def split_layers( self, text):
# try if we have a xml document in hand
try:
doc = dom.parseString( text)
except:
# it seems not to be the case
if text.startswith( "InChI="):
text = text[6:]
layers = re.split( "/", text.strip())
# fixed hydrogen layer is marked stupidly by f/h :(, we have to deal with it
i = None
for l in layers:
if l.startswith("f"):
i = layers.index( l)
break
if i != None:
del layers[i]
layers[i] = 'f'+layers[i][1:]
return layers
structs = doc.getElementsByTagName( 'structure')
if not structs:
raise "no structures found in xml string %s" % text
struct = structs[0]
layers = []
for name in ('version','formula','connections','H'):
try:
layer = struct.getElementsByTagName( name)[0]
except IndexError:
raise "no '%s' tag found in xml string" % name
layers.append( dom_extensions.getTextFromElement( layer))
return layers
def split_layers(self, text):
# try if we have a xml document in hand
try:
doc = dom.parseString(text)
except:
# it seems not to be the case
if text.startswith("InChI="):
text = text[6:]
layers = re.split("/", text.strip())
# fixed hydrogen layer is marked stupidly by f/h :(, we have to deal with it
i = None
for l in layers:
if l.startswith("f"):
i = layers.index(l)
break
if i != None:
del layers[i]
layers[i] = 'f' + layers[i][1:]
return layers
structs = doc.getElementsByTagName('structure')
if not structs:
raise "no structures found in xml string %s" % text
struct = structs[0]
layers = []
for name in ('version', 'formula', 'connections', 'H'):
try:
layer = struct.getElementsByTagName(name)[0]
except IndexError:
raise "no '%s' tag found in xml string" % name
layers.append(dom_extensions.getTextFromElement(layer))
return layers
def read_CML( self, cml):
# id could be attribute
if cml.getAttribute( 'id'):
self.id = cml.getAttribute( 'id')
for e in cml.childNodes:
if e.nodeValue:
continue
attr = e.getAttribute( 'builtin')
if attr == 'atomId':
self.id = dom_ext.getTextFromElement( e)
elif attr == 'elementType':
self.symbol = dom_ext.getTextFromElement( e)
elif attr in ['x2', 'x3']:
self.x = float( dom_ext.getTextFromElement( e))
elif attr in ['y2', 'y3']:
self.y = float( dom_ext.getTextFromElement( e))
elif attr == 'z3':
self.z = float( dom_ext.getTextFromElement( e))
def read_CML( self, cml):
for e in cml.childNodes:
if e.nodeValue:
continue
attr = e.getAttribute( 'builtin')
if attr == 'atomRef':
if not self.atom1:
self.atom1 = dom_ext.getTextFromElement( e)
else:
self.atom2 = dom_ext.getTextFromElement( e)
elif attr == 'order':
order = dom_ext.getTextFromElement( e)
if order == 'A':
self.order = 1
else:
try:
self.order = int( order)
except ValueError:
raise cml_exception( "Wrong bond order '%s'" % order)
elif attr == 'stereo':
stereo = dom_ext.getTextFromElement( e)
if stereo:
self.stereo = stereo.upper()
def read_CML( self, cml):
if cml.getAttribute( 'order'):
self.order = cml.getAttribute( 'order')
if self.order.isdigit():
self.order = int( self.order)
else:
types = ['s','d','t']
if self.order.lower() in types:
self.order = types.index( self.order.lower()) + 1
else:
raise plugin.import_exception("unknown bond type %s" % self.order)
if cml.getAttribute( 'atomRefs2'):
atoms = cml.getAttribute( 'atomRefs2').split( ' ')
if len( atoms) == 2:
self.atom1, self.atom2 = atoms
stereo = cml.getElementsByTagName( 'stereo')
if stereo:
stereo = stereo[0]
text = dom_ext.getTextFromElement( stereo)
if text.lower() in 'wh':
self.stereo = text.lower()
else:
self.stereo = 'n'
def read_CML(self, cml):
if cml.getAttribute('order'):
self.order = cml.getAttribute('order')
if self.order.isdigit():
self.order = int(self.order)
else:
types = ['s', 'd', 't']
if self.order.lower() in types:
self.order = types.index(self.order.lower()) + 1
else:
raise plugin.import_exception, "unknown bond type %s" % self.order
if cml.getAttribute('atomRefs2'):
atoms = cml.getAttribute('atomRefs2').split(' ')
if len(atoms) == 2:
self.atom1, self.atom2 = atoms
stereo = cml.getElementsByTagName('stereo')
if stereo:
stereo = stereo[0]
text = dom_ext.getTextFromElement(stereo)
if text.lower() in 'wh':
self.stereo = text.lower()
else:
self.stereo = 'n'
