def present_mol(sdf):
if not sdf.rstrip().endswith("$$$$"):
return 0
try:
mol = StringIO.StringIO(sdf)
molec = oasa_bridge.read_molfile(mol, App.paper)
mol.close()
except:
return 0
if len(molec.atoms)<2:
return 0
averagey = sum([atom.y for atom in molec.atoms]) / float(len(molec.atoms))
for atom in molec.atoms:
atom.y = 2*averagey - atom.y
N = 0
for minimol in molec.get_disconnected_subgraphs():
N += 1
App.paper.stack.append(minimol)
minimol.draw()
App.paper.add_bindings()
App.paper.start_new_undo_record()
return N
def present_mol(sdf):
if not sdf.rstrip().endswith("$$$$"):
return 0
try:
mol = StringIO.StringIO(sdf)
molec = oasa_bridge.read_molfile(mol, App.paper)
mol.close()
except:
return 0
if len(molec.atoms) < 2:
return 0
averagey = sum([atom.y for atom in molec.atoms]) / float(len(molec.atoms))
for atom in molec.atoms:
atom.y = 2 * averagey - atom.y
N = 0
for minimol in molec.get_disconnected_subgraphs():
N += 1
App.paper.stack.append(minimol)
minimol.draw()
App.paper.add_bindings()
App.paper.start_new_undo_record()
return N
def get_molecules(self, name):
file = open(name, 'r')
mols = oasa_bridge.read_molfile(file, self.paper)
file.close()
[invert_coords(mol) for mol in mols]
return mols
label_text=_('Give the name of a molecule to fetch:'),
entryfield_labelpos = 'n',
buttons=(_('OK'),_('Cancel')))
res = dial.activate()
if res == _('OK'):
name = dial.get()
# fetch the molfile
try:
from io import StringIO
except ImportError:
from StringIO import StringIO
molcas = get_mol_from_web_molfile(name)
if molcas:
mol, cas = molcas
mol = StringIO(mol)
molec = oasa_bridge.read_molfile(mol, App.paper)[0]
mol.close()
App.paper.stack.append(molec)
molec.draw()
if cas:
t = App.paper.new_text(280, 300, text="CAS: " + cas.strip())
t.draw()
App.paper.add_bindings()
App.paper.start_new_undo_record()
else:
App.update_status(_("Sorry, molecule with name %s was not found") % name)
def get_molecules(self, name):
with open(name, 'r') as f:
mols = oasa_bridge.read_molfile(f, self.paper)
[invert_coords(mol) for mol in mols]
return mols
def get_molecules(self, name):
with open(name, 'r') as f:
mols = oasa_bridge.read_molfile(f, self.paper)
[invert_coords(mol) for mol in mols]
return mols