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"