rdworks 0.35.1__py3-none-any.whl → 0.36.2__py3-none-any.whl

rdworks/__init__.py

@@ -1,4 +1,4 @@
-__version__ = '0.35.1'
+__version__ = '0.36.2'
 
 from rdworks.conf    import Conf
 from rdworks.mol     import Mol

rdworks/conf.py

@@ -11,7 +11,7 @@ from mendeleev import element
 from ase.optimize import FIRE
 
 from rdkit import Chem
-from rdkit.Chem import rdMolTransforms, AllChem, rdMolAlign
+from rdkit.Chem import rdMolTransforms, AllChem, rdMolAlign, rdmolops
 from rdkit.Chem.Draw import rdMolDraw2D
 from PIL import Image
 
@@ -39,6 +39,8 @@ class Conf:
         self.rdmol = None # must contain one and only one rdkit conformer
         self.name = name
         self.natoms = 0
+        self.charge = 0 # molecular charge
+        self.spin = 1 # molecular spin multiplicity for ASE
         self.props = {}
 
         if molecule is None:
@@ -60,6 +62,7 @@ class Conf:
         tot_atoms = self.rdmol.GetNumAtoms(onlyExplicit=False)
         assert num_atoms == tot_atoms, "Conf() Error: missing hydrogens"
         self.natoms = num_atoms
+        self.charge = rdmolops.GetFormalCharge(self.rdmol)
         self.props.update({'atoms': num_atoms})
      
         assert self.rdmol.GetConformer().Is3D(), "Conf() Error: not 3D"
@@ -214,6 +217,8 @@ class Conf:
             # assuming ASE calculator
             with io.StringIO() as logfile:
                 ase_atoms = ase.Atoms(symbols=self.symbols(), positions=self.positions())
+                ase_atoms.info['charge'] = self.charge
+                ase_atoms.info['spin'] = self.spin
                 ase_atoms.calc = calculator
                 FIRE(ase_atoms, logfile=logfile).run(fmax=fmax)
                 lines = [l.strip().split()[1:] for l in logfile.getvalue().split('\n') if l.startswith('FIRE')]
@@ -366,9 +371,14 @@ class Conf:
         else:
             try:
                 ase_atoms = ase.Atoms(symbols=self.symbols(), positions=self.positions())
+                ase_atoms.info['charge'] = self.charge
+                ase_atoms.info['spin'] = self.spin
                 ase_atoms.calc = calculator
                 PE = ase_atoms.get_potential_energy() # np.array
-                PE = ev2kcalpermol * float(PE[0]) # np.float64 to float
+                if isinstance(PE, float):
+                    PE = ev2kcalpermol * PE
+                elif isinstance(PE, np.ndarray | list):
+                    PE = ev2kcalpermol * float(PE[0]) # np.float64 to float
                 self.props.update({'E_tot(kcal/mol)': PE})
             
                 return PE

rdworks/mol.py

@@ -3,6 +3,7 @@ import itertools
 import json
 import logging
 import tempfile
+import os
 
 from io import StringIO, BytesIO
 from pathlib import Path
@@ -367,7 +368,7 @@ class Mol:
                 self.confs.append(conf)
         
         elif method.upper() == 'CONFORGE':
-            with tempfile.NamedTemporaryFile() as tmpfile:
+            with tempfile.NamedTemporaryFile(suffix='.sdf', delete=False) as tmpfile:
                 mol = CDPL.Chem.parseSMILES(self.smiles)
                 # create and initialize an instance of the class ConfGen.ConformerGenerator which
                 # will perform the actual conformer ensemble generation work
@@ -390,7 +391,7 @@ class Mol:
                     CDPL.ConfGen.ReturnCode.TORSION_DRIVING_FAILED         : 'torsion driving failed',
                     CDPL.ConfGen.ReturnCode.CONF_GEN_FAILED                : 'conformer generation failed',
                     }
-                writer = CDPL.Chem.MolecularGraphWriter( f"{tmpfile.name}.sdf", "sdf" )
+                writer = CDPL.Chem.MolecularGraphWriter(tmpfile.name, "sdf" )
                 # SB - io.StringIO does not work with Chem.MolecularGraphWriter()
                 # We have to create a temporary file and re-read it for storing individual conformers. 
                 try:
@@ -403,15 +404,20 @@ class Mol:
                     if status == CDPL.ConfGen.ReturnCode.SUCCESS or status == CDPL.ConfGen.ReturnCode.TOO_MUCH_SYMMETRY:
                         # TOO_MUCH_SYMMETRY: output ensemble may contain duplicates
                         conf_gen.setConformers(mol)
-                        writer.write(mol)
-                        with Chem.SDMolSupplier(f"{tmpfile.name}.sdf", sanitize=True, removeHs=False) as sdf:
-                            self.confs = [ Conf(m) for m in sdf if m is not None ]                            
+                        writer.write(mol)                            
                     else:
                         raise RuntimeError('Error: conformer generation failed: %s' % status_to_str[status])
                 except Exception as e:
                     raise RuntimeError('Error: conformer generation failed: %s' % str(e))
-            # tmpfile is automatically closed and deleted here
-
+            
+            # tmpfile is automatically closed here
+            
+            with Chem.SDMolSupplier(tmpfile.name, sanitize=True, removeHs=False) as sdf:
+                self.confs = [ Conf(m) for m in sdf if m is not None ]
+            
+            # tmpfile is not deleted here because delete=False
+            # we should remove the file when it is no longer needed
+            os.remove(tmpfile.name)
 
         # energy evaluations for ranking
         for conf in self.confs:

{rdworks-0.35.1.dist-info → rdworks-0.36.2.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: rdworks
-Version: 0.35.1
+Version: 0.36.2
 Summary: Frequently used tasks built on RDKit and other tools
 Author-email: Sung-Hun Bae <sunghun.bae@gmail.com>
 Maintainer-email: Sung-Hun Bae <sunghun.bae@gmail.com>

{rdworks-0.35.1.dist-info → rdworks-0.36.2.dist-info}/RECORD

@@ -1,10 +1,10 @@
-rdworks/__init__.py,sha256=UPZKHw1RajTvab15-wzdsP4UjD27yQT0n6Q5waUaJQE,1368
-rdworks/conf.py,sha256=BPp_uZAXXOU53tKzjZz8SsUdAvi7aK1s_zCeHfiRATk,21744
+rdworks/__init__.py,sha256=IQYmK2AVX7BA--tFniboPkU1P1f3KlwhLFIUmnYtaUQ,1368
+rdworks/conf.py,sha256=hi8qqcEhDMfiGAj10I7Pl65svVNeV-ihjM7lRKX7OaM,22284
 rdworks/descriptor.py,sha256=34T_dQ6g8v3u-ym8TLKbQtxIIV5TEo-d3pdedq3o-cg,2106
 rdworks/display.py,sha256=JR0gR26UpH-JCxVOaqXZCUj2MiGZSrx9Me87FncspVI,13469
 rdworks/ionized.py,sha256=5oIjMRpkX792RIpEEE2Ir96icfFaN_h21mSihhfQPAw,6713
 rdworks/matchedseries.py,sha256=A3ON4CUpQV159mu9VqgNiJ8uoQ9ePOry9d3ra4NCAgc,10377
-rdworks/mol.py,sha256=5ZaBIpCnKIqxbIZM0IAJ2uG5fEIlZotw1Lb2QT_IXe0,71145
+rdworks/mol.py,sha256=lF5b_AIueYCfHWgrrnxbcZOFtSPe6dO4oOcovJ3GWhA,71338
 rdworks/mollibr.py,sha256=X4UBO6Ga-QmNS7RwUiaDYAx0Q5hnWs71yTkEpH02Qb4,37696
 rdworks/pka.py,sha256=NVJVfpcNEMlX5QRyLBgUM7GIT7VMjO-llAR4LWc8J2c,1656
 rdworks/readin.py,sha256=0bnVcZcAmSLqc6zu1mYcv0LdBv2agQfOpKGwpSRL9VE,11742
@@ -65,8 +65,8 @@ rdworks/predefined/misc/reactive-part-3.xml,sha256=LgWHSEbRTVmgBoIO45xbTo1xQJs0X
 rdworks/predefined/misc/reactive.xml,sha256=syedoQ6VYUfRLnxy99ObuDniJ_a_WhrWAJbTKFfJ6VY,11248
 rdworks/xtb/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 rdworks/xtb/wrapper.py,sha256=I0nW89vlJZ5Za5pCjIpjsEOFbTm7HpeNGiPgssheWn8,11350
-rdworks-0.35.1.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
-rdworks-0.35.1.dist-info/METADATA,sha256=cmN6_DkuVc8s0zE1LClwGTv2RGbwP6lrVxPOt2hST5k,1183
-rdworks-0.35.1.dist-info/WHEEL,sha256=zaaOINJESkSfm_4HQVc5ssNzHCPXhJm0kEUakpsEHaU,91
-rdworks-0.35.1.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
-rdworks-0.35.1.dist-info/RECORD,,
+rdworks-0.36.2.dist-info/licenses/LICENSE,sha256=UOkJSBqYyQUvtCp7a-vdCANeEcLE2dnTie_eB1By5SY,1074
+rdworks-0.36.2.dist-info/METADATA,sha256=GRcE_cV1nVX4j60RB1Cm_Y69Ad_y3HrZgOwnNau177Y,1183
+rdworks-0.36.2.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+rdworks-0.36.2.dist-info/top_level.txt,sha256=05C98HbvBK2axUBogC_hAT_CdpOeQYGnQ6vRAgawr8s,8
+rdworks-0.36.2.dist-info/RECORD,,

{rdworks-0.35.1.dist-info → rdworks-0.36.2.dist-info}/WHEEL

@@ -1,5 +1,5 @@
 Wheel-Version: 1.0
-Generator: setuptools (80.8.0)
+Generator: setuptools (80.9.0)
 Root-Is-Purelib: true
 Tag: py3-none-any