def _hydrogenize(block, hydro):
mol = Chem.MolFromMolBlock(block, sanitize=False)
_call([mol], 'UpdatePropertyCache', strict=False)
_apply([mol], ct._sssr)
res = Chem.AddHs(mol, addCoords=True) if hydro else Chem.RemoveHs(
mol, sanitize=False)
return MolToMarvin(Chem.MolToMolBlock(res))
def _mols2svg(mols,
size,
kekulize=False,
atomMapNumber=False,
computeCoords=False,
highlightAtomLists=None):
if not mols:
return ''
else:
# process only one molecule
mols = mols[0:1]
_call(mols, 'UpdatePropertyCache', strict=False)
_apply(mols, ct._sssr)
if computeCoords:
_apply(mols, _computeCoords, True)
if atomMapNumber:
_apply(mols, _atomMapNumber)
if kekulize:
_apply(mols, _kekulize)
if highlightAtomLists:
highlightAtomLists = highlightAtomLists[0]
drawer = rdMolDraw2D.MolDraw2DSVG(size, size)
opts = drawer.drawOptions()
opts.clearBackground = False
drawer.DrawMolecule(mols[0], highlightAtoms=highlightAtomLists)
drawer.FinishDrawing()
return drawer.GetDrawingText()
def _similarityMapSVG(ms,
width=500,
height=500,
radius=2,
fingerprint='morgan',
format='svg'):
if matplotlib is None:
raise ValueError('matplotlib not useable')
_call(ms, 'UpdatePropertyCache', strict=False)
_apply(ms, ct._sssr)
fn = None
if fingerprint == 'morgan':
fn = lambda x, i: SimilarityMaps.GetMorganFingerprint(
x, i, radius=radius)
elif fingerprint == 'tt':
fn = SimilarityMaps.GetAPFingerprint
elif fingerprint == 'ap':
fn = SimilarityMaps.GetTTFingerprint
SimilarityMaps.GetSimilarityMapForFingerprint(ms[0],
ms[1],
fn,
size=(width, height))
sio = io.StringIO()
pyplot.savefig(sio, format=format, bbox_inches='tight', dpi=100)
return sio.getvalue()
def MolToMarvin(mol):
if mol.endswith('.mol') and os.path.exists(mol):
mol = Chem.MolFromMolFile(mol, False, False, False)
else:
mol = Chem.MolFromMolBlock(mol, False, False, False)
_call([mol], 'UpdatePropertyCache', strict=False)
_apply([mol], ct._sssr)
rdmolops.SetAromaticity(mol)
js = _molsToJson([mol], MOL_MARVIN_SCALE)
return _dataToXml(js)
def _parseSMILESData(data, computeCoords=False, delimiter=' ', smilesColumn=0, nameColumn=1, titleLine=True,
sanitize=True):
fd, fpath = tempfile.mkstemp(text=True)
os.write(fd, data)
os.close(fd)
suppl = Chem.SmilesMolSupplier(fpath, delimiter=delimiter, smilesColumn=smilesColumn, nameColumn=nameColumn,
titleLine=titleLine, sanitize=sanitize)
mols = [x for x in suppl if x]
if computeCoords:
_apply(mols, ct._computeCoords, True)
_apply(mols, ct._wedgeMolBonds)
_call(mols, 'SetProp', '_Name', '')
os.remove(fpath)
return mols
def _clean(mrv, dim=2, cgen=False):
block = MarvinToMol(mrv)
mol = Chem.MolFromMolBlock(block, sanitize=False)
_call([mol], 'UpdatePropertyCache', strict=False)
_apply([mol], ct._sssr)
if not mol:
print("No mol for block:\n %s" % block)
return mrv
if cgen:
Chem.rdDepictor.SetPreferCoordGen(True)
else:
Chem.rdDepictor.SetPreferCoordGen(False)
Chem.rdDepictor.Compute2DCoords(mol, bondLength=0.8)
return MolToMarvin(Chem.MolToMolBlock(mol))
def get_matches(mol):
_call([mol], 'UpdatePropertyCache', strict=False)
_apply([mol], ct._sssr)
matches = []
for alert in alerts:
try:
match = mol.HasSubstructMatch(alert['rdmol'])
if match:
malert = copy.deepcopy(alert)
del malert['rdmol']
matches.append(malert)
except Exception as e:
print(e)
return matches
def _molExport(structure, **kwargs):
input_f = kwargs.get('input', None)
output_f = kwargs.get('output', None)
if not input_f:
mol = _autoDetect(str(structure))
elif input_f == 'mrv':
mol = Chem.MolFromMolBlock(MarvinToMol(structure), sanitize=False)
elif input_f == 'smiles':
mol = Chem.MolFromSmiles(str(structure), sanitize=False)
elif input_f == 'inchi':
mol = Chem.MolFromInchi(str(structure))
else:
mol = Chem.MolFromMolBlock(structure, sanitize=False)
_call([mol], 'UpdatePropertyCache', strict=False)
_apply([mol], ct._sssr)
if not mol.GetNumConformers() or mol.GetConformer().Is3D():
Chem.rdDepictor.SetPreferCoordGen(True)
Chem.rdDepictor.Compute2DCoords(mol, bondLength=0.8)
if output_f == 'smiles':
out_structure = Chem.MolToSmiles(mol)
elif output_f == 'inchi':
out_structure = Chem.MolToInchi(mol)
elif output_f == 'inchikey':
out_structure = Chem.InchiToInchiKey(Chem.MolToInchi(mol))
elif output_f == 'mol':
out_structure = Chem.MolToMolBlock(mol)
elif output_f == 'sdf':
out_structure = Chem.MolToMolBlock(mol) + '\n$$$$\n'
elif output_f == 'mrv':
out_structure = MolToMarvin(Chem.MolToMolBlock(mol))
return {
"structure": out_structure,
"format": output_f,
"contentUrl": "",
"contentBaseUrl": ""
}
def _autoDetect(structure):
mol = None
if Chem.MolFromSmiles(structure.strip(), sanitize=False):
mol = Chem.MolFromSmiles(structure.strip(), sanitize=False)
elif Chem.MolFromMolBlock(structure, sanitize=False):
return Chem.MolFromMolBlock(structure, sanitize=False)
elif Chem.INCHI_AVAILABLE and Chem.inchi.MolFromInchi(
structure.strip(), sanitize=True, removeHs=True):
mol = Chem.inchi.MolFromInchi(structure.strip(),
sanitize=True,
removeHs=True)
elif hasattr(Chem, 'MolFromSmarts') and Chem.MolFromSmarts(structure):
mol = Chem.MolFromSmarts(structure)
elif hasattr(Chem,
'MolFromMol2Block') and Chem.MolFromMol2Block(structure):
mol = Chem.MolFromMol2Block(structure)
elif hasattr(Chem, 'MolFromPDBBlock') and Chem.MolFromPDBBlock(structure):
mol = Chem.MolFromPDBBlock(structure)
elif hasattr(Chem, 'MolFromTPLBlock') and Chem.MolFromTPLBlock(structure):
mol = Chem.MolFromTPLBlock(structure)
else:
try:
mol = Chem.MolFromMolBlock(MarvinToMol(structure))
except:
pass
_call([mol], 'UpdatePropertyCache', strict=False)
_apply([mol], ct._sssr)
return mol
def _align(mols, pattern, force=False):
if all(mol.HasSubstructMatch(pattern) for mol in mols):
_apply(mols, GenerateDepictionMatching2DStructure, pattern)
return mols
if not force:
return
pattern = _adjustQuery(pattern)
matches = _call(mols, 'HasSubstructMatch', pattern)
if all(matches):
_apply(mols, GenerateDepictionMatching2DStructure, pattern)
return mols
if any(matches):
_apply(mols,
GenerateDepictionMatching2DStructure,
pattern,
acceptFailure=True)
return compress(mols, matches)
def _getMatches(mols, smarts, force=False):
_call(mols, 'UpdatePropertyCache', strict=False)
_apply(mols, ct._sssr)
return _apply(mols, ct._getSubstructMatch, _molFromSmarts(smarts), force)