def read_package(self, package):
"""reads the dom element package and sets internal state according to it"""
# the standard
std = self.paper and self.paper.standard or None
self.name = package.getAttribute('name')
if package.getAttribute('id'):
self.id = package.getAttribute('id')
for name, cls in {
'atom': atom,
'group': group,
'text': textatom,
'query': queryatom
}.iteritems():
for a in dom_extensions.simpleXPathSearch(package, name):
self.insert_atom(cls(standard=std, package=a, molecule=self))
self._id_map = [a.id for a in self.atoms]
for b in dom_extensions.simpleXPathSearch(package, 'bond'):
bnd = bond(standard=std, package=b, molecule=self)
self.add_edge(bnd.atom1, bnd.atom2, bnd)
# template related attributes
temp = package.getElementsByTagName('template')
if temp:
temp = temp[0]
self.t_atom = Store.id_manager.get_object_with_id(
temp.getAttribute('atom'))
if temp.getAttribute('bond_first') and temp.getAttribute(
'bond_second'):
self.t_bond_first = Store.id_manager.get_object_with_id(
temp.getAttribute('bond_first'))
self.t_bond_second = Store.id_manager.get_object_with_id(
temp.getAttribute('bond_second'))
self.next_to_t_atom = self.t_atom.neighbors[0]
# display form
df = package.getElementsByTagName('display-form')
if df:
df = df[0]
self.display_form = ''.join([e.toxml() for e in df.childNodes
]).encode('utf-8')
# fragments
for fel in dom_extensions.simpleXPathSearch(package, "fragment"):
f = fragment()
try:
f.read_package(fel)
except bkchem_exceptions.bkchem_fragment_error:
pass
else:
self.fragments.add(f)
ud = dom_extensions.getChildrenNamed(package, "user-data")
if ud:
self.user_data = [u.cloneNode(True) for u in ud]
# final check of atoms valecies
[
a.raise_valency_to_senseful_value() for a in self.vertices
if isinstance(a, atom)
]
def read_package(self, doc):
self.id = doc.getAttribute("id")
self.type = doc.getAttribute("type") or "explicit"
name = dom_ext.getFirstChildNamed(doc, "name")
if name:
self.name = dom_ext.getAllTextFromElement(name)
for b in dom_ext.simpleXPathSearch(doc, "bond"):
try:
self.edges.add(
Store.id_manager.get_object_with_id(b.getAttribute("id")))
except KeyError:
raise bkchem_fragment_error("inconsistent", "")
for v in dom_ext.simpleXPathSearch(doc, "vertex"):
try:
self.vertices.add(
Store.id_manager.get_object_with_id(v.getAttribute("id")))
except KeyError:
raise bkchem_fragment_error("inconsistent", "")
for p in dom_ext.simpleXPathSearch(doc, "property"):
k = p.getAttribute("name")
v = p.getAttribute("value")
t = p.getAttribute("type")
typ = types.__dict__[t]
self.properties[k] = typ(v)
def read_data_definition(self, filename):
doc = dom.parse(filename)
root = doc.childNodes[0]
for ecls in dom_ext.simpleXPathSearch(root, "class"):
cls = ecls.getAttribute('name')
self.definitions[cls] = {}
for eobj in dom_ext.simpleXPathSearch(ecls, "object"):
obj = eobj.getAttribute('type')
self.definitions[cls][obj] = {}
for evalue in dom_ext.simpleXPathSearch(eobj, "value"):
vname = evalue.getAttribute('name')
vtype = evalue.getAttribute('type')
# try to decode list style types
if vtype.startswith("[") and vtype.endswith("]"):
try:
vtype = eval(vtype)
except ValueError:
pass
text = dom_ext.getAllTextFromElement(
dom_ext.getFirstChildNamed(evalue, "text"))
self.definitions[cls][obj][vname] = {
'type': vtype,
'text': text
}
self.records[cls] = {}
def read_plugin_file( self, dir, name):
doc = dom.parse( os.path.join( dir, name))
root = doc.childNodes[0]
plugin_type = root.getAttribute( 'type') or 'script'
sources = dom_ext.simpleXPathSearch( doc, "/plugin/source")
if sources:
source = sources[0]
files = dom_ext.simpleXPathSearch( source, "file")
names = dom_ext.simpleXPathSearch( source, "menu-text")
descs = dom_ext.simpleXPathSearch( source, "/plugin/meta/description")
menus = dom_ext.simpleXPathSearch( source, "menu")
if files and names:
file = dom_ext.getAllTextFromElement( files[0])
if not os.path.isabs( file):
file = os.path.normpath( os.path.join( dir, file))
name = self._select_correct_text( names)
if menus:
menu = dom_ext.getAllTextFromElement( menus[0])
else:
menu = ""
plugin = plugin_handler( name, file, type=plugin_type,
desc=self._select_correct_text( descs),
menu=menu)
self.plugins[ name] = plugin
def read_cdml(text):
"""returns the last molecule for now"""
doc = dom.parseString(text)
#if doc.childNodes()[0].nodeName == 'svg':
# path = "/svg/cdml/molecule"
#else:
# path = "/cdml/molecule"
path = "//molecule"
do_not_continue_this_mol = 0
for mol_el in dom_ext.simpleXPathSearch(doc, path):
atom_id_remap = {}
mol = molecule()
groups = []
for atom_el in dom_ext.simpleXPathSearch(mol_el, "atom"):
name = atom_el.getAttribute('name')
if not name:
#print "this molecule has an invalid symbol"
do_not_continue_this_mol = 1
break
pos = dom_ext.simpleXPathSearch(atom_el, 'point')[0]
x = cm_to_float_coord(pos.getAttribute('x'))
y = cm_to_float_coord(pos.getAttribute('y'))
z = cm_to_float_coord(pos.getAttribute('z'))
if name in PT:
# its really an atom
a = atom(symbol=name,
charge=atom_el.getAttribute('charge')
and int(atom_el.getAttribute('charge')) or 0,
coords=(x, y, z))
mol.add_vertex(v=a)
elif name in cdml_to_smiles:
# its a known group
group = smiles.text_to_mol(cdml_to_smiles[name], calc_coords=0)
a = group.vertices[0]
a.x = x
a.y = y
a.z = z
mol.insert_a_graph(group)
atom_id_remap[atom_el.getAttribute('id')] = a
if do_not_continue_this_mol:
break
for bond_el in dom_ext.simpleXPathSearch(mol_el, "bond"):
type = bond_el.getAttribute('type')
if type[1] == u'0':
# we ignore bonds with order 0
continue
v1 = atom_id_remap[bond_el.getAttribute('start')]
v2 = atom_id_remap[bond_el.getAttribute('end')]
e = bond(order=int(type[1]), type=type[0])
mol.add_edge(v1, v2, e=e)
if mol.is_connected():
# this is here to handle diborane and similar weird things
yield mol
else:
for comp in mol.get_disconnected_subgraphs():
yield comp
def read_cdml( text):
"""returns the last molecule for now"""
doc = dom.parseString( text)
#if doc.childNodes()[0].nodeName == 'svg':
# path = "/svg/cdml/molecule"
#else:
# path = "/cdml/molecule"
path = "//molecule"
do_not_continue_this_mol = 0
for mol_el in dom_ext.simpleXPathSearch( doc, path):
atom_id_remap = {}
mol = molecule()
groups = []
for atom_el in dom_ext.simpleXPathSearch( mol_el, "atom"):
name = atom_el.getAttribute( 'name')
if not name:
#print "this molecule has an invalid symbol"
do_not_continue_this_mol = 1
break
pos = dom_ext.simpleXPathSearch( atom_el, 'point')[0]
x = cm_to_float_coord( pos.getAttribute('x'))
y = cm_to_float_coord( pos.getAttribute('y'))
z = cm_to_float_coord( pos.getAttribute('z'))
if name in PT:
# its really an atom
a = atom( symbol=name,
charge=atom_el.getAttribute( 'charge') and int( atom_el.getAttribute( 'charge')) or 0,
coords=( x, y, z))
mol.add_vertex( v=a)
elif name in cdml_to_smiles:
# its a known group
group = smiles.text_to_mol( cdml_to_smiles[ name], calc_coords=0)
a = group.vertices[0]
a.x = x
a.y = y
a.z = z
mol.insert_a_graph( group)
atom_id_remap[ atom_el.getAttribute( 'id')] = a
if do_not_continue_this_mol:
break
for bond_el in dom_ext.simpleXPathSearch( mol_el, "bond"):
type = bond_el.getAttribute( 'type')
if type[1] == u'0':
# we ignore bonds with order 0
continue
v1 = atom_id_remap[ bond_el.getAttribute( 'start')]
v2 = atom_id_remap[ bond_el.getAttribute( 'end')]
e = bond( order=int( type[1]), type=type[0])
mol.add_edge( v1, v2, e=e)
if mol.is_connected():
# this is here to handle diborane and similar weird things
yield mol
else:
for comp in mol.get_disconnected_subgraphs():
yield comp
def read_package( self, root):
"""reads the data from xml (CDML) format. Is not intended for reading of definition
files, use read_data_definition instead"""
for ecls in dom_ext.simpleXPathSearch( root, "class"):
cls = ecls.getAttribute( 'name')
if not cls in self.records.keys():
self.records[ cls] = {}
for eobj in dom_ext.simpleXPathSearch( ecls, "object"):
obj = Store.id_manager.get_object_with_id( eobj.getAttribute( 'ref'))
for evalue in dom_ext.simpleXPathSearch( eobj, "value"):
vcat = evalue.getAttribute( 'category')
vvalue = evalue.getAttribute( 'value')
self.set_data( cls, obj, vcat, vvalue)
def read_package( self, root):
"""reads the data from xml (CDML) format. Is not intended for reading of definition
files, use read_data_definition instead"""
for ecls in dom_ext.simpleXPathSearch( root, "class"):
cls = ecls.getAttribute( 'name')
if not cls in self.records.keys():
self.records[ cls] = {}
for eobj in dom_ext.simpleXPathSearch( ecls, "object"):
obj = Store.id_manager.get_object_with_id( eobj.getAttribute( 'ref'))
for evalue in dom_ext.simpleXPathSearch( eobj, "value"):
vcat = evalue.getAttribute( 'category')
vvalue = evalue.getAttribute( 'value')
self.set_data( cls, obj, vcat, vvalue)
def read_package( self, package):
"""reads the dom element package and sets internal state according to it"""
# the standard
std = self.paper and self.paper.standard or None
self.name = package.getAttribute( 'name')
if package.getAttribute( 'id'):
self.id = package.getAttribute( 'id')
for name, cls in {'atom': atom, 'group': group, 'text': textatom, 'query': queryatom}.items():
for a in dom_extensions.simpleXPathSearch( package, name):
self.insert_atom( cls( standard=std, package=a, molecule=self))
self._id_map = [a.id for a in self.atoms]
for b in dom_extensions.simpleXPathSearch( package, 'bond'):
bnd = bond( standard=std, package=b, molecule=self)
self.add_edge( bnd.atom1, bnd.atom2, bnd)
# template related attributes
temp = package.getElementsByTagName('template')
if temp:
temp = temp[0]
self.t_atom = Store.id_manager.get_object_with_id( temp.getAttribute( 'atom'))
if temp.getAttribute('bond_first') and temp.getAttribute('bond_second'):
self.t_bond_first = Store.id_manager.get_object_with_id( temp.getAttribute( 'bond_first'))
self.t_bond_second = Store.id_manager.get_object_with_id( temp.getAttribute( 'bond_second'))
self.next_to_t_atom = self.t_atom.neighbors[0]
# display form
df = package.getElementsByTagName('display-form')
if df:
df = df[0]
self.display_form = ''.join( [e.toxml('utf-8') for e in df.childNodes])
# fragments
for fel in dom_extensions.simpleXPathSearch( package, "fragment"):
f = fragment()
try:
f.read_package( fel)
except bkchem_exceptions.bkchem_fragment_error:
pass
else:
self.fragments.add( f)
ud = dom_extensions.getChildrenNamed( package, "user-data")
if ud:
self.user_data = [u.cloneNode( True) for u in ud]
# final check of atoms valecies
[a.raise_valency_to_senseful_value() for a in self.vertices if isinstance( a, atom)]
def read_data_definition( self, filename):
doc = dom.parse( filename)
root = doc.childNodes[0]
for ecls in dom_ext.simpleXPathSearch( root, "class"):
cls = ecls.getAttribute( 'name')
self.definitions[ cls] = {}
for eobj in dom_ext.simpleXPathSearch( ecls, "object"):
obj = eobj.getAttribute( 'type')
self.definitions[ cls][ obj] = {}
for evalue in dom_ext.simpleXPathSearch( eobj, "value"):
vname = evalue.getAttribute( 'name')
vtype = evalue.getAttribute( 'type')
# try to decode list style types
if vtype.startswith( "[") and vtype.endswith( "]"):
try:
vtype = eval( vtype)
except ValueError:
pass
text = dom_ext.getAllTextFromElement( dom_ext.getFirstChildNamed( evalue, "text"))
self.definitions[ cls][ obj][ vname] = {'type': vtype,
'text': text }
self.records[ cls] = {}
def read_package( self, doc):
self.id = doc.getAttribute( "id")
self.type = doc.getAttribute( "type") or "explicit"
name = dom_ext.getFirstChildNamed( doc, "name")
if name:
self.name = dom_ext.getAllTextFromElement( name)
for b in dom_ext.simpleXPathSearch( doc, "bond"):
try:
self.edges.add( Store.id_manager.get_object_with_id( b.getAttribute( "id")))
except KeyError:
raise bkchem_fragment_error( "inconsistent", "")
for v in dom_ext.simpleXPathSearch( doc, "vertex"):
try:
self.vertices.add( Store.id_manager.get_object_with_id( v.getAttribute( "id")))
except KeyError:
raise bkchem_fragment_error( "inconsistent", "")
for p in dom_ext.simpleXPathSearch( doc, "property"):
k = p.getAttribute( "name")
v = p.getAttribute( "value")
t = p.getAttribute( "type")
typ = types.__dict__[ t]
self.properties[k] = typ( v)