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])