def _getDescriptors(data, ds, loadMol=True, useRDKitChemistry=True):
if ds:
ds = ds.split(',')
return _apply(
_parseMolData(data,
loadMol=loadMol,
useRDKitChemistry=useRDKitChemistry), _desc_list, ds)
def _removeHs(data):
mols = _parseMolData(data, loadMol=False, useRDKitChemistry=False)
ms = []
for molblock in mols:
mol = parse_molblock(molblock, useRDKitChemistry=False)
props = molblock.split("M END")[1].strip()
props = props if len(props) > 1 else None
Chem.FastFindRings(mol)
mol.UpdatePropertyCache(strict=False)
Chem.AssignAtomChiralTagsFromStructure(mol)
Chem.AssignStereochemistry(mol, cleanIt=True, force=True)
ms.append((remove_hs_from_mol(mol), props))
return _getSDFString(ms)
def _mcs(data, asSmiles, atomCompare, bondCompare, threshold, ringMatchesRingOnly, completeRingsOnly, loadMol=False, useRDKitChemistry=False,
isomericSmiles=False, canonical=True, kekuleSmiles=False):
ms = _parseMolData(data, loadMol=loadMol,
useRDKitChemistry=useRDKitChemistry)
if not ms:
return
if len(ms) == 1:
if asSmiles:
return Chem.MolToSmiles(ms[0])
else:
return Chem.MolToSmarts(ms[0])
if threshold:
threshold = float(threshold)
try:
mcs = MCS.FindMCS(ms,
atomCompare=atomCompare,
bondCompare=bondCompare,
ringMatchesRingOnly=ringMatchesRingOnly,
completeRingsOnly=completeRingsOnly,
threshold=threshold)
except TypeError:
ac = MCS.AtomCompare.CompareAny
if hasattr(MCS.AtomCompare, atomCompare):
ac = getattr(MCS.AtomCompare, atomCompare)
bc = MCS.BondCompare.CompareOrder
if hasattr(MCS.BondCompare, bondCompare):
bc = getattr(MCS.BondCompare, bondCompare)
th = 1.0
if threshold:
th = threshold
mcs = MCS.FindMCS(ms,
atomCompare=ac,
bondCompare=bc,
ringMatchesRingOnly=ringMatchesRingOnly,
completeRingsOnly=completeRingsOnly,
threshold=th
)
if hasattr(mcs, 'smarts'):
res = mcs.smarts
else:
res = mcs.smartsString
if asSmiles:
p = Chem.MolFromSmarts(res)
for m in ms:
if m.HasSubstructMatch(p):
match = m.GetSubstructMatch(p)
res = Chem.MolFragmentToSmiles(m, atomsToUse=match, isomericSmiles=isomericSmiles, canonical=canonical,
kekuleSmiles=kekuleSmiles)
break
return res
def _ctab2svg(data,
size,
loadMol=True,
useRDKitChemistry=False,
kekulize=False,
atomMapNumber=False,
computeCoords=False):
return _mols2svg(_parseMolData(data,
loadMol=loadMol,
useRDKitChemistry=useRDKitChemistry),
size,
kekulize=kekulize,
atomMapNumber=atomMapNumber,
computeCoords=computeCoords)
def _sdf2SimilarityMapSVG(data,
width=500,
height=500,
radius=2,
fingerprint='morgan',
loadMol=True,
useRDKitChemistry=True,
format='svg'):
return _similarityMapSVG(_parseMolData(
data, loadMol=loadMol, useRDKitChemistry=useRDKitChemistry),
width=width,
height=height,
radius=radius,
fingerprint=fingerprint,
format=format)
def _highlightCtabFragmentSVG(data,
smarts,
size,
loadMol=True,
useRDKitChemistry=False,
kekulize=False,
atomMapNumber=False,
computeCoords=False,
force=False):
mols = _parseMolData(data,
loadMol=loadMol,
useRDKitChemistry=useRDKitChemistry)
matches = _getMatches(mols, smarts, force)
return _mols2svg(mols,
size,
kekulize=kekulize,
atomMapNumber=atomMapNumber,
computeCoords=computeCoords,
highlightAtomLists=matches)
def _ctab22D(data, loadMol=True, useRDKitChemistry=False):
mols = _parseMolData(data, loadMol=True, useRDKitChemistry=False)
optimisedMols = _apply(mols, _2D22D)
return _getSDFString(optimisedMols)
def _get_alerts(data, loadMol=True, useRDKitChemistry=False):
mols = _parseMolData(data,
loadMol=loadMol,
useRDKitChemistry=useRDKitChemistry)
res = _apply(mols, get_matches)
return json.dumps(res)
def _ctab2inchi(data, loadMol=False, useRDKitChemistry=False):
return '\n'.join(_apply(_parseMolData(data, loadMol=False, useRDKitChemistry=False), Chem.MolBlockToInchi))
def _ctab2smiles(data, loadMol=True, useRDKitChemistry=True, delimiter=' ', nameHeader='Name', includeHeader=True):
return _getSMILESString(_parseMolData(data, loadMol=True, useRDKitChemistry=True),
delimiter=delimiter, nameHeader=nameHeader, includeHeader=includeHeader)
def _ctab2smarts(data, loadMol=True, useRDKitChemistry=True):
return _getSMARTSString(_parseMolData(data, loadMol=True, useRDKitChemistry=True))
def _is3D(data, loadMol=True, useRDKitChemistry=True):
mols = _parseMolData(data,
loadMol=loadMol,
useRDKitChemistry=useRDKitChemistry)
flags = _apply(mols, _check3Dcoords)
return json.dumps(flags)
def _getChemblDescriptors(data, loadMol=True, useRDKitChemistry=True):
return _apply(
_parseMolData(data,
loadMol=loadMol,
useRDKitChemistry=useRDKitChemistry), _chembl_desc_list)
def _check(data, loadMol=False, useRDKitChemistry=False):
mols = _parseMolData(data, loadMol=loadMol, useRDKitChemistry=useRDKitChemistry)
res = _apply(mols, checker.check_molblock)
return json.dumps(res)
def _exclude(data, loadMol=True, useRDKitChemistry=False):
mols = _parseMolData(data, loadMol=loadMol, useRDKitChemistry=useRDKitChemistry)
res = _apply(mols, exclude_flag, False)
return json.dumps(res)
def _standardize(data, loadMol=False, useRDKitChemistry=False):
mols = _parseMolData(data, loadMol=loadMol, useRDKitChemistry=useRDKitChemistry)
res = _apply(mols, standardizer.standardize_molblock)
res_list = [{'standard_molblock': m} for m in res]
return json.dumps(res_list)
def _get_parent(data, loadMol=False, useRDKitChemistry=False):
mols = _parseMolData(data, loadMol=loadMol, useRDKitChemistry=useRDKitChemistry)
res = _apply(mols, standardizer.get_parent_molblock)
res_dict = [{k: v for e in m for k, v in zip(('parent_molblock', 'exclude'), m)} for m in res]
return json.dumps(res_dict)