def transform_atom( self, a, doc):
out = doc.createElement( 'atom')
try:
atom = self.CML_atom( cml=a)
except cml_exception, detail:
# problems converting cml to atom
raise plugin.import_exception( detail)
def transform_bond( self, b, doc):
out = doc.createElement( 'bond')
try:
bond = self.CML_bond( cml=b)
except cml_exception, detail:
# problems converting cml to bond
raise plugin.import_exception( str( detail))
def transform_CML_bond( self, bond, doc):
"""called by transform_bond in order to do the transform from CML_bond instance to CDML"""
if bond.not_enough_data():
# bond does not have sufficient data to be safely converted to cdml
raise plugin.import_exception( "missing "+str( bond.not_enough_data())+" in bond specification")
out = doc.createElement( 'bond')
type = (bond.stereo.lower() or 'n') + str( bond.order)
dom_ext.setAttributes( out, (('type', type),
('start', bond.atom1),
('end', bond.atom2)))
return out
class CML_importer( plugin.importer):
"""Imports a CML (Chemical Markup Language) document, uses version 1.0 of the CML standard."""
doc_string = _("Imports a CML (Chemical Markup Language) document, uses version 1.0 of the CML standard.")
def __init__( self):
# this makes implementing CML2 much easier - just supply different CML_atom and CML_bond
self.CML_atom = CML_atom
self.CML_bond = CML_bond
self.xs = []
self.ys = []
def on_begin( self):
self.xs = []
self.ys = []
self.atoms = []
return 1
def get_cdml_dom( self, file_name):
tree = dom.parse( file_name)
out = dom.Document()
root = dom_ext.elementUnder( out, 'cdml', (('version','0.11'),))
for m in tree.getElementsByTagName( 'molecule'):
out_m = self.transform_molecule( m, out)
if out_m:
root.appendChild( out_m)
view = self.on_end_set_viewport()
if view:
viewport = out.createElement( 'viewport')
viewport.setAttribute( 'viewport', '%f %f %f %f' % view)
root.insertBefore( viewport, root.firstChild)
return root
def transform_molecule( self, mol, doc):
#atoms
out = doc.createElement( 'molecule')
for a in mol.getElementsByTagName( 'atom'):
out_a = self.transform_atom( a, doc)
if out_a:
out.appendChild( out_a)
# bonds
ar = mol.getElementsByTagName( 'bondArray')
if ar:
ar = ar[0]
for b in ar.getElementsByTagName( 'bond'):
out_b = self.transform_bond( b, doc)
if out_b:
out.appendChild( out_b)
else:
for b in self.add_nonexisting_bonds():
out.appendChild( b)
return out
def transform_atom( self, a, doc):
out = doc.createElement( 'atom')
try:
atom = self.CML_atom( cml=a)
except cml_exception, detail:
# problems converting cml to atom
raise plugin.import_exception( detail)
if atom.not_enough_data():
# atom does not have sufficient data to be safely converted to cdml
raise plugin.import_exception( "missing "+str( atom.not_enough_data())+" in atom specification")
self.atoms.append( atom)
dom_ext.setAttributes( out, (('name', atom.symbol),
('id', atom.id)))
pnt = dom_ext.elementUnder( out, 'point', (('x', str( atom.x)),
('y', str( atom.y))))
if atom.z != None:
pnt.setAttribute( 'z', str( atom.z))
self.xs.append( atom.x)
self.ys.append( atom.y)
return out
