def render(self, mode="human"):
"""
Generates a 3D rendering of the current molecule in the environment.
Parameters
-------
mode: string
Just a way of indicating whether the rendering is mainly for humans vs machines in OpenAI
"""
if self.check_valency() and self.check_chemical_validity():
if not self.pymol_window_flag:
self.start_pymol()
molecule = self.mol
self.mol.UpdatePropertyCache(
strict=False) # Update valence information
FastFindRings(
self.mol
) # Quick for finding out if an atom is in a ring, use Chem.GetSymmSSR() if more reliability is desired
Chem.AddHs(
molecule) # Add explicit hydrogen atoms for rendering purposes
# remove stereochemistry information
rdmolops.RemoveStereochemistry(molecule)
# Generate 3D structure
AllChem.EmbedMolecule(molecule)
AllChem.MMFFOptimizeMolecule(molecule)
v = MolViewer()
v.ShowMol(molecule)
v.GetPNG(h=400)
# Save the rendering in pse format
pymol.cmd.save("./pymol_renderings/" + Chem.MolToSmiles(molecule) +
".pse",
format="pse")
Chem.RemoveHs(molecule) # Remove explicit hydrogen
else:
print(
"The molecule is not chemically valid, and rendering has been terminated."
)
parser.add_option('--verbose',
default=False,
action='store_true',
help='be verbose')
if __name__ == '__main__':
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem.PyMol import MolViewer
options, args = parser.parse_args()
if len(args) < 1:
parser.error('please provide either at least one sd or mol file')
try:
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)
print 'm1:'
s1 = b.GenerateSubshapeShape(m1)
cPickle.dump(s1,file('test_data/square1.shp.pkl','wb+'))
print 'm2:'
s2 = b.GenerateSubshapeShape(m2)
cPickle.dump(s2,file('test_data/square2.shp.pkl','wb+'))
ns1 = b.CombineSubshapes(s1,s2)
b.GenerateSubshapeSkeleton(ns1)
cPickle.dump(ns1,file('test_data/combined.shp.pkl','wb+'))
else:
s1 = cPickle.load(file('test_data/square1.shp.pkl','rb'))
s2 = cPickle.load(file('test_data/square2.shp.pkl','rb'))
#ns1 = cPickle.load(file('test_data/combined.shp.pkl','rb'))
ns1=cPickle.load(file('test_data/combined.shp.pkl','rb'))
v = MolViewer()
SubshapeObjects.DisplaySubshape(v,s1,'shape1')
SubshapeObjects.DisplaySubshape(v,ns1,'ns1')
#SubshapeObjects.DisplaySubshape(v,s2,'shape2')
a = SubshapeAligner.SubshapeAligner()
pruneStats={}
algs =a.GetSubshapeAlignments(None,ns1,m1,s1,b,pruneStats=pruneStats)
print len(algs)
print pruneStats
import os,tempfile
from rdkit import Geometry
fName = tempfile.mktemp('.grd')
Geometry.WriteGridToFile(ns1.coarseGrid.grid,fName)
v.server.loadSurface(fName,'coarse','',2.5)
from rdkit import Chem
from rdkit.Chem.PyMol import MolViewer
from rdkit.Chem import AllChem
import gzip
try:
v = MolViewer()
v.DeleteAll()
except Exception:
v = None
outf = open('chembl_20_chiral.problems.smi', 'w+')
noconff = open('chembl_20_chiral.noconfs.smi', 'w+')
for i, line in enumerate(gzip.open('../Data/chembl_20_chiral.smi.gz')):
line = line.strip().decode().split(' ')
mol = Chem.MolFromSmiles(line[0])
if not mol:
continue
cents = Chem.FindMolChiralCenters(mol, includeUnassigned=True)
if len([y for x, y in cents if y == '?']):
continue
nm = line[1]
csmi = Chem.MolToSmiles(mol, True)
for j in range(100):
mh = Chem.AddHs(mol)
ok = AllChem.EmbedMolecule(mh, randomSeed=j + 1)
if ok >= 0:
Chem.AssignAtomChiralTagsFromStructure(mh)
newm = Chem.RemoveHs(mh)
smi = Chem.MolToSmiles(newm, True)
if smi != csmi:
from rdkit.Chem.PyMol import MolViewer
#cmpd = Chem.MolFromSmiles('CCCc1cc(C(=O)O)ccc1')
#cmpd = Chem.AddHs(cmpd)
if 1:
cmpd = Chem.MolFromSmiles('C1=CC=C1C#CC1=CC=C1')
cmpd = Chem.AddHs(cmpd)
AllChem.EmbedMolecule(cmpd)
AllChem.UFFOptimizeMolecule(cmpd)
AllChem.CanonicalizeMol(cmpd)
print >> file('testmol.mol', 'w+'), Chem.MolToMolBlock(cmpd)
else:
cmpd = Chem.MolFromMolFile('testmol.mol')
builder = SubshapeBuilder()
if 1:
shape = builder.GenerateSubshapeShape(cmpd)
v = MolViewer()
if 1:
import tempfile
tmpFile = tempfile.mktemp('.grd')
v.server.deleteAll()
Geometry.WriteGridToFile(shape.grid, tmpFile)
time.sleep(1)
v.ShowMol(cmpd, name='testMol', showOnly=True)
v.server.loadSurface(tmpFile, 'testGrid', '', 2.5)
v.server.resetCGO('*')
cPickle.dump(shape, file('subshape.pkl', 'w+'))
for i, pt in enumerate(shape.skelPts):
v.server.sphere(tuple(pt.location), .5, (1, 0, 1), 'Pt-%d' % i)
if not hasattr(pt, 'shapeDirs'): continue
momBeg = pt.location - pt.shapeDirs[0]
targetConf=tgtConf,
queryConf=queryConf,
pruneStats=pruneStats):
continue
# if we made it this far, it's a good alignment
yield alignment
if __name__ == '__main__':
from rdkit.six.moves import cPickle
tgtMol, tgtShape = cPickle.load(file('target.pkl', 'rb'))
queryMol, queryShape = cPickle.load(file('query.pkl', 'rb'))
builder = cPickle.load(file('builder.pkl', 'rb'))
aligner = SubshapeAligner()
algs = aligner.GetSubshapeAlignments(tgtMol, tgtShape, queryMol,
queryShape, builder)
print(len(algs))
from rdkit.Chem.PyMol import MolViewer
v = MolViewer()
v.ShowMol(tgtMol, name='Target', showOnly=True)
v.ShowMol(queryMol, name='Query', showOnly=False)
SubshapeObjects.DisplaySubshape(v,
tgtShape,
'target_shape',
color=(.8, .2, .2))
SubshapeObjects.DisplaySubshape(v,
queryShape,
'query_shape',
color=(.2, .2, .8))