def text_to_mol(text):
gen = read_cdml(text)
try:
mol = gen.next()
except StopIteration:
return None
calculate_coords(mol, bond_length=-1)
return mol
def text_to_mol( text):
gen = read_cdml( text)
try:
mol = gen.next()
except StopIteration:
return None
calculate_coords( mol, bond_length=-1)
return mol
def text_to_mol( text, calc_coords=1, localize_aromatic_bonds=True):
sm = smiles()
sm.read_smiles( text)
mol = sm.structure
if localize_aromatic_bonds:
mol.localize_aromatic_bonds()
for b in mol.bonds:
b.aromatic = 0
if calc_coords:
coords_generator.calculate_coords( mol, bond_length=calc_coords)
return mol
def text_to_mol( text, include_hydrogens=True, mark_aromatic_bonds=False, calc_coords=1):
try:
inc = inchi()
inc.read_inchi( text)
mol = inc.structure
#mol.add_missing_bond_orders()
if not include_hydrogens:
mol.remove_unimportant_hydrogens()
if calc_coords:
coords_generator.calculate_coords( mol, bond_length=calc_coords)
if mark_aromatic_bonds:
mol.mark_aromatic_bonds()
return mol
except oasa_inchi_error:
raise
except oasa_not_implemented_error:
raise
except:
raise
def text_to_mol(text,
include_hydrogens=True,
mark_aromatic_bonds=False,
calc_coords=1):
try:
inc = inchi()
inc.read_inchi(text)
mol = inc.structure
#mol.add_missing_bond_orders()
if not include_hydrogens:
mol.remove_unimportant_hydrogens()
if calc_coords:
coords_generator.calculate_coords(mol, bond_length=calc_coords)
if mark_aromatic_bonds:
mol.mark_aromatic_bonds()
return mol
except oasa_inchi_error:
raise
except oasa_not_implemented_error:
raise
except:
raise
def show_dump():
from molecule import molecule
from graph.graph import graph
imp = molecule()
imp.read_simple_text_file(file("aaa9.txt", "r"))
removed = True
while removed:
removed = False
for e in list(imp.edges):
a1, a2 = e.vertices
for e2 in list(imp.edges):
if (e is not e2) and set(e.vertices) == set(e2.vertices):
imp.disconnect_edge(e2)
removed = True
break
if removed:
break
import coords_generator
for part in imp.get_disconnected_subgraphs():
if len(part.vertices) > 1:
coords_generator.calculate_coords(part, force=1)
coords_generator.show_mol(part)
def show_dump():
from molecule import molecule
from graph.graph import graph
imp = molecule()
imp.read_simple_text_file( file("aaa9.txt","r"))
removed = True
while removed:
removed = False
for e in list(imp.edges):
a1,a2 = e.vertices
for e2 in list(imp.edges):
if (e is not e2) and set(e.vertices) == set(e2.vertices):
imp.disconnect_edge( e2)
removed = True
break
if removed:
break
import coords_generator
for part in imp.get_disconnected_subgraphs():
if len( part.vertices) > 1:
coords_generator.calculate_coords( part, force=1)
coords_generator.show_mol( part)
all_chunks.append( chunk)
else:
for chunk, count in gen_formula_fragments_helper( form):
if count:
all_chunks.append(")")
if chunk:
all_chunks.extend( reverse_formula( chunk))
if count:
all_chunks.append("(")
#
# if count:
# all_chunks.append( str(count))
print all_chunks
#all_chunks.reverse()
return all_chunks
if __name__ == "__main__":
form = 'CH3(CH2)7'
#form = 'CH3((CH2)2)2O'
a = linear_formula( form , start_valency=0, end_valency=1)
if a.molecule:
m = a.molecule
coords_generator.calculate_coords( m)
coords_generator.show_mol( m)
else:
print "nothing"
