def test_multimol_molfile2():
import molfile, smiles
mols = [smiles.text_to_mol(t) for t in ["CCC(=O)[O-].[K+]"]]
for mol in mols:
mol.remove_zero_order_bonds()
m = molfile.converter()
text = m.mols_to_text(mols)
f = file("multi2.mol", "w")
f.write(text)
f.close()
f = file("prase.sdf", "r")
for mol in m.read_text(text):
print smiles.mol_to_text(mol)
f.close()
def test_multimol_molfile2():
import molfile, smiles
mols = [smiles.text_to_mol( t) for t in ["CCC(=O)[O-].[K+]"]]
for mol in mols:
mol.remove_zero_order_bonds()
m = molfile.converter()
text = m.mols_to_text( mols)
f = file("multi2.mol","w")
f.write( text)
f.close()
f = file("prase.sdf","r")
for mol in m.read_text( text):
print smiles.mol_to_text( mol)
f.close()
def find_rings_in_mol(self, mol, detect_aromatic=True):
hits = []
if detect_aromatic:
# this is necessary to correctly process fused aromatic rings
# with improperly localized bonds
mol.mark_aromatic_bonds()
for ering in mol.get_smallest_independent_cycles_e():
vring = mol.edge_subgraph_to_vertex_subgraph(ering)
ring_mol = mol.get_new_induced_subgraph(vring, ering)
# here we need to take care of aromatic bonds
# this is needed to properly match naphthalene, etc.
if detect_aromatic:
for e in ring_mol.edges:
if e.aromatic:
e.order = 4
ring_mol.localize_aromatic_bonds()
ring_hash = ring_mol.get_structure_hash()
if ring_hash in self.rings:
hit = ring_match(vring, self.rings[ring_hash])
else:
ring_obj = ring(None,
smiles.mol_to_text(ring_mol),
ring_hash=ring_hash)
self.rings[ring_hash] = ring_obj
hit = ring_match(vring, ring_obj)
hits.append(hit)
return hits
def find_rings_in_mol( self, mol, detect_aromatic=True):
hits = []
if detect_aromatic:
# this is necessary to correctly process fused aromatic rings
# with improperly localized bonds
mol.mark_aromatic_bonds()
for ering in mol.get_smallest_independent_cycles_e():
vring = mol.edge_subgraph_to_vertex_subgraph( ering)
ring_mol = mol.get_new_induced_subgraph( vring, ering)
# here we need to take care of aromatic bonds
# this is needed to properly match naphthalene, etc.
if detect_aromatic:
for e in ring_mol.edges:
if e.aromatic:
e.order = 4
ring_mol.localize_aromatic_bonds()
ring_hash = ring_mol.get_structure_hash()
if ring_hash in self.rings:
hit = ring_match( vring, self.rings[ ring_hash])
else:
ring_obj = ring( None, smiles.mol_to_text( ring_mol), ring_hash=ring_hash)
self.rings[ ring_hash] = ring_obj
hit = ring_match( vring, ring_obj)
hits.append( hit)
return hits
def test_fullerene_lockdown():
import inchi
import smiles
from time import time
t = time()
#mol = inchi.text_to_mol( "InChI=1/C60/c1-2-5-6-3(1)8-12-10-4(1)9-11-7(2)17-21-13(5)23-24-14(6)22-18(8)28-20(12)30-26-16(10)15(9)25-29-19(11)27(17)37-41-31(21)33(23)43-44-34(24)32(22)42-38(28)48-40(30)46-36(26)35(25)45-39(29)47(37)55-49(41)51(43)57-52(44)50(42)56(48)59-54(46)53(45)58(55)60(57)59")
string = "C12=C3C4=C5C6=C1C7=C8C9=C1C%10=C%11C(=C29)C3=C2C3=C4C4=C5C5=C9C6=C7C6=C7C8=C1C1=C8C%10=C%10C%11=C2C2=C3C3=C4C4=C5C5=C%11C%12=C(C6=C95)C7=C1C1=C%12C5=C%11C4=C3C3=C5C(=C81)C%10=C23"
#string = "C12C3C2C13"
string = "c1=%31c%25c8c%23c%19c%18c7c8c%17c%25c%29C=%21C=%31c%12c2-c%11c=%21c%20c%24c=4c%11C=6c2c9c(c5%28)c%12c1c%23c5c%19c3c%16c%18c%14c7c(c%17c%10c%20%29)c%22c%10c%24c%26c-%13c%22c%14c(c-%13c%15=C%27C=4%26)c%16c(c%15=%30)=c3c%28=C9C=%30C=6%27"
mol = smiles.text_to_mol(string, calc_coords=True)
print time() - t
t = time()
#print mol.get_all_cycles()
print smiles.mol_to_text(mol)
print time() - t
print mol
def test_fullerene_lockdown():
import inchi
import smiles
from time import time
t = time()
#mol = inchi.text_to_mol( "InChI=1/C60/c1-2-5-6-3(1)8-12-10-4(1)9-11-7(2)17-21-13(5)23-24-14(6)22-18(8)28-20(12)30-26-16(10)15(9)25-29-19(11)27(17)37-41-31(21)33(23)43-44-34(24)32(22)42-38(28)48-40(30)46-36(26)35(25)45-39(29)47(37)55-49(41)51(43)57-52(44)50(42)56(48)59-54(46)53(45)58(55)60(57)59")
string = "C12=C3C4=C5C6=C1C7=C8C9=C1C%10=C%11C(=C29)C3=C2C3=C4C4=C5C5=C9C6=C7C6=C7C8=C1C1=C8C%10=C%10C%11=C2C2=C3C3=C4C4=C5C5=C%11C%12=C(C6=C95)C7=C1C1=C%12C5=C%11C4=C3C3=C5C(=C81)C%10=C23"
#string = "C12C3C2C13"
string = "c1=%31c%25c8c%23c%19c%18c7c8c%17c%25c%29C=%21C=%31c%12c2-c%11c=%21c%20c%24c=4c%11C=6c2c9c(c5%28)c%12c1c%23c5c%19c3c%16c%18c%14c7c(c%17c%10c%20%29)c%22c%10c%24c%26c-%13c%22c%14c(c-%13c%15=C%27C=4%26)c%16c(c%15=%30)=c3c%28=C9C=%30C=6%27"
mol = smiles.text_to_mol( string, calc_coords=True)
print time()-t
t = time()
#print mol.get_all_cycles()
print smiles.mol_to_text( mol)
print time()-t
print mol
def main( text, cycles):
t1 = time.time()
for jj in range( cycles):
mol = text_to_mol( text, calc_coords=True, include_hydrogens=False)
print map( str, [b for b in mol.bonds if b.order == 0])
print " smiles: ", smiles.mol_to_text( mol)
print " inchi: ", generate_inchi( mol, fixed_hs=False, program="/home/beda/bin/stdinchi-1")
print " charge: ", sum( [a.charge for a in mol.vertices])
print " mw: ", mol.weight
print generate_inchi_and_inchikey( mol, fixed_hs=False, program="/home/beda/bin/stdinchi-1")
t1 = time.time() - t1
print 'time per cycle', round( 1000*t1/cycles, 2), 'ms'
def main(text, cycles):
t1 = time.time()
for jj in range(cycles):
mol = text_to_mol(text, calc_coords=True, include_hydrogens=False)
print map(str, [b for b in mol.bonds if b.order == 0])
print " smiles: ", smiles.mol_to_text(mol)
print " inchi: ", generate_inchi(
mol, fixed_hs=False, program="/home/beda/bin/stdinchi-1")
print " charge: ", sum([a.charge for a in mol.vertices])
print " mw: ", mol.weight
print generate_inchi_and_inchikey(mol,
fixed_hs=False,
program="/home/beda/bin/stdinchi-1")
t1 = time.time() - t1
print 'time per cycle', round(1000 * t1 / cycles, 2), 'ms'
def stereo_from_coords():
f = file("ez_stereo2.mol", "r")
mol = molfile.file_to_mol(f)
f.close()
mol.detect_stereochemistry_from_coords()
print smiles.mol_to_text(mol)
def stereo_from_coords():
f = file( "ez_stereo2.mol", "r")
mol = molfile.file_to_mol( f)
f.close()
mol.detect_stereochemistry_from_coords()
print smiles.mol_to_text( mol)