def __init__(
self,
pubchem_templates_path: str = '',
general_templates_path: str = config.general_templates) -> None:
"""
Initialize component which does the ligand depiction.
If Nones is provided as parameters just the defalt RDKit
functionality is going to be used.
Args:
pubchem_templates_path (str, optional): Defaults to ''.
Path to the library with 2D structures downloaded from
PubChem. Use `setup_pubchem_library` for this task.
general_templates_path (str, optional): Defaults to
config.general_templates (supplied with the pdbeccdutils).
Path to the library with general templates to be used
for depicting ligand e.g. porphyrin rings.
"""
self.coordgen_params = rdCoordGen.CoordGenParams()
self.coordgen_params.coordgenScaling = 50 / 1.5
self.coordgen_params.templateFileDir = config.coordgen_templates
self.pubchem_templates = pubchem_templates_path if os.path.isdir(
pubchem_templates_path) else ''
self.templates: Dict[str, rdkit.Chem.rdchem.Mol] = OrderedDict()
if os.path.isdir(general_templates_path):
for k in sorted(os.listdir(general_templates_path)):
template = self._load_template(
os.path.join(general_templates_path, k))
template_name = k.split('.')[0]
self.templates[template_name] = template
def test_template3(self):
# the easier way, test lifetime...
template = Chem.MolFromSmiles('C1OCOCOCOCCCNCCC1')
mol = Chem.MolFromSmiles('C1OCOCOCOCCCNC(OC(=O)C2CC2)CC1')
rdCoordGen.AddCoords(template)
template2 = Chem.Mol(template)
ps = rdCoordGen.CoordGenParams()
ps.SetTemplateMol(template2)
template2 = None
ps.dbg_useFixed = True
rdCoordGen.AddCoords(mol,ps)
self.assertTrue(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
def test_template2(self):
# the easier way...
template = Chem.MolFromSmiles('C1OCOCOCOCCCNCCC1')
template.SetProp("_Name",'template')
mol = Chem.MolFromSmiles('C1OCOCOCOCCCNC(OC(=O)C2CC2)CC1')
mol.SetProp("_Name","mol")
rdCoordGen.AddCoords(template)
ps = rdCoordGen.CoordGenParams()
ps.SetTemplateMol(template)
ps.dbg_useFixed = True
rdCoordGen.AddCoords(mol,ps)
self.assertTrue(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
def test_template1(self):
template = Chem.MolFromSmiles('C1OCOCOCOCCCNCCC1')
template.SetProp("_Name",'template')
mol = Chem.MolFromSmiles('C1OCOCOCOCCCNC(OC(=O)C2CC2)CC1')
mol.SetProp("_Name","mol")
rdCoordGen.AddCoords(template)
rdCoordGen.AddCoords(mol)
self.assertFalse(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
match = mol.GetSubstructMatch(template)
mapd = dict()
for i,aid in enumerate(match):
p = template.GetConformer().GetAtomPosition(i)
mapd[aid] = Geometry.Point2D(p.x,p.y)
ps = rdCoordGen.CoordGenParams()
ps.SetCoordMap(mapd)
ps.dbg_useFixed = True
rdCoordGen.AddCoords(mol,ps)
self.assertTrue(compareConfs(mol.GetConformer(),template.GetConformer(),mol.GetSubstructMatch(template)))
def testMinimizeOnly(self):
m = Chem.MolFromMolBlock('''
Mrv2014 08052005392D
0 0 0 0 0 999 V3000
M V30 BEGIN CTAB
M V30 COUNTS 14 15 0 0 0
M V30 BEGIN ATOM
M V30 1 C -1.4287 -1.4523 0 0
M V30 2 C -2.9638 -1.5752 0 0
M V30 3 C -3.8377 -0.3072 0 0
M V30 4 C -3.1766 1.0837 0 0
M V30 5 C -1.6416 1.2066 0 0
M V30 6 C -0.7675 -0.0614 0 0
M V30 7 C 0.7675 0.0614 0 0
M V30 8 C 1.6416 -1.2066 0 0
M V30 9 C 0.9804 -2.5975 0 0
M V30 10 N 3.1766 -1.0837 0 0
M V30 11 C 3.8377 0.3072 0 0
M V30 12 C 2.9638 1.5752 0 0
M V30 13 C 1.4287 1.4523 0 0
M V30 14 F -0.5548 -2.7203 0 0
M V30 END ATOM
M V30 BEGIN BOND
M V30 1 2 1 2
M V30 2 1 2 3
M V30 3 2 3 4
M V30 4 1 4 5
M V30 5 2 5 6
M V30 6 1 6 7
M V30 7 2 7 8
M V30 8 1 8 9
M V30 9 1 8 10
M V30 10 2 10 11
M V30 11 1 11 12
M V30 12 2 12 13
M V30 13 1 6 1
M V30 14 1 13 7
M V30 15 1 1 14
M V30 END BOND
M V30 END CTAB
M END
''')
ref = Chem.MolFromMolBlock('''
RDKit 2D
14 15 0 0 0 0 0 0 0 0999 V2000
-1.5379 -1.4859 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1218 -1.5958 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.9595 -0.2554 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2641 1.1663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.6778 1.2217 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7941 -0.0886 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7983 0.0383 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7524 -1.2209 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.1246 -2.6443 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.3306 -1.0787 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
3.9439 0.3747 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.0337 1.6656 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.4617 1.4692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6924 -2.7917 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 7 1 0
7 8 2 0
8 9 1 0
8 10 1 0
10 11 2 0
11 12 1 0
12 13 2 0
6 1 1 0
13 7 1 0
1 14 1 0
M END''')
ps = rdCoordGen.CoordGenParams()
ps.minimizeOnly = True
m2 = Chem.Mol(m)
rdCoordGen.AddCoords(m2, ps)
self.assertGreater(rdMolAlign.AlignMol(m, ref), 0.1)
self.assertLess(rdMolAlign.AlignMol(m2, ref), 0.1)
def testMinimizeOnly(self):
m = Chem.MolFromMolBlock('''
Mrv2014 03252113022D
14 15 0 0 0 0 999 V2000
-0.7654 -0.7780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5877 -0.8439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.0559 -0.1646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7017 0.5805 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.8794 0.6464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.4112 -0.0329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4112 0.0329 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.8794 -0.6464 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7771 -1.4237 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7017 -0.5805 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
2.0559 0.1646 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5877 0.8439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7654 0.7780 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7654 -1.6519 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0 0 0 0
2 3 1 0 0 0 0
3 4 2 0 0 0 0
4 5 1 0 0 0 0
5 6 2 0 0 0 0
6 7 1 0 0 0 0
7 8 2 0 0 0 0
8 9 1 0 0 0 0
8 10 1 0 0 0 0
10 11 2 0 0 0 0
11 12 1 0 0 0 0
12 13 2 0 0 0 0
6 1 1 0 0 0 0
13 7 1 0 0 0 0
1 14 1 0 0 0 0
M END
''')
ref = Chem.MolFromMolBlock('''
RDKit 2D
14 15 0 0 0 0 0 0 0 0999 V2000
-0.5957 -0.8221 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4185 -0.8441 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8520 -0.1434 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4595 0.5814 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.6368 0.6072 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2063 -0.0955 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.2087 -0.0625 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7102 -0.7158 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.4040 -1.4774 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5259 -0.6099 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
1.8401 0.1516 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.3405 0.8062 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.5252 0.6981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1735 -1.5240 0.0000 F 0 0 0 0 0 0 0 0 0 0 0 0
1 2 2 0
2 3 1 0
3 4 2 0
4 5 1 0
5 6 2 0
6 7 1 0
7 8 2 0
8 9 1 0
8 10 1 0
10 11 2 0
11 12 1 0
12 13 2 0
6 1 1 0
13 7 1 0
1 14 1 0
M END
''')
ps = rdCoordGen.CoordGenParams()
ps.minimizeOnly = True
m2 = Chem.Mol(m)
rdCoordGen.AddCoords(m2, ps)
self.assertGreater(rdMolAlign.AlignMol(m, ref), 0.1)
self.assertLess(rdMolAlign.AlignMol(m2, ref), 0.1)