def cairo_out_test(): import molfile import time cid = 22646404 #cid = 1373132 #cid = 18305969 #cid = 19815256 f = file("%d.mol" % cid, "r") mol = molfile.file_to_mol(f) f.close() import cairo_out mol.normalize_bond_length(25) mol.remove_unimportant_hydrogens() c = cairo_out.cairo_out(scaling=4.0, margin=10, font_size=16, bond_second_line_shortening=0.15, bond_width=6, line_width=2.0, antialias_drawing=True, antialias_text=True) #c.background_color = (1,1,0.6) c.show_hydrogens_on_hetero = True t = time.time() c.mol_to_cairo(mol, "%d.png" % cid) c.mol_to_cairo(mol, "%d.pdf" % cid, format="pdf") c.mol_to_cairo(mol, "%d.svg" % cid, format="svg") print time.time() - t
def test_multimol_molfile(): import molfile f = file('test.mol', 'r') mol = molfile.file_to_mol(f) f.close() print mol.is_connected() for mol in mol.get_disconnected_subgraphs(): print mol
def test_multimol_molfile(): import molfile f = file( 'test.mol', 'r') mol = molfile.file_to_mol( f) f.close() print mol.is_connected() for mol in mol.get_disconnected_subgraphs(): print mol
def test_charge_property_line(): import molfile f = file('fromOBabel.mol', 'r') mol = molfile.file_to_mol(f) f.close() print mol.is_connected() for mol in mol.get_disconnected_subgraphs(): for atom in mol.atoms: print atom.charge
def test_charge_property_line(): import molfile f = file( 'fromOBabel.mol', 'r') mol = molfile.file_to_mol( f) f.close() print mol.is_connected() for mol in mol.get_disconnected_subgraphs(): for atom in mol.atoms: print atom.charge
def cairo_out_test_wedge(): import molfile import time f = file( "untitled0.mol", "r") mol = molfile.file_to_mol( f) f.close() import cairo_out mol.normalize_bond_length( 30) mol.remove_unimportant_hydrogens() c = cairo_out.cairo_out( scaling=1.0, antialias_text=True, color_bonds=True, color_atoms=True) t = time.time() c.mol_to_cairo( mol, "untitled0.png") print time.time()-t
def cairo_out_test3d(): import molfile f = file( "1.mol", "r") mol = molfile.file_to_mol( f) f.close() import cairo_out #mol.normalize_bond_length( 25) #mol.remove_unimportant_hydrogens() c = cairo_out.cairo_out( scaling=1.0, margin=30, font_size=16, bond_second_line_shortening=0.15, bond_width=6, line_width=2.0, antialias_drawing=True, antialias_text=True) c.show_hydrogens_on_hetero = True c.mol_to_cairo( mol, "1.png")
def cairo_out_test_wedge(): import molfile import time f = file("untitled0.mol", "r") mol = molfile.file_to_mol(f) f.close() import cairo_out mol.normalize_bond_length(30) mol.remove_unimportant_hydrogens() c = cairo_out.cairo_out(scaling=1.0, antialias_text=True, color_bonds=True, color_atoms=True) t = time.time() c.mol_to_cairo(mol, "untitled0.png") print time.time() - t
def cairo_out_test3d(): import molfile f = file("1.mol", "r") mol = molfile.file_to_mol(f) f.close() import cairo_out #mol.normalize_bond_length( 25) #mol.remove_unimportant_hydrogens() c = cairo_out.cairo_out(scaling=1.0, margin=30, font_size=16, bond_second_line_shortening=0.15, bond_width=6, line_width=2.0, antialias_drawing=True, antialias_text=True) c.show_hydrogens_on_hetero = True c.mol_to_cairo(mol, "1.png")
def cairo_out_test(): import molfile import time cid = 22646404 #cid = 1373132 #cid = 18305969 #cid = 19815256 f = file( "%d.mol" % cid, "r") mol = molfile.file_to_mol( f) f.close() import cairo_out mol.normalize_bond_length( 25) mol.remove_unimportant_hydrogens() c = cairo_out.cairo_out( scaling=4.0, margin=10, font_size=16, bond_second_line_shortening=0.15, bond_width=6, line_width=2.0, antialias_drawing=True, antialias_text=True) #c.background_color = (1,1,0.6) c.show_hydrogens_on_hetero = True t = time.time() c.mol_to_cairo( mol, "%d.png" % cid) c.mol_to_cairo( mol, "%d.pdf" % cid, format="pdf") c.mol_to_cairo( mol, "%d.svg" % cid, format="svg") print time.time()-t
( 'ry', str( radius)), ( 'stroke-width', "1"), ( 'fill', fill_color), ( 'stroke', stroke_color), ( 'fill-opacity', str(opacity)), ( 'stroke-opacity', str(opacity)), )) if id: el.setAttribute( "id", id) def mol_to_svg( mol, filename): c = svg_out() tree = c.mol_to_svg( mol) f = file( filename, "w") f.write( tree.toxml()) f.close() if __name__ == "__main__": #import inchi #mol = inchi.text_to_mol( "1/C7H6O2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H,8,9)", include_hydrogens=False, calc_coords=30) #import smiles #mol = smiles.text_to_mol( "CC[CH]", calc_coords=40) import molfile mol = molfile.file_to_mol( file( "/home/beda/bkchem/bkchem/untitled0.mol", "r")) mol_to_svg( mol, "output.svg")
import time pmol = pybel.readstring("smi", "CC(=O)O") omol = PybelConverter.pybel_to_oasa_molecule(pmol) print(omol) import smiles c = smiles.converter() print(c.mols_to_text([omol])) #print(get_supported_input_formats()) #print(get_supported_output_formats()) if False: import molfile with open("tbu-benzen.mol", 'r') as f: mol = molfile.file_to_mol(f) print(PybelConverter.oasa_to_pybel_molecule(mol)) t = time.time() ff = ForceFieldOptimizer(mol) gen = ff.conjugate_gradients() for step in gen: print(step, ff.ff.Energy()) ff.update_coords() print([a.coords for a in mol.atoms]) print(time.time() - t) a = pybel.readstring("smi", "CCCC\nCCC") for mol in PybelConverter.read_text("smi", "CCCC\nCCC"):
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_coords2(): f = file("cis_trans_cycles.mol", "r") mol = molfile.file_to_mol(f) f.close() c = smiles.converter() print c.mols_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)
('rx', str(radius)), ('ry', str(radius)), ('stroke-width', "1"), ('fill', fill_color), ('stroke', stroke_color), ('fill-opacity', str(opacity)), ('stroke-opacity', str(opacity)), )) if id: el.setAttribute("id", id) def mol_to_svg(mol, filename): c = svg_out() tree = c.mol_to_svg(mol) f = file(filename, "w") f.write(tree.toxml()) f.close() if __name__ == "__main__": #import inchi #mol = inchi.text_to_mol( "1/C7H6O2/c8-7(9)6-4-2-1-3-5-6/h1-5H,(H,8,9)", include_hydrogens=False, calc_coords=30) #import smiles #mol = smiles.text_to_mol( "CC[CH]", calc_coords=40) import molfile mol = molfile.file_to_mol( file("/home/beda/bkchem/bkchem/untitled0.mol", "r")) mol_to_svg(mol, "output.svg")
import time pmol = pybel.readstring("smi", "CC(=O)O") omol = PybelConverter.pybel_to_oasa_molecule( pmol) print(omol) import smiles c = smiles.converter() print(c.mols_to_text([omol])) #print(get_supported_input_formats()) #print(get_supported_output_formats()) if False: import molfile with open("tbu-benzen.mol", 'r') as f: mol = molfile.file_to_mol(f) print(PybelConverter.oasa_to_pybel_molecule(mol)) t = time.time() ff = ForceFieldOptimizer( mol) gen = ff.conjugate_gradients() for step in gen: print(step, ff.ff.Energy()) ff.update_coords() print([a.coords for a in mol.atoms]) print(time.time() - t) a = pybel.readstring( "smi", "CCCC\nCCC") for mol in PybelConverter.read_text( "smi", "CCCC\nCCC"):
def stereo_from_coords2(): f = file( "cis_trans_cycles.mol", "r") mol = molfile.file_to_mol( f) f.close() c = smiles.converter() print c.mols_to_text( [mol])