use Lomap package's bindings (#478)

* use Lomap package's bindings * fix mypy complaints * Code via suggestions because local branch is borked Why can't I push this from my local? * Update openfe/setup/atom_mapping/lomap_scorers.py * try exporting __all__ (make RTD happy too) * guess mypy didn't like that at __all__ * Oh, *that* would be how to fix the warning about mocks * Update environment.yaml * Update environment.yml * Update conf.py * remove lomap docs * try adding lomap to docs build * try adding lomap scorer docs back * add generate_lomap_network to docs * Update environment.yml --------- Co-authored-by: David W.H. Swenson <[email protected]>
OpenFreeEnergy · Nov 3, 2023 · e60580c · e60580c
1 parent 195b9e8
commit e60580c
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diff --git a/docs/conf.py b/docs/conf.py
@@ -103,7 +103,6 @@
 
 autodoc_mock_imports = [
     "matplotlib",
-    "lomap",
     "openmmtools",
     "mdtraj",
     "openmmforcefields",

diff --git a/docs/environment.yaml b/docs/environment.yaml
@@ -4,6 +4,7 @@ channels:
 - https://conda.anaconda.org/conda-forge
 dependencies:
 - autodoc-pydantic<2.0
+- lomap2>=3.0.0
 - openff-models>=0.0.5
 - openff-toolkit >=0.13.0
 - openff-units

diff --git a/docs/reference/api/ligand_network.rst b/docs/reference/api/ligand_network.rst
@@ -32,6 +32,9 @@ Functions that build a :class:`.LigandNetwork` from a collection of :class:`Smal
     generate_radial_network
     generate_maximal_network
     generate_minimal_spanning_network
+    generate_minimal_redundant_network
+    generate_lomap_network
+
 
 .. _Ligand Network Loaders:
 
@@ -90,15 +93,15 @@ Atom Map Scorers
 
 Scoring functions for a mapping between ligands. These are used as objective functions for :any:`Ligand Network Planners`.
 
-LOMAP Scorers
+
+Lomap Scorers
 ~~~~~~~~~~~~~
 
 Scorers implemented by the `LOMAP <https://github.com/OpenFreeEnergy/Lomap>`_ package.
 
 .. apparently we need the atom_mapping because internally autofunction is
     trying ``import openfe.setup.lomap_scorers``, which doesn't work (whereas
     ``from openfe.setup import lomap_scorers`` does)
-
 .. module:: openfe.setup.atom_mapping.lomap_scorers
 
 .. autosummary::

diff --git a/environment.yml b/environment.yml
@@ -4,6 +4,7 @@ channels:
   - conda-forge
 dependencies:
   - duecredit
+  - lomap2>=3.0.0
   - numpy<1.24
   - networkx
   - rdkit

diff --git a/openfe/setup/atom_mapping/lomap_mapper.py b/openfe/setup/atom_mapping/lomap_mapper.py
@@ -5,72 +5,4 @@
 The MCS class from Lomap shamelessly wrapped and used here to match our API.
 
 """
-from lomap import mcs as lomap_mcs
-
-from .ligandatommapper import LigandAtomMapper
-
-
-class LomapAtomMapper(LigandAtomMapper):
-    time: int
-    threed: bool
-    max3d: float
-    element_change: bool
-    seed: str
-    shift: bool
-
-    def __init__(self, *, time: int = 20, threed: bool = True,
-                 max3d: float = 1000.0, element_change: bool = True,
-                 seed: str = '', shift: bool = True):
-        """
-        Suggest atom mappings with the MCS atom mapper from Lomap.
-
-        Keyword arguments are passed directly to the MCS class from Lomap for
-        each mapping created.
-
-        Parameters
-        ----------
-        time : int, optional
-          timeout of MCS algorithm, passed to RDKit
-          default 20
-        threed : bool, optional
-          if true, positional info is used to choose between symmetrically
-          equivalent mappings and prune the mapping, default True
-        max3d : float, optional
-          maximum discrepancy in Angstroms between atoms before mapping is not
-          allowed, default 1000.0, which effectively trims no atoms
-        element_change: bool, optional
-          whether to allow element changes in the mappings, default True
-        seed: str, optional
-          SMARTS string to use as seed for MCS searches.  When used across an entire set
-          of ligands, this can create
-        shift: bool, optional
-          when determining 3D overlap, if to translate the two molecules MCS to minimise
-          RMSD to boost potential alignment.
-        """
-        self.time = time
-        self.threed = threed
-        self.max3d = max3d
-        self.element_change = element_change
-        self.seed = seed
-        self.shift = shift
-
-    def _mappings_generator(self, componentA, componentB):
-        try:
-            mcs = lomap_mcs.MCS(componentA.to_rdkit(), componentB.to_rdkit(),
-                                time=self.time,
-                                threed=self.threed, max3d=self.max3d,
-                                element_change=self.element_change, seed=self.seed,
-                                shift=self.shift)
-        except ValueError:
-            # if no match found, Lomap throws ValueError, so we just yield
-            # generator with no contents
-            return
-
-        mapping_string = mcs.all_atom_match_list()
-        # lomap spits out "1:1,2:2,...,x:y", so split around commas,
-        # then colons and coerce to ints
-        mapping_dict = dict((map(int, v.split(':'))
-                             for v in mapping_string.split(',')))
-
-        yield mapping_dict
-        return
+from lomap import LomapAtomMapper