From c20311f804ba3e4674b49a13288602eede84db74 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 16 Aug 2021 17:22:50 +0200 Subject: [PATCH 01/74] ignore vscode --- .gitignore | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 9f92f8f..1faf115 100644 --- a/.gitignore +++ b/.gitignore @@ -160,4 +160,6 @@ Thumbs.db #thumbnail cache on Windows .prof -# End of https://www.toptal.com/developers/gitignore/api/jupyternotebooks,python \ No newline at end of file +# End of https://www.toptal.com/developers/gitignore/api/jupyternotebooks,python + +.vscode/ \ No newline at end of file From e5951f54c5645c8ce49709753bc51bd79b7927c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 16 Aug 2021 17:34:22 +0200 Subject: [PATCH 02/74] fix save function --- mols2grid/dispatch.py | 17 ++++++++++------- 1 file changed, 10 insertions(+), 7 deletions(-) diff --git a/mols2grid/dispatch.py b/mols2grid/dispatch.py index 57bb0fc..46f7568 100644 --- a/mols2grid/dispatch.py +++ b/mols2grid/dispatch.py @@ -24,9 +24,6 @@ def _prepare_kwargs(kwargs, kind): render_kwargs = {"width": kwargs.pop("width", "100%"), "height": kwargs.pop("height", None), **render_kwargs} - elif kind == "save": - render_kwargs = {"output": kwargs.pop("output"), - **render_kwargs} return template, kwargs, render_kwargs @singledispatch @@ -135,27 +132,33 @@ def save(arg, **kwargs): Parameters ---------- + arg : pandas.DataFrame, SDF file or list of molecules + The input containing your molecules output : str Name and path of the output document See `mols2grid.display` for the full list of arguments """ - raise TypeError(f"No display method registered for type {type(arg)!r}") + raise TypeError(f"No save method registered for type {type(arg)!r}") @save.register(DataFrame) def _(df, **kwargs): template, kwargs, render_kwargs = _prepare_kwargs(kwargs, "save") - return MolGrid(df, **kwargs).save(template=template, **render_kwargs) + output = kwargs.pop("output") + return MolGrid(df, **kwargs).save(output, template=template, + **render_kwargs) @save.register(str) def _(sdf, **kwargs): template, kwargs, render_kwargs = _prepare_kwargs(kwargs, "save") - return MolGrid.from_sdf(sdf, **kwargs).save(template=template, + output = kwargs.pop("output") + return MolGrid.from_sdf(sdf, **kwargs).save(output, template=template, **render_kwargs) @save.register(Series) @save.register(list) def _(mols, **kwargs): template, kwargs, render_kwargs = _prepare_kwargs(kwargs, "save") - return MolGrid.from_mols(mols, **kwargs).save(template=template, + output = kwargs.pop("output") + return MolGrid.from_mols(mols, **kwargs).save(output, template=template, **render_kwargs) \ No newline at end of file From 7d80a410b97eb728ee8a40235ca9efdb3a11aa91 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 17 Aug 2021 19:08:56 +0200 Subject: [PATCH 03/74] allow multiple grids selection --- mols2grid/__init__.py | 4 +++- mols2grid/molgrid.py | 17 +++++++++++++++-- mols2grid/select.py | 33 ++++++++++++++++++++++++--------- mols2grid/templates/pages.html | 30 +++++++++++++++++++----------- 4 files changed, 61 insertions(+), 23 deletions(-) diff --git a/mols2grid/__init__.py b/mols2grid/__init__.py index 804fb6d..07c5133 100644 --- a/mols2grid/__init__.py +++ b/mols2grid/__init__.py @@ -1,4 +1,6 @@ from .molgrid import MolGrid from .dispatch import display, save -from .select import selection, reset_selection, set_selection, del_selection +from .select import ( + selection, get_selection, + _update_current_grid, _set_selection, _del_selection) from ._version import __version__ \ No newline at end of file diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index a7dfc73..4f73f9e 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -10,6 +10,7 @@ from rdkit.Chem import Draw from jinja2 import Environment, FileSystemLoader from .utils import requires, tooltip_formatter, mol_to_record, mol_to_smiles +from .select import get_selection, selection as SELECTION try: from IPython.display import HTML except ModuleNotFoundError: @@ -27,6 +28,8 @@ class MolGrid: """Class that handles drawing molecules, rendering the HTML document and saving or displaying it in a notebook """ + _n_instances = 0 + def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, useSVG=True, mapping=None, **kwargs): """ @@ -78,6 +81,10 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, self.mol_col = mol_col self.img_size = kwargs.get("size", (160, 120)) self.smiles_col = smiles_col + # register instance + self._grid_id = MolGrid._n_instances + SELECTION[self._grid_id] = {} + MolGrid._n_instances += 1 @classmethod def from_mols(cls, mols, **kwargs): @@ -362,10 +369,11 @@ def to_pages(self, subset=None, tooltip=None, selection = selection, smiles_col = smiles, sort_cols = sort_cols, + grid_id = self._grid_id, ) return template.render(**template_kwargs) - def get(self, selection): + def get_selection(self, selection=None): """Retrieve the dataframe subset corresponding to a selection Parameters @@ -378,7 +386,12 @@ def get(self, selection): ------- pandas.DataFrame """ - sel = list(selection.keys()) if isinstance(selection, dict) else selection + if isinstance(selection, list): + sel = selection + elif isinstance(selection, int) or selection is None: + sel = list(get_selection(selection).keys()) + else: + raise TypeError(f"`selection` must be list, int or None") return (self.dataframe.loc[self.dataframe["mols2grid-id"].isin(sel)] .drop(columns=self._extra_columns)) diff --git a/mols2grid/select.py b/mols2grid/select.py index 8e52593..c567bd2 100644 --- a/mols2grid/select.py +++ b/mols2grid/select.py @@ -1,22 +1,37 @@ +from copy import deepcopy + selection = {} +current_selection = 0 + +def _update_current_grid(grid_id): + global current_selection + current_selection = grid_id -def reset_selection(): +def _set_selection(_id, smiles): global selection - selection.clear() + global current_selection + selection[current_selection][_id] = smiles -def set_selection(_id, smiles): +def _del_selection(_id): global selection - selection[_id] = smiles + global current_selection + del selection[current_selection][_id] -def del_selection(_id): +def get_selection(grid_id=None): + """Returns the selection for a specific MolGrid instance. If grid_id is + `None`, the most recently updated grid is returned.""" global selection - del selection[_id] + global current_selection + grid_id = current_selection if grid_id is None else grid_id + sel = selection[grid_id] + return deepcopy(sel) try: from google import colab except (ModuleNotFoundError, ImportError): pass else: - colab.output.register_callback('m2g.reset_selection', reset_selection) - colab.output.register_callback('m2g.set_selection', set_selection) - colab.output.register_callback('m2g.del_selection', del_selection) + colab.output.register_callback('m2g._update_current_grid', + _update_current_grid) + colab.output.register_callback('m2g._set_selection', _set_selection) + colab.output.register_callback('m2g._del_selection', _del_selection) diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index 7c2e30f..a741611 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -112,27 +112,34 @@ // Jupyter notebook var kernel = window.parent.IPython.notebook.kernel; kernel.execute('import mols2grid') - kernel.execute('mols2grid.reset_selection()') + function update_current_grid(grid_id) { + kernel.execute("mols2grid._update_current_grid("+grid_id+")"); + } function set_selection(_id, smiles) { - kernel.execute("mols2grid.set_selection("+_id+",'"+smiles+"')") + kernel.execute("mols2grid._set_selection("+_id+",'"+smiles+"')"); } function del_selection(_id) { - kernel.execute("mols2grid.del_selection("+_id+")"); + kernel.execute("mols2grid._del_selection("+_id+")"); } } else if (window.parent.google !== undefined) { // Google colab var kernel = window.parent.google.colab.kernel; - (async function() { - const result = await kernel.invokeFunction('m2g.reset_selection', [], {}); - })(); + function update_current_grid(grid_id) { + (async function() { + const result = await kernel.invokeFunction('m2g._update_current_grid', + [grid_id], {}); + })(); + } function set_selection(_id, smiles) { (async function() { - const result = await kernel.invokeFunction('m2g.set_selection', [_id, smiles], {}); + const result = await kernel.invokeFunction('m2g._set_selection', + [_id, smiles], {}); })(); } function del_selection(_id) { (async function() { - const result = await kernel.invokeFunction('m2g.del_selection', [_id], {}); + const result = await kernel.invokeFunction('m2g._del_selection', + [_id], {}); })(); } } @@ -202,7 +209,7 @@ if (search_type === "Text") { listObj.search(query, {{ search_cols }}); } else { - listObj.search(query, ["data-"+"{{ smiles_col }}"], SmartsSearch); + listObj.search(query, ["data-{{ smiles_col }}"], SmartsSearch); } }); {% if tooltip %} @@ -228,12 +235,13 @@ if (kernel !== undefined) { listObj.on("updated", function (list) { $("input:checkbox").change(function() { + update_current_grid({{ grid_id }}); var _id = parseInt($(this).closest(".cell").attr("data-mols2grid-id")); var _smiles = $($(this).siblings(".data-{{ smiles_col }}")[0]).text(); if (this.checked) { - set_selection(_id, _smiles) + set_selection(_id, _smiles); } else { - del_selection(_id) + del_selection(_id); } }); }); From 08c37438a32986bc543a324af0c2109dfbe64085 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 17 Aug 2021 19:09:45 +0200 Subject: [PATCH 04/74] update demo nb --- demo.ipynb | 215 ++++++++++++++++++++++++++++++----------------------- 1 file changed, 123 insertions(+), 92 deletions(-) diff --git a/demo.ipynb b/demo.ipynb index be90853..37d550b 100755 --- a/demo.ipynb +++ b/demo.ipynb @@ -136,7 +136,7 @@ " // pages\n", " var listObj = new List('mols2grid',\n", " {\n", - " valueNames: [{data: ['mols2grid-id']}, 'data-img', 'data-Solubility', 'data-SMILES', 'data-ID', {attr: 'data-content', name: 'mols2grid-tooltip'}, { attr: 'style', name: 'style-Solubility' }],\n", + " valueNames: [{data: ['mols2grid-id']}, 'data-SMILES', 'data-ID', 'data-img', 'data-Solubility', {attr: 'data-content', name: 'mols2grid-tooltip'}, { attr: 'style', name: 'style-Solubility' }],\n", " item: '<div class="cell" data-mols2grid-id="0"><input type="checkbox" class="position-relative float-left"><div class="data data-ID"></div><div class="data data-img mols2grid-tooltip" data-toggle="popover" data-content="foo"></div><div class="data data-Solubility style-Solubility" style=""></div><div class="data data-SMILES" style="display: none;"></div></div>',\n", " page: 15,\n", " pagination: {\n", @@ -148,34 +148,41 @@ " }\n", " );\n", " listObj.remove("mols2grid-id", "0")\n", - " listObj.add([{"data-img": "<?xml version='1.0' encoding='iso-8859-1'?>\\n<svg version='1.1' baseProfile='full'\\n xmlns='http://www.w3.org/2000/svg'\\n xmlns:rdkit='http://www.rdkit.org/xml'\\n xmlns:xlink='http://www.w3.org/1999/xlink'\\n xml:space='preserve'\\nwidth='160px' height='120px' viewBox='0 0 160 120'>\\n<!-- END OF HEADER -->\\n<rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='160' height='120' x='0' y='0'> </rect>\\n<path class='bond-0 atom-0 atom-1' d='M 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window.parent.IPython.notebook.kernel;\n", " kernel.execute('import mols2grid')\n", - " kernel.execute('mols2grid.reset_selection()')\n", + " function update_current_grid(grid_id) {\n", + " kernel.execute("mols2grid._update_current_grid("+grid_id+")");\n", + " }\n", " function set_selection(_id, smiles) {\n", - " kernel.execute("mols2grid.set_selection("+_id+",'"+smiles+"')")\n", + " kernel.execute("mols2grid._set_selection("+_id+",'"+smiles+"')");\n", " }\n", " function del_selection(_id) {\n", - " kernel.execute("mols2grid.del_selection("+_id+")");\n", + " kernel.execute("mols2grid._del_selection("+_id+")");\n", " }\n", " } else if (window.parent.google !== undefined) {\n", " // Google colab\n", " var kernel = window.parent.google.colab.kernel;\n", - " (async function() {\n", - " const result = await kernel.invokeFunction('m2g.reset_selection', [], {});\n", - " })();\n", + " function update_current_grid(grid_id) {\n", + " (async function() {\n", + " const result = await kernel.invokeFunction('m2g._update_current_grid',\n", + " [grid_id], {});\n", + " })();\n", + " }\n", " function set_selection(_id, smiles) {\n", " (async function() {\n", - " const result = await kernel.invokeFunction('m2g.set_selection', [_id, smiles], {});\n", + " const result = await kernel.invokeFunction('m2g._set_selection',\n", + " [_id, smiles], {});\n", " })();\n", " }\n", " function del_selection(_id) {\n", " (async function() {\n", - " const result = await kernel.invokeFunction('m2g.del_selection', [_id], {});\n", + " const result = await kernel.invokeFunction('m2g._del_selection',\n", + " [_id], {});\n", " })();\n", " }\n", " }\n", @@ -245,7 +252,7 @@ " if (search_type === "Text") {\n", " listObj.search(query, ['data-ID', 'data-Solubility', 'mols2grid-tooltip']);\n", " } else {\n", - " listObj.search(query, ["data-"+"SMILES"], SmartsSearch);\n", + " listObj.search(query, ["data-SMILES"], SmartsSearch);\n", " }\n", " });\n", " \n", @@ -271,12 +278,13 @@ " if (kernel !== undefined) {\n", " listObj.on("updated", function (list) {\n", " $("input:checkbox").change(function() {\n", + " update_current_grid(0);\n", " var _id = parseInt($(this).closest(".cell").attr("data-mols2grid-id"));\n", " var _smiles = $($(this).siblings(".data-SMILES")[0]).text();\n", " if (this.checked) {\n", - " set_selection(_id, _smiles)\n", + " set_selection(_id, _smiles);\n", " } else {\n", - " del_selection(_id)\n", + " del_selection(_id);\n", " }\n", " }); \n", " });\n", @@ -341,7 +349,7 @@ ], "source": [ "# retrieve the index and SMILES of your selection\n", - "mols2grid.selection" + "mols2grid.get_selection()" ] }, { @@ -353,7 +361,7 @@ }, { "cell_type": "code", - "execution_count": 3, + "execution_count": 4, "metadata": {}, "outputs": [ { @@ -456,7 +464,7 @@ " // pages\n", " var listObj = new List('mols2grid',\n", " {\n", - " valueNames: [{data: ['mols2grid-id']}, 'data-img', 'data-id', 'data-smi'],\n", + " valueNames: [{data: ['mols2grid-id']}, 'data-id', 'data-smi', 'data-img'],\n", " item: '<div class="cell" data-mols2grid-id="0"><input type="checkbox" class="position-relative float-left"><div class="data data-id"></div><div class="data data-img"></div><div class="data data-smi" style="display: none;"></div></div>',\n", " page: 21,\n", " pagination: {\n", @@ -468,34 +476,41 @@ " }\n", " );\n", " listObj.remove("mols2grid-id", "0")\n", - " listObj.add([{"data-img": "<?xml version='1.0' encoding='iso-8859-1'?>\\n<svg version='1.1' baseProfile='full'\\n xmlns='http://www.w3.org/2000/svg'\\n xmlns:rdkit='http://www.rdkit.org/xml'\\n xmlns:xlink='http://www.w3.org/1999/xlink'\\n xml:space='preserve'\\nwidth='110px' height='90px' viewBox='0 0 110 90'>\\n<!-- END OF HEADER -->\\n<rect style='opacity:1.0;fill:#FFFFFF;stroke:none' width='110' height='90' x='0' y='0'> </rect>\\n<path class='bond-0 atom-0 atom-1' d='M 105,51.1326 L 67.191,29.2579' 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kernel.execute("mols2grid._update_current_grid("+grid_id+")");\n", + " }\n", " function set_selection(_id, smiles) {\n", - " kernel.execute("mols2grid.set_selection("+_id+",'"+smiles+"')")\n", + " kernel.execute("mols2grid._set_selection("+_id+",'"+smiles+"')");\n", " }\n", " function del_selection(_id) {\n", - " kernel.execute("mols2grid.del_selection("+_id+")");\n", + " kernel.execute("mols2grid._del_selection("+_id+")");\n", " }\n", " } else if (window.parent.google !== undefined) {\n", " // Google colab\n", " var kernel = window.parent.google.colab.kernel;\n", - " (async function() {\n", - " const result = await kernel.invokeFunction('m2g.reset_selection', [], {});\n", - " })();\n", + " function update_current_grid(grid_id) {\n", + " (async function() {\n", + " const result = await kernel.invokeFunction('m2g._update_current_grid',\n", + " [grid_id], {});\n", + " })();\n", + " }\n", " function set_selection(_id, smiles) {\n", " (async function() {\n", - " const result = await kernel.invokeFunction('m2g.set_selection', [_id, smiles], {});\n", + " const result = await kernel.invokeFunction('m2g._set_selection',\n", + " [_id, smiles], {});\n", " })();\n", " }\n", " function del_selection(_id) {\n", " (async function() {\n", - " const result = await kernel.invokeFunction('m2g.del_selection', [_id], {});\n", + " const result = await kernel.invokeFunction('m2g._del_selection',\n", + " [_id], {});\n", " })();\n", " }\n", " }\n", @@ -565,7 +580,7 @@ " if (search_type === "Text") {\n", " listObj.search(query, ['data-id']);\n", " } else {\n", - " listObj.search(query, ["data-"+"smi"], SmartsSearch);\n", + " listObj.search(query, ["data-smi"], SmartsSearch);\n", " }\n", " });\n", " \n", @@ -574,12 +589,13 @@ " if (kernel !== undefined) {\n", " listObj.on("updated", function (list) {\n", " $("input:checkbox").change(function() {\n", + " update_current_grid(1);\n", " var _id = parseInt($(this).closest(".cell").attr("data-mols2grid-id"));\n", " var _smiles = $($(this).siblings(".data-smi")[0]).text();\n", " if (this.checked) {\n", - " set_selection(_id, _smiles)\n", + " set_selection(_id, _smiles);\n", " } else {\n", - " del_selection(_id)\n", + " del_selection(_id);\n", " }\n", " }); \n", " });\n", @@ -596,7 +612,7 @@ "" ] }, - "execution_count": 3, + "execution_count": 4, "metadata": {}, "output_type": "execute_result" } @@ -609,8 +625,15 @@ "df = pd.DataFrame({\"smi\": smiles,\n", " \"id\": range(1, len(smiles) + 1)})\n", "# setup the grid\n", - "mg = mols2grid.MolGrid(df, smiles_col=\"smi\", size=(110, 90))\n", - "mg.display(subset=[\"id\", \"img\"], n_cols=7)" + "grid = mols2grid.MolGrid(df, smiles_col=\"smi\", size=(110, 90))\n", + "grid.display(subset=[\"id\", \"img\"], n_cols=7)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "As soon as you click on a checkbox on the new grid, calling `mols2grid.get_selection()` will return this latest selection instead. " ] }, { @@ -620,48 +643,8 @@ "outputs": [ { "data": { - "text/html": [ - "
\n", - "\n", - "\n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - " \n", - "
smiid
0CCO1
4O=S(=O)(-O)(-O)5
\n", - "
" - ], "text/plain": [ - " smi id\n", - "0 CCO 1\n", - "4 O=S(=O)(-O)(-O) 5" + "{4: 'O=S(=O)(-O)(-O)'}" ] }, "execution_count": 5, @@ -670,14 +653,76 @@ } ], "source": [ - "# retrieve your selection as a dataframe\n", - "mg.get(mols2grid.selection)" + "# retrieve the index and SMILES of the current selection\n", + "mols2grid.get_selection()" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "You can also specify which grid you want to get the selection from:" ] }, { "cell_type": "code", "execution_count": 6, "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{14: 'c1c(C)cc2ccccc2c1C', 0: 'CCC(C)CC', 7: 'c1ccccc1CC'}" + ] + }, + "execution_count": 6, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "mols2grid.get_selection(0)" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "If you need access to both grids, you can use `mols2grid.selection` which contains all selections in separate dictionnaries:" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": {}, + "outputs": [ + { + "data": { + "text/plain": [ + "{0: {14: 'c1c(C)cc2ccccc2c1C', 0: 'CCC(C)CC', 7: 'c1ccccc1CC'},\n", + " 1: {4: 'O=S(=O)(-O)(-O)'}}" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "mols2grid.selection" + ] + }, + { + "cell_type": "markdown", + "metadata": {}, + "source": [ + "The advantage of using the MolGrid class is that you can retrieve your selection in the input dataframe with `MolGrid.get_selection()`" + ] + }, + { + "cell_type": "code", + "execution_count": 8, + "metadata": {}, "outputs": [ { "data": { @@ -706,11 +751,6 @@ " \n", " \n", " \n", - " 0\n", - " CCO\n", - " 1\n", - " \n", - " \n", " 4\n", " O=S(=O)(-O)(-O)\n", " 5\n", @@ -721,18 +761,16 @@ ], "text/plain": [ " smi id\n", - "0 CCO 1\n", "4 O=S(=O)(-O)(-O) 5" ] }, - "execution_count": 6, + "execution_count": 8, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "# retrieve specific indexes\n", - "mg.get([0, 4])" + "grid.get_selection()" ] }, { @@ -744,7 +782,7 @@ }, { "cell_type": "code", - "execution_count": 4, + "execution_count": 9, "metadata": {}, "outputs": [ { @@ -1422,7 +1460,7 @@ "" ] }, - "execution_count": 4, + "execution_count": 9, "metadata": {}, "output_type": "execute_result" } @@ -1454,13 +1492,6 @@ " subset=[\"img\"], size=(120, 100),\n", " MolDrawOptions=opts, selection=False)" ] - }, - { - "cell_type": "code", - "execution_count": null, - "metadata": {}, - "outputs": [], - "source": [] } ], "metadata": { From 493df834f0ecd43bc05d8aeea7a157b15076104b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Wed, 18 Aug 2021 18:09:48 +0200 Subject: [PATCH 05/74] fix transform not applied to tooltips --- mols2grid/molgrid.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 4f73f9e..b32d47b 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -321,13 +321,6 @@ def to_pages(self, subset=None, tooltip=None, column_map[smiles] = f"data-{smiles}" # set mapping for list.js value_names = "[{data: ['mols2grid-id']}, " + str(value_names)[1:] - - if tooltip: - df["mols2grid-tooltip"] = df.apply(tooltip_formatter, axis=1, - args=(tooltip, tooltip_fmt, style)) - final_columns = final_columns + ["mols2grid-tooltip"] - value_names = (value_names[:-1] + - ", {attr: 'data-content', name: 'mols2grid-tooltip'}]") # apply CSS styles for col, func in style.items(): @@ -340,6 +333,13 @@ def to_pages(self, subset=None, tooltip=None, for col, func in transform.items(): df[col] = df[col].apply(func) + if tooltip: + df["mols2grid-tooltip"] = df.apply(tooltip_formatter, axis=1, + args=(tooltip, tooltip_fmt, style)) + final_columns = final_columns + ["mols2grid-tooltip"] + value_names = (value_names[:-1] + + ", {attr: 'data-content', name: 'mols2grid-tooltip'}]") + checkbox = '' item = '
{}{}
'.format( checkbox if selection else "", From 84776bed0ff8d9ff981a4ea32f1f4d0a690fcc85 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Wed, 18 Aug 2021 19:02:09 +0200 Subject: [PATCH 06/74] add sort by tooltip items --- mols2grid/molgrid.py | 29 +++++++++++++++++++++-------- mols2grid/templates/pages.html | 5 +++-- 2 files changed, 24 insertions(+), 10 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index b32d47b..bfaf0bf 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -273,28 +273,41 @@ def to_pages(self, subset=None, tooltip=None, df = self.dataframe.drop(columns=self.mol_col).copy() cell_width = self.img_size[0] smiles = self.smiles_col + content = [] + column_map = {} + width = n_cols * (cell_width + 2 * (gap + 2)) + if subset is None: subset = df.columns.tolist() subset = [subset.pop(subset.index("img"))] + subset - # define fields that are searchable + # define fields that are searchable and sortable search_cols = [f"data-{col}" for col in subset if col != "img"] if tooltip: search_cols.append("mols2grid-tooltip") - sort_cols = search_cols[:-1] if tooltip else search_cols[:] + sort_cols = search_cols[:-1] + sort_cols.extend([f"data-{col}" for col in tooltip]) + for col in tooltip: + if col not in subset: + s = f'' + content.append(s) + column_map[col] = f"data-{col}" + else: + sort_cols = search_cols[:] sort_cols = ["mols2grid-id"] + sort_cols + # get unique list but keep order + sort_cols = list(dict.fromkeys(sort_cols)) if style is None: style = {} if transform is None: transform = {} - value_names = list(set(subset + [smiles])) + value_names = list(set(subset + [smiles] + tooltip)) value_names = [f"data-{col}" for col in value_names] - width = n_cols * (cell_width + 2 * (gap + 2)) - content = [] - # force id and SMILES to be present in the data + + # force id, SMILES, and tooltip values to be present in the data final_columns = subset[:] - final_columns.extend(["mols2grid-id", smiles]) + final_columns.extend(["mols2grid-id", smiles] + tooltip) final_columns = list(set(final_columns)) - column_map = {} + # make a copy if id shown explicitely if "mols2grid-id" in subset: id_name = "mols2grid-id-copy" diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index a741611..3d9e024 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -67,7 +67,7 @@ {% if loop.first %} {% else %} - + {% endif %} {% endfor %} @@ -166,11 +166,12 @@ } $('#mols2grid button.sort-btn').click(function(e) { var _field = $(this).attr("data-name"); + console.log(_field); if (_field == sort_field) { $(this).removeClass("arrow-" + sort_order) sort_order = (sort_order === "desc") ? "asc" : "desc"; } else { - $('#mols2grid button.sort-btn.active').removeClass("active "+"arrow-"+sort_order); + $('#mols2grid button.sort-btn.active').removeClass("active arrow-" + sort_order); sort_order = "asc"; sort_field = _field; $(this).addClass("active"); From 0800b34a45790b2a0357eb65ff5554afb6a11ac2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 31 Aug 2021 20:35:25 +0200 Subject: [PATCH 07/74] allow custom names --- mols2grid/molgrid.py | 11 +++++++---- mols2grid/templates/pages.html | 3 ++- 2 files changed, 9 insertions(+), 5 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index bfaf0bf..7653ddc 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -31,7 +31,7 @@ class MolGrid: _n_instances = 0 def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, - useSVG=True, mapping=None, **kwargs): + useSVG=True, mapping=None, name=None, **kwargs): """ Parameters ---------- @@ -51,6 +51,9 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, Use SVG instead of PNG mapping : dict or None Rename the properties/fields stored in the molecule + name : int or str or None + Name of the grid, as shown in `mols2grid.selection`. If `None`, + the name is automatically set. kwargs : object Arguments passed to the `draw_mol` method """ @@ -82,7 +85,7 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, self.img_size = kwargs.get("size", (160, 120)) self.smiles_col = smiles_col # register instance - self._grid_id = MolGrid._n_instances + self._grid_id = MolGrid._n_instances if name is None else name SELECTION[self._grid_id] = {} MolGrid._n_instances += 1 @@ -401,10 +404,10 @@ def get_selection(self, selection=None): """ if isinstance(selection, list): sel = selection - elif isinstance(selection, int) or selection is None: + elif isinstance(selection, (int, str)) or selection is None: sel = list(get_selection(selection).keys()) else: - raise TypeError(f"`selection` must be list, int or None") + raise TypeError(f"`selection` must be list, int, str, or None") return (self.dataframe.loc[self.dataframe["mols2grid-id"].isin(sel)] .drop(columns=self._extra_columns)) diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index 3d9e024..391b795 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -113,6 +113,7 @@ var kernel = window.parent.IPython.notebook.kernel; kernel.execute('import mols2grid') function update_current_grid(grid_id) { + grid_id = typeof grid_id === "string" ? "'"+grid_id+"'" : grid_id; kernel.execute("mols2grid._update_current_grid("+grid_id+")"); } function set_selection(_id, smiles) { @@ -236,7 +237,7 @@ if (kernel !== undefined) { listObj.on("updated", function (list) { $("input:checkbox").change(function() { - update_current_grid({{ grid_id }}); + update_current_grid({{ grid_id | tojson }}); var _id = parseInt($(this).closest(".cell").attr("data-mols2grid-id")); var _smiles = $($(this).siblings(".data-{{ smiles_col }}")[0]).text(); if (this.checked) { From bf2d1d900b3072a9f45af7d3618d5dfd7cc47e14 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 31 Aug 2021 20:38:19 +0200 Subject: [PATCH 08/74] fix no tooltip --- mols2grid/molgrid.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 7653ddc..39c654d 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -303,12 +303,17 @@ def to_pages(self, subset=None, tooltip=None, style = {} if transform is None: transform = {} - value_names = list(set(subset + [smiles] + tooltip)) + if tooltip: + value_names = list(set(subset + [smiles] + tooltip)) + else: + value_names = list(set(subset + [smiles])) value_names = [f"data-{col}" for col in value_names] # force id, SMILES, and tooltip values to be present in the data final_columns = subset[:] - final_columns.extend(["mols2grid-id", smiles] + tooltip) + final_columns.extend(["mols2grid-id", smiles]) + if tooltip: + final_columns.extend(tooltip) final_columns = list(set(final_columns)) # make a copy if id shown explicitely From 176cca46d0af34e55d0ca978c980ccc9e9e7759a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 31 Aug 2021 20:39:07 +0200 Subject: [PATCH 09/74] fix tooltip_trigger="focus" --- mols2grid/molgrid.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 39c654d..fe2d10b 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -183,7 +183,7 @@ def mol_to_img(self, mol, **kwargs): if self.useSVG: return img data = b64encode(img).decode() - return f'molecule' + return f'' def smi_to_img(self, smi, **kwargs): """Convert a SMILES string to an HTML img tag containing a drawing of @@ -326,8 +326,8 @@ def to_pages(self, subset=None, tooltip=None, # organize data for col in subset: if col == "img" and tooltip: - s = (f'
') + s = (f'') else: if style.get(col): s = f'
' From 3e2d2f6ae699bdc757559bbfa49fc48792c24914 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 31 Aug 2021 20:59:12 +0200 Subject: [PATCH 10/74] get_selection copy kwarg --- mols2grid/select.py | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/mols2grid/select.py b/mols2grid/select.py index c567bd2..502953a 100644 --- a/mols2grid/select.py +++ b/mols2grid/select.py @@ -17,14 +17,24 @@ def _del_selection(_id): global current_selection del selection[current_selection][_id] -def get_selection(grid_id=None): - """Returns the selection for a specific MolGrid instance. If grid_id is - `None`, the most recently updated grid is returned.""" +def get_selection(grid_id=None, copy=True): + """Returns the selection for a specific MolGrid instance + + Parameters + ---------- + grid_id : int, str or None + Name of the grid to fetch the selection from. If `None`, the most + recently updated grid is returned + copy : bool + Return a copy of the selection instead of the original object + """ global selection global current_selection grid_id = current_selection if grid_id is None else grid_id sel = selection[grid_id] - return deepcopy(sel) + if copy: + return deepcopy(sel) + return sel try: from google import colab From 322d07773c87549c0ed912d51d6d9e4646c4ad4f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 31 Aug 2021 20:59:37 +0200 Subject: [PATCH 11/74] MolGrid.get_selection remove selection kwarg --- mols2grid/molgrid.py | 17 +++-------------- 1 file changed, 3 insertions(+), 14 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index fe2d10b..3648c90 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -394,25 +394,14 @@ def to_pages(self, subset=None, tooltip=None, ) return template.render(**template_kwargs) - def get_selection(self, selection=None): - """Retrieve the dataframe subset corresponding to a selection - - Parameters - ---------- - selection : list or dict - Either a list of indices or a dict with keys corresponding to - indices to select in the internal dataframe + def get_selection(self): + """Retrieve the dataframe subset corresponding to your selection Returns ------- pandas.DataFrame """ - if isinstance(selection, list): - sel = selection - elif isinstance(selection, (int, str)) or selection is None: - sel = list(get_selection(selection).keys()) - else: - raise TypeError(f"`selection` must be list, int, str, or None") + sel = list(get_selection().keys()) return (self.dataframe.loc[self.dataframe["mols2grid-id"].isin(sel)] .drop(columns=self._extra_columns)) From e1b4683f1fa23d563f12240dd74dde7d260b1b7e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Thu, 2 Sep 2021 16:10:47 +0200 Subject: [PATCH 12/74] ignore vscode --- .gitignore | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/.gitignore b/.gitignore index 9f92f8f..1faf115 100644 --- a/.gitignore +++ b/.gitignore @@ -160,4 +160,6 @@ Thumbs.db #thumbnail cache on Windows .prof -# End of https://www.toptal.com/developers/gitignore/api/jupyternotebooks,python \ No newline at end of file +# End of https://www.toptal.com/developers/gitignore/api/jupyternotebooks,python + +.vscode/ \ No newline at end of file From 17876af4477af07fe77298e4f69ab6ad4a23d091 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Fri, 3 Sep 2021 01:52:14 +0200 Subject: [PATCH 13/74] add selection modifiers and export --- mols2grid/templates/pages.html | 151 +++++++++++++++++++++++++-------- 1 file changed, 114 insertions(+), 37 deletions(-) diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index 7c2e30f..3761cf1 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -53,32 +53,34 @@
-
+
{{ item }}
-
-
    -
    - -
    - {% for name in sort_cols %} - {% if loop.first %} - - {% else %} - - {% endif %} - {% endfor %} +
    +
      +
      + -
      -
      - -
      - -
      - - +
      + +
      + +
      + + +
      @@ -108,15 +110,40 @@ listObj.add({{ data }}) {% if selection %} // checkbox + class MolStorage extends Map { + to_dict() { + var content = "{"; + for (let [key, value] of this) { + content += key + ":" + JSON.stringify(value) + ","; + } + content = content.length > 1 ? content.slice(0, -1) : content; + content += "}"; + return content + } + download_smi(fileName) { + var content = ""; + for (let [key, value] of this) { + content += value + "\n"; + } + var a = document.createElement("a"); + var file = new Blob([content], {type: "text/plain"}); + a.href = URL.createObjectURL(file); + a.download = fileName; + a.click(); + } + } + var SELECTION = new MolStorage(); if (window.parent.IPython !== undefined) { // Jupyter notebook var kernel = window.parent.IPython.notebook.kernel; kernel.execute('import mols2grid') kernel.execute('mols2grid.reset_selection()') function set_selection(_id, smiles) { + SELECTION.set(_id, smiles); kernel.execute("mols2grid.set_selection("+_id+",'"+smiles+"')") } function del_selection(_id) { + SELECTION.delete(_id); kernel.execute("mols2grid.del_selection("+_id+")"); } } else if (window.parent.google !== undefined) { @@ -126,17 +153,25 @@ const result = await kernel.invokeFunction('m2g.reset_selection', [], {}); })(); function set_selection(_id, smiles) { + SELECTION.set(_id, smiles); (async function() { const result = await kernel.invokeFunction('m2g.set_selection', [_id, smiles], {}); })(); } function del_selection(_id) { + SELECTION.delete(_id); (async function() { const result = await kernel.invokeFunction('m2g.del_selection', [_id], {}); })(); } + } else { + function set_selection(_id, smiles) { + SELECTION.set(_id, smiles); + } + function del_selection(_id) { + SELECTION.delete(_id); + } } - {% endif %} // sort var sort_field = "mols2grid-id"; @@ -224,20 +259,62 @@ }); {% endif %} {% if selection %} + // add "copy to clipboard" and save buttons + $("#sort-dropdown").before(` + ` + ); + $('#btn-chkbox-all').click(function (e) { + var current_page = parseInt($("li.page-item.active > a").text()); + var n_items = {{ n_items_per_page }}; + var last_page = parseInt($("li.page-item > a").last().text()); + for (let i = 0; i < last_page; i++) { + listObj.show(i * n_items + 1, n_items); + $("input:checkbox").each(function() { + this.checked = true; + $(this).trigger("change"); + }); + } + listObj.show((current_page - 1) * n_items + 1, n_items); + }); + $('#btn-chkbox-invert').click(function (e) { + var current_page = parseInt($("li.page-item.active > a").text()); + var n_items = {{ n_items_per_page }}; + var last_page = parseInt($("li.page-item > a").last().text()); + for (let i = 0; i < last_page; i++) { + listObj.show(i * n_items + 1, n_items); + $("input:checkbox").each(function() { + this.checked = !this.checked; + $(this).trigger("change"); + }); + } + listObj.show((current_page - 1) * n_items + 1, n_items); + }); + $("#btn-chkbox-copy").click(function(e) { + navigator.clipboard.writeText(SELECTION.to_dict()); + }); + $("#btn-chkbox-dlsmi").click(function(e) { + SELECTION.download_smi("selection.smi"); + }); // update selection on checkbox click - if (kernel !== undefined) { - listObj.on("updated", function (list) { - $("input:checkbox").change(function() { - var _id = parseInt($(this).closest(".cell").attr("data-mols2grid-id")); - var _smiles = $($(this).siblings(".data-{{ smiles_col }}")[0]).text(); - if (this.checked) { - set_selection(_id, _smiles) - } else { - del_selection(_id) - } - }); - }); - } + listObj.on("updated", function (list) { + $("input:checkbox").change(function() { + var _id = parseInt($(this).closest(".cell").attr("data-mols2grid-id")); + var _smiles = $($(this).siblings(".data-{{ smiles_col }}")[0]).text(); + if (this.checked) { + set_selection(_id, _smiles); + } else { + del_selection(_id); + } + }); + }); {% endif %} {% if tooltip or selection %} listObj.update(); From 64c38a7fbdf738f6736865286cbf13712df01671 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Wed, 15 Sep 2021 17:07:11 +0200 Subject: [PATCH 14/74] drop created rdmol column --- mols2grid/molgrid.py | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 3648c90..f092b4f 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -80,8 +80,7 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, dataframe.dropna(axis=0, subset=[mol_col], inplace=True) # generate drawings dataframe["img"] = dataframe[mol_col].apply(self.mol_to_img, **kwargs) - self.dataframe = dataframe - self.mol_col = mol_col + self.dataframe = dataframe if mol_col else dataframe.drop(columns=mol_col) self.img_size = kwargs.get("size", (160, 120)) self.smiles_col = smiles_col # register instance @@ -273,7 +272,7 @@ def to_pages(self, subset=None, tooltip=None, before (MP) and after (°C) the value. These transformations only affect columns in `subset` (not `tooltip`) and are applied independantly from `style` """ - df = self.dataframe.drop(columns=self.mol_col).copy() + df = self.dataframe.copy() cell_width = self.img_size[0] smiles = self.smiles_col content = [] @@ -465,7 +464,7 @@ def to_table(self, subset=None, tooltip=None, n_cols=6, """ tr = [] data = [] - df = self.dataframe.drop(columns=self.mol_col) + df = self.dataframe cell_width = self.img_size[0] if subset is None: From 2268287760e839b6d55f6a74610b6324d0ac1707 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 20 Sep 2021 20:31:29 +0200 Subject: [PATCH 15/74] add sdf_to_dataframe function --- mols2grid/__init__.py | 4 +--- mols2grid/utils.py | 14 ++++++++++---- 2 files changed, 11 insertions(+), 7 deletions(-) diff --git a/mols2grid/__init__.py b/mols2grid/__init__.py index 07c5133..547daa0 100644 --- a/mols2grid/__init__.py +++ b/mols2grid/__init__.py @@ -1,6 +1,4 @@ from .molgrid import MolGrid from .dispatch import display, save -from .select import ( - selection, get_selection, - _update_current_grid, _set_selection, _del_selection) +from .utils import sdf_to_dataframe from ._version import __version__ \ No newline at end of file diff --git a/mols2grid/utils.py b/mols2grid/utils.py index 026e25e..5027b41 100644 --- a/mols2grid/utils.py +++ b/mols2grid/utils.py @@ -1,6 +1,7 @@ from functools import wraps from importlib.util import find_spec -from rdkit.Chem import MolToSmiles +from rdkit import Chem +import pandas as pd def requires(module): def inner(func): @@ -36,10 +37,15 @@ def tooltip_formatter(s, subset, fmt, style): def mol_to_smiles(mol): """Returns a SMILES from an RDKit molecule, or None if not an RDKit mol""" - return MolToSmiles(mol) if mol else None + return Chem.MolToSmiles(mol) if mol else None def mol_to_record(mol, mol_col="mol"): """Function to create a dict of data from an RDKit molecule""" - return {"SMILES": MolToSmiles(mol), + return {"SMILES": Chem.MolToSmiles(mol), **mol.GetPropsAsDict(includePrivate=True), - mol_col: mol} if mol else {} \ No newline at end of file + mol_col: mol} if mol else {} + +def sdf_to_dataframe(sdf_path): + """Returns a dataframe of molecules from an SDF file""" + return pd.DataFrame([mol_to_record(mol, "mol") + for mol in Chem.SDMolSupplier(sdf_path)]) From 93b3613407938c8e1ea6d6c1caf261cbedc560fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 20 Sep 2021 20:32:29 +0200 Subject: [PATCH 16/74] keep old selection API available --- mols2grid/__init__.py | 3 +- mols2grid/molgrid.py | 7 ++- mols2grid/select.py | 105 ++++++++++++++++++++------------- mols2grid/templates/pages.html | 14 ++--- 4 files changed, 77 insertions(+), 52 deletions(-) diff --git a/mols2grid/__init__.py b/mols2grid/__init__.py index 547daa0..5b3cdb2 100644 --- a/mols2grid/__init__.py +++ b/mols2grid/__init__.py @@ -1,4 +1,5 @@ from .molgrid import MolGrid from .dispatch import display, save +from .select import get_selection, selection from .utils import sdf_to_dataframe -from ._version import __version__ \ No newline at end of file +from ._version import __version__ diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index f092b4f..fb2564e 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -10,7 +10,7 @@ from rdkit.Chem import Draw from jinja2 import Environment, FileSystemLoader from .utils import requires, tooltip_formatter, mol_to_record, mol_to_smiles -from .select import get_selection, selection as SELECTION +from .select import register try: from IPython.display import HTML except ModuleNotFoundError: @@ -85,7 +85,8 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, self.smiles_col = smiles_col # register instance self._grid_id = MolGrid._n_instances if name is None else name - SELECTION[self._grid_id] = {} + register.SELECTIONS[self._grid_id] = {} + register.current_selection = self._grid_id MolGrid._n_instances += 1 @classmethod @@ -400,7 +401,7 @@ def get_selection(self): ------- pandas.DataFrame """ - sel = list(get_selection().keys()) + sel = list(register.get_selection().keys()) return (self.dataframe.loc[self.dataframe["mols2grid-id"].isin(sel)] .drop(columns=self._extra_columns)) diff --git a/mols2grid/select.py b/mols2grid/select.py index 502953a..41e9fba 100644 --- a/mols2grid/select.py +++ b/mols2grid/select.py @@ -1,47 +1,70 @@ -from copy import deepcopy - -selection = {} -current_selection = 0 - -def _update_current_grid(grid_id): - global current_selection - current_selection = grid_id - -def _set_selection(_id, smiles): - global selection - global current_selection - selection[current_selection][_id] = smiles - -def _del_selection(_id): - global selection - global current_selection - del selection[current_selection][_id] - -def get_selection(grid_id=None, copy=True): - """Returns the selection for a specific MolGrid instance - - Parameters - ---------- - grid_id : int, str or None - Name of the grid to fetch the selection from. If `None`, the most - recently updated grid is returned - copy : bool - Return a copy of the selection instead of the original object - """ - global selection - global current_selection - grid_id = current_selection if grid_id is None else grid_id - sel = selection[grid_id] - if copy: - return deepcopy(sel) - return sel +import warnings +from collections import UserDict +class SelectionRegister: + """Register for grid selections""" + def __init__(self): + self.SELECTIONS = {} + self.current_selection = 0 + + def _update_current_grid(self, grid_id): + self.current_selection = grid_id + + def _set_selection(self, _id, smiles): + self.SELECTIONS[self.current_selection][_id] = smiles + + def _del_selection(self, _id): + del self.SELECTIONS[self.current_selection][_id] + + def get_selection(self, grid_id=None): + """Returns the selection for a specific MolGrid instance + + Parameters + ---------- + grid_id : int, str or None + Name of the grid to fetch the selection from. If `None`, the most + recently updated grid is returned + """ + grid_id = self.current_selection if grid_id is None else grid_id + return self.SELECTIONS.get(grid_id, {}) + + +class _OldSelection(UserDict): + def __init__(self, register): + self._sel = register.get_selection + super().__init__() + + def __repr__(self): + warnings.warn( + "Accessing the current grid's selection through " + "`mols2grid.selection` is deprecated and will be removed soon. " + "Please use `mols2grid.get_selection()` instead") + return repr(self._sel()) + + def __iter__(self): + return iter(self._sel()) + + def __len__(self): + return len(self._sel()) + + def __missing__(self, key): + return self._sel()[key] + + +register = SelectionRegister() +get_selection = register.get_selection +selection = _OldSelection(register) + + +# Callbacks for Google Colab try: from google import colab except (ModuleNotFoundError, ImportError): pass else: - colab.output.register_callback('m2g._update_current_grid', - _update_current_grid) - colab.output.register_callback('m2g._set_selection', _set_selection) - colab.output.register_callback('m2g._del_selection', _del_selection) + colab.output.register_callback('m2g_sel._update_current_grid', + register._update_current_grid) + colab.output.register_callback('m2g_sel._set_selection', + register._set_selection) + colab.output.register_callback('m2g_sel._del_selection', + register._del_selection) diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index 391b795..5a09c76 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -111,35 +111,35 @@ if (window.parent.IPython !== undefined) { // Jupyter notebook var kernel = window.parent.IPython.notebook.kernel; - kernel.execute('import mols2grid') + kernel.execute('from mols2grid.select import register as m2g_sel') function update_current_grid(grid_id) { grid_id = typeof grid_id === "string" ? "'"+grid_id+"'" : grid_id; - kernel.execute("mols2grid._update_current_grid("+grid_id+")"); + kernel.execute("m2g_sel._update_current_grid("+grid_id+")"); } function set_selection(_id, smiles) { - kernel.execute("mols2grid._set_selection("+_id+",'"+smiles+"')"); + kernel.execute("m2g_sel._set_selection("+_id+",'"+smiles+"')"); } function del_selection(_id) { - kernel.execute("mols2grid._del_selection("+_id+")"); + kernel.execute("m2g_sel._del_selection("+_id+")"); } } else if (window.parent.google !== undefined) { // Google colab var kernel = window.parent.google.colab.kernel; function update_current_grid(grid_id) { (async function() { - const result = await kernel.invokeFunction('m2g._update_current_grid', + const result = await kernel.invokeFunction('m2g_sel._update_current_grid', [grid_id], {}); })(); } function set_selection(_id, smiles) { (async function() { - const result = await kernel.invokeFunction('m2g._set_selection', + const result = await kernel.invokeFunction('m2g_sel._set_selection', [_id, smiles], {}); })(); } function del_selection(_id) { (async function() { - const result = await kernel.invokeFunction('m2g._del_selection', + const result = await kernel.invokeFunction('m2g_sel._del_selection', [_id], {}); })(); } From bfc7f6bc6695e4d53d3be9ca8a9674af5d5f0da3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 21 Sep 2021 02:11:52 +0200 Subject: [PATCH 17/74] fix rendering svg in tooltips --- mols2grid/templates/pages.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index 5a09c76..5073924 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -167,7 +167,6 @@ } $('#mols2grid button.sort-btn').click(function(e) { var _field = $(this).attr("data-name"); - console.log(_field); if (_field == sort_field) { $(this).removeClass("arrow-" + sort_order) sort_order = (sort_order === "desc") ? "asc" : "desc"; @@ -228,6 +227,7 @@ placement: {{ tooltip_placement }}, trigger: {{ tooltip_trigger }}, html: true, + sanitize: false, }); }) }); From 137a172d54f6129da7a5de93b866279e5375f27c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 21 Sep 2021 02:12:15 +0200 Subject: [PATCH 18/74] automatically resize iframe to fit content --- mols2grid/molgrid.py | 30 ++++++++++++++---------------- 1 file changed, 14 insertions(+), 16 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index fb2564e..a490df9 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -530,22 +530,20 @@ def display(self, width="100%", height=None, **kwargs): """Render and display the grid in a Jupyter notebook""" code = self.render(**kwargs) template = kwargs.get("template", "pages") - if not height: - n_cols = kwargs.get("n_cols", 5) - tot_rows = ceil(self.dataframe.shape[0] / n_cols) - n_rows = min([kwargs.get("n_rows", 3), tot_rows]) - img_height = self.img_size[1] - gap = kwargs.get("gap", 0) - border = 1 - fontsize = 12 - subset = kwargs.get("subset", self.dataframe.columns) - subset = self.dataframe.columns if subset is None else subset - n_txt_fields = len(subset) - 1 - cell_height = img_height + 2 * (gap + 2 * border) + n_txt_fields * (2 * fontsize) - searchbar_height = 70 if template == "pages" else 0 - height = n_rows * cell_height + searchbar_height - iframe = ('') + if height: + iframe = ( + '') + else: + # automatically resize iframe + iframe = ( + '' + '' + ) return HTML(iframe.format(width=width, height=height, code=escape(code))) From 112799ea031c4aa78bbcc77763d5e3bb24030558 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 21 Sep 2021 02:42:24 +0200 Subject: [PATCH 19/74] deprecation warning on mg.selection use --- mols2grid/select.py | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/mols2grid/select.py b/mols2grid/select.py index 41e9fba..30696d4 100644 --- a/mols2grid/select.py +++ b/mols2grid/select.py @@ -29,24 +29,35 @@ def get_selection(self, grid_id=None): return self.SELECTIONS.get(grid_id, {}) +# deprecate old selection system +def warn(func): + def wrapper(*args, **kwargs): + warnings.warn( + "Accessing the current grid's selection through " + "`mols2grid.selection` is deprecated and will be removed soon. " + "Please use `mols2grid.get_selection()` instead") + return func(*args, **kwargs) + return wrapper + + class _OldSelection(UserDict): def __init__(self, register): self._sel = register.get_selection super().__init__() + @warn def __repr__(self): - warnings.warn( - "Accessing the current grid's selection through " - "`mols2grid.selection` is deprecated and will be removed soon. " - "Please use `mols2grid.get_selection()` instead") return repr(self._sel()) + @warn def __iter__(self): return iter(self._sel()) + @warn def __len__(self): return len(self._sel()) + @warn def __missing__(self, key): return self._sel()[key] From 00d48f4717093c0eb27348b99a55c30d928bb768 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 21 Sep 2021 02:42:51 +0200 Subject: [PATCH 20/74] add func to get list of grid names --- mols2grid/__init__.py | 2 +- mols2grid/select.py | 5 +++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/mols2grid/__init__.py b/mols2grid/__init__.py index 5b3cdb2..2d715bb 100644 --- a/mols2grid/__init__.py +++ b/mols2grid/__init__.py @@ -1,5 +1,5 @@ from .molgrid import MolGrid from .dispatch import display, save -from .select import get_selection, selection +from .select import get_selection, selection, list_grids from .utils import sdf_to_dataframe from ._version import __version__ diff --git a/mols2grid/select.py b/mols2grid/select.py index 30696d4..334da0e 100644 --- a/mols2grid/select.py +++ b/mols2grid/select.py @@ -28,6 +28,10 @@ def get_selection(self, grid_id=None): grid_id = self.current_selection if grid_id is None else grid_id return self.SELECTIONS.get(grid_id, {}) + def list_grids(self): + """Returns a list of grid names""" + return list(self.SELECTIONS.keys()) + # deprecate old selection system def warn(func): @@ -64,6 +68,7 @@ def __missing__(self, key): register = SelectionRegister() get_selection = register.get_selection +list_grids = register.list_grids selection = _OldSelection(register) From ec1b5f25e542f02efc2a9ae2a035381d4f78dfae Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 21 Sep 2021 04:22:08 +0200 Subject: [PATCH 21/74] add style for whole cell --- mols2grid/molgrid.py | 36 +++++++++++++++++++++++++--------- mols2grid/templates/pages.html | 18 ++++++++++++++--- 2 files changed, 42 insertions(+), 12 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index a490df9..715615e 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -341,15 +341,25 @@ def to_pages(self, subset=None, tooltip=None, content.append(s) column_map[smiles] = f"data-{smiles}" # set mapping for list.js - value_names = "[{data: ['mols2grid-id']}, " + str(value_names)[1:] - + if "__all__" in style.keys(): + whole_cell_style = True + x = "[{data: ['mols2grid-id', 'cellstyle']}, " + else: + whole_cell_style = False + x = "[{data: ['mols2grid-id']}, " + value_names = x + str(value_names)[1:] + # apply CSS styles for col, func in style.items(): - name = f"style-{col}" - df[name] = df[col].apply(func) + if col == "__all__": + name = "cellstyle" + df[name] = df.apply(func, axis=1) + else: + name = f"style-{col}" + df[name] = df[col].apply(func) final_columns.append(name) value_names = value_names[:-1] + f", {{ attr: 'style', name: {name!r} }}]" - + # apply custom user function for col, func in transform.items(): df[col] = df[col].apply(func) @@ -361,10 +371,17 @@ def to_pages(self, subset=None, tooltip=None, value_names = (value_names[:-1] + ", {attr: 'data-content', name: 'mols2grid-tooltip'}]") - checkbox = '' - item = '
      {}{}
      '.format( - checkbox if selection else "", - "".join(content)) + if selection: + checkbox = '' + else: + checkbox = "" + if whole_cell_style: + item = ('
      {checkbox}{content}
      ') + else: + item = ('
      ' + '{checkbox}{content}
      ') + item = item.format(checkbox=checkbox, content="".join(content)) df = df[final_columns].rename(columns=column_map) @@ -391,6 +408,7 @@ def to_pages(self, subset=None, tooltip=None, smiles_col = smiles, sort_cols = sort_cols, grid_id = self._grid_id, + whole_cell_style = whole_cell_style, ) return template.render(**template_kwargs) diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index 5073924..a00a361 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -104,8 +104,8 @@ }, } ); - listObj.remove("mols2grid-id", "0") - listObj.add({{ data }}) + listObj.remove("mols2grid-id", "0"); + listObj.add({{ data }}); {% if selection %} // checkbox if (window.parent.IPython !== undefined) { @@ -213,6 +213,18 @@ listObj.search(query, ["data-{{ smiles_col }}"], SmartsSearch); } }); + {% if whole_cell_style %} + // add style for whole cell + listObj.on("updated", function (list) { + $('#mols2grid div.cell').each(function() { + var $t = $(this); + $t.attr({ + style: $t.attr('data-cellstyle') + }) + .removeAttr('data-cellstyle'); + }); + }); + {% endif %} {% if tooltip %} // tooltips $.fn.tooltip.Constructor.Default.whiteList.span = ['style'] @@ -249,7 +261,7 @@ }); } {% endif %} - {% if tooltip or selection %} + {%if tooltip or selection or whole_cell_style %} listObj.update(); {% endif %} From 7f5aefee01488ddc2e3a2cf2be7f594c78b30753 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 21 Sep 2021 16:29:36 +0200 Subject: [PATCH 22/74] fix iframe resizing --- mols2grid/molgrid.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 715615e..02314b3 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -547,7 +547,6 @@ def to_table(self, subset=None, tooltip=None, n_cols=6, def display(self, width="100%", height=None, **kwargs): """Render and display the grid in a Jupyter notebook""" code = self.render(**kwargs) - template = kwargs.get("template", "pages") if height: iframe = ( '' ) return HTML(iframe.format(width=width, height=height, From 8b58a83d43b1247aea01c48c8d1198616b8298c4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 21 Sep 2021 17:33:33 +0200 Subject: [PATCH 23/74] fix tooltip formatting --- mols2grid/molgrid.py | 11 ++++++----- mols2grid/utils.py | 5 ++++- 2 files changed, 10 insertions(+), 6 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 02314b3..7bdc4e5 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -360,17 +360,18 @@ def to_pages(self, subset=None, tooltip=None, final_columns.append(name) value_names = value_names[:-1] + f", {{ attr: 'style', name: {name!r} }}]" - # apply custom user function - for col, func in transform.items(): - df[col] = df[col].apply(func) - if tooltip: df["mols2grid-tooltip"] = df.apply(tooltip_formatter, axis=1, - args=(tooltip, tooltip_fmt, style)) + args=(tooltip, tooltip_fmt, style, + transform)) final_columns = final_columns + ["mols2grid-tooltip"] value_names = (value_names[:-1] + ", {attr: 'data-content', name: 'mols2grid-tooltip'}]") + # apply custom user function + for col, func in transform.items(): + df[col] = df[col].apply(func) + if selection: checkbox = '' else: diff --git a/mols2grid/utils.py b/mols2grid/utils.py index 5027b41..2ac2676 100644 --- a/mols2grid/utils.py +++ b/mols2grid/utils.py @@ -15,7 +15,7 @@ def wrapper(*args, **kwargs): return wrapper return inner -def tooltip_formatter(s, subset, fmt, style): +def tooltip_formatter(s, subset, fmt, style, transform): """Function to generate tooltips from a pandas Series Parameters @@ -28,9 +28,12 @@ def tooltip_formatter(s, subset, fmt, style): Format string for each key-value pair of the tooltip style : dict CSS styling applied to each item independently + transform : dict + Functions applied to each value before rendering """ items = [] for k, v in s[subset].to_dict().items(): + v = transform[k](v) if transform.get(k) else v v = f'{v}' if style.get(k) else v items.append(fmt.format(key=k, value=v)) return "
      ".join(items) From 013fbb167bdfa95466d3e4670e337e4a2efa85c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 21 Sep 2021 17:34:21 +0200 Subject: [PATCH 24/74] reorganize files --- mols2grid/templates/css/pages.css | 42 +++ .../templates/html/checkbox_dropdown.html | 9 + mols2grid/templates/html/pages_header.html | 5 + mols2grid/templates/js/kernel.js | 47 +++ mols2grid/templates/js/molstorage.js | 22 ++ mols2grid/templates/js/pages.js | 66 ++++ mols2grid/templates/js/search.js | 33 ++ mols2grid/templates/js/selection_actions.js | 51 +++ mols2grid/templates/js/sort.js | 32 ++ mols2grid/templates/pages.html | 306 +----------------- 10 files changed, 312 insertions(+), 301 deletions(-) create mode 100644 mols2grid/templates/css/pages.css create mode 100644 mols2grid/templates/html/checkbox_dropdown.html create mode 100644 mols2grid/templates/html/pages_header.html create mode 100644 mols2grid/templates/js/kernel.js create mode 100644 mols2grid/templates/js/molstorage.js create mode 100644 mols2grid/templates/js/pages.js create mode 100644 mols2grid/templates/js/search.js create mode 100644 mols2grid/templates/js/selection_actions.js create mode 100644 mols2grid/templates/js/sort.js diff --git a/mols2grid/templates/css/pages.css b/mols2grid/templates/css/pages.css new file mode 100644 index 0000000..a344c89 --- /dev/null +++ b/mols2grid/templates/css/pages.css @@ -0,0 +1,42 @@ +#mols2grid.gridcontainer { + display: block; + padding-left: 1em; + max-width: {{ width }}px; + width: {{ width }}px; +} +#mols2grid .cell { + border: {{ border }}; + text-align: {{ textalign }}; + vertical-align: top; + max-width: {{ cell_width }}px; + width: {{ cell_width }}px; + font-family: {{ fontfamily }}; + font-size: {{ fontsize }}; + padding: 0; + margin: {{ gap }}; + float: left; +} +#mols2grid .cell:hover { + background-color: {{ hover_color }}; +} +#mols2grid .cell img, #mols2grid .cell svg { + max-width: 100%; + height: auto; + padding: 0; +} +#mols2grid .data { + overflow: hidden; + white-space: nowrap; + text-overflow: ellipsis; + display: block; +} +#mols2grid .arrow-asc:after { + content: '↑'; + text-align: right; + float:right; +} +#mols2grid .arrow-desc:after { + content: '↓'; + text-align: right; + float:right; +} \ No newline at end of file diff --git a/mols2grid/templates/html/checkbox_dropdown.html b/mols2grid/templates/html/checkbox_dropdown.html new file mode 100644 index 0000000..551a63b --- /dev/null +++ b/mols2grid/templates/html/checkbox_dropdown.html @@ -0,0 +1,9 @@ + \ No newline at end of file diff --git a/mols2grid/templates/html/pages_header.html b/mols2grid/templates/html/pages_header.html new file mode 100644 index 0000000..7854c47 --- /dev/null +++ b/mols2grid/templates/html/pages_header.html @@ -0,0 +1,5 @@ + + + + + \ No newline at end of file diff --git a/mols2grid/templates/js/kernel.js b/mols2grid/templates/js/kernel.js new file mode 100644 index 0000000..1ce98cb --- /dev/null +++ b/mols2grid/templates/js/kernel.js @@ -0,0 +1,47 @@ +if (window.parent.IPython !== undefined) { + // Jupyter notebook + var kernel = window.parent.IPython.notebook.kernel; + kernel.execute('from mols2grid.select import register as m2g_sel') + function update_current_grid(grid_id) { + grid_id = typeof grid_id === "string" ? "'"+grid_id+"'" : grid_id; + kernel.execute("m2g_sel._update_current_grid("+grid_id+")"); + } + function set_selection(_id, smiles) { + SELECTION.set(_id, smiles); + kernel.execute("m2g_sel._set_selection("+_id+",'"+smiles+"')") + } + function del_selection(_id) { + SELECTION.delete(_id); + kernel.execute("m2g_sel._del_selection("+_id+")"); + } +} else if (window.parent.google !== undefined) { + // Google colab + var kernel = window.parent.google.colab.kernel; + function update_current_grid(grid_id) { + (async function() { + const result = await kernel.invokeFunction('m2g_sel._update_current_grid', + [grid_id], {}); + })(); + } + function set_selection(_id, smiles) { + SELECTION.set(_id, smiles); + (async function() { + const result = await kernel.invokeFunction('m2g_sel._set_selection', + [_id, smiles], {}); + })(); + } + function del_selection(_id) { + SELECTION.delete(_id); + (async function() { + const result = await kernel.invokeFunction('m2g_sel._del_selection', + [_id], {}); + })(); + } +} else { + function set_selection(_id, smiles) { + SELECTION.set(_id, smiles); + } + function del_selection(_id) { + SELECTION.delete(_id); + } +} \ No newline at end of file diff --git a/mols2grid/templates/js/molstorage.js b/mols2grid/templates/js/molstorage.js new file mode 100644 index 0000000..c1045aa --- /dev/null +++ b/mols2grid/templates/js/molstorage.js @@ -0,0 +1,22 @@ +class MolStorage extends Map { + to_dict() { + var content = "{"; + for (let [key, value] of this) { + content += key + ":" + JSON.stringify(value) + ","; + } + content = content.length > 1 ? content.slice(0, -1) : content; + content += "}"; + return content + } + download_smi(fileName) { + var content = ""; + for (let [key, value] of this) { + content += value + "\n"; + } + var a = document.createElement("a"); + var file = new Blob([content], {type: "text/plain"}); + a.href = URL.createObjectURL(file); + a.download = fileName; + a.click(); + } +} \ No newline at end of file diff --git a/mols2grid/templates/js/pages.js b/mols2grid/templates/js/pages.js new file mode 100644 index 0000000..8fb32ea --- /dev/null +++ b/mols2grid/templates/js/pages.js @@ -0,0 +1,66 @@ +// RDKit +onRuntimeInitialized: initRDKitModule().then(function(instance) { + RDKitModule = instance; + console.log('RDKit version: ' + RDKitModule.version()); +}); +// list.js +var listObj = new List('mols2grid', { + valueNames: {{ value_names }}, + item: {{ item_repr }}, + page: {{ n_items_per_page }}, + pagination: { + name: "pagination", + item: '
      • ', + innerWindow: 1, + outerWindow: 1, + }, +}); +listObj.remove("mols2grid-id", "0"); +listObj.add({{ data }}); +{% if selection %} +// selection +{% include 'js/molstorage.js' %} +var SELECTION = new MolStorage(); +{% include 'js/kernel.js' %} +{% endif %} +// sort +{% include 'js/sort.js' %} +// search bar +{% include 'js/search.js' %} +{% if whole_cell_style %} +// add style for whole cell +listObj.on("updated", function (list) { + $('#mols2grid div.cell').each(function() { + var $t = $(this); + $t.attr({ + style: $t.attr('data-cellstyle') + }) + .removeAttr('data-cellstyle'); + }); +}); +{% endif %} +{% if tooltip %} +// tooltips +$.fn.tooltip.Constructor.Default.whiteList.span = ['style'] +listObj.on("updated", function (list) { + $(function () { + // hide previous popovers + $('#mols2grid a.page-link').click(function(e) { + $('.mols2grid-tooltip[data-toggle="popover"]').popover('hide') + }); + // create new popover + $('.mols2grid-tooltip[data-toggle="popover"]').popover({ + placement: {{ tooltip_placement }}, + trigger: {{ tooltip_trigger }}, + html: true, + sanitize: false, + }); + }) +}); +{% endif %} +{% if selection %} +{% include 'js/selection_actions.js' %} +{% endif %} +{%if tooltip or selection or whole_cell_style %} +listObj.update(); +{% endif %} \ No newline at end of file diff --git a/mols2grid/templates/js/search.js b/mols2grid/templates/js/search.js new file mode 100644 index 0000000..22ee496 --- /dev/null +++ b/mols2grid/templates/js/search.js @@ -0,0 +1,33 @@ +function SmartsSearch(query, columns) { + query = $('#mols2grid #searchbar').val(); + var smiles = columns[0]; + var qmol = RDKitModule.get_qmol(query); + if (qmol.is_valid()) { + for (var k = 0, kl = listObj.items.length; k < kl; k++) { + var item = listObj.items[k]; + var mol = RDKitModule.get_mol(item.values()[smiles]); + var results = JSON.parse(mol.get_substruct_match(qmol)); + if (results.atoms) { + item.found = true; + } else { + item.found = false; + } + mol.delete(); + } + } + qmol.delete(); +} +var search_type = "Text"; +$('#mols2grid .search-btn').click(function() { + search_type = $(this).text(); + $('#mols2grid button.search-btn.active').removeClass("active"); + $(this).addClass("active"); +}); +$('#mols2grid #searchbar').on("keyup", function(e) { + var query = e.target.value; + if (search_type === "Text") { + listObj.search(query, {{ search_cols }}); + } else { + listObj.search(query, ["data-{{ smiles_col }}"], SmartsSearch); + } +}); \ No newline at end of file diff --git a/mols2grid/templates/js/selection_actions.js b/mols2grid/templates/js/selection_actions.js new file mode 100644 index 0000000..06078b2 --- /dev/null +++ b/mols2grid/templates/js/selection_actions.js @@ -0,0 +1,51 @@ +// add selection buttons +$("#sort-dropdown").before(`{% include 'html/checkbox_dropdown.html' %}`); +// check all +$('#btn-chkbox-all').click(function (e) { + var current_page = parseInt($("li.page-item.active > a").text()); + var n_items = {{ n_items_per_page }}; + var last_page = parseInt($("li.page-item > a").last().text()); + for (let i = 0; i < last_page; i++) { + listObj.show(i * n_items + 1, n_items); + $("input:checkbox").each(function() { + this.checked = true; + $(this).trigger("change"); + }); + } + listObj.show((current_page - 1) * n_items + 1, n_items); +}); +// invert +$('#btn-chkbox-invert').click(function (e) { + var current_page = parseInt($("li.page-item.active > a").text()); + var n_items = {{ n_items_per_page }}; + var last_page = parseInt($("li.page-item > a").last().text()); + for (let i = 0; i < last_page; i++) { + listObj.show(i * n_items + 1, n_items); + $("input:checkbox").each(function() { + this.checked = !this.checked; + $(this).trigger("change"); + }); + } + listObj.show((current_page - 1) * n_items + 1, n_items); +}); +// copy to clipboard +$("#btn-chkbox-copy").click(function(e) { + navigator.clipboard.writeText(SELECTION.to_dict()); +}); +// export smiles +$("#btn-chkbox-dlsmi").click(function(e) { + SELECTION.download_smi("selection.smi"); +}); +// update selection on checkbox click +listObj.on("updated", function (list) { + $("input:checkbox").change(function() { + update_current_grid({{ grid_id | tojson }}); + var _id = parseInt($(this).closest(".cell").attr("data-mols2grid-id")); + var _smiles = $($(this).siblings(".data-{{ smiles_col }}")[0]).text(); + if (this.checked) { + set_selection(_id, _smiles); + } else { + del_selection(_id); + } + }); +}); \ No newline at end of file diff --git a/mols2grid/templates/js/sort.js b/mols2grid/templates/js/sort.js new file mode 100644 index 0000000..59c1653 --- /dev/null +++ b/mols2grid/templates/js/sort.js @@ -0,0 +1,32 @@ +var sort_field = "mols2grid-id"; +var sort_order = "asc"; +function coerce_type(str) { + if (isNaN(str)) return null; + var num = parseFloat(str) + return isNaN(num) ? str : num; +} +function mols2gridSortFunction(itemA, itemB, options) { + var x = coerce_type(itemA.values()[options.valueName]); + var y = coerce_type(itemB.values()[options.valueName]); + if (x > y) { + return 1; + } else if (x < y) { + return -1; + } else { + return 0; + } +} +$('#mols2grid button.sort-btn').click(function(e) { + var _field = $(this).attr("data-name"); + if (_field == sort_field) { + $(this).removeClass("arrow-" + sort_order) + sort_order = (sort_order === "desc") ? "asc" : "desc"; + } else { + $('#mols2grid button.sort-btn.active').removeClass("active arrow-" + sort_order); + sort_order = "asc"; + sort_field = _field; + $(this).addClass("active"); + } + $(this).addClass("arrow-" + sort_order) + listObj.sort(_field, {order: sort_order, sortFunction: mols2gridSortFunction}); +}); \ No newline at end of file diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index e669a66..0f4e1c5 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -2,54 +2,11 @@ - - - - - + {% include 'html/pages_header.html' %}
      @@ -87,260 +44,7 @@
      \ No newline at end of file From 0e78a28ee0f0cce9575a04242c7221bd3d62bb00 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 21 Sep 2021 18:21:04 +0200 Subject: [PATCH 25/74] add custom css --- mols2grid/molgrid.py | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 7bdc4e5..c8ae433 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -214,7 +214,8 @@ def to_pages(self, subset=None, tooltip=None, fontsize="12pt", fontfamily="'DejaVu', sans-serif", textalign="center", tooltip_fmt="{key}: {value}", tooltip_trigger="click hover", tooltip_placement="bottom", - hover_color="#e7e7e7", style=None, selection=True, transform=None): + hover_color="#e7e7e7", style=None, selection=True, transform=None, + custom_css=None): """Returns the HTML document for the "pages" template Parameters @@ -256,7 +257,10 @@ def to_pages(self, subset=None, tooltip=None, input, and outputs a valid CSS styling, for example `style={"Solubility": lambda x: "color: red" if x < -5 else "color: black"}` if you want to color the text corresponding to the "Solubility" - column in your dataframe + column in your dataframe. You can also style a whole cell using the `__all__` + key, the corresponding function then has access to all values for each cell: + `style={"__all__": lambda x: "color: red" if x["Solubility"] < -5 else + "color: black"}` selection : bool Enables the selection of molecules and displays a checkbox at the top of each cell. This is only usefull in the context of a Jupyter notebook, which gives @@ -264,14 +268,16 @@ def to_pages(self, subset=None, tooltip=None, transform : dict or None Functions applied to specific items in all cells. The dict must follow a `key: function` structure where the key must correspond to one of the columns - in `subset`. The function takes the item's value as input and transforms it, - for example: + in `subset` or `tooltip`. The function takes the item's value as input and + transforms it, for example: `transform={"Solubility": lambda x: f"{x:.2f}", - "Melting point": lambda x: f"MP: {5/9*(x-32):.1f}°C"}` + "Melting point": lambda x: f"MP: {5/9*(x-32):.1f}°C"}` will round the solubility to 2 decimals, and display the melting point in Celsius instead of Fahrenheit with a single digit precision and some text before (MP) and after (°C) the value. These transformations only affect - columns in `subset` (not `tooltip`) and are applied independantly from `style` + columns in `subset` and `tooltip`, and do not interfere with `style`. + custom_css : str + Custom CSS properties applied to the content of the HTML document. """ df = self.dataframe.copy() cell_width = self.img_size[0] @@ -410,6 +416,7 @@ def to_pages(self, subset=None, tooltip=None, sort_cols = sort_cols, grid_id = self._grid_id, whole_cell_style = whole_cell_style, + custom_css = custom_css if custom_css else "", ) return template.render(**template_kwargs) From 880508da1b663571b9a0518b0a87159f0714d76d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 21 Sep 2021 18:40:00 +0200 Subject: [PATCH 26/74] fix hover_color with style __all__ --- mols2grid/templates/css/pages.css | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/mols2grid/templates/css/pages.css b/mols2grid/templates/css/pages.css index a344c89..839a83f 100644 --- a/mols2grid/templates/css/pages.css +++ b/mols2grid/templates/css/pages.css @@ -17,7 +17,7 @@ float: left; } #mols2grid .cell:hover { - background-color: {{ hover_color }}; + background-color: {{ hover_color }} !important; } #mols2grid .cell img, #mols2grid .cell svg { max-width: 100%; From 28f51fe87ff6e2743e7fd4ccda2079d430b44f9d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 21 Sep 2021 23:20:12 +0200 Subject: [PATCH 27/74] missing indent --- mols2grid/templates/js/search.js | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/mols2grid/templates/js/search.js b/mols2grid/templates/js/search.js index 22ee496..7ff4246 100644 --- a/mols2grid/templates/js/search.js +++ b/mols2grid/templates/js/search.js @@ -4,15 +4,15 @@ function SmartsSearch(query, columns) { var qmol = RDKitModule.get_qmol(query); if (qmol.is_valid()) { for (var k = 0, kl = listObj.items.length; k < kl; k++) { - var item = listObj.items[k]; - var mol = RDKitModule.get_mol(item.values()[smiles]); - var results = JSON.parse(mol.get_substruct_match(qmol)); - if (results.atoms) { - item.found = true; - } else { - item.found = false; - } - mol.delete(); + var item = listObj.items[k]; + var mol = RDKitModule.get_mol(item.values()[smiles]); + var results = JSON.parse(mol.get_substruct_match(qmol)); + if (results.atoms) { + item.found = true; + } else { + item.found = false; + } + mol.delete(); } } qmol.delete(); From f749cb9adc58afbd1a7a3a21c257c5b7e31c7875 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Wed, 22 Sep 2021 00:53:10 +0200 Subject: [PATCH 28/74] add filtering --- mols2grid/molgrid.py | 33 ++++++++++++++++++++++++++++++-- mols2grid/templates/js/filter.js | 7 +++++++ mols2grid/templates/js/pages.js | 6 +++++- mols2grid/templates/pages.html | 2 +- 4 files changed, 44 insertions(+), 4 deletions(-) create mode 100644 mols2grid/templates/js/filter.js diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index c8ae433..086fef7 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -4,15 +4,15 @@ import json from pathlib import Path from copy import deepcopy -from math import ceil import pandas as pd +import numpy as np from rdkit import Chem from rdkit.Chem import Draw from jinja2 import Environment, FileSystemLoader from .utils import requires, tooltip_formatter, mol_to_record, mol_to_smiles from .select import register try: - from IPython.display import HTML + from IPython.display import HTML, Javascript except ModuleNotFoundError: pass else: @@ -430,6 +430,35 @@ def get_selection(self): sel = list(register.get_selection().keys()) return (self.dataframe.loc[self.dataframe["mols2grid-id"].isin(sel)] .drop(columns=self._extra_columns)) + + def filter(self, mask): + """Filters the grid using a mask (boolean array) + + Parameters + ---------- + mask : list, pd.Series, np.ndarray + Boolean array: `True` when the item should be displayed, `False` if it should + be filtered out. + """ + # convert mask to mols2grid-id + ids = self.dataframe.loc[mask]["mols2grid-id"] + return self._filter_by_id(ids) + + def filter_by_index(self, indices): + """Filters the grid using the dataframe's index""" + # convert index to mols2grid-id + ids = self.dataframe.loc[self.dataframe.index.isin(indices)]["mols2grid-id"] + return self._filter_by_id(ids) + + def _filter_by_id(self, ids): + """Filters the grid using the values in the `mols2grid-id` column""" + if isinstance(ids, (pd.Series, np.ndarray)): + ids = ids.to_list() + code = env.get_template('js/filter.js').render( + grid_id = self._grid_id, + ids = ids, + ) + return Javascript(code) def to_table(self, subset=None, tooltip=None, n_cols=6, cell_width=160, border="1px solid #cccccc", gap=0, diff --git a/mols2grid/templates/js/filter.js b/mols2grid/templates/js/filter.js new file mode 100644 index 0000000..478b09a --- /dev/null +++ b/mols2grid/templates/js/filter.js @@ -0,0 +1,7 @@ +var iframe = mols2grid_iframe["{{ grid_id }}"]; +var listObj = iframe.listObj; +var kl = listObj.items.length; +var ids = {{ ids }}; +listObj.filter(function (item) { + return ids.includes(item.values()["mols2grid-id"]); +}); diff --git a/mols2grid/templates/js/pages.js b/mols2grid/templates/js/pages.js index 8fb32ea..1ba21ca 100644 --- a/mols2grid/templates/js/pages.js +++ b/mols2grid/templates/js/pages.js @@ -18,6 +18,9 @@ var listObj = new List('mols2grid', { listObj.remove("mols2grid-id", "0"); listObj.add({{ data }}); {% if selection %} +if (window.parent.mols2grid_iframe === undefined) { + window.parent.mols2grid_iframe = {}; +} // selection {% include 'js/molstorage.js' %} var SELECTION = new MolStorage(); @@ -63,4 +66,5 @@ listObj.on("updated", function (list) { {% endif %} {%if tooltip or selection or whole_cell_style %} listObj.update(); -{% endif %} \ No newline at end of file +{% endif %} +window.parent.mols2grid_iframe["{{ grid_id }}"] = window; diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index 0f4e1c5..28eadff 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -9,7 +9,7 @@ {% include 'html/pages_header.html' %} -
      +
      {{ item }}
      From 2c3a26ef5988033f689221caa5de04bb49cfeed1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Wed, 22 Sep 2021 13:56:17 +0200 Subject: [PATCH 29/74] sort by selection --- mols2grid/templates/js/sort.js | 27 ++++++++++++++++++++++++++- mols2grid/templates/pages.html | 3 +++ 2 files changed, 29 insertions(+), 1 deletion(-) diff --git a/mols2grid/templates/js/sort.js b/mols2grid/templates/js/sort.js index 59c1653..f90faed 100644 --- a/mols2grid/templates/js/sort.js +++ b/mols2grid/templates/js/sort.js @@ -16,6 +16,27 @@ function mols2gridSortFunction(itemA, itemB, options) { return 0; } } +function checkboxSort(itemA, itemB, options) { + if (itemA.elm !== undefined) { + var checkedA = itemA.elm.firstChild.checked; + if (itemB.elm !== undefined) { + var checkedB = itemB.elm.firstChild.checked; + if (checkedA && !checkedB) { + return -1; + } else if (!checkedA && checkedB) { + return 1; + } else { + return 0; + } + } else { + return -1; + } + } else if (itemB.elm !== undefined) { + return 1; + } else { + return 0; + } +} $('#mols2grid button.sort-btn').click(function(e) { var _field = $(this).attr("data-name"); if (_field == sort_field) { @@ -28,5 +49,9 @@ $('#mols2grid button.sort-btn').click(function(e) { $(this).addClass("active"); } $(this).addClass("arrow-" + sort_order) - listObj.sort(_field, {order: sort_order, sortFunction: mols2gridSortFunction}); + if (sort_field == "checkbox") { + listObj.sort("mols2grid-id", {order: sort_order, sortFunction: checkboxSort}); + } else { + listObj.sort(_field, {order: sort_order, sortFunction: mols2gridSortFunction}); + } }); \ No newline at end of file diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index 28eadff..4c6cfbd 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -28,6 +28,9 @@ {% endif %} {% endfor %} + {% if selection %} + + {% endif %}
      From ffbf4810f3c91f45feb643a473fa58339340c810 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Wed, 22 Sep 2021 14:06:46 +0200 Subject: [PATCH 30/74] fix selection when no kernel --- mols2grid/templates/js/kernel.js | 3 +++ 1 file changed, 3 insertions(+) diff --git a/mols2grid/templates/js/kernel.js b/mols2grid/templates/js/kernel.js index 1ce98cb..8b5c20e 100644 --- a/mols2grid/templates/js/kernel.js +++ b/mols2grid/templates/js/kernel.js @@ -38,6 +38,9 @@ if (window.parent.IPython !== undefined) { })(); } } else { + function update_current_grid(grid_id) { + null; + } function set_selection(_id, smiles) { SELECTION.set(_id, smiles); } From 5161181d8de6932ae3cf049f9140b144892ecc7b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Wed, 22 Sep 2021 17:44:52 +0200 Subject: [PATCH 31/74] add JS callbacks --- mols2grid/molgrid.py | 7 ++++++- mols2grid/templates/js/callback.js | 14 ++++++++++++++ mols2grid/templates/js/pages.js | 3 +++ 3 files changed, 23 insertions(+), 1 deletion(-) create mode 100644 mols2grid/templates/js/callback.js diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 086fef7..56413cb 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -215,7 +215,7 @@ def to_pages(self, subset=None, tooltip=None, textalign="center", tooltip_fmt="{key}: {value}", tooltip_trigger="click hover", tooltip_placement="bottom", hover_color="#e7e7e7", style=None, selection=True, transform=None, - custom_css=None): + custom_css=None, callback=None): """Returns the HTML document for the "pages" template Parameters @@ -278,6 +278,10 @@ def to_pages(self, subset=None, tooltip=None, columns in `subset` and `tooltip`, and do not interfere with `style`. custom_css : str Custom CSS properties applied to the content of the HTML document. + callback : str + JavaScript callback to be executed when clicking on an image. A dictionnary + containing the data for the full cell is available as `data`. All the values + are parsed as strings, except "mols2grid-id" which is always an integer. """ df = self.dataframe.copy() cell_width = self.img_size[0] @@ -417,6 +421,7 @@ def to_pages(self, subset=None, tooltip=None, grid_id = self._grid_id, whole_cell_style = whole_cell_style, custom_css = custom_css if custom_css else "", + callback = callback, ) return template.render(**template_kwargs) diff --git a/mols2grid/templates/js/callback.js b/mols2grid/templates/js/callback.js new file mode 100644 index 0000000..b94a911 --- /dev/null +++ b/mols2grid/templates/js/callback.js @@ -0,0 +1,14 @@ +listObj.on("updated", function (list) { + $('#mols2grid .data-img').click(function(e) { + var data = {} + data["mols2grid-id"] = parseInt($(this).closest(".cell") + .attr("data-mols2grid-id")); + $(this).siblings(".data").each(function() { + let name = this.className.split(" ") + .filter(cls => cls.startsWith("data-"))[0] + .substring(5); + data[name] = this.innerHTML; + }); + {{ callback }} + }); +}); \ No newline at end of file diff --git a/mols2grid/templates/js/pages.js b/mols2grid/templates/js/pages.js index 1ba21ca..73bd35a 100644 --- a/mols2grid/templates/js/pages.js +++ b/mols2grid/templates/js/pages.js @@ -64,6 +64,9 @@ listObj.on("updated", function (list) { {% if selection %} {% include 'js/selection_actions.js' %} {% endif %} +{% if callback %} +{% include 'js/callback.js' %} +{% endif %} {%if tooltip or selection or whole_cell_style %} listObj.update(); {% endif %} From 4b22236e9827060b680cc93abebf4bdfcaa0c1f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Wed, 22 Sep 2021 17:59:02 +0200 Subject: [PATCH 32/74] fix displaying sdf or mols directly --- mols2grid/molgrid.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 56413cb..dc9253c 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -83,6 +83,7 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, self.dataframe = dataframe if mol_col else dataframe.drop(columns=mol_col) self.img_size = kwargs.get("size", (160, 120)) self.smiles_col = smiles_col + self.mol_col = mol_col # register instance self._grid_id = MolGrid._n_instances if name is None else name register.SELECTIONS[self._grid_id] = {} @@ -283,7 +284,7 @@ def to_pages(self, subset=None, tooltip=None, containing the data for the full cell is available as `data`. All the values are parsed as strings, except "mols2grid-id" which is always an integer. """ - df = self.dataframe.copy() + df = self.dataframe.drop(columns=self.mol_col).copy() cell_width = self.img_size[0] smiles = self.smiles_col content = [] From 99438a54f7ad10b5a4a2e7a8c3b61ad8a74b891d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Wed, 22 Sep 2021 19:50:50 +0200 Subject: [PATCH 33/74] bump changelog and version --- CHANGELOG.md | 27 +++++++++++++++++++++++++++ mols2grid/_version.py | 2 +- 2 files changed, 28 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 44fe2c0..e22431a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,33 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). +## [0.0.7] - 2021/09/?? +### Added +- The grid can be filtered using pandas DataFrame's `query` and `loc` logic (mostly + useful to combine with ipywidgets). +- Selections can now be modified (select all, or invert) and exported (to clipboard or a + SMILES file) even without a notebook kernel. Fixes: Issue #16. +- The grid can be sorted according to the selection status and to values in the tooltips. +- Added tracking the selection in multiple grids at the same time (i.e. it's not a + global object that get's overwritten anymore). +- Added support for executing custom JavaScript code when clicking on a molecule's image + through the `callback` argument. +- Added styling for the whole cell through `style={"__all__": userfunction}`. +- Added `mols2grid.get_selection()` allowing users to specify which grid selection should + be returned. Without argument, the most recently updated grid is returned. +- Added `mols2grid.list_grids()` to return a list of grid names available. +- Added a function to easily convert an SDF file to a pandas DataFrame. +- Added the `custom_css` argument to pass custom CSS for the HTML document. +### Changed +- The functions in `style` and `transform` are now also applied to tooltips. +- The sizing of the iframe displaying the grid is now fully automated and more precise. +### Fixed +- Fixed `mols2grid.save` that returned an error about missing the `output` argument. +- The tooltip is now compatible with the "focus" mode: `tooltip_trigger="focus"`. +- Fixed rendering SVG images in tooltips. +### Deprecated +- Deprecated `mols2grid.selection` in favor of `mols2grid.get_selection()`. + ## [0.0.6] - 2021/05/14 ### Changed - Javascript module for RDKit is now sourced from `unpkg.com` and pinned to `v2021.3.2` diff --git a/mols2grid/_version.py b/mols2grid/_version.py index d85b28e..7d53ea3 100644 --- a/mols2grid/_version.py +++ b/mols2grid/_version.py @@ -1 +1 @@ -__version__ = "0.0.6" \ No newline at end of file +__version__ = "0.0.7" \ No newline at end of file From 57727ae92f78ed13f56ec3dacf95f3362de1f1b6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 26 Sep 2021 01:21:32 +0200 Subject: [PATCH 34/74] update docs --- mols2grid/dispatch.py | 43 ++++++++++++++++++++++++++++++++++++++----- mols2grid/molgrid.py | 12 ++++++------ 2 files changed, 44 insertions(+), 11 deletions(-) diff --git a/mols2grid/dispatch.py b/mols2grid/dispatch.py index 46f7568..83b0e61 100644 --- a/mols2grid/dispatch.py +++ b/mols2grid/dispatch.py @@ -14,6 +14,7 @@ def _prepare_kwargs(kwargs, kind): + """Separate kwargs for the init and render methods of MolGrid""" template = kwargs.pop("template", _SIGNATURE["render"]["template"].default) render_kwargs = {key: value for key, value in kwargs.items() @@ -43,15 +44,18 @@ def display(arg, **kwargs): coordGen : bool (True) Use the coordGen library instead of the RDKit one to depict the molecules in 2D - use_coords : bool + use_coords : bool (True) Use the coordinates of the molecules (only relevant when an SDF file, a list of molecules or a DataFrame of RDKit molecules were used as input) - remove_Hs : bool + remove_Hs : bool (False) Remove hydrogen atoms from the drawings size : tuple ((160, 120)) Size of each image - mapping : dict (None) + rename : dict (None) Rename the properties in the final document + name : str ("default") + Name of the grid. Used when retrieving selections from multiple grids + at the same time template : str ("pages") One of {pages, table} width : str ("100%) @@ -62,7 +66,8 @@ def display(arg, **kwargs): subset: list (None) Columns to be displayed in each cell of the grid. Each column's value will be displayed from top to bottom in the same order given here. - Use "img" for the image of the molecule. + Use "img" for the image of the molecule, and "mols2grid-id" for the + molecule's index in your input file. Default: all columns (with "img" in first position) tooltip : list (None) Columns to be displayed as a tooltip when hovering/clicking on the @@ -76,7 +81,7 @@ def display(arg, **kwargs): n_cols : int (5) Number of columns per page n_rows` : int (3) - Number of rows per page (only available for the "pages" template) + Only available for the "pages" template. Number of rows per page border : str ("1px solid #cccccc") Styling of the border around each cell (CSS) gap : int or str (0) @@ -99,6 +104,34 @@ def display(arg, **kwargs): ```python style={"Solubility": lambda x: "color: red" if x < -5 else "color: black"} ``` + You can also style a whole cell using the `__all__` key, the corresponding function then has access to all values for each cell: + ```python + style={"__all__": lambda x: "color: red" if x["Solubility"] < -5 else "color: black"}` + ``` + selection : bool (True) + Only available for the "pages" template. Enables the selection of molecules and + displays a checkbox at the top of each cell. To access your selection (index and + SMILES), use `mols2grid.get_selection()` or the export options in the bottom + checkbox dropdown menu. + transform : dict (None) + Functions applied to specific items in all cells. The dict must follow a + `key: function` structure where the key must correspond to one of the columns + in `subset` or `tooltip`. The function takes the item's value as input and + transforms it, for example: + `transform={"Solubility": lambda x: f"{x:.2f}", + "Melting point": lambda x: f"MP: {5/9*(x-32):.1f}°C"}` + will round the solubility to 2 decimals, and display the melting point in + Celsius instead of Fahrenheit with a single digit precision and some text + before (MP) and after (°C) the value. These transformations only affect + columns in `subset` and `tooltip`, and do not interfere with `style`. + custom_css : str + Only available for the "pages" template. Custom CSS properties applied to the + content of the HTML document. + callback : str + Only available for the "pages" template. JavaScript callback to be executed when + clicking on an image. A dictionnary containing the data for the full cell is + available as `data`. All the values are parsed as strings, except "mols2grid-id" + which is always an integer. Notes ----- diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index dc9253c..7d8228f 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -36,9 +36,9 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, Parameters ---------- df : pandas.DataFrame or dict or list - Dataframe containing a SMILES or mol column, or dictionary containing - a list of SMILES, or list of dictionnaries containing a SMILES - field + Dataframe containing a SMILES or mol column, or dictionary + containing a list of SMILES, or list of dictionnaries containing a + SMILES field smiles_col : str or None Name of the SMILES column in the dataframe, if available mol_col : str or None @@ -51,9 +51,9 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, Use SVG instead of PNG mapping : dict or None Rename the properties/fields stored in the molecule - name : int or str or None - Name of the grid, as shown in `mols2grid.selection`. If `None`, - the name is automatically set. + name : str + Name of the grid. Used when retrieving selections from multiple + grids at the same time kwargs : object Arguments passed to the `draw_mol` method """ From 7887d0d949c42fc4f6a3a9b6b891d3b6f30a0355 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 26 Sep 2021 01:24:32 +0200 Subject: [PATCH 35/74] force name to be a string --- mols2grid/molgrid.py | 17 +++++++++++------ mols2grid/select.py | 1 - mols2grid/templates/js/kernel.js | 3 +-- mols2grid/templates/js/selection_actions.js | 2 +- 4 files changed, 13 insertions(+), 10 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 7d8228f..a4c1e75 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -28,10 +28,9 @@ class MolGrid: """Class that handles drawing molecules, rendering the HTML document and saving or displaying it in a notebook """ - _n_instances = 0 def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, - useSVG=True, mapping=None, name=None, **kwargs): + useSVG=True, mapping=None, name="default", **kwargs): """ Parameters ---------- @@ -59,6 +58,8 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, """ if not (smiles_col or mol_col): raise ValueError("One of `smiles_col` or `mol_col` must be set") + if not isinstance(name, str): + raise TypeError(f"`name` must be a string. Currently of type {type(name)}") Draw.rdDepictor.SetPreferCoordGen(coordGen) self.useSVG = useSVG if isinstance(df, pd.DataFrame): @@ -85,10 +86,14 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, self.smiles_col = smiles_col self.mol_col = mol_col # register instance - self._grid_id = MolGrid._n_instances if name is None else name - register.SELECTIONS[self._grid_id] = {} - register.current_selection = self._grid_id - MolGrid._n_instances += 1 + self._grid_id = name + overwrite = register.SELECTIONS.get(name, False) + if overwrite: + warnings.warn( + f"Overwriting non-empty {name!r} grid selection: {str(overwrite)}" + ) + register.SELECTIONS[name] = {} + register.current_selection = name @classmethod def from_mols(cls, mols, **kwargs): diff --git a/mols2grid/select.py b/mols2grid/select.py index 334da0e..e9430c9 100644 --- a/mols2grid/select.py +++ b/mols2grid/select.py @@ -5,7 +5,6 @@ class SelectionRegister: """Register for grid selections""" def __init__(self): self.SELECTIONS = {} - self.current_selection = 0 def _update_current_grid(self, grid_id): self.current_selection = grid_id diff --git a/mols2grid/templates/js/kernel.js b/mols2grid/templates/js/kernel.js index 8b5c20e..2eb9123 100644 --- a/mols2grid/templates/js/kernel.js +++ b/mols2grid/templates/js/kernel.js @@ -3,8 +3,7 @@ if (window.parent.IPython !== undefined) { var kernel = window.parent.IPython.notebook.kernel; kernel.execute('from mols2grid.select import register as m2g_sel') function update_current_grid(grid_id) { - grid_id = typeof grid_id === "string" ? "'"+grid_id+"'" : grid_id; - kernel.execute("m2g_sel._update_current_grid("+grid_id+")"); + kernel.execute("m2g_sel._update_current_grid('"+grid_id+"')"); } function set_selection(_id, smiles) { SELECTION.set(_id, smiles); diff --git a/mols2grid/templates/js/selection_actions.js b/mols2grid/templates/js/selection_actions.js index 06078b2..6535f34 100644 --- a/mols2grid/templates/js/selection_actions.js +++ b/mols2grid/templates/js/selection_actions.js @@ -39,7 +39,7 @@ $("#btn-chkbox-dlsmi").click(function(e) { // update selection on checkbox click listObj.on("updated", function (list) { $("input:checkbox").change(function() { - update_current_grid({{ grid_id | tojson }}); + update_current_grid({{ grid_id }}); var _id = parseInt($(this).closest(".cell").attr("data-mols2grid-id")); var _smiles = $($(this).siblings(".data-{{ smiles_col }}")[0]).text(); if (this.checked) { From 018b246c6ec08f4255a2d009bc0b66af809bb8ea Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 26 Sep 2021 01:25:52 +0200 Subject: [PATCH 36/74] replace mapping by rename --- mols2grid/molgrid.py | 15 +++++++++++++-- 1 file changed, 13 insertions(+), 2 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index a4c1e75..cc4de55 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -30,7 +30,7 @@ class MolGrid: """ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, - useSVG=True, mapping=None, name="default", **kwargs): + useSVG=True, rename=None, name="default", **kwargs): """ Parameters ---------- @@ -55,6 +55,9 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, grids at the same time kwargs : object Arguments passed to the `draw_mol` method + + ..versionchanged: 0.0.7 + Added `rename` argument to replace `mapping` """ if not (smiles_col or mol_col): raise ValueError("One of `smiles_col` or `mol_col` must be set") @@ -65,9 +68,17 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, if isinstance(df, pd.DataFrame): dataframe = df.copy() else: + # list of dicts or other input formats for dataframes dataframe = pd.DataFrame(df) + mapping = kwargs.pop("mapping", None) if mapping: - dataframe.rename(columns=mapping, inplace=True) + warnings.warn( + "`mapping` is deprecated and will be removed soon. Consider " + "using `rename` in the future." + ) + rename = mapping or rename + if rename: + dataframe.rename(columns=rename, inplace=True) self._extra_columns = ["img", "mols2grid-id"] if smiles_col and not mol_col: mol_col = "mol" From ece9dbe1bfec028f862ba5aac918d18be57a1210 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 26 Sep 2021 01:26:33 +0200 Subject: [PATCH 37/74] add removeHs --- mols2grid/molgrid.py | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index cc4de55..9848cc2 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -30,7 +30,7 @@ class MolGrid: """ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, - useSVG=True, rename=None, name="default", **kwargs): + useSVG=True, removeHs=False, rename=None, name="default", **kwargs): """ Parameters ---------- @@ -48,7 +48,9 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, RDKit depiction library useSVG : bool Use SVG instead of PNG - mapping : dict or None + removeHs : bool + Remove hydrogen atoms from the drawings + rename : dict or None Rename the properties/fields stored in the molecule name : str Name of the grid. Used when retrieving selections from multiple @@ -84,7 +86,9 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, mol_col = "mol" self._extra_columns.append(mol_col) dataframe[mol_col] = dataframe[smiles_col].apply(Chem.MolFromSmiles) - elif mol_col and (smiles_col not in dataframe.columns): + if removeHs: + dataframe[mol_col] = dataframe[mol_col].apply(Chem.RemoveHs) + if mol_col and (smiles_col not in dataframe.columns): dataframe[smiles_col] = dataframe[mol_col].apply(mol_to_smiles) # add index dataframe["mols2grid-id"] = list(range(len(dataframe))) From d12c5a7420b817c4a96c988a6ef4c8d0ec7cbe26 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 26 Sep 2021 01:32:54 +0200 Subject: [PATCH 38/74] __all__ style and transform on tooltips for table --- mols2grid/molgrid.py | 13 ++++++++++--- 1 file changed, 10 insertions(+), 3 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 9848cc2..2b5b2db 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -542,7 +542,7 @@ def to_table(self, subset=None, tooltip=None, n_cols=6, will round the solubility to 2 decimals, and display the melting point in Celsius instead of Fahrenheit with a single digit precision and some text before (MP) and after (°C) the value. These transformations only affect - columns in `subset` (not `tooltip`) and are applied independantly from `style` + columns in `subset` and `tooltip`, and are applied independantly from `style` """ tr = [] data = [] @@ -561,11 +561,18 @@ def to_table(self, subset=None, tooltip=None, n_cols=6, ncell = i + 1 nrow, ncol = divmod(i, n_cols) td = [f''] + if "__all__" in style.keys(): + s = style["__all__"](row) + div = [f'
      '] + else: + div = [f'
      '] for col in subset: v = row[col] if col == "img" and tooltip: - popover = tooltip_formatter(row, tooltip, tooltip_fmt, style) + popover = tooltip_formatter(row, tooltip, tooltip_fmt, style, + transform) + func = transform.get(col) + v = func(v) if func else v item = (f'
      {v}
      ') else: From fc45acfb8f745451b460297658cf8f220ee778d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 26 Sep 2021 01:33:36 +0200 Subject: [PATCH 39/74] modify mol_col name in sdf_to_df --- mols2grid/utils.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mols2grid/utils.py b/mols2grid/utils.py index 2ac2676..d8bb749 100644 --- a/mols2grid/utils.py +++ b/mols2grid/utils.py @@ -48,7 +48,7 @@ def mol_to_record(mol, mol_col="mol"): **mol.GetPropsAsDict(includePrivate=True), mol_col: mol} if mol else {} -def sdf_to_dataframe(sdf_path): +def sdf_to_dataframe(sdf_path, mol_col="mol"): """Returns a dataframe of molecules from an SDF file""" - return pd.DataFrame([mol_to_record(mol, "mol") + return pd.DataFrame([mol_to_record(mol, mol_col) for mol in Chem.SDMolSupplier(sdf_path)]) From 69f070e1856981ce04487004cb030644dcea1b66 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 26 Sep 2021 01:48:36 +0200 Subject: [PATCH 40/74] make from_sdf use utils.sdf_to_df --- mols2grid/molgrid.py | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 2b5b2db..1026339 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -9,7 +9,11 @@ from rdkit import Chem from rdkit.Chem import Draw from jinja2 import Environment, FileSystemLoader -from .utils import requires, tooltip_formatter, mol_to_record, mol_to_smiles +from .utils import (requires, + tooltip_formatter, + mol_to_record, + mol_to_smiles, + sdf_to_dataframe) from .select import register try: from IPython.display import HTML, Javascript @@ -138,8 +142,7 @@ def from_sdf(cls, sdf_file, **kwargs): Other arguments passed on initialization """ mol_col = kwargs.pop("mol_col", "mol") - df = pd.DataFrame([mol_to_record(mol, mol_col) - for mol in Chem.SDMolSupplier(sdf_file)]) + df = sdf_to_dataframe(sdf_file, mol_col=mol_col) return cls(df, mol_col=mol_col, **kwargs) @property From 5da31f5be89be51c48534d906f18395df52da984 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 26 Sep 2021 22:43:22 +0200 Subject: [PATCH 41/74] refactoring MolGrid class --- mols2grid/molgrid.py | 108 +++++++++----------- mols2grid/templates/js/selection_actions.js | 2 +- mols2grid/utils.py | 6 ++ 3 files changed, 56 insertions(+), 60 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 1026339..f93b8ae 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -3,7 +3,6 @@ from html import escape import json from pathlib import Path -from copy import deepcopy import pandas as pd import numpy as np from rdkit import Chem @@ -13,7 +12,8 @@ tooltip_formatter, mol_to_record, mol_to_smiles, - sdf_to_dataframe) + sdf_to_dataframe, + remove_coordinates) from .select import register try: from IPython.display import HTML, Javascript @@ -33,8 +33,9 @@ class MolGrid: saving or displaying it in a notebook """ - def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, - useSVG=True, removeHs=False, rename=None, name="default", **kwargs): + def __init__(self, df, smiles_col="SMILES", mol_col=None, removeHs=False, + use_coords=True, coordGen=True, useSVG=True, size=(160, 120), + MolDrawOptions=None, rename=None, name="default", **kwargs): """ Parameters ---------- @@ -47,20 +48,31 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, mol_col : str or None Name of an RDKit molecule column. If available, coordinates and atom/bonds annotations from this will be used for depiction + removeHs : bool + Remove hydrogen atoms from the drawings + use_coords : bool + Use the existing coordinates of the molecule coordGen : bool Sets whether or not the CoordGen library should be preferred to the RDKit depiction library useSVG : bool Use SVG instead of PNG - removeHs : bool - Remove hydrogen atoms from the drawings + size : tuple + The size of the drawing canvas + MolDrawOptions : rdkit.Chem.Draw.MolDrawOptions or None + Drawing options. Useful for making highly customized drawings rename : dict or None Rename the properties/fields stored in the molecule name : str Name of the grid. Used when retrieving selections from multiple grids at the same time kwargs : object - Arguments passed to the `draw_mol` method + MolDrawOptions attributes + + Notes + ----- + The list of supported MolDrawOptions attributes are available in + https://www.rdkit.org/docs/source/rdkit.Chem.Draw.rdMolDraw2D.html#rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions ..versionchanged: 0.0.7 Added `rename` argument to replace `mapping` @@ -68,9 +80,9 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, if not (smiles_col or mol_col): raise ValueError("One of `smiles_col` or `mol_col` must be set") if not isinstance(name, str): - raise TypeError(f"`name` must be a string. Currently of type {type(name)}") + raise TypeError( + f"`name` must be a string. Currently of type {type(name).__name__}") Draw.rdDepictor.SetPreferCoordGen(coordGen) - self.useSVG = useSVG if isinstance(df, pd.DataFrame): dataframe = df.copy() else: @@ -82,16 +94,24 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, "`mapping` is deprecated and will be removed soon. Consider " "using `rename` in the future." ) - rename = mapping or rename + rename = rename or mapping if rename: dataframe.rename(columns=rename, inplace=True) self._extra_columns = ["img", "mols2grid-id"] + # generate temporary RDKit molecules if smiles_col and not mol_col: mol_col = "mol" + keep_mols = False self._extra_columns.append(mol_col) dataframe[mol_col] = dataframe[smiles_col].apply(Chem.MolFromSmiles) + else: + keep_mols = True + # remove hydrogens if removeHs: dataframe[mol_col] = dataframe[mol_col].apply(Chem.RemoveHs) + if not use_coords: + dataframe[mol_col] = dataframe[mol_col].apply(remove_coordinates) + # generate smiles col if mol_col and (smiles_col not in dataframe.columns): dataframe[smiles_col] = dataframe[mol_col].apply(mol_to_smiles) # add index @@ -99,9 +119,15 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, coordGen=True, # drop None dataframe.dropna(axis=0, subset=[mol_col], inplace=True) # generate drawings - dataframe["img"] = dataframe[mol_col].apply(self.mol_to_img, **kwargs) - self.dataframe = dataframe if mol_col else dataframe.drop(columns=mol_col) - self.img_size = kwargs.get("size", (160, 120)) + self.useSVG = useSVG + opts = MolDrawOptions or Draw.MolDrawOptions() + for key, value in kwargs.items(): + setattr(opts, key, value) + self.MolDrawOptions = opts + self._MolDraw2D = Draw.MolDraw2DSVG if useSVG else Draw.MolDraw2DCairo + self.img_size = size + dataframe["img"] = dataframe[mol_col].apply(self.mol_to_img) + self.dataframe = dataframe if keep_mols else dataframe.drop(columns=mol_col) self.smiles_col = smiles_col self.mol_col = mol_col # register instance @@ -127,7 +153,8 @@ def from_mols(cls, mols, **kwargs): Other arguments passed on initialization """ mol_col = kwargs.pop("mol_col", "mol") - df = pd.DataFrame([mol_to_record(mol, mol_col) for mol in mols]) + df = pd.DataFrame([mol_to_record(mol, mol_col=mol_col) + for mol in mols]) return cls(df, mol_col=mol_col, **kwargs) @classmethod @@ -160,60 +187,23 @@ def template(self, value): "Use one of 'pages' or 'table'") self._template = value - def draw_mol(self, mol, size=(160, 120), use_coords=True, - MolDrawOptions=None, **kwargs): - """Draw a molecule - - Parameters - ---------- - mol : rdkit.Chem.rdchem.Mol - The molecule to draw - size : tuple - The size of the drawing canvas - use_coords : bool - Use the 2D or 3D coordinates of the molecule - MolDrawOptions : rdkit.Chem.Draw.MolDrawOptions or None - Directly set the drawing options. Useful for making highly - customized drawings - **kwargs : object - Attributes of the rdkit.Chem.Draw.MolDrawOptions class like - `fixedBondLength=35, bondLineWidth=2` - - Notes - ----- - The list of supported MolDrawOptions attributes are available in - https://www.rdkit.org/docs/source/rdkit.Chem.Draw.rdMolDraw2D.html#rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions - """ - if self.useSVG: - d2d = Draw.MolDraw2DSVG(*size) - else: - d2d = Draw.MolDraw2DCairo(*size) - MolDrawOptions = MolDrawOptions or Draw.MolDrawOptions() - for key, value in kwargs.items(): - setattr(MolDrawOptions, key, value) - d2d.SetDrawOptions(MolDrawOptions) - if not use_coords: - mol = deepcopy(mol) - mol.RemoveAllConformers() + def draw_mol(self, mol): + """Draw a molecule""" + d2d = self._MolDraw2D(*self.img_size) + d2d.SetDrawOptions(self.MolDrawOptions) hl_atoms = getattr(mol, "__sssAtoms", []) d2d.DrawMolecule(mol, highlightAtoms=hl_atoms) d2d.FinishDrawing() return d2d.GetDrawingText() - - def mol_to_img(self, mol, **kwargs): - """Convert an RDKit mol to an HTML img tag containing a drawing of the + + def mol_to_img(self, mol): + """Convert an RDKit mol to an HTML image containing a drawing of the molecule""" - img = self.draw_mol(mol, **kwargs) + img = self.draw_mol(mol) if self.useSVG: return img data = b64encode(img).decode() return f'' - - def smi_to_img(self, smi, **kwargs): - """Convert a SMILES string to an HTML img tag containing a drawing of - the molecule""" - mol = Chem.MolFromSmiles(smi) - return self.mol_to_img(mol, **kwargs) def render(self, template="pages", **kwargs): """Returns the HTML document corresponding to the "pages" or "table" diff --git a/mols2grid/templates/js/selection_actions.js b/mols2grid/templates/js/selection_actions.js index 6535f34..06078b2 100644 --- a/mols2grid/templates/js/selection_actions.js +++ b/mols2grid/templates/js/selection_actions.js @@ -39,7 +39,7 @@ $("#btn-chkbox-dlsmi").click(function(e) { // update selection on checkbox click listObj.on("updated", function (list) { $("input:checkbox").change(function() { - update_current_grid({{ grid_id }}); + update_current_grid({{ grid_id | tojson }}); var _id = parseInt($(this).closest(".cell").attr("data-mols2grid-id")); var _smiles = $($(this).siblings(".data-{{ smiles_col }}")[0]).text(); if (this.checked) { diff --git a/mols2grid/utils.py b/mols2grid/utils.py index d8bb749..e7b97d2 100644 --- a/mols2grid/utils.py +++ b/mols2grid/utils.py @@ -52,3 +52,9 @@ def sdf_to_dataframe(sdf_path, mol_col="mol"): """Returns a dataframe of molecules from an SDF file""" return pd.DataFrame([mol_to_record(mol, mol_col) for mol in Chem.SDMolSupplier(sdf_path)]) + +def remove_coordinates(mol): + """Removes the existing coordinates from the molecule. The molecule is + modified inplace""" + mol.RemoveAllConformers() + return mol From a0adf9c12b97e46ce128a190aab0fe73adbc7703 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 26 Sep 2021 22:43:44 +0200 Subject: [PATCH 42/74] add tests --- setup.cfg | 8 +- tests/__init__.py | 0 tests/test_molgrid.py | 217 ++++++++++++++++++++++++++++++++++++++++++ 3 files changed, 224 insertions(+), 1 deletion(-) create mode 100644 tests/__init__.py create mode 100644 tests/test_molgrid.py diff --git a/setup.cfg b/setup.cfg index 6cc72ee..0ee8f28 100644 --- a/setup.cfg +++ b/setup.cfg @@ -37,4 +37,10 @@ install_requires = zip_safe = False [options.package_data] -mols2grid = templates/*.html +* = *.html, *.js, *.css + +[options.extras_require] +tests = + pytest>=6.2.5 + pytest-cov>=2.12.1 + codecov>=2.1.12 diff --git a/tests/__init__.py b/tests/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/tests/test_molgrid.py b/tests/test_molgrid.py new file mode 100644 index 0000000..4e4456a --- /dev/null +++ b/tests/test_molgrid.py @@ -0,0 +1,217 @@ +import pytest +from numpy.testing import assert_equal +from tempfile import NamedTemporaryFile +from pathlib import Path +from rdkit import RDConfig, Chem +from rdkit.Chem import Draw +from rdkit.Chem.rdDepictor import Compute2DCoords +from mols2grid import MolGrid, sdf_to_dataframe +from mols2grid.select import register + +_len_df = 5 +sdf = f"{RDConfig.RDDocsDir}/Book/data/solubility.test.sdf" + +def _make_df(): + return sdf_to_dataframe(sdf).iloc[:_len_df] + +default_df = _make_df() + +def _make_grid(**kwargs): + kwargs["mol_col"] = kwargs.pop("mol_col", "mol") + return MolGrid(default_df, **kwargs) + +@pytest.fixture(scope="module") +def df(): + return _make_df() + +@pytest.fixture(scope="module") +def grid(): + return _make_grid() + +@pytest.fixture(scope="module") +def mols(): + return default_df["mol"] + +def test_no_input_specified(): + with pytest.raises(ValueError, + match="One of `smiles_col` or `mol_col` must be set"): + _make_grid(smiles_col=None, mol_col=None) + +def test_name_not_str(): + with pytest.raises(TypeError, + match="`name` must be a string. Currently of type int"): + _make_grid(name=0) + +def test_uses_svg(grid): + assert grid.useSVG == True + data = grid.dataframe.loc[0, "img"] + assert " Date: Mon, 27 Sep 2021 00:04:08 +0200 Subject: [PATCH 43/74] fix python build --- .github/workflows/build.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index e4e02f7..fba7c42 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -18,7 +18,7 @@ jobs: - name: Install python with pip uses: actions/setup-python@v2 with: - python-version: pypy-3.6 + python-version: 3.6 architecture: x64 - name: Install dependencies for packaging From aeb0d305c9ff4aeb691147079c8d5a1ef88bd879 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 27 Sep 2021 00:06:32 +0200 Subject: [PATCH 44/74] add ci with coverage --- .github/workflows/ci.yml | 106 +++++++++++++++++++++++++++++++++++++++ 1 file changed, 106 insertions(+) create mode 100644 .github/workflows/ci.yml diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 0000000..053639d --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,106 @@ +name: CI +on: + push: + branches: + - "*" + pull_request: + branches: + - master + workflow_dispatch: + +defaults: + run: + shell: bash -l {0} + +concurrency: + group: "${{ github.ref }}-${{ github.head_ref }}" + cancel-in-progress: true + +jobs: + tests: + name: CI-${{ matrix.os }} | py${{ matrix.python-version }} | rdkit-${{ matrix.rdkit-version }} + runs-on: ${{ matrix.os }} + strategy: + matrix: + os: [ubuntu-latest] + python-version: [3.6, 3.8] + rdkit-version: ["rdkit>=2020.03.1"] + include: + - name: CI min version + os: ubuntu-latest + python-version: 3.6 + rdkit-version: "rdkit==2019.09.3" + + steps: + - uses: actions/checkout@v2 + + - name: Cache conda + uses: actions/cache@v2 + env: + CACHE_NUMBER: 0 + with: + path: ~/conda_pkgs_dir + key: + ${{ runner.os }}-conda-${{ env.CACHE_NUMBER }}-${{ + hashFiles('etc/example-environment.yml') }} + + - name: Setup Conda + uses: conda-incubator/setup-miniconda@v2 + with: + python-version: ${{ matrix.python-version }} + mamba-version: "*" + channels: conda-forge,defaults + use-only-tar-bz2: true + + - name: Check conda and pip + run: | + which python + python --version + pip --version + conda --version + mamba --version + + - name: Install conda dependencies + run: | + mamba install ${{ matrix.rdkit-version }} + mamba list + + - name: Install package through pip + run: | + pip install .[tests] + pip list + + - name: Run tests + run: | + pytest --color=yes --disable-pytest-warnings --cov=mols2grid --cov-report=xml tests/ + + - name: Measure tests coverage + uses: codecov/codecov-action@v1 + with: + file: coverage.xml + fail_ci_if_error: True + verbose: True + + - name: Prepare for build + run: | + pip uninstall -y mols2grid + python setup.py sdist bdist_wheel + echo "$SCRIPT" > test_install.py + cat test_install.py + env: + - SCRIPT: | + import mols2grid as mg + from rdkit import RDConfig + sdf = f"{RDConfig.RDDocsDir}/Book/data/solubility.test.sdf" + mg.save("/dev/null", sdf, subset=["img", "mols2grid-id"]) + + - name: Test tar.gz build + run: | + pip install dist/mols2grid-*.tar.gz + python test_install.py + pip uninstall -y mols2grid + + - name: Test wheel build + run: | + pip install dist/mols2grid-*.whl + python test_install.py From a138c00ec49beedc839ece9454e88733e7ce8354 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 27 Sep 2021 00:22:19 +0200 Subject: [PATCH 45/74] fix ci script --- .github/workflows/ci.yml | 66 ++++++++++++++++++++-------------------- 1 file changed, 33 insertions(+), 33 deletions(-) diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 053639d..72ff6ba 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -18,18 +18,18 @@ concurrency: jobs: tests: - name: CI-${{ matrix.os }} | py${{ matrix.python-version }} | rdkit-${{ matrix.rdkit-version }} + name: CI-${{ matrix.os }} | py${{ matrix.python-version }} | ${{ matrix.rdkit-version }} runs-on: ${{ matrix.os }} strategy: matrix: os: [ubuntu-latest] python-version: [3.6, 3.8] - rdkit-version: ["rdkit>=2020.03.1"] + rdkit-version: ["rdkit>2020.03.1"] include: - name: CI min version os: ubuntu-latest python-version: 3.6 - rdkit-version: "rdkit==2019.09.3" + rdkit-version: "rdkit==2020.03.1" steps: - uses: actions/checkout@v2 @@ -70,37 +70,37 @@ jobs: pip install .[tests] pip list - - name: Run tests - run: | - pytest --color=yes --disable-pytest-warnings --cov=mols2grid --cov-report=xml tests/ + - name: Run tests + run: | + pytest --color=yes --disable-pytest-warnings --cov=mols2grid --cov-report=xml tests/ - - name: Measure tests coverage - uses: codecov/codecov-action@v1 - with: - file: coverage.xml - fail_ci_if_error: True - verbose: True + - name: Measure tests coverage + uses: codecov/codecov-action@v1 + with: + file: coverage.xml + fail_ci_if_error: True + verbose: True - - name: Prepare for build - run: | - pip uninstall -y mols2grid - python setup.py sdist bdist_wheel - echo "$SCRIPT" > test_install.py - cat test_install.py - env: - - SCRIPT: | - import mols2grid as mg - from rdkit import RDConfig - sdf = f"{RDConfig.RDDocsDir}/Book/data/solubility.test.sdf" - mg.save("/dev/null", sdf, subset=["img", "mols2grid-id"]) + - name: Prepare for build + run: | + pip uninstall -y mols2grid + python setup.py sdist bdist_wheel + echo "$SCRIPT" > test_install.py + cat test_install.py + env: + SCRIPT: | + import mols2grid as mg + from rdkit import RDConfig + sdf = f"{RDConfig.RDDocsDir}/Book/data/solubility.test.sdf" + mg.save(sdf, output="/dev/null", subset=["img", "mols2grid-id"]) - - name: Test tar.gz build - run: | - pip install dist/mols2grid-*.tar.gz - python test_install.py - pip uninstall -y mols2grid + - name: Test tar.gz build + run: | + pip install dist/mols2grid-*.tar.gz + python test_install.py + pip uninstall -y mols2grid - - name: Test wheel build - run: | - pip install dist/mols2grid-*.whl - python test_install.py + - name: Test wheel build + run: | + pip install dist/mols2grid-*.whl + python test_install.py From 764efb5fcb785631272adba14a2bf2faecabe111 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 27 Sep 2021 01:45:02 +0200 Subject: [PATCH 46/74] fix js error with filter --- mols2grid/molgrid.py | 3 +-- mols2grid/templates/js/filter.js | 16 +++++++++------- mols2grid/templates/js/pages.js | 9 +++++---- 3 files changed, 15 insertions(+), 13 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index f93b8ae..69f8f24 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -475,8 +475,7 @@ def _filter_by_id(self, ids): ids = ids.to_list() code = env.get_template('js/filter.js').render( grid_id = self._grid_id, - ids = ids, - ) + ids = ids) return Javascript(code) def to_table(self, subset=None, tooltip=None, n_cols=6, diff --git a/mols2grid/templates/js/filter.js b/mols2grid/templates/js/filter.js index 478b09a..3bb9411 100644 --- a/mols2grid/templates/js/filter.js +++ b/mols2grid/templates/js/filter.js @@ -1,7 +1,9 @@ -var iframe = mols2grid_iframe["{{ grid_id }}"]; -var listObj = iframe.listObj; -var kl = listObj.items.length; -var ids = {{ ids }}; -listObj.filter(function (item) { - return ids.includes(item.values()["mols2grid-id"]); -}); +let name = {{ grid_id | tojson }}; +if ((typeof mols2grid_lists !== "undefined") && (name in mols2grid_lists)) { + var listObj = mols2grid_lists[name]; + var kl = listObj.items.length; + var ids = {{ ids }}; + listObj.filter(function (item) { + return ids.includes(item.values()["mols2grid-id"]); + }); +} diff --git a/mols2grid/templates/js/pages.js b/mols2grid/templates/js/pages.js index 73bd35a..00d669d 100644 --- a/mols2grid/templates/js/pages.js +++ b/mols2grid/templates/js/pages.js @@ -17,10 +17,12 @@ var listObj = new List('mols2grid', { }); listObj.remove("mols2grid-id", "0"); listObj.add({{ data }}); -{% if selection %} -if (window.parent.mols2grid_iframe === undefined) { - window.parent.mols2grid_iframe = {}; +// filter +if (window.parent.mols2grid_lists === undefined) { + window.parent.mols2grid_lists = {}; } +window.parent.mols2grid_lists[{{ grid_id | tojson }}] = listObj; +{% if selection %} // selection {% include 'js/molstorage.js' %} var SELECTION = new MolStorage(); @@ -70,4 +72,3 @@ listObj.on("updated", function (list) { {%if tooltip or selection or whole_cell_style %} listObj.update(); {% endif %} -window.parent.mols2grid_iframe["{{ grid_id }}"] = window; From ba79149c6c8c704a9affd5e42ead8728f398e633 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 27 Sep 2021 01:55:49 +0200 Subject: [PATCH 47/74] move overwrite warning to register --- mols2grid/molgrid.py | 8 +------- mols2grid/select.py | 17 ++++++++++++++++- 2 files changed, 17 insertions(+), 8 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 69f8f24..1536531 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -132,13 +132,7 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, removeHs=False, self.mol_col = mol_col # register instance self._grid_id = name - overwrite = register.SELECTIONS.get(name, False) - if overwrite: - warnings.warn( - f"Overwriting non-empty {name!r} grid selection: {str(overwrite)}" - ) - register.SELECTIONS[name] = {} - register.current_selection = name + register._init_grid(name) @classmethod def from_mols(cls, mols, **kwargs): diff --git a/mols2grid/select.py b/mols2grid/select.py index e9430c9..19a3bd9 100644 --- a/mols2grid/select.py +++ b/mols2grid/select.py @@ -9,6 +9,15 @@ def __init__(self): def _update_current_grid(self, grid_id): self.current_selection = grid_id + def _init_grid(self, grid_id): + overwrite = self.SELECTIONS.get(grid_id, False) + if overwrite: + warnings.warn( + f"Overwriting non-empty {grid_id!r} grid selection: {str(overwrite)}" + ) + self.SELECTIONS[grid_id] = {} + self._update_current_grid(grid_id) + def _set_selection(self, _id, smiles): self.SELECTIONS[self.current_selection][_id] = smiles @@ -25,12 +34,18 @@ def get_selection(self, grid_id=None): recently updated grid is returned """ grid_id = self.current_selection if grid_id is None else grid_id - return self.SELECTIONS.get(grid_id, {}) + return self.SELECTIONS[grid_id] def list_grids(self): """Returns a list of grid names""" return list(self.SELECTIONS.keys()) + def _clear(self): + """Clears all selections""" + if hasattr(self, "current_selection"): + del self.current_selection + self.SELECTIONS.clear() + # deprecate old selection system def warn(func): From d841553baf1a642e9a9101e1187f98f752636863 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 27 Sep 2021 01:56:03 +0200 Subject: [PATCH 48/74] add register tests --- tests/test_molgrid.py | 10 ------- tests/test_select.py | 61 +++++++++++++++++++++++++++++++++++++++++++ 2 files changed, 61 insertions(+), 10 deletions(-) create mode 100644 tests/test_select.py diff --git a/tests/test_molgrid.py b/tests/test_molgrid.py index 4e4456a..9ff5848 100644 --- a/tests/test_molgrid.py +++ b/tests/test_molgrid.py @@ -127,16 +127,6 @@ def test_update_current_grid_on_init(): assert register.get_selection("foo") is register.get_selection() assert register.get_selection() == {} -def test_overwrite_warning(): - _make_grid() - register._set_selection(0, "C") - with pytest.warns( - UserWarning, - match=f"Overwriting non-empty 'default' grid selection: {{0: 'C'}}" - ): - _make_grid() - assert register.get_selection() == {} - def test_from_mols(mols): grid = MolGrid.from_mols(mols) assert "mol" in grid.dataframe.columns diff --git a/tests/test_select.py b/tests/test_select.py new file mode 100644 index 0000000..ec560dd --- /dev/null +++ b/tests/test_select.py @@ -0,0 +1,61 @@ +import pytest +import mols2grid as mg +from mols2grid.select import register + +data = [{"SMILES": "C"*i, "ID": i} for i in range(1, 5)] + +@pytest.fixture(autouse=True) +def clear_register_before_each_test(): + register._clear() + register._init_grid("foo") + yield + +def test_update_current_grid(): + register._clear() + assert not hasattr(register, "current_selection") + grid = mg.MolGrid(data, name="foo") + assert register.current_selection == "foo" + +def test_init_grid(): + assert "foo" in register.SELECTIONS.keys() + assert register.current_selection == "foo" + +def test_overwrite_warning(): + register._set_selection(0, "C") + with pytest.warns( + UserWarning, + match=f"Overwriting non-empty 'foo' grid selection: {{0: 'C'}}" + ): + register._init_grid("foo") + assert register.get_selection() == {} + +def test_set_selection(): + for index, smi in [(0, "C"), (1, "CC")]: + register._set_selection(index, smi) + assert register.SELECTIONS["foo"][index] == smi + +def test_del_selection(): + for index, smi in [(0, "C"), (1, "CC")]: + register._set_selection(index, smi) + register._del_selection(0) + assert 0 not in register.SELECTIONS["foo"].keys() + assert "C" not in register.SELECTIONS["foo"].values() + +def test_get_selection(): + assert register.get_selection() == {} + d = {0: "C", 1: "CC"} + for index, smi in d.items(): + register._set_selection(index, smi) + assert register.get_selection() == d + +def test_list_grids(): + assert register.list_grids() == ["foo"] + register._init_grid("bar") + assert register.list_grids() == ["foo", "bar"] + register._init_grid("foo") + assert register.list_grids() == ["foo", "bar"] + +def test_warn_selection(): + with pytest.warns(UserWarning, + match="`mols2grid.selection` is deprecated"): + len(mg.selection) From b912640728bfc92500a53ee3d00d67e1bbf38973 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 27 Sep 2021 16:03:03 +0200 Subject: [PATCH 49/74] refactor selection code --- mols2grid/select.py | 84 ++++++++++++++++----- mols2grid/templates/js/kernel.js | 38 ++++------ mols2grid/templates/js/selection_actions.js | 5 +- tests/test_select.py | 23 +++++- 4 files changed, 99 insertions(+), 51 deletions(-) diff --git a/mols2grid/select.py b/mols2grid/select.py index 19a3bd9..b787e93 100644 --- a/mols2grid/select.py +++ b/mols2grid/select.py @@ -2,39 +2,87 @@ from collections import UserDict class SelectionRegister: - """Register for grid selections""" + """Register for grid selections + + Attributes + ---------- + SELECTIONS : dict + Stores each grid selection according to their name + current_selection : str + Name of the most recently updated grid + """ def __init__(self): self.SELECTIONS = {} - def _update_current_grid(self, grid_id): - self.current_selection = grid_id + def _update_current_grid(self, name): + self.current_selection = name - def _init_grid(self, grid_id): - overwrite = self.SELECTIONS.get(grid_id, False) + def _init_grid(self, name): + overwrite = self.SELECTIONS.get(name, False) if overwrite: warnings.warn( - f"Overwriting non-empty {grid_id!r} grid selection: {str(overwrite)}" + f"Overwriting non-empty {name!r} grid selection: {str(overwrite)}" ) - self.SELECTIONS[grid_id] = {} - self._update_current_grid(grid_id) + self.SELECTIONS[name] = {} + self._update_current_grid(name) def _set_selection(self, _id, smiles): self.SELECTIONS[self.current_selection][_id] = smiles - def _del_selection(self, _id): + def _unset_selection(self, _id): del self.SELECTIONS[self.current_selection][_id] - def get_selection(self, grid_id=None): + def add_selection(self, name, _id, smiles): + """Add an entry to a grid + + Parameters + ---------- + name : str + Name of the grid to update + _id : int + Identifier (`mols2grid-id`) of the entry + smiles : str + SMILES of the entry + + Notes + ----- + Manually using this function will not affect the checkbox displayed + on the grid. It is only usefull when retrieving selections from Python + with `mols2grid.get_selection()`. + """ + self._update_current_grid(name) + self._set_selection(_id, smiles) + + def del_selection(self, name, _id): + """Remove an entry from a grid + + Parameters + ---------- + name : str + Name of the grid to update + _id : int + Identifier (`mols2grid-id`) of the entry + + Notes + ----- + Manually using this function will not affect the checkbox displayed + on the grid. It is only usefull when retrieving selections from Python + with `mols2grid.get_selection()`. + """ + self._update_current_grid(name) + self._unset_selection(_id) + + def get_selection(self, name=None): """Returns the selection for a specific MolGrid instance Parameters ---------- - grid_id : int, str or None + name : str or None Name of the grid to fetch the selection from. If `None`, the most recently updated grid is returned """ - grid_id = self.current_selection if grid_id is None else grid_id - return self.SELECTIONS[grid_id] + name = self.current_selection if name is None else name + return self.SELECTIONS[name] def list_grids(self): """Returns a list of grid names""" @@ -92,9 +140,7 @@ def __missing__(self, key): except (ModuleNotFoundError, ImportError): pass else: - colab.output.register_callback('m2g_sel._update_current_grid', - register._update_current_grid) - colab.output.register_callback('m2g_sel._set_selection', - register._set_selection) - colab.output.register_callback('m2g_sel._del_selection', - register._del_selection) + colab.output.register_callback('_m2g_reg.add_selection', + register.add_selection) + colab.output.register_callback('_m2g_reg.del_selection', + register.del_selection) diff --git a/mols2grid/templates/js/kernel.js b/mols2grid/templates/js/kernel.js index 2eb9123..9f14f06 100644 --- a/mols2grid/templates/js/kernel.js +++ b/mols2grid/templates/js/kernel.js @@ -1,49 +1,37 @@ if (window.parent.IPython !== undefined) { // Jupyter notebook var kernel = window.parent.IPython.notebook.kernel; - kernel.execute('from mols2grid.select import register as m2g_sel') - function update_current_grid(grid_id) { - kernel.execute("m2g_sel._update_current_grid('"+grid_id+"')"); - } - function set_selection(_id, smiles) { + kernel.execute('from mols2grid.select import register as _m2g_reg') + function add_selection(grid_id, _id, smiles) { SELECTION.set(_id, smiles); - kernel.execute("m2g_sel._set_selection("+_id+",'"+smiles+"')") + kernel.execute("_m2g_reg.add_selection('"+grid_id+"', "+_id+",'"+smiles+"')") } - function del_selection(_id) { + function del_selection(grid_id, _id) { SELECTION.delete(_id); - kernel.execute("m2g_sel._del_selection("+_id+")"); + kernel.execute("_m2g_reg.del_selection('"+grid_id+"', "+_id+")"); } } else if (window.parent.google !== undefined) { // Google colab var kernel = window.parent.google.colab.kernel; - function update_current_grid(grid_id) { - (async function() { - const result = await kernel.invokeFunction('m2g_sel._update_current_grid', - [grid_id], {}); - })(); - } - function set_selection(_id, smiles) { + function add_selection(grid_id, _id, smiles) { SELECTION.set(_id, smiles); (async function() { - const result = await kernel.invokeFunction('m2g_sel._set_selection', - [_id, smiles], {}); + const result = await kernel.invokeFunction('_m2g_reg.add_selection', + [grid_id, _id, smiles], {}); })(); } - function del_selection(_id) { + function del_selection(grid_id, _id) { SELECTION.delete(_id); (async function() { - const result = await kernel.invokeFunction('m2g_sel._del_selection', - [_id], {}); + const result = await kernel.invokeFunction('_m2g_reg.del_selection', + [grid_id, _id], {}); })(); } } else { - function update_current_grid(grid_id) { - null; - } - function set_selection(_id, smiles) { + function add_selection(grid_id, _id, smiles) { SELECTION.set(_id, smiles); } - function del_selection(_id) { + function del_selection(grid_id, _id) { SELECTION.delete(_id); } } \ No newline at end of file diff --git a/mols2grid/templates/js/selection_actions.js b/mols2grid/templates/js/selection_actions.js index 06078b2..71abe33 100644 --- a/mols2grid/templates/js/selection_actions.js +++ b/mols2grid/templates/js/selection_actions.js @@ -39,13 +39,12 @@ $("#btn-chkbox-dlsmi").click(function(e) { // update selection on checkbox click listObj.on("updated", function (list) { $("input:checkbox").change(function() { - update_current_grid({{ grid_id | tojson }}); var _id = parseInt($(this).closest(".cell").attr("data-mols2grid-id")); var _smiles = $($(this).siblings(".data-{{ smiles_col }}")[0]).text(); if (this.checked) { - set_selection(_id, _smiles); + add_selection({{ grid_id | tojson }}, _id, _smiles); } else { - del_selection(_id); + del_selection({{ grid_id | tojson }}, _id); } }); }); \ No newline at end of file diff --git a/tests/test_select.py b/tests/test_select.py index ec560dd..6d9e126 100644 --- a/tests/test_select.py +++ b/tests/test_select.py @@ -10,10 +10,14 @@ def clear_register_before_each_test(): register._init_grid("foo") yield -def test_update_current_grid(): +def test_clear_register(): register._clear() assert not hasattr(register, "current_selection") - grid = mg.MolGrid(data, name="foo") + assert register.SELECTIONS == {} + +def test_update_current_grid(): + register._clear() + mg.MolGrid(data, name="foo") assert register.current_selection == "foo" def test_init_grid(): @@ -34,13 +38,24 @@ def test_set_selection(): register._set_selection(index, smi) assert register.SELECTIONS["foo"][index] == smi -def test_del_selection(): +def test_unset_selection(): for index, smi in [(0, "C"), (1, "CC")]: register._set_selection(index, smi) - register._del_selection(0) + register._unset_selection(0) assert 0 not in register.SELECTIONS["foo"].keys() assert "C" not in register.SELECTIONS["foo"].values() +def test_add_selection(): + register._init_grid("bar") + register.add_selection("foo", 0, "C") + assert register.get_selection()[0] == "C" + +def test_del_selection(): + register._set_selection(0, "C") + register._init_grid("bar") + register.del_selection("foo", 0) + assert register.get_selection() == {} + def test_get_selection(): assert register.get_selection() == {} d = {0: "C", 1: "CC"} From e593c5f6bbd075e72b41ec0456d71f2c8467b550 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 28 Sep 2021 17:28:34 +0200 Subject: [PATCH 50/74] add utils tests --- tests/test_utils.py | 119 ++++++++++++++++++++++++++++++++++++++++++++ 1 file changed, 119 insertions(+) create mode 100644 tests/test_utils.py diff --git a/tests/test_utils.py b/tests/test_utils.py new file mode 100644 index 0000000..5c139dc --- /dev/null +++ b/tests/test_utils.py @@ -0,0 +1,119 @@ +import pytest +import pandas as pd +from rdkit import RDConfig, Chem +from rdkit.Chem.rdDepictor import Compute2DCoords +from mols2grid import utils + +sdf = f"{RDConfig.RDDocsDir}/Book/data/solubility.test.sdf" + +def test_requires(): + @utils.requires("_not_a_module") + def func(): + pass + with pytest.raises(ModuleNotFoundError, + match="The module '_not_a_module' is required"): + func() + +@pytest.mark.parametrize(["subset", "fmt", "style", "transform", "exp"], [ + (["SMILES", "ID"], "{key}: {value}", {}, {}, + "SMILES: CCO
      ID: 0"), + (["ID"], "foo-{value}", {}, {}, "foo-0"), + (["ID"], "{value}", {"ID": lambda x: "color: red"}, {}, + '0'), + (["Activity"], "{value}", {}, {"Activity": lambda x: f"{x:.2f}"}, + "42.01"), + (["Activity"], "{key}: {value}", + {"Activity": lambda x: "color: red" if x.endswith("1") else ""}, + {"Activity": lambda x: f"{x:.2f}"}, + 'Activity: 42.01'), +]) +def test_tooltip_formatter(subset, fmt, style, transform, exp): + row = pd.Series({ + "ID": 0, + "SMILES": "CCO", + "Activity": 42.012345, + }) + tooltip = utils.tooltip_formatter(row, subset, fmt, style, transform) + assert tooltip == exp + +@pytest.mark.parametrize(["smi", "exp"], [ + ("CCO", "CCO"), + ("blabla", None), + (None, None) +]) +def test_mol_to_smiles(smi, exp): + if smi: + mol = Chem.MolFromSmiles(smi) + else: + mol = smi + assert utils.mol_to_smiles(mol) == exp + +def test_mol_to_record(): + mol = Chem.MolFromSmiles("CCO") + props = { + "NAME": "ethanol", + "foo": 42, + "_bar": 42.01, + "__baz": 0, + } + for prop, value in props.items(): + if isinstance(value, int): + mol.SetIntProp(prop, value) + elif isinstance(value, float): + mol.SetDoubleProp(prop, value) + else: + mol.SetProp(prop, value) + new = utils.mol_to_record(mol) + for default_col in ["mol", "SMILES"]: + assert default_col in new.keys() + new.pop(default_col) + assert new == props + +def test_mol_to_record_none(): + new = utils.mol_to_record(None) + assert new == {} + +def test_mol_to_record_overwrite_smiles(): + mol = Chem.MolFromSmiles("CCO") + mol.SetProp("SMILES", "foo") + new = utils.mol_to_record(mol) + assert new["SMILES"] == "foo" + +def test_mol_to_record_custom_mol_col(): + mol = Chem.MolFromSmiles("CCO") + new = utils.mol_to_record(mol, mol_col="foo") + assert new["foo"] is mol + +def test_sdf_to_dataframe(df): + df = utils.sdf_to_dataframe(sdf) + exp = { + 'ID': 5, + 'NAME': '3-methylpentane', + 'SMILES': 'CCC(C)CC', + 'SOL': -3.68, + 'SOL_classification': '(A) low', + '_MolFileComments': '', + '_MolFileInfo': ' SciTegic05121109362D', + '_Name': '3-methylpentane', + } + new = ( + df + .iloc[0] + .drop(["mol"]) + .to_dict() + ) + assert new == exp + +def test_sdf_to_dataframe_custom_mol_col(): + df = utils.sdf_to_dataframe(sdf, mol_col="foo") + assert "mol" not in df.columns + assert "foo" in df.columns + +def test_remove_coordinates(): + mol = Chem.MolFromSmiles("CCO") + Compute2DCoords(mol) + mol.GetConformer() + new = utils.remove_coordinates(mol) + assert new is mol + with pytest.raises(ValueError, match="Bad Conformer Id"): + new.GetConformer() From d6526108a301013107a96bdfbf5560a8603bbae8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 28 Sep 2021 18:39:29 +0200 Subject: [PATCH 51/74] fix molgrid.display without mol_col --- mols2grid/molgrid.py | 11 +++++++++-- 1 file changed, 9 insertions(+), 2 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 1536531..b90f7db 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -127,7 +127,11 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, removeHs=False, self._MolDraw2D = Draw.MolDraw2DSVG if useSVG else Draw.MolDraw2DCairo self.img_size = size dataframe["img"] = dataframe[mol_col].apply(self.mol_to_img) - self.dataframe = dataframe if keep_mols else dataframe.drop(columns=mol_col) + if keep_mols: + self.dataframe = dataframe + else: + self.dataframe = dataframe.drop(columns=mol_col) + mol_col = None self.smiles_col = smiles_col self.mol_col = mol_col # register instance @@ -291,7 +295,10 @@ def to_pages(self, subset=None, tooltip=None, containing the data for the full cell is available as `data`. All the values are parsed as strings, except "mols2grid-id" which is always an integer. """ - df = self.dataframe.drop(columns=self.mol_col).copy() + if self.mol_col: + df = self.dataframe.drop(columns=self.mol_col).copy() + else: + df = self.dataframe.copy() cell_width = self.img_size[0] smiles = self.smiles_col content = [] From c26c0ed1e86ef277196a95ff56d6a7bc20bd1a9e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 28 Sep 2021 19:17:02 +0200 Subject: [PATCH 52/74] fix setup.cfg --- MANIFEST.in | 2 ++ setup.cfg | 4 +--- 2 files changed, 3 insertions(+), 3 deletions(-) create mode 100644 MANIFEST.in diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..8ed5c51 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,2 @@ +include README.md LICENSE CHANGELOG.md +recursive-include mols2grid/templates * diff --git a/setup.cfg b/setup.cfg index 0ee8f28..cf93334 100644 --- a/setup.cfg +++ b/setup.cfg @@ -35,9 +35,7 @@ install_requires = pandas jinja2 zip_safe = False - -[options.package_data] -* = *.html, *.js, *.css +include_package_data = True [options.extras_require] tests = From 83a9a53c8629b9b4ceb526516ecd6eb9aa61a735 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Tue, 28 Sep 2021 19:39:33 +0200 Subject: [PATCH 53/74] fix test --- tests/test_utils.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_utils.py b/tests/test_utils.py index 5c139dc..4d02e2b 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -84,7 +84,7 @@ def test_mol_to_record_custom_mol_col(): new = utils.mol_to_record(mol, mol_col="foo") assert new["foo"] is mol -def test_sdf_to_dataframe(df): +def test_sdf_to_dataframe(): df = utils.sdf_to_dataframe(sdf) exp = { 'ID': 5, From feabee12c5e158abf45cae1bbf943ea705d01460 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Wed, 29 Sep 2021 23:21:56 +0200 Subject: [PATCH 54/74] add integration tests for both templates --- mols2grid/molgrid.py | 2 +- tests/test_molgrid.py | 34 +++++++++++++++++++++++++++++++++- 2 files changed, 34 insertions(+), 2 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index b90f7db..b87539a 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -252,7 +252,7 @@ def to_pages(self, subset=None, tooltip=None, Number of rows per page border : str Styling of the border around each cell (CSS) - gap : int or str + gap : int Size of the margin around each cell (CSS) fontsize : str Font size of the text displayed in each cell (CSS) diff --git a/tests/test_molgrid.py b/tests/test_molgrid.py index 9ff5848..114956e 100644 --- a/tests/test_molgrid.py +++ b/tests/test_molgrid.py @@ -204,4 +204,36 @@ def test_save(grid): grid.save(f.name) assert Path(f.name).is_file() -# TODO: test filters and renderers \ No newline at end of file +@pytest.mark.parametrize("kind", ["pages", "table"]) +def test_render(grid, kind): + grid.render(template=kind) + +def test_render_wrong_template(grid): + with pytest.raises(ValueError, match="template='foo' not supported"): + grid.render(template="foo") + +@pytest.mark.parametrize("kwargs", [ + dict(), + dict(subset=["ID"]), + dict(tooltip=["ID"]), + dict(selection=False), + dict(style={"ID": lambda x: "color: red" if x == 1 else ""}), + dict(transform={"ID": lambda x: f"Id. #{x}"}), + dict(custom_css="* {color: red;}"), + dict(callback="console.log(JSON.stringify(data));"), +]) +def test_integration_pages(grid, kwargs): + grid.to_pages(**kwargs) + +@pytest.mark.parametrize("kwargs", [ + dict(), + dict(subset=["ID"]), + dict(tooltip=["ID"]), + dict(gap="5px"), + dict(style={"ID": lambda x: "color: red" if x == 1 else ""}), + dict(transform={"ID": lambda x: f"Id. #{x}"}), +]) +def test_integration_table(grid, kwargs): + grid.to_table(**kwargs) + +# TODO: test filters and display \ No newline at end of file From 2ebacaa93e5254d7ae8c6b984c735e74b390c8cc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Fri, 1 Oct 2021 01:25:16 +0200 Subject: [PATCH 55/74] add badges to readme --- README.md | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index a647b10..c0c1633 100644 --- a/README.md +++ b/README.md @@ -1,7 +1,12 @@ # 👀 mols2grid -[![Pypi Version](https://img.shields.io/pypi/v/mols2grid.svg)](https://pypi.python.org/pypi/mols2grid) +[![Pypi version](https://img.shields.io/pypi/v/mols2grid.svg)](https://pypi.python.org/pypi/mols2grid) +![Conda version](https://img.shields.io/conda/vn/conda-forge/mols2grid) + +[![Tests status](https://github.com/cbouy/mols2grid/workflows/CI/badge.svg)](https://github.com/cbouy/mols2grid/actions/workflows/ci.yml) +[![Code coverage](https://codecov.io/gh/cbouy/mols2grid/branch/master/graph/badge.svg?token=QDI1XQSDUC)](https://codecov.io/gh/cbouy/mols2grid) [![Build status](https://github.com/cbouy/mols2grid/workflows/build/badge.svg)](https://github.com/cbouy/mols2grid/actions/workflows/build.yml) + [![Powered by RDKit](https://img.shields.io/static/v1?label=Powered%20by&message=RDKit&color=3838ff&style=flat&logo=data:image/x-icon;base64,AAABAAEAEBAQAAAAAABoAwAAFgAAACgAAAAQAAAAIAAAAAEAGAAAAAAAAAMAABILAAASCwAAAAAAAAAAAADc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nz/FBT/FBT/FBT/FBT/FBT/FBTc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nz/FBT/PBT/PBT/PBT/PBT/PBT/PBT/FBTc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nz/FBT/PBT/ZGT/ZGT/ZGT/ZGT/ZGT/ZGT/PBT/FBTc3Nzc3Nzc3Nzc3Nzc3Nz/FBT/PBT/ZGT/ZGT/ZGT/ZGT/ZGT/ZGT/ZGT/ZGT/PBT/FBTc3Nzc3Nzc3Nz/FBT/PBT/ZGT/ZGT/ZGT/jIz/jIz/jIz/jIz/ZGT/ZGT/ZGT/PBT/FBTc3Nzc3Nz/FBT/PBT/ZGT/ZGT/jIz/jIz/jIz/jIz/jIz/jIz/ZGT/ZGT/PBT/FBTc3Nzc3Nz/FBT/PBT/ZGT/ZGT/jIz/jIz/tLT/tLT/jIz/jIz/ZGT/ZGT/PBT/FBTc3Nzc3Nz/FBT/PBT/ZGT/ZGT/jIz/jIz/tLT/tLT/jIz/jIz/ZGT/ZGT/PBT/FBTc3Nzc3Nz/FBT/PBT/ZGT/ZGT/jIz/jIz/jIz/jIz/jIz/jIz/ZGT/ZGT/PBT/FBTc3Nzc3Nz/FBT/PBT/ZGT/ZGT/ZGT/jIz/jIz/jIz/jIz/ZGT/ZGT/ZGT/PBT/FBTc3Nzc3Nzc3Nz/FBT/PBT/ZGT/ZGT/ZGT/ZGT/ZGT/ZGT/ZGT/ZGT/PBT/FBTc3Nzc3Nzc3Nzc3Nzc3Nz/FBT/PBT/ZGT/ZGT/ZGT/ZGT/ZGT/ZGT/PBT/FBTc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nz/FBT/PBT/PBT/PBT/PBT/PBT/PBT/FBTc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nz/FBT/FBT/FBT/FBT/FBT/FBTc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nzc3Nz/////+B////AP///gB///wAP//4AB//+AAf//gAH//4AB//+AAf//gAH//8AD///gB///8A////gf////////)](https://www.rdkit.org/) [![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/github/cbouy/mols2grid/blob/master/demo.ipynb) From 88ca172a5bc283811389f4146c82177045244b56 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Thu, 7 Oct 2021 23:05:26 +0200 Subject: [PATCH 56/74] add custom header param --- mols2grid/molgrid.py | 9 ++++++--- mols2grid/templates/js/pages.js | 2 ++ mols2grid/templates/pages.html | 2 ++ 3 files changed, 10 insertions(+), 3 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index b87539a..e62f87c 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -227,7 +227,7 @@ def to_pages(self, subset=None, tooltip=None, textalign="center", tooltip_fmt="{key}: {value}", tooltip_trigger="click hover", tooltip_placement="bottom", hover_color="#e7e7e7", style=None, selection=True, transform=None, - custom_css=None, callback=None): + custom_css=None, custom_header=None, callback=None): """Returns the HTML document for the "pages" template Parameters @@ -289,7 +289,9 @@ def to_pages(self, subset=None, tooltip=None, before (MP) and after (°C) the value. These transformations only affect columns in `subset` and `tooltip`, and do not interfere with `style`. custom_css : str - Custom CSS properties applied to the content of the HTML document. + Custom CSS properties applied to the content of the HTML document + custom_header : str + Custom libraries to be loaded in the header of the document callback : str JavaScript callback to be executed when clicking on an image. A dictionnary containing the data for the full cell is available as `data`. All the values @@ -435,7 +437,8 @@ def to_pages(self, subset=None, tooltip=None, sort_cols = sort_cols, grid_id = self._grid_id, whole_cell_style = whole_cell_style, - custom_css = custom_css if custom_css else "", + custom_css = custom_css or "", + custom_header = custom_header or "", callback = callback, ) return template.render(**template_kwargs) diff --git a/mols2grid/templates/js/pages.js b/mols2grid/templates/js/pages.js index 00d669d..11b5ffe 100644 --- a/mols2grid/templates/js/pages.js +++ b/mols2grid/templates/js/pages.js @@ -64,9 +64,11 @@ listObj.on("updated", function (list) { }); {% endif %} {% if selection %} +// selection modifyers and export options {% include 'js/selection_actions.js' %} {% endif %} {% if callback %} +// callback {% include 'js/callback.js' %} {% endif %} {%if tooltip or selection or whole_cell_style %} diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index 4c6cfbd..c832ad3 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -7,6 +7,8 @@ {{ custom_css }} {% include 'html/pages_header.html' %} + + {{ custom_header }}
      From 0d6026c701b320f168cebf02802e88001fdc9c98 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Thu, 7 Oct 2021 23:06:43 +0200 Subject: [PATCH 57/74] add popup helper function --- mols2grid/__init__.py | 10 +++++++--- mols2grid/molgrid.py | 9 ++------- mols2grid/templates/js/popup.js | 30 ++++++++++++++++++++++++++++++ mols2grid/utils.py | 29 +++++++++++++++++++++++++++++ 4 files changed, 68 insertions(+), 10 deletions(-) create mode 100644 mols2grid/templates/js/popup.js diff --git a/mols2grid/__init__.py b/mols2grid/__init__.py index 2d715bb..6981758 100644 --- a/mols2grid/__init__.py +++ b/mols2grid/__init__.py @@ -1,5 +1,9 @@ from .molgrid import MolGrid -from .dispatch import display, save -from .select import get_selection, selection, list_grids -from .utils import sdf_to_dataframe +from .dispatch import (display, + save) +from .select import (get_selection, + selection, + list_grids) +from .utils import (sdf_to_dataframe, + make_popup_callback) from ._version import __version__ diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index e62f87c..5e38fe0 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -2,13 +2,12 @@ from base64 import b64encode from html import escape import json -from pathlib import Path import pandas as pd import numpy as np from rdkit import Chem from rdkit.Chem import Draw -from jinja2 import Environment, FileSystemLoader -from .utils import (requires, +from .utils import (env, + requires, tooltip_formatter, mol_to_record, mol_to_smiles, @@ -24,10 +23,6 @@ "Consider using IPython.display.IFrame instead") -env = Environment(loader=FileSystemLoader(Path(__file__).parent / 'templates'), - autoescape=False) - - class MolGrid: """Class that handles drawing molecules, rendering the HTML document and saving or displaying it in a notebook diff --git a/mols2grid/templates/js/popup.js b/mols2grid/templates/js/popup.js new file mode 100644 index 0000000..86632c7 --- /dev/null +++ b/mols2grid/templates/js/popup.js @@ -0,0 +1,30 @@ +// prerequisite JavaScript code +{{ js }} +// HTML template for the popup +var html = ` + +` +// create container element where the popup will be inserted +if ($("#modal-container").length === 0) { + $('').insertAfter("#mols2grid"); +} +// insert the code inside the container element +$('#modal-container').html(html); +// trigger display of popup window +$('#m2g-modal').modal('show'); \ No newline at end of file diff --git a/mols2grid/utils.py b/mols2grid/utils.py index e7b97d2..cf8a9dd 100644 --- a/mols2grid/utils.py +++ b/mols2grid/utils.py @@ -1,8 +1,14 @@ from functools import wraps from importlib.util import find_spec +from jinja2 import Environment, FileSystemLoader +from pathlib import Path from rdkit import Chem import pandas as pd + +env = Environment(loader=FileSystemLoader(Path(__file__).parent / 'templates'), + autoescape=False) + def requires(module): def inner(func): @wraps(func) @@ -58,3 +64,26 @@ def remove_coordinates(mol): modified inplace""" mol.RemoveAllConformers() return mol + +def make_popup_callback(title, html, js="", style=""): + """Creates a JavaScript callback that displays a popup window + + Parameters + ---------- + title : str + Title of the popup. Use `title='${data["Name"]}'` to use the value + of the column "Name" as a title + html : str + Content of the popup window + js : str + JavaScript code executed before making the content of the popup window. + This allows you to create variables and reuse them later in the `html` + content of the popup, using the `${my_variable}` syntax + style : str + CSS style assigned to the popup window + """ + return (env.get_template('js/popup.js') + .render(js=js, + html=html, + title=title, + style=style)) From 6d6d4f092c30fe87350aef4ab24fed6e3e6654d7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Thu, 7 Oct 2021 23:07:43 +0200 Subject: [PATCH 58/74] add index and header to smiles selection export --- mols2grid/templates/js/molstorage.js | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/mols2grid/templates/js/molstorage.js b/mols2grid/templates/js/molstorage.js index c1045aa..ea199bb 100644 --- a/mols2grid/templates/js/molstorage.js +++ b/mols2grid/templates/js/molstorage.js @@ -2,16 +2,16 @@ class MolStorage extends Map { to_dict() { var content = "{"; for (let [key, value] of this) { - content += key + ":" + JSON.stringify(value) + ","; + content += key + ":" + JSON.stringify(value) + ","; } content = content.length > 1 ? content.slice(0, -1) : content; content += "}"; return content } download_smi(fileName) { - var content = ""; + var content = "SMILES index\n"; for (let [key, value] of this) { - content += value + "\n"; + content += value + " " + key + "\n"; } var a = document.createElement("a"); var file = new Blob([content], {type: "text/plain"}); From 9fd63649b2d585c988a86d7b5ff552d3895b938b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Thu, 7 Oct 2021 23:27:19 +0200 Subject: [PATCH 59/74] add python callbacks --- mols2grid/molgrid.py | 8 ++++++++ mols2grid/templates/js/callback.js | 13 +++++++++++++ mols2grid/templates/js/kernel.js | 5 ++++- 3 files changed, 25 insertions(+), 1 deletion(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 5e38fe0..311c852 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -406,6 +406,13 @@ def to_pages(self, subset=None, tooltip=None, '{checkbox}{content}
      ') item = item.format(checkbox=checkbox, content="".join(content)) + # callback + if callable(callback): + callback_type = "python" + callback = callback.__name__ + else: + callback_type = "js" + df = df[final_columns].rename(columns=column_map) template = env.get_template('pages.html') @@ -435,6 +442,7 @@ def to_pages(self, subset=None, tooltip=None, custom_css = custom_css or "", custom_header = custom_header or "", callback = callback, + callback_type = callback_type, ) return template.render(**template_kwargs) diff --git a/mols2grid/templates/js/callback.js b/mols2grid/templates/js/callback.js index b94a911..73ad8ca 100644 --- a/mols2grid/templates/js/callback.js +++ b/mols2grid/templates/js/callback.js @@ -9,6 +9,19 @@ listObj.on("updated", function (list) { .substring(5); data[name] = this.innerHTML; }); + {% if callback_type == "python" %} + // call python func + if (kernel_env === "jupyter") { + kernel.execute("{{ callback }}("+JSON.stringify(data)+")"); + } else if (kernel_env === "colab") { + (async function() { + const result = await kernel.invokeFunction("{{ callback }}", + [data], {}); + })(); + } + {% else %} + // custom js callback {{ callback }} + {% endif %} }); }); \ No newline at end of file diff --git a/mols2grid/templates/js/kernel.js b/mols2grid/templates/js/kernel.js index 9f14f06..686345f 100644 --- a/mols2grid/templates/js/kernel.js +++ b/mols2grid/templates/js/kernel.js @@ -1,10 +1,12 @@ +var kernel_env = null; if (window.parent.IPython !== undefined) { // Jupyter notebook + kernel_env = "jupyter"; var kernel = window.parent.IPython.notebook.kernel; kernel.execute('from mols2grid.select import register as _m2g_reg') function add_selection(grid_id, _id, smiles) { SELECTION.set(_id, smiles); - kernel.execute("_m2g_reg.add_selection('"+grid_id+"', "+_id+",'"+smiles+"')") + kernel.execute("_m2g_reg.add_selection('"+grid_id+"', "+_id+",'"+smiles+"')"); } function del_selection(grid_id, _id) { SELECTION.delete(_id); @@ -12,6 +14,7 @@ if (window.parent.IPython !== undefined) { } } else if (window.parent.google !== undefined) { // Google colab + kernel_env = "colab"; var kernel = window.parent.google.colab.kernel; function add_selection(grid_id, _id, smiles) { SELECTION.set(_id, smiles); From 732e44e31782aee40a13a9b16826f8cbe14eba9a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Fri, 8 Oct 2021 00:36:28 +0200 Subject: [PATCH 60/74] test callbacks --- mols2grid/molgrid.py | 5 +++++ mols2grid/templates/js/callback.js | 6 ++++-- tests/test_molgrid.py | 12 ++++++++++++ 3 files changed, 21 insertions(+), 2 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 311c852..5c17abe 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -1,3 +1,4 @@ +from typing import Type import warnings from base64 import b64encode from html import escape @@ -408,6 +409,10 @@ def to_pages(self, subset=None, tooltip=None, # callback if callable(callback): + if callback.__name__ == "": + raise TypeError( + "Lambda functions are not supported as callbacks. Please " + "use a regular function instead.") callback_type = "python" callback = callback.__name__ else: diff --git a/mols2grid/templates/js/callback.js b/mols2grid/templates/js/callback.js index 73ad8ca..3ccd540 100644 --- a/mols2grid/templates/js/callback.js +++ b/mols2grid/templates/js/callback.js @@ -10,7 +10,7 @@ listObj.on("updated", function (list) { data[name] = this.innerHTML; }); {% if callback_type == "python" %} - // call python func + // call custom python callback if (kernel_env === "jupyter") { kernel.execute("{{ callback }}("+JSON.stringify(data)+")"); } else if (kernel_env === "colab") { @@ -18,9 +18,11 @@ listObj.on("updated", function (list) { const result = await kernel.invokeFunction("{{ callback }}", [data], {}); })(); + } else { + // no kernel detected for callback } {% else %} - // custom js callback + // call custom js callback {{ callback }} {% endif %} }); diff --git a/tests/test_molgrid.py b/tests/test_molgrid.py index 114956e..b59b91f 100644 --- a/tests/test_molgrid.py +++ b/tests/test_molgrid.py @@ -221,6 +221,7 @@ def test_render_wrong_template(grid): dict(transform={"ID": lambda x: f"Id. #{x}"}), dict(custom_css="* {color: red;}"), dict(callback="console.log(JSON.stringify(data));"), + dict(custom_header=''), ]) def test_integration_pages(grid, kwargs): grid.to_pages(**kwargs) @@ -236,4 +237,15 @@ def test_integration_pages(grid, kwargs): def test_integration_table(grid, kwargs): grid.to_table(**kwargs) +def test_python_callback(grid): + def myfunc(): + pass + html = grid.to_pages(subset=["ID"], callback=myfunc) + assert "// call custom python callback" in html + assert "// no kernel detected for callback" + +def test_python_callback_lambda(grid): + with pytest.raises(TypeError, match="Lambda functions are not supported"): + grid.to_pages(subset=["ID"], callback=lambda x: None) + # TODO: test filters and display \ No newline at end of file From 056def6b972e2a8986d07a3d2efb7fbd9bd1e417 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Fri, 8 Oct 2021 00:42:57 +0200 Subject: [PATCH 61/74] add popup callback tests --- tests/test_utils.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/tests/test_utils.py b/tests/test_utils.py index 4d02e2b..cdf3b6a 100644 --- a/tests/test_utils.py +++ b/tests/test_utils.py @@ -117,3 +117,15 @@ def test_remove_coordinates(): assert new is mol with pytest.raises(ValueError, match="Bad Conformer Id"): new.GetConformer() + +def test_make_popup_callback(): + popup = utils.make_popup_callback( + title="${title}", + html='${title}', + js='var title = "FOOBAR";', + style="max-width: 42%;", + ) + assert '
      ${title}
      ' in popup + assert '${title}' in popup + assert '// prerequisite JavaScript code\nvar title = "FOOBAR";' in popup + assert '
      ' in popup From 3ab1e7cff71b8c9c152abc632724b768f7584b1d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Fri, 8 Oct 2021 11:10:15 +0200 Subject: [PATCH 62/74] add clipboard-write permissions --- mols2grid/molgrid.py | 20 ++++++-------------- mols2grid/templates/html/iframe.html | 11 +++++++++++ 2 files changed, 17 insertions(+), 14 deletions(-) create mode 100644 mols2grid/templates/html/iframe.html diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 5c17abe..9830016 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -620,20 +620,12 @@ def to_table(self, subset=None, tooltip=None, n_cols=6, @requires("IPython.display") def display(self, width="100%", height=None, **kwargs): """Render and display the grid in a Jupyter notebook""" - code = self.render(**kwargs) - if height: - iframe = ( - '') - else: - # automatically resize iframe - iframe = ( - '' - ) - return HTML(iframe.format(width=width, height=height, - code=escape(code))) + iframe_allow = kwargs.pop("iframe_allow", "clipboard-write") + doc = self.render(**kwargs) + iframe = (env.get_template("html/iframe.html") + .render(width=width, height=height, padding=18, + allow=iframe_allow, doc=escape(doc))) + return HTML(iframe) def save(self, output, **kwargs): """Render and save the grid in an HTML document""" diff --git a/mols2grid/templates/html/iframe.html b/mols2grid/templates/html/iframe.html new file mode 100644 index 0000000..49d5cc6 --- /dev/null +++ b/mols2grid/templates/html/iframe.html @@ -0,0 +1,11 @@ + \ No newline at end of file From 70323b033d8407576ecee62ec0a684e95e358d7d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Fri, 8 Oct 2021 17:02:12 +0200 Subject: [PATCH 63/74] fix filtering for streamlit --- mols2grid/templates/js/filter.js | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/mols2grid/templates/js/filter.js b/mols2grid/templates/js/filter.js index 3bb9411..6a21c91 100644 --- a/mols2grid/templates/js/filter.js +++ b/mols2grid/templates/js/filter.js @@ -1,7 +1,10 @@ let name = {{ grid_id | tojson }}; -if ((typeof mols2grid_lists !== "undefined") && (name in mols2grid_lists)) { +if (typeof mols2grid_lists !== "undefined") { var listObj = mols2grid_lists[name]; - var kl = listObj.items.length; +} else if (typeof window.parent.mols2grid_lists !== "undefined") { + var listObj = window.parent.mols2grid_lists[name]; +} +if (typeof listObj !== "undefined") { var ids = {{ ids }}; listObj.filter(function (item) { return ids.includes(item.values()["mols2grid-id"]); From 0919d268ca6228212900cdd840fe118118096bc8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 10 Oct 2021 18:36:33 +0200 Subject: [PATCH 64/74] fix assert in py callback test --- tests/test_molgrid.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_molgrid.py b/tests/test_molgrid.py index b59b91f..f7b1988 100644 --- a/tests/test_molgrid.py +++ b/tests/test_molgrid.py @@ -242,7 +242,7 @@ def myfunc(): pass html = grid.to_pages(subset=["ID"], callback=myfunc) assert "// call custom python callback" in html - assert "// no kernel detected for callback" + assert "// no kernel detected for callback" in html def test_python_callback_lambda(grid): with pytest.raises(TypeError, match="Lambda functions are not supported"): From b23a378c6d1a34f39416d8f51d85c2c5ba9f736e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 10 Oct 2021 18:54:36 +0200 Subject: [PATCH 65/74] refactored kwargs detection for display --- mols2grid/dispatch.py | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) diff --git a/mols2grid/dispatch.py b/mols2grid/dispatch.py index 83b0e61..db64b71 100644 --- a/mols2grid/dispatch.py +++ b/mols2grid/dispatch.py @@ -6,25 +6,22 @@ _SIGNATURE = { method: dict(inspect.signature(getattr(MolGrid, method)).parameters.items()) - for method in ["render", "to_pages", "to_table"] + for method in ["render", "to_pages", "to_table", "display"] } -for method in ["render", "to_pages", "to_table"]: +for method in ["render", "to_pages", "to_table", "display"]: _SIGNATURE[method].pop("self") -_SIGNATURE["render"].pop("kwargs") + if method in ["render", "display"]: + _SIGNATURE[method].pop("kwargs") def _prepare_kwargs(kwargs, kind): """Separate kwargs for the init and render methods of MolGrid""" template = kwargs.pop("template", _SIGNATURE["render"]["template"].default) - render_kwargs = {key: value - for key, value in kwargs.items() - if key in _SIGNATURE[f'to_{template}'].keys()} - for key in render_kwargs.keys(): - kwargs.pop(key) + render_kwargs = {param: kwargs.pop(param, sig.default) + for param, sig in _SIGNATURE[f'to_{template}'].items()} if kind == "display": - render_kwargs = {"width": kwargs.pop("width", "100%"), - "height": kwargs.pop("height", None), - **render_kwargs} + render_kwargs.update({param: kwargs.pop(param, sig.default) + for param, sig in _SIGNATURE["display"].items()}) return template, kwargs, render_kwargs @singledispatch From 708bc57f6ebe6bb3204e9e5589a5bea16a194a29 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 10 Oct 2021 18:56:06 +0200 Subject: [PATCH 66/74] allow clipboard-write by default on iframe --- mols2grid/molgrid.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 9830016..1d83f70 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -618,9 +618,9 @@ def to_table(self, subset=None, tooltip=None, n_cols=6, return template.render(**template_kwargs) @requires("IPython.display") - def display(self, width="100%", height=None, **kwargs): + def display(self, width="100%", height=None, iframe_allow="clipboard-write", + **kwargs): """Render and display the grid in a Jupyter notebook""" - iframe_allow = kwargs.pop("iframe_allow", "clipboard-write") doc = self.render(**kwargs) iframe = (env.get_template("html/iframe.html") .render(width=width, height=height, padding=18, From dab628a2c20b77669725f7bc23ce1988f1bc722c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 10 Oct 2021 18:56:14 +0200 Subject: [PATCH 67/74] bump version --- CHANGELOG.md | 19 ++++++++++++------- mols2grid/_version.py | 2 +- mols2grid/molgrid.py | 2 +- 3 files changed, 14 insertions(+), 9 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index e22431a..ce817af 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,32 +4,37 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [0.0.7] - 2021/09/?? +## [0.1.0] - 2021/10/?? ### Added - The grid can be filtered using pandas DataFrame's `query` and `loc` logic (mostly - useful to combine with ipywidgets). -- Selections can now be modified (select all, or invert) and exported (to clipboard or a - SMILES file) even without a notebook kernel. Fixes: Issue #16. + useful to combine with ipywidgets) with `MolGrid.filter_by_index` and `MolGrid.filter`. +- Selections can now be modified (select and unselect all, or invert) and exported (to + clipboard or a SMILES file) even without a notebook kernel. Fixes: Issue #16. - The grid can be sorted according to the selection status and to values in the tooltips. - Added tracking the selection in multiple grids at the same time (i.e. it's not a global object that get's overwritten anymore). -- Added support for executing custom JavaScript code when clicking on a molecule's image - through the `callback` argument. +- Added support for executing custom JavaScript code or Python function when clicking on + a molecule's image through the `callback` argument. +- Added the `mols2grid.make_popup_callback` helper function to create a popup-like window + as a JavaScript callback. - Added styling for the whole cell through `style={"__all__": userfunction}`. - Added `mols2grid.get_selection()` allowing users to specify which grid selection should be returned. Without argument, the most recently updated grid is returned. - Added `mols2grid.list_grids()` to return a list of grid names available. -- Added a function to easily convert an SDF file to a pandas DataFrame. +- Added the `mols2grid.sdf_to_dataframe` function to easily convert an SDF file to a + pandas DataFrame. - Added the `custom_css` argument to pass custom CSS for the HTML document. ### Changed - The functions in `style` and `transform` are now also applied to tooltips. - The sizing of the iframe displaying the grid is now fully automated and more precise. +- Reorganized the code to separate the JS, CSS and HTML templates. ### Fixed - Fixed `mols2grid.save` that returned an error about missing the `output` argument. - The tooltip is now compatible with the "focus" mode: `tooltip_trigger="focus"`. - Fixed rendering SVG images in tooltips. ### Deprecated - Deprecated `mols2grid.selection` in favor of `mols2grid.get_selection()`. +- Deprecated `mapping` in favor of `rename` in the MolGrid class and `mols2grid.display`. ## [0.0.6] - 2021/05/14 ### Changed diff --git a/mols2grid/_version.py b/mols2grid/_version.py index 7d53ea3..a68927d 100644 --- a/mols2grid/_version.py +++ b/mols2grid/_version.py @@ -1 +1 @@ -__version__ = "0.0.7" \ No newline at end of file +__version__ = "0.1.0" \ No newline at end of file diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 1d83f70..4ab116d 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -70,7 +70,7 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, removeHs=False, The list of supported MolDrawOptions attributes are available in https://www.rdkit.org/docs/source/rdkit.Chem.Draw.rdMolDraw2D.html#rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions - ..versionchanged: 0.0.7 + ..versionchanged: 0.1.0 Added `rename` argument to replace `mapping` """ if not (smiles_col or mol_col): From 6aa5f1f587a61e382f90d63f15c5716aabc303ce Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 10 Oct 2021 19:52:32 +0200 Subject: [PATCH 68/74] fix duplicated smiles when shown in tooltip --- mols2grid/molgrid.py | 28 ++++++++++++++-------------- 1 file changed, 14 insertions(+), 14 deletions(-) diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index 4ab116d..c8fc4e2 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -98,7 +98,6 @@ def __init__(self, df, smiles_col="SMILES", mol_col=None, removeHs=False, if smiles_col and not mol_col: mol_col = "mol" keep_mols = False - self._extra_columns.append(mol_col) dataframe[mol_col] = dataframe[smiles_col].apply(Chem.MolFromSmiles) else: keep_mols = True @@ -263,16 +262,16 @@ def to_pages(self, subset=None, tooltip=None, `key: function` structure where the key must correspond to one of the columns in `subset` or `tooltip`. The function takes the item's value as input, and outputs a valid CSS styling, for example - `style={"Solubility": lambda x: "color: red" if x < -5 else "color: black"}` + `style={"Solubility": lambda x: "color: red" if x < -5 else ""}` if you want to color the text corresponding to the "Solubility" column in your dataframe. You can also style a whole cell using the `__all__` key, the corresponding function then has access to all values for each cell: - `style={"__all__": lambda x: "color: red" if x["Solubility"] < -5 else - "color: black"}` + `style={"__all__": lambda x: "color: red" if x["Solubility"] < -5 else ""}` selection : bool Enables the selection of molecules and displays a checkbox at the top of each cell. This is only usefull in the context of a Jupyter notebook, which gives - you access to your selection (index and SMILES) through `mols2grid.selection` + you access to your selection (index and SMILES) through + `mols2grid.get_selection()` transform : dict or None Functions applied to specific items in all cells. The dict must follow a `key: function` structure where the key must correspond to one of the columns @@ -288,10 +287,12 @@ def to_pages(self, subset=None, tooltip=None, Custom CSS properties applied to the content of the HTML document custom_header : str Custom libraries to be loaded in the header of the document - callback : str - JavaScript callback to be executed when clicking on an image. A dictionnary - containing the data for the full cell is available as `data`. All the values - are parsed as strings, except "mols2grid-id" which is always an integer. + callback : str or callable + JavaScript or Python callback to be executed when clicking on an image. A + dictionnary containing the data for the full cell is directly available as + `data` in JS. For Python, the callback function must have `data` as the first + argument to the function. All the values in the `data` dict are parsed as + strings, except "mols2grid-id" which is always an integer. """ if self.mol_col: df = self.dataframe.drop(columns=self.mol_col).copy() @@ -326,10 +327,9 @@ def to_pages(self, subset=None, tooltip=None, style = {} if transform is None: transform = {} - if tooltip: - value_names = list(set(subset + [smiles] + tooltip)) - else: - value_names = list(set(subset + [smiles])) + if tooltip is None: + tooltip = [] + value_names = list(set(subset + [smiles] + tooltip)) value_names = [f"data-{col}" for col in value_names] # force id, SMILES, and tooltip values to be present in the data @@ -359,7 +359,7 @@ def to_pages(self, subset=None, tooltip=None, content.append(s) column_map[col] = f"data-{col}" # add but hide SMILES div if not present - if smiles not in subset: + if smiles not in (subset + tooltip): s = f'' content.append(s) column_map[smiles] = f"data-{smiles}" From 49b7d48fc9fd8e4598c42a0ddefbe89ea255575a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Sun, 10 Oct 2021 20:03:45 +0200 Subject: [PATCH 69/74] Add uncheck all button --- mols2grid/templates/html/checkbox_dropdown.html | 2 ++ mols2grid/templates/js/selection_actions.js | 16 +++++++++++++++- 2 files changed, 17 insertions(+), 1 deletion(-) diff --git a/mols2grid/templates/html/checkbox_dropdown.html b/mols2grid/templates/html/checkbox_dropdown.html index 551a63b..a168144 100644 --- a/mols2grid/templates/html/checkbox_dropdown.html +++ b/mols2grid/templates/html/checkbox_dropdown.html @@ -2,7 +2,9 @@
      + +
      diff --git a/mols2grid/templates/js/selection_actions.js b/mols2grid/templates/js/selection_actions.js index 71abe33..3c7f482 100644 --- a/mols2grid/templates/js/selection_actions.js +++ b/mols2grid/templates/js/selection_actions.js @@ -7,13 +7,27 @@ $('#btn-chkbox-all').click(function (e) { var last_page = parseInt($("li.page-item > a").last().text()); for (let i = 0; i < last_page; i++) { listObj.show(i * n_items + 1, n_items); - $("input:checkbox").each(function() { + $("input:checkbox:not(:checked)").each(function() { this.checked = true; $(this).trigger("change"); }); } listObj.show((current_page - 1) * n_items + 1, n_items); }); +// uncheck all +$('#btn-chkbox-none').click(function (e) { + var current_page = parseInt($("li.page-item.active > a").text()); + var n_items = {{ n_items_per_page }}; + var last_page = parseInt($("li.page-item > a").last().text()); + for (let i = 0; i < last_page; i++) { + listObj.show(i * n_items + 1, n_items); + $("input:checkbox:checked").each(function() { + this.checked = false; + $(this).trigger("change"); + }); + } + listObj.show((current_page - 1) * n_items + 1, n_items); +}); // invert $('#btn-chkbox-invert').click(function (e) { var current_page = parseInt($("li.page-item.active > a").text()); From e0163a6a8d1a94842d4d56be3fcda515cb970654 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 11 Oct 2021 00:11:55 +0200 Subject: [PATCH 70/74] add sort_by option --- CHANGELOG.md | 3 ++- mols2grid/dispatch.py | 3 +++ mols2grid/molgrid.py | 20 ++++++++++++++++---- 3 files changed, 21 insertions(+), 5 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index ce817af..d37f234 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,7 @@ All notable changes to this project will be documented in this file. The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/), and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [0.1.0] - 2021/10/?? +## [0.1.0] - 2021/10/11 ### Added - The grid can be filtered using pandas DataFrame's `query` and `loc` logic (mostly useful to combine with ipywidgets) with `MolGrid.filter_by_index` and `MolGrid.filter`. @@ -24,6 +24,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - Added the `mols2grid.sdf_to_dataframe` function to easily convert an SDF file to a pandas DataFrame. - Added the `custom_css` argument to pass custom CSS for the HTML document. +- Added the `sort_by` argument to change how the grid elements are ordered ### Changed - The functions in `style` and `transform` are now also applied to tooltips. - The sizing of the iframe displaying the grid is now fully automated and more precise. diff --git a/mols2grid/dispatch.py b/mols2grid/dispatch.py index db64b71..5f067f5 100644 --- a/mols2grid/dispatch.py +++ b/mols2grid/dispatch.py @@ -129,6 +129,9 @@ def display(arg, **kwargs): clicking on an image. A dictionnary containing the data for the full cell is available as `data`. All the values are parsed as strings, except "mols2grid-id" which is always an integer. + sort_by : str or None + Sort the grid according to the following field (which must be present in `subset` + or `tooltip`). Notes ----- diff --git a/mols2grid/molgrid.py b/mols2grid/molgrid.py index c8fc4e2..0766837 100644 --- a/mols2grid/molgrid.py +++ b/mols2grid/molgrid.py @@ -222,7 +222,7 @@ def to_pages(self, subset=None, tooltip=None, textalign="center", tooltip_fmt="{key}: {value}", tooltip_trigger="click hover", tooltip_placement="bottom", hover_color="#e7e7e7", style=None, selection=True, transform=None, - custom_css=None, custom_header=None, callback=None): + custom_css=None, custom_header=None, callback=None, sort_by=None): """Returns the HTML document for the "pages" template Parameters @@ -283,9 +283,9 @@ def to_pages(self, subset=None, tooltip=None, Celsius instead of Fahrenheit with a single digit precision and some text before (MP) and after (°C) the value. These transformations only affect columns in `subset` and `tooltip`, and do not interfere with `style`. - custom_css : str + custom_css : str or None Custom CSS properties applied to the content of the HTML document - custom_header : str + custom_header : str or None Custom libraries to be loaded in the header of the document callback : str or callable JavaScript or Python callback to be executed when clicking on an image. A @@ -293,6 +293,9 @@ def to_pages(self, subset=None, tooltip=None, `data` in JS. For Python, the callback function must have `data` as the first argument to the function. All the values in the `data` dict are parsed as strings, except "mols2grid-id" which is always an integer. + sort_by : str or None + Sort the grid according to the following field (which must be present in + `subset` or `tooltip`). """ if self.mol_col: df = self.dataframe.drop(columns=self.mol_col).copy() @@ -418,7 +421,15 @@ def to_pages(self, subset=None, tooltip=None, else: callback_type = "js" - df = df[final_columns].rename(columns=column_map) + if sort_by and sort_by != "mols2grid-id": + if sort_by in (subset + tooltip): + sort_by = f"data-{sort_by}" + else: + raise ValueError(f"{sort_by} is not an available field in " + "`subset` or `tooltip`") + else: + sort_by = "mols2grid-id" + df = df[final_columns].rename(columns=column_map).sort_values(sort_by) template = env.get_template('pages.html') template_kwargs = dict( @@ -448,6 +459,7 @@ def to_pages(self, subset=None, tooltip=None, custom_header = custom_header or "", callback = callback, callback_type = callback_type, + sort_by = sort_by, ) return template.render(**template_kwargs) From 8aacd171945509a23af9692038cc31c37f0bd167 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 11 Oct 2021 00:12:12 +0200 Subject: [PATCH 71/74] fix sorting --- mols2grid/templates/js/sort.js | 25 ++++++++++++------------- mols2grid/templates/pages.html | 7 +++++-- 2 files changed, 17 insertions(+), 15 deletions(-) diff --git a/mols2grid/templates/js/sort.js b/mols2grid/templates/js/sort.js index f90faed..7492fd3 100644 --- a/mols2grid/templates/js/sort.js +++ b/mols2grid/templates/js/sort.js @@ -1,19 +1,18 @@ -var sort_field = "mols2grid-id"; +var sort_field = "{{ sort_by }}"; var sort_order = "asc"; -function coerce_type(str) { - if (isNaN(str)) return null; - var num = parseFloat(str) - return isNaN(num) ? str : num; -} function mols2gridSortFunction(itemA, itemB, options) { - var x = coerce_type(itemA.values()[options.valueName]); - var y = coerce_type(itemB.values()[options.valueName]); - if (x > y) { - return 1; - } else if (x < y) { - return -1; + var x = itemA.values()[options.valueName]; + var y = itemB.values()[options.valueName]; + if (typeof x === "number") { + if (isFinite(x - y)) { + return x - y; + } else { + return isFinite(x) ? -1 : 1; + } } else { - return 0; + x = x.toLowerCase(); + y = y.toLowerCase(); + return (x < y) ? -1: (x > y) ? 1: 0; } } function checkboxSort(itemA, itemB, options) { diff --git a/mols2grid/templates/pages.html b/mols2grid/templates/pages.html index c832ad3..2aeff9d 100644 --- a/mols2grid/templates/pages.html +++ b/mols2grid/templates/pages.html @@ -23,11 +23,14 @@ Sort by
      + {% set default_sort = sort_by.replace("data-", "", 1) %} {% for name in sort_cols %} + {% set col_name = name.replace("data-", "", 1) %} + {% set is_active = "arrow-asc active" if default_sort == col_name else "" %} {% if loop.first %} - + {% else %} - + {% endif %} {% endfor %} {% if selection %} From 282e66b478736289e4ef08595c361b6d411ccddd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 11 Oct 2021 00:15:24 +0200 Subject: [PATCH 72/74] update readme and demo to 0.1.0 --- README.md | 45 +- demo.ipynb | 2068 +++++++++++++++++++++------------------------------- 2 files changed, 852 insertions(+), 1261 deletions(-) diff --git a/README.md b/README.md index c0c1633..7aca162 100644 --- a/README.md +++ b/README.md @@ -39,9 +39,9 @@ mols2grid.display("path/to/molecules.sdf", # RDKit's MolDrawOptions parameters fixedBondLength=25, # rename fields for the output document - mapping={"SOL": "Solubility", - "SOL_classification": "Class", - "NAME": "Name"}, + rename={"SOL": "Solubility", + "SOL_classification": "Class", + "NAME": "Name"}, # set what's displayed on the grid subset=["ID", "img", "Solubility"], # set what's displayed on the tooltips @@ -59,12 +59,13 @@ You can setup the grid from various inputs: * a list of **RDKit molecules** (with properties accessible through the `mol.GetPropsAsDict()` method), * or an **SDF file** -You can also rename each field of your input with the `mapping` parameter. Please note that 3 fields are automatically added regardless of your input: `mols2grid-id`, `SMILES` and `img`. If a "SMILES" field already exists, it will not be overwritten. +You can also rename each field of your input with the `rename` parameter. Please note that 3 fields are automatically added regardless of your input: `mols2grid-id`, `SMILES` and `img`. If a "SMILES" field already exists, it will not be overwritten. #### Parameters for the drawing of each molecule * `useSVG=True`: use SVG images or PNG * `coordGen=True`: use the coordGen library instead of the RDKit one to depict the molecules in 2D +* `removeHs=False`: remove explicit hydrogen atoms from the drawings * `size=(160, 120)`: size of each image * `use_coords=True`: use the coordinates of the input molecules if available * `MolDrawOptions=None`: RDKit's [MolDrawOptions](https://www.rdkit.org/docs/source/rdkit.Chem.Draw.rdMolDraw2D.html#rdkit.Chem.Draw.rdMolDraw2D.MolDrawOptions) class. Useful for making highly customized drawings. You can also leave this to `None`, and directly use the attributes of this class as parameters like `addStereoAnnotation=True` @@ -75,7 +76,8 @@ You can control the general look of the document through the `template` argument * `template="pages"` (default) which is displayed above. It integrates nicely with Jupyter notebooks and has a search bar * `template="table"`, which displays the full list of molecules (no pages). Useful if you ever need to print the full list of molecules on paper (or print to PDF) -Both templates can be configured with the same parameters (a lot of which are [CSS](https://www.w3schools.com/cssref/) declarations): +Both templates can be configured with the same parameters (a lot of which are [CSS](https://www.w3schools.com/cssref/) declarations). +For the `pages` template, the following parameters are available: * `subset=None`: list or None Columns to be displayed in each cell of the grid. Each column's value will be displayed from top to bottom in the same order given here. Use `"img"` for the image of the molecule. Default: all columns (with "img" in first position) @@ -89,6 +91,8 @@ Both templates can be configured with the same parameters (a lot of which are [C Position of the tooltip: auto, top, bottom, left, right * `n_cols=5`: int Number of columns per page +* `n_rows=3` : int + Number of rows per page * `border="1px solid #cccccc"`: str Styling of the border around each cell (CSS) * `gap=0`: int or str @@ -105,29 +109,36 @@ Both templates can be configured with the same parameters (a lot of which are [C CSS styling applied to each item in a cell. The dict must follow a `key: function` structure where the key must correspond to one of the columns in `subset` or `tooltip`. The function takes the item's value as input, and outputs a valid CSS styling. For example, if you want to color the text corresponding to the "Solubility" column in your dataframe: ```python - style={"Solubility": lambda x: "color: red" if x < -3 else "color: black"} + style={"Solubility": lambda x: "color: red" if x < -3 else ""} + ``` + You can also style a whole cell using `__all__` as a key, the corresponding function then has access to all values for each cell: + ```python + style={"__all__": lambda x: "background-color: yellow" if x["Solubility"] < -5 else ""} ``` * `transform=None`: dict or None - Functions applied to specific items in all cells. The dict must follow a `key: function` structure where the key must correspond to one of the columns in `subset`. The function takes the item's value as input and transforms it. For example, to round the "Solubility" to 2 decimals, and display the "Melting point" in Celsius instead of Fahrenheit with a single digit precision and some text before ("MP") and after ("°C") the value: + Functions applied to specific items in all cells. The dict must follow a `key: function` structure where the key must correspond to one of the columns in `subset` or `tooltip`. The function takes the item's value as input and transforms it. For example, to round the "Solubility" to 2 decimals, and display the "Melting point" in Celsius instead of Fahrenheit with a single digit precision and some text before ("MP") and after ("°C") the value: ```python transform={"Solubility": lambda x: f"{x:.2f}", "Melting point": lambda x: f"MP: {5/9*(x-32):.1f}°C"} ``` - These transformations only affect columns in `subset` (not `tooltip`) and are applied independantly from `style`. - -The `pages` template comes with additional parameters: - -* `n_rows=3` : int - Number of rows per page + These transformations only affect columns in `subset` and `tooltip` and do not interfere with `style`. * `selection=True` : bool - Enables the selection of molecules using a checkbox. Only usefull in the context of a Jupyter notebook. You can retrieve your selection of molecules (index and SMILES) through `mols2grid.selection` - -The `pages` template also allows searching (by text or SMARTS) and sorting the grid. + Enables the selection of molecules using a checkbox. Only usefull in the context of a Jupyter notebook. You can retrieve your selection of molecules (index and SMILES) through `mols2grid.get_selection()` +* `custom_css=None` : str or None + Custom CSS properties applied to the content of the HTML document +* `custom_header=None` : str or None + Custom libraries (CSS or JS) to be loaded in the header of the document +* `callback=None` : str or callable + JavaScript or Python callback to be executed when clicking on an image. A dictionnary containing the data for the full cell is directly available as `data` in JS. For Python, the callback function must have `data` as the first argument to the function. All the values in the `data` dict are parsed as strings, except "mols2grid-id" which is always an integer. +* `sort_by` : str or None + Sort the grid according to the following field (which must be present in `subset` or `tooltip`). + +Less options are available for the `table` template, you can check the complete list of arguments with `help(mols2grid.MolGrid.to_table)` #### Output parameters You can either: -* save the grid with `mols2grid.save(output_path, ...)`. The file that is generated is a standalone HTML document that should work with most web browsers. +* save the grid with `mols2grid.save(input, output_path, ...)`. The file that is generated is a standalone HTML document that should work with most web browsers. * display it directly in a Jupyter notebook with `mols2grid.display(...)` (optionnal argument: `width="100%"`, `height=None`) diff --git a/demo.ipynb b/demo.ipynb index 37d550b..ecc5a24 100755 --- a/demo.ipynb +++ b/demo.ipynb @@ -3,7 +3,9 @@ { "cell_type": "code", "execution_count": null, - "metadata": {}, + "metadata": { + "scrolled": true + }, "outputs": [], "source": [ "%%capture\n", @@ -15,7 +17,9 @@ { "cell_type": "code", "execution_count": 1, - "metadata": {}, + "metadata": { + "scrolled": true + }, "outputs": [], "source": [ "import mols2grid\n", @@ -35,264 +39,434 @@ { "data": { "text/html": [ - "" @@ -307,39 +481,55 @@ } ], "source": [ - "mols2grid.display(SDF_PATH,\n", - " # RDKit's MolDrawOptions parameters\n", - " fixedBondLength=25,\n", - " # rename fields for the output document\n", - " mapping={\"SOL\": \"Solubility\",\n", - " \"SOL_classification\": \"Class\",\n", - " \"NAME\": \"Name\"},\n", - " # set what's displayed on the grid\n", - " subset=[\"ID\", \"img\", \"Solubility\"],\n", - " # set what's displayed on the tooltips\n", - " tooltip=[\"Name\", \"SMILES\", \"Class\", \"Solubility\"],\n", - " # style for the grid labels and tooltips\n", - " style={\"Solubility\": lambda x: \"color: red\" if x < -3 else \"color: black\"},\n", - " # change the precision and format (or other transformations)\n", - " transform={\"Solubility\": lambda x: round(x, 2)})" + "mols2grid.display(\n", + " SDF_PATH,\n", + " # RDKit's MolDrawOptions parameters\n", + " fixedBondLength=25, clearBackground=False,\n", + " # rename fields for the output document\n", + " rename={\"SOL\": \"Solubility\",\n", + " \"SOL_classification\": \"Class\",\n", + " \"NAME\": \"Name\"},\n", + " # set what's displayed on the grid\n", + " subset=[\"ID\", \"img\", \"Solubility\"],\n", + " # set what's displayed on the tooltips\n", + " tooltip=[\"Name\", \"SMILES\", \"Class\", \"Solubility\"],\n", + " # style for the grid labels and tooltips\n", + " style={\n", + " \"Solubility\": lambda x: \"color: red; font-weight: bold;\" if x < -3 else \"\",\n", + " \"__all__\": lambda x: \"background-color: azure;\" if x[\"Solubility\"] > -1 else \"\"\n", + " },\n", + " # change the precision and format (or other transformations)\n", + " transform={\"Solubility\": lambda x: round(x, 2)},\n", + " # sort the grid molecules in a different order\n", + " sort_by=\"Name\"\n", + ")" ] }, { "cell_type": "markdown", "metadata": {}, "source": [ - "If we click on the checkbox of the last, first and middle molecules on the first page (id 75, 5 and 40), we can retrieve the corresponding index and SMILES (in the same order):" + "For a complete list of properties that can be applied to **style** each cell, click [here](https://developer.mozilla.org/en-US/docs/Web/CSS/Reference#index).\n", + "\n", + "In the lower right, the searchbar let's you make text queries. If you click on the \"🔎\" icon, you can switch to **[SMARTS queries](https://en.wikipedia.org/wiki/SMILES_arbitrary_target_specification)** for substructure search.\n", + "\n", + "Next to it, the \"**Sort by**\" menu let's you change the order in which the molecules are displayed. If you click on a sort option that is already selected, the results will be displayed in reversed order.\n", + "\n", + "Finaly, you can **select** specific molecules by clicking on the checkbox next to each cell. If you click on the \"☑\" icon, you can either modify your selections (select all, unselect all, or invert the current selection), or export them to your clipboard or a SMILES file. \n", + "If we click on the checkbox of the last, first and middle molecules on the first page (id 171, 130 and 201), we can also retrieve the corresponding index and SMILES (in the same order) from Python:" ] }, { "cell_type": "code", "execution_count": 3, - "metadata": {}, + "metadata": { + "scrolled": true + }, "outputs": [ { "data": { "text/plain": [ - "{14: 'c1c(C)cc2ccccc2c1C', 0: 'CCC(C)CC', 7: 'c1ccccc1CC'}" + "{33: 'CCCCCCCBr', 25: 'ClC(Cl)C(Cl)Cl', 39: 'c1ccc(Br)cc1Br'}" ] }, "execution_count": 3, @@ -356,254 +546,397 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "You can also retrieve your selection (and the data that came with it) in a pandas DataFrame if you use the `MolGrid` class (which is used by the `mols2grid.display` function implicitely). The MolGrid class takes a dataframe as input, but you can also use the `MolGrid.from_mols` and `MolGrid.from_sdf` classmethods if needed." + "Please note that retrieving the selection in Python is currently only available for Jupyter and Google Colab notebooks, not notebooks run through Visual Studio Code, JupyterLab, and not in Streamlit (although the other export options should still work).\n", + "\n", + "You can also retrieve your selection (and the data that came with it) in a pandas DataFrame if you use the `MolGrid` class (which is used by the `mols2grid.display` function implicitely) with `grid.get_selection()`. \n", + "The MolGrid class takes a dataframe as input, but you can also use the `MolGrid.from_mols` and `MolGrid.from_sdf` classmethods if needed.\n" ] }, { "cell_type": "code", "execution_count": 4, - "metadata": {}, + "metadata": { + "scrolled": true + }, "outputs": [ { "data": { "text/html": [ - "" @@ -625,104 +958,16 @@ "df = pd.DataFrame({\"smi\": smiles,\n", " \"id\": range(1, len(smiles) + 1)})\n", "# setup the grid\n", - "grid = mols2grid.MolGrid(df, smiles_col=\"smi\", size=(110, 90))\n", + "grid = mols2grid.MolGrid(df, smiles_col=\"smi\", size=(110, 90), name=\"something\")\n", "grid.display(subset=[\"id\", \"img\"], n_cols=7)" ] }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "As soon as you click on a checkbox on the new grid, calling `mols2grid.get_selection()` will return this latest selection instead. " - ] - }, { "cell_type": "code", "execution_count": 5, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{4: 'O=S(=O)(-O)(-O)'}" - ] - }, - "execution_count": 5, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "# retrieve the index and SMILES of the current selection\n", - "mols2grid.get_selection()" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "You can also specify which grid you want to get the selection from:" - ] - }, - { - "cell_type": "code", - "execution_count": 6, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{14: 'c1c(C)cc2ccccc2c1C', 0: 'CCC(C)CC', 7: 'c1ccccc1CC'}" - ] - }, - "execution_count": 6, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "mols2grid.get_selection(0)" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "If you need access to both grids, you can use `mols2grid.selection` which contains all selections in separate dictionnaries:" - ] - }, - { - "cell_type": "code", - "execution_count": 7, - "metadata": {}, - "outputs": [ - { - "data": { - "text/plain": [ - "{0: {14: 'c1c(C)cc2ccccc2c1C', 0: 'CCC(C)CC', 7: 'c1ccccc1CC'},\n", - " 1: {4: 'O=S(=O)(-O)(-O)'}}" - ] - }, - "execution_count": 7, - "metadata": {}, - "output_type": "execute_result" - } - ], - "source": [ - "mols2grid.selection" - ] - }, - { - "cell_type": "markdown", - "metadata": {}, - "source": [ - "The advantage of using the MolGrid class is that you can retrieve your selection in the input dataframe with `MolGrid.get_selection()`" - ] - }, - { - "cell_type": "code", - "execution_count": 8, - "metadata": {}, + "metadata": { + "scrolled": true + }, "outputs": [ { "data": { @@ -764,12 +1009,13 @@ "4 O=S(=O)(-O)(-O) 5" ] }, - "execution_count": 8, + "execution_count": 5, "metadata": {}, "output_type": "execute_result" } ], "source": [ + "# select a molecule, then run this cell\n", "grid.get_selection()" ] }, @@ -777,720 +1023,54 @@ "cell_type": "markdown", "metadata": {}, "source": [ - "Here's an example with annotations and highlights of molecules, and more complex drawing options:" + "If you need to manipulate several grids at the same time, it's possible to get the selection for each grid separately as long as you give a unique name to each grid with `name=\"something\"` (`name=\"default\"` by default).\n", + "\n", + "As soon as you click on a checkbox on the new grid, calling `mols2grid.get_selection()` will return this latest selection instead. If you want to access a specific grid, you can also pass its name: `mols2grid.get_selection(\"something\")`." ] }, { "cell_type": "code", - "execution_count": 9, - "metadata": {}, + "execution_count": 6, + "metadata": { + "scrolled": true + }, "outputs": [ { "data": { - "text/html": [ - "" - ], "text/plain": [ - "" + "{4: 'O=S(=O)(-O)(-O)'}" ] }, - "execution_count": 9, + "execution_count": 6, "metadata": {}, "output_type": "execute_result" } ], "source": [ - "from rdkit import Chem\n", - "from rdkit.Chem import Draw\n", - "\n", - "# drawing options\n", - "opts = Draw.MolDrawOptions()\n", - "opts.useBWAtomPalette() # black and white atom palette\n", - "opts.setHighlightColour((0, 1, 1)) # cyan highlights\n", - "opts.setAnnotationColour((0.8, 0, 0.8)) # purple notes\n", - "opts.annotationFontScale = 0.8 # notes font scale\n", - "opts.clearBackground = False # transparent bg\n", - "Draw.SetComicMode(opts) # xkcd style\n", - "\n", - "mols = [Chem.MolFromSmiles(smi) for smi in smiles]\n", - "# annotate atom in first molecule\n", - "mols[0].GetAtomWithIdx(0).SetProp(\"atomNote\", \"1\")\n", - "# annotate bond\n", - "mols[1].GetBondWithIdx(0).SetProp(\"bondNote\", \"2\")\n", - "# highlight atoms manually\n", - "mols[3].__sssAtoms = [0]\n", - "# highlight atoms through SMARTS querry\n", - "mols[4].GetSubstructMatch(Chem.MolFromSmarts(\"S=O\"))\n", - "# display\n", - "mols2grid.display(mols, template=\"table\", n_cols=7,\n", - " subset=[\"img\"], size=(120, 100),\n", - " MolDrawOptions=opts, selection=False)" + "# retrieve the index and SMILES of the current selection\n", + "mols2grid.get_selection()" + ] + }, + { + "cell_type": "code", + "execution_count": 7, + "metadata": { + "scrolled": true + }, + "outputs": [ + { + "data": { + "text/plain": [ + "{33: 'CCCCCCCBr', 25: 'ClC(Cl)C(Cl)Cl', 39: 'c1ccc(Br)cc1Br'}" + ] + }, + "execution_count": 7, + "metadata": {}, + "output_type": "execute_result" + } + ], + "source": [ + "mols2grid.get_selection(\"default\")" ] } ], From de64d5a32613b9c73cf882d7ff15db50bde386b7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 11 Oct 2021 00:20:52 +0200 Subject: [PATCH 73/74] fix formatting --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 7aca162..4cf4e1a 100644 --- a/README.md +++ b/README.md @@ -115,22 +115,22 @@ For the `pages` template, the following parameters are available: ```python style={"__all__": lambda x: "background-color: yellow" if x["Solubility"] < -5 else ""} ``` -* `transform=None`: dict or None +* `transform=None`: dict or None Functions applied to specific items in all cells. The dict must follow a `key: function` structure where the key must correspond to one of the columns in `subset` or `tooltip`. The function takes the item's value as input and transforms it. For example, to round the "Solubility" to 2 decimals, and display the "Melting point" in Celsius instead of Fahrenheit with a single digit precision and some text before ("MP") and after ("°C") the value: ```python transform={"Solubility": lambda x: f"{x:.2f}", "Melting point": lambda x: f"MP: {5/9*(x-32):.1f}°C"} ``` These transformations only affect columns in `subset` and `tooltip` and do not interfere with `style`. -* `selection=True` : bool +* `selection=True` : bool Enables the selection of molecules using a checkbox. Only usefull in the context of a Jupyter notebook. You can retrieve your selection of molecules (index and SMILES) through `mols2grid.get_selection()` -* `custom_css=None` : str or None +* `custom_css=None` : str or None Custom CSS properties applied to the content of the HTML document -* `custom_header=None` : str or None +* `custom_header=None` : str or None Custom libraries (CSS or JS) to be loaded in the header of the document -* `callback=None` : str or callable +* `callback=None` : str or callable JavaScript or Python callback to be executed when clicking on an image. A dictionnary containing the data for the full cell is directly available as `data` in JS. For Python, the callback function must have `data` as the first argument to the function. All the values in the `data` dict are parsed as strings, except "mols2grid-id" which is always an integer. -* `sort_by` : str or None +* `sort_by` : str or None Sort the grid according to the following field (which must be present in `subset` or `tooltip`). Less options are available for the `table` template, you can check the complete list of arguments with `help(mols2grid.MolGrid.to_table)` @@ -138,7 +138,7 @@ Less options are available for the `table` template, you can check the complete #### Output parameters You can either: -* save the grid with `mols2grid.save(input, output_path, ...)`. The file that is generated is a standalone HTML document that should work with most web browsers. +* save the grid with `mols2grid.save(input, output="path/grid.html", ...)`. The file that is generated is a standalone HTML document that should work with most web browsers. * display it directly in a Jupyter notebook with `mols2grid.display(...)` (optionnal argument: `width="100%"`, `height=None`) From 59644ee3b99eae9d5d7d480f8c0b912410b5659f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?C=C3=A9dric=20Bouysset?= Date: Mon, 11 Oct 2021 00:24:24 +0200 Subject: [PATCH 74/74] fix temp mol column test --- tests/test_molgrid.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/test_molgrid.py b/tests/test_molgrid.py index f7b1988..46c08fa 100644 --- a/tests/test_molgrid.py +++ b/tests/test_molgrid.py @@ -74,7 +74,7 @@ def test_smi_only_makes_mol_temporary(df): df["SMILES"] = df["mol"].apply(Chem.MolToSmiles) df = df.drop(columns=["mol"]) grid = MolGrid(df) - assert "mol" in grid._extra_columns + assert "mol" not in grid._extra_columns assert "mol" not in grid.dataframe.columns def test_keep_mol_col_if_input(grid):