Merge pull request #185 from hjkgrp/importlib_resources

Importlib resources

devtools/conda-envs/mols.yml

@@ -8,9 +8,11 @@ dependencies:
   - pandas
   - scipy
   - libffi
+  - importlib_resources
   - pip
   - pip:
     - pytest
+    - pytest-resource-path
 
   # Optional
   # GUI / plotting

devtools/conda-envs/mols_minimal.yml

@@ -8,6 +8,8 @@ dependencies:
   - pandas
   - scipy
   - libffi
+  - importlib_resources
   - pip
   - pip:
     - pytest
+    - pytest-resource-path

molSimplify/Classes/mGUI.py

@@ -39,7 +39,7 @@
 import glob
 import tempfile
 import re
-from pkg_resources import resource_filename, Requirement
+from importlib_resources import files as resource_files
 import xml.etree.ElementTree as ET
 
 try:
@@ -142,8 +142,7 @@ def initGUI(self, app):
         helpAction.triggered.connect(self.qshowhelp)
         menu2.addAction(helpAction)
         # ## place title top ###
-        f = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/icons/logo.png")
+        f = resource_files("molSimplify").joinpath("icons/logo.png")
         clogo = mQPixmap(f)
         self.grid.addWidget(clogo, 2, 8, 1, 10)
         self.txtdev = mQLabel('Developed by Kulik group @ MIT', '', 'c', 16)
@@ -363,8 +362,7 @@ def initGUI(self, app):
         if globs.custom_path:
             f = globs.custom_path + "/Ligands/ligands.dict"
         else:
-            f = resource_filename(Requirement.parse(
-                "molSimplify"), "molSimplify/Ligands/ligands.dict")
+            f = str(resource_files("molSimplify").joinpath("Ligands/ligands.dict"))
         qcav0 = getligroups(readdict(f))
         qcav = [_f for _f in qcav0.split(' ') if _f]
         self.etliggrp = mQComboBox(qcav, ctip, 12)
@@ -613,8 +611,7 @@ def initGUI(self, app):
         self.qctWindow.setPalette(p)  # set background color
         self.qctWindow.setLayout(self.qctgrid)  # set layout
 
-        f = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/icons/petachem.png")
+        f = resource_files("molSimplify").joinpath("icons/petachem.png")
         c0 = mQPixmap(f)
         self.qctgrid.addWidget(c0, 0, 2, 1, 1)
         # top text
@@ -876,10 +873,8 @@ def initGUI(self, app):
         self.sgrid.addWidget(self.jWindow)  # add to stacked grid
         self.jWindow.setPalette(p)  # set background color
         self.jWindow.setLayout(self.jgrid)  # set layout
-        f1 = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/icons/sge.png")
-        f2 = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/icons/slurm.png")
+        f1 = resource_files("molSimplify").joinpath("icons/sge.png")
+        f2 = resource_files("molSimplify").joinpath("icons/slurm.png")
         c1 = mQPixmap(f1)
         c2 = mQPixmap(f2)
         self.jgrid.addWidget(c1, 1, 2, 1, 1)
@@ -1181,8 +1176,7 @@ def initGUI(self, app):
         self.etcDBmw1 = mQLineEdit('', ctip, 'l', 14)
         self.cDBgrid.addWidget(self.etcDBmw1, 11, 8, 1, 1)
         # aspirin icon
-        f = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/icons/chemdb.png")
+        f = resource_files("molSimplify").joinpath("icons/chemdb.png")
         c = mQPixmap(f)
         relresize(c, c, 0.4)
         self.cDBgrid.addWidget(c, 7, 0, 4, 2)
@@ -1271,8 +1265,7 @@ def initGUI(self, app):
         self.butpret.clicked.connect(self.qretmain)
         self.pgrid.addWidget(self.butpret, 7, 3, 1, 2)
         # c1p = mPic(self.pWindow,globs.installdir+'/icons/wft1.png',0.04,0.7,0.2)
-        f = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/icons/wft3.png")
+        f = resource_files("molSimplify").joinpath("icons/wft3.png")
         c3p = mQPixmap(f)
         self.pgrid.addWidget(c3p, 3, 0, 4, 1)
         # c2p = mPic(self.pWindow,globs.installdir+'/icons/wft2.png',0.04,0.035,0.2)
@@ -1746,8 +1739,7 @@ def qaddg(self):
             if globs.custom_path:
                 f = globs.custom_path + "/Data/coordinations.dict"
             else:
-                f = resource_filename(Requirement.parse(
-                    "molSimplify"), "molSimplify/Data/coordinations.dict")
+                f = str(resource_files("molSimplify").joinpath("Data/coordinations.dict"))
             with open(f, 'r') as fl:
                 s = fl.read().splitlines()
             if gname.lower() in s:
@@ -1790,8 +1782,7 @@ def qaddg(self):
                 fl.write(xyzl)
             # write png file
             if glob.glob(cfile):
-                f = resource_filename(Requirement.parse(
-                    "molSimplify"), "molSimplify/icons/geoms/")
+                f = str(resource_files("molSimplify").joinpath("icons/geoms/"))
                 shutil.copy2(cfile, f+gshort+'.png')
             choice = QMessageBox.information(
                 self.geWindow, 'Add', 'Successfully added to the database!')
@@ -1827,8 +1818,7 @@ def qdelg(self):
             if globs.custom_path:
                 f = globs.custom_path + "/Data/coordinations.dict"
             else:
-                f = resource_filename(Requirement.parse(
-                    "molSimplify"), "molSimplify/Data/coordinations.dict")
+                f = str(resource_files("molSimplify").joinpath("Data/coordinations.dict"))
             with open(f, 'r') as fl:
                 s = fl.read()
             if gname.lower() not in s and gshort.lower() not in s:
@@ -1847,8 +1837,7 @@ def qdelg(self):
             if globs.custom_path:
                 f = globs.custom_path + "/Data/coordinations.dict"
             else:
-                f = resource_filename(Requirement.parse(
-                    "molSimplify"), "molSimplify/Data/coordinations.dict")
+                f = str(resource_files("molSimplify").joinpath("Data/coordinations.dict"))
             with open(f, 'w') as fl:
                 fl.write(snew)
             # remove file
@@ -2076,8 +2065,7 @@ def drawligs_svg(self):
     def viewgeom(self):
         # get geometry
         geom = self.dcoordg.currentText()
-        gfname = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/icons/geoms/" + geom + ".png")
+        gfname = str(resource_files("molSimplify").joinpath(f"icons/geoms/{geom}.png"))
         if glob.glob(gfname):
             rows = self.lgrid.rowCount()
             # Clear existing widgets in layout
@@ -2268,8 +2256,7 @@ def matchgeomcoord(self):
         # add to box
         for i, t in enumerate(qc):
             # File f is never actually used? RM 2022/02/17
-            f = resource_filename(Requirement.parse(  # noqa F841
-                "molSimplify"), "molSimplify/icons/geoms/" + t + ".png")
+            f = str(resource_files("molSimplify").joinpath(f"icons/geoms/{t}.png"))  # noqa F841
             self.dcoordg.addItem(QIcon(t), t)
         self.dcoordg.setIconSize(QSize(60, 60))
         # set default geometry

molSimplify/Classes/mol3D.py

@@ -2672,7 +2672,7 @@ def returnxyz(self):
             ss += "%s \t%f\t%f\t%f\n" % (atom.sym, xyz[0], xyz[1], xyz[2])
         return (ss)
 
-    def readfromxyz(self, filename, ligand_unique_id=False, read_final_optim_step=False):
+    def readfromxyz(self, filename: str, ligand_unique_id=False, read_final_optim_step=False):
         """
         Read XYZ into a mol3D class instance.
 
@@ -2693,8 +2693,7 @@ def readfromxyz(self, filename, ligand_unique_id=False, read_final_optim_step=Fa
         amassdict = globs.amass()
         self.graph = []
         self.xyzfile = filename
-        fname = filename.split('.xyz')[0]
-        with open(fname + '.xyz', 'r') as f:
+        with open(filename, 'r') as f:
             s = f.read().splitlines()
         try:
             atom_count = int(s[0])

molSimplify/Informatics/MOF/MOF_functionalizer.py

@@ -16,7 +16,7 @@
 	XYZ_connected,
 	write_cif,
 	)
-from pkg_resources import resource_filename, Requirement
+from importlib_resources import files as resource_files
 import numpy as np
 import scipy
 import networkx as nx
@@ -1257,8 +1257,7 @@ def functionalize_MOF_at_indices_mol3D_merge(cif_file, path2write, functional_gr
 
 	# Load in the mol3D from the folder molSimplify folder monofunctionalized_BDC.
 	functional_group_template = mol3D()
-	func_group_xyz_path = resource_filename(Requirement.parse(
-				"molSimplify"), f"molSimplify/Informatics/MOF/monofunctionalized_BDC/{functional_group}.xyz")
+	func_group_xyz_path = str(resource_files("molSimplify").joinpath(f"Informatics/MOF/monofunctionalized_BDC/{functional_group}.xyz"))
 	functional_group_template.readfromxyz(func_group_xyz_path) # This is a whole BDC linker with the requested functional group on it.
 
 	# Read information about the important indices of the functional_group_template.

molSimplify/Informatics/geometrics.py

@@ -1,7 +1,7 @@
 
 import numpy as np
 import json
-from pkg_resources import resource_filename, Requirement
+from importlib_resources import files as resource_files
 from molSimplify.Classes.mol3D import mol3D
 
 
@@ -17,7 +17,7 @@ def get_percentile_csd_geometrics(geometrics_csd, geodict, geotype, maxdent,
     metrics: list, a list of geometric considered.
     path2metric: str, the molSimplify path to load geometrics_csd if geometrics_csd is not specified
     '''
-    jsonpath = resource_filename(Requirement.parse("molSimplify"), path2metric)
+    jsonpath = resource_files("molSimplify").joinpath(path2metric)
     if not isinstance(geometrics_csd, dict):
         print("loading csd geometrics...")
         with open(jsonpath, "r") as f:

molSimplify/Scripts/io.py

@@ -19,7 +19,7 @@
 except ImportError:
     import openbabel  # fallback to version 2
 from typing import Any, List, Dict, Tuple, Union, Optional
-from pkg_resources import resource_filename, Requirement
+from importlib_resources import files as resource_files
 
 from molSimplify.Classes.globalvars import (globalvars,
                                             romans)
@@ -34,8 +34,7 @@ def printgeoms():
     if globs.custom_path:
         f = globs.custom_path + "/Data/coordinations.dict"
     else:
-        f = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/Data/coordinations.dict")
+        f = resource_files("molSimplify").joinpath("Data/coordinations.dict")
     with open(f, 'r') as f:
         s = f.read().splitlines()
     s = [_f for _f in s if _f]
@@ -64,8 +63,7 @@ def getgeoms():
     if globs.custom_path:
         f = globs.custom_path + "/Data/coordinations.dict"
     else:
-        f = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/Data/coordinations.dict")
+        f = resource_files("molSimplify").joinpath("Data/coordinations.dict")
     with open(f, 'r') as f:
         s = f.read().splitlines()
     s = [_f for _f in s if _f]
@@ -164,8 +162,7 @@ def getlicores(flip: bool = True) -> Dict[str, Any]:
     if globs.custom_path:  # test if a custom path is used:
         licores_path = str(globs.custom_path).rstrip('/') + "/Ligands/ligands.dict"
     else:
-        licores_path = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/Ligands/ligands.dict")
+        licores_path = resource_files("molSimplify").joinpath("Ligands/ligands.dict")
     licores = readdict(licores_path)
     if flip:
         for ligand in list(licores.keys()):
@@ -195,8 +192,7 @@ def getslicores() -> Dict[str, Any]:
         slicores_path = str(globs.custom_path).rstrip(
             '/') + "/Ligands/simple_ligands.dict"
     else:
-        slicores_path = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/Ligands/simple_ligands.dict")
+        slicores_path = resource_files("molSimplify").joinpath("Ligands/simple_ligands.dict")
     slicores = readdict(slicores_path)
     return slicores
 
@@ -245,8 +241,7 @@ def getbcores() -> dict:
     if globs.custom_path:  # test if a custom path is used:
         bcores_path = str(globs.custom_path).rstrip('/') + "/Bind/bind.dict"
     else:
-        bcores_path = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/Bind/bind.dict")
+        bcores_path = resource_files("molSimplify").joinpath("Bind/bind.dict")
     bcores = readdict(bcores_path)
     return bcores
 
@@ -275,8 +270,7 @@ def getmcores():
     if globs.custom_path:  # test if a custom path is used:
         mcores = str(globs.custom_path).rstrip('/') + "/Cores/cores.dict"
     else:
-        mcores = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/Cores/cores.dict")
+        mcores = resource_files("molSimplify").joinpath("Cores/cores.dict")
     mcores = readdict(mcores)
     return mcores
 
@@ -306,8 +300,7 @@ def getsubcores():
         subcores = str(globs.custom_path).rstrip(
             '/') + "/Substrates/substrates.dict"
     else:
-        subcores = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/Substrates/substrates.dict")
+        subcores = resource_files("molSimplify").joinpath("Substrates/substrates.dict")
     subcores = readdict_sub(subcores)
     return subcores
 
@@ -323,8 +316,7 @@ def loaddata(path: str) -> dict:
     if globs.custom_path:  # test if a custom path is used:
         fname = str(globs.custom_path).rstrip('/') + path
     else:
-        fname = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify"+path)
+        fname = resource_files("molSimplify").joinpath(path.strip('/'))
     d = dict()
 
     with open(fname) as f:
@@ -348,8 +340,7 @@ def loaddata_ts(path: str) -> dict:
     if globs.custom_path:  # test if a custom path is used:
         fname = str(globs.custom_path).rstrip('/') + path
     else:
-        fname = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify"+path)
+        fname = resource_files("molSimplify").joinpath(path.strip('/'))
     d = dict()
 
     with open(fname) as f:
@@ -452,8 +443,7 @@ def loadcoord(coord: str) -> List[List[float]]:
     if globs.custom_path:
         f = globs.custom_path + "/Data/" + coord + ".dat"
     else:
-        f = resource_filename(Requirement.parse(
-            "molSimplify"), "molSimplify/Data/" + coord + ".dat")
+        f = resource_files("molSimplify").joinpath(f"Data/{coord}.dat")
     with open(f) as f:
         txt = [_f for _f in f.read().splitlines() if _f]
     b = []
@@ -485,8 +475,7 @@ def core_load(usercore: str, mcores: Optional[dict] = None) -> Tuple[Union[mol3D
         if globs.custom_path:
             fcore = globs.custom_path + "/Cores/" + dbentry[0]
         else:
-            fcore = resource_filename(Requirement.parse(
-                "molSimplify"), "molSimplify/Cores/" + dbentry[0])
+            fcore = str(resource_files("molSimplify").joinpath(f"Cores/{dbentry[0]}"))
         # check if core xyz/mol file exists
         if not glob.glob(fcore):
             emsg = "We can't find the core structure file %s right now! Something is amiss. Exiting..\n" % fcore
@@ -582,8 +571,7 @@ def substr_load(usersubstrate: str,
         if globs.custom_path:
             fsubst = globs.custom_path + "/Substrates/" + var_list_sub_i[0]
         else:
-            fsubst = resource_filename(Requirement.parse(
-                "molSimplify"), "molSimplify/Substrates/" + var_list_sub_i[0])
+            fsubst = str(resource_files("molSimplify").joinpath(f"Substrates/{var_list_sub_i[0]}"))
         # check if substrate xyz/mol file exists
         if not glob.glob(fsubst):
             emsg = "We can't find the substrate structure file %s right now! Something is amiss. Exiting..\n" % fsubst
@@ -706,8 +694,7 @@ def lig_load(userligand: str, licores: Optional[dict] = None) -> Tuple[Any, str]
         if globs.custom_path:
             flig = globs.custom_path + "/Ligands/" + dbentry[0]
         else:
-            flig = resource_filename(Requirement.parse(
-                "molSimplify"), "molSimplify/Ligands/" + dbentry[0])
+            flig = str(resource_files("molSimplify").joinpath(f"Ligands/{dbentry[0]}"))
         # check if ligand xyz/mol file exists
         print(('looking for '+flig))
         if not os.path.isfile(flig):
@@ -753,7 +740,6 @@ def lig_load(userligand: str, licores: Optional[dict] = None) -> Tuple[Any, str]
             lig.ffopt = dbentry[4][0]
     # load from file
     elif ('.mol' in userligand or '.xyz' in userligand or '.smi' in userligand or '.sdf' in userligand):
-        # flig = resource_filename(Requirement.parse("molSimplify"),"molSimplify/" +userligand)
         if glob.glob(userligand):
             ftype = userligand.split('.')[-1]
             # try and catch error if conversion doesn't work
@@ -818,8 +804,7 @@ def bind_load(userbind: str, bindcores: dict) -> Tuple[Union[mol3D, None], bool,
         if globs.custom_path:
             fbind = globs.custom_path + "/Bind/" + bindcores[userbind][0]
         else:
-            fbind = resource_filename(Requirement.parse(
-                "molSimplify"), "molSimplify/Bind/" + bindcores[userbind][0])
+            fbind = str(resource_files("molSimplify").joinpath(f"Bind/{bindcores[userbind][0]}"))
         # check if bind xyz/mol file exists
         if not glob.glob(fbind):
             emsg = "We can't find the binding species structure file %s right now! Something is amiss. Exiting..\n" % fbind
@@ -903,8 +888,7 @@ def getinputargs(args, fname: str):
 
 
 def plugin_defs() -> str:
-    plugin_path = resource_filename(Requirement.parse(
-        "molSimplify"), "molSimplify/plugindefines_reference.txt")
+    plugin_path = str(resource_files("molSimplify").joinpath("plugindefines_reference.txt"))
     return plugin_path
 
 # def get_name(args,rootdir,core,ligname,bind = False,bsmi = False):
@@ -1144,16 +1128,11 @@ def copy_to_custom_path():
     if not os.path.exists(globs.custom_path):
         os.makedirs(globs.custom_path)
     # copytree cannot overwrite, need to enusre directory does not exist already
-    core_dir = resource_filename(Requirement.parse(
-        "molSimplify"), "molSimplify/Cores")
-    li_dir = resource_filename(Requirement.parse(
-        "molSimplify"), "molSimplify/Ligands")
-    bind_dir = (resource_filename(
-        Requirement.parse("molSimplify"), "molSimplify/Bind"))
-    data_dir = (resource_filename(
-        Requirement.parse("molSimplify"), "molSimplify/Data"))
-    subs_dir = (resource_filename(Requirement.parse(
-        "molSimplify"), "molSimplify/Substrates"))
+    core_dir = resource_files("molSimplify").joinpath("Cores")
+    li_dir = resource_files("molSimplify").joinpath("Ligands")
+    bind_dir = resource_files("molSimplify").joinpath("Bind")
+    data_dir = resource_files("molSimplify").joinpath("Data")
+    subs_dir = resource_files("molSimplify").joinpath("Substrates")
     if os.path.exists(str(globs.custom_path).rstrip("/")+"/Cores"):
         print('Note: removing old molSimplify data')
         shutil.rmtree(str(globs.custom_path).rstrip("/")+"/Cores")