def _read_in_library(self, path, header, delimiter, quotechar):
"""Fragment library parser
Args:
path (str): Path to the fragment library.
header (bool): Whether or not the library contains a header.
delimiter (str): Delimiter symbol.
quotechar (str): Quotechar symbol.
"""
rdkit.rdBase.DisableLog("rdApp.*")
rdCoordGen.SetDefaultTemplateFileDir(config.coordgen_templates)
rdCoordGen.CoordGenParams.coordgenScaling = 33 # to get single bond length 1.5
with open(path, "r") as csvfile:
library_reader = csv.reader(
csvfile, delimiter=delimiter, quotechar=quotechar
)
if header:
next(library_reader)
for row in library_reader:
mol = None
if row[1] == "SMARTS":
mol = Chem.MolFromSmarts(row[2])
else:
mol = Chem.MolFromSmiles(row[2])
if row[1] == "LIKE":
for bond in mol.GetBonds():
bond.SetBondType(Chem.rdchem.BondType.UNSPECIFIED)
Chem.SanitizeMol(mol, catchErrors=True)
rdCoordGen.AddCoords(mol)
self.library[row[0]] = FragmentEntry(row[0], row[6], mol)
rdkit.rdBase.EnableLog("rdApp.*")
# This is an optional component of the build
from rdkit.Chem.rdMolInterchange import *
except ImportError:
pass
# Coordgen needs to know where its template file is.
# The default install puts it in RDDataDir
try:
from rdkit.Chem import rdCoordGen
except ImportError:
pass
else:
templDir = RDConfig.RDDataDir
if templDir[-1] != '/':
templDir += '/'
rdCoordGen.SetDefaultTemplateFileDir(templDir)
def QuickSmartsMatch(smi, sma, unique=True, display=False):
m = MolFromSmiles(smi)
p = MolFromSmarts(sma)
res = m.GetSubstructMatches(p, unique)
if display:
pass
return res
def CanonSmiles(smi, useChiral=1):
m = MolFromSmiles(smi)
return MolToSmiles(m, useChiral)
