import os, sys, math
import cPickle
from rdkit import Chem
from rdkit import RDConfig
from rdkit import Geometry
from rdkit.Chem import AllChem
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem.Pharm3D import Pharmacophore
from rdkit.Chem.FeatMaps import FeatMapPoint
# feature Def
feat_def = "BaseFeatures_seri.fdef"
feat_fact = AllChem.BuildFeatureFactoryFromString(file(feat_def, "r").read())
# Get Pharmacophore from q_mol
q_mol = Chem.SDMolSupplier(sys.argv[1])[0]
feats = feat_fact.GetFeaturesForMol(q_mol)
pcophore = Pharmacophore.Pharmacophore(feats)
# GetFeatures As nested list
# [[x,y,x],
# [x,y,z],
# [x,y,z]]
pos_list = []
for feat in feats:
geom = list(feat.GetPos())
pos_list.append(geom)
for i in range(len(pos_list)):
print pos_list[i], feats[i].GetFamily()
v = MolViewer()
except Exception:
logger.error(
'Unable to connect to PyMol server.\nPlease run ~landrgr1/extern/PyMol/launch.sh to start it.'
)
sys.exit(1)
if options.clearAll:
v.DeleteAll()
try:
fdef = open(options.fdef, 'r').read()
except IOError:
logger.error('ERROR: Could not open fdef file %s' % options.fdef)
sys.exit(1)
factory = AllChem.BuildFeatureFactoryFromString(fdef)
if options.writeFeats:
print('# Family \tX \tY \tZ \tRadius\t # Atom_ids')
if options.featMapFile:
if options.featMapFile == '-':
options.featMapFile = sys.stdout
else:
options.featMapFile = file(options.featMapFile, 'w+')
print('# Feature map generated by ShowFeats v%s' % _version,
file=options.featMapFile)
print("ScoreMode=All", file=options.featMapFile)
print("DirScoreMode=Ignore", file=options.featMapFile)
print("BeginParams", file=options.featMapFile)
for family in factory.GetFeatureFamilies():
def get_feats(molecule):
fdef = open(os.path.join(RDConfig.RDDataDir, 'BaseFeatures.fdef'), 'r').read()
factory = AllChem.BuildFeatureFactoryFromString(fdef)
return ShowMolFeats(molecule, factory, transparency=0.25,
showOnly=False, includeArrowheads=True,
writeFeats=True, showMol=True)
