def read_package(self, p):
for attr in ('line_width', 'font_size', 'font_family', 'line_color',
'area_color', 'paper_crop_svg', 'paper_orientation',
'paper_type', 'paper_crop_margin'):
if p.getAttribute(attr):
self.__dict__[attr] = p.getAttribute(attr)
self.font_size = int(self.font_size)
self.paper_crop_svg = int(self.paper_crop_svg)
self.paper_crop_margin = int(self.paper_crop_margin)
b = dom_extensions.getFirstChildNamed(p, 'bond')
if b:
self.bond_length = b.getAttribute('length') or self.bond_length
self.bond_width = b.getAttribute('width') or self.bond_width
self.double_length_ratio = b.getAttribute(
'double-ratio') or self.double_length_ratio
self.double_length_ratio = float(self.double_length_ratio)
self.wedge_width = b.getAttribute(
'wedge-width') or self.wedge_width
a = dom_extensions.getFirstChildNamed(p, 'arrow')
if a:
self.arrow_length = a.getAttribute('length')
a = dom_extensions.getFirstChildNamed(p, 'atom')
if a:
show_hydrogens = a.getAttribute('show_hydrogens')
if show_hydrogens == "False":
show_hydrogens = 0
elif show_hydrogens == "True":
show_hydrogens = 1
self.show_hydrogens = int(show_hydrogens)
def read_package( self, p):
for attr in ('line_width', 'font_size', 'font_family', 'line_color','area_color',
'paper_crop_svg','paper_orientation','paper_type','paper_crop_margin'):
if p.getAttribute( attr):
self.__dict__[ attr] = p.getAttribute( attr)
self.font_size = int( self.font_size)
self.paper_crop_svg = int( self.paper_crop_svg)
self.paper_crop_margin = int( self.paper_crop_margin)
b = dom_extensions.getFirstChildNamed( p, 'bond')
if b:
self.bond_length = b.getAttribute( 'length') or self.bond_length
self.bond_width = b.getAttribute( 'width') or self.bond_width
self.double_length_ratio = b.getAttribute( 'double-ratio') or self.double_length_ratio
self.double_length_ratio = float( self.double_length_ratio)
self.wedge_width = b.getAttribute( 'wedge-width') or self.wedge_width
a = dom_extensions.getFirstChildNamed( p, 'arrow')
if a:
self.arrow_length = a.getAttribute( 'length')
a = dom_extensions.getFirstChildNamed( p, 'atom')
if a:
show_hydrogens = a.getAttribute('show_hydrogens')
if show_hydrogens == "False":
show_hydrogens = 0
elif show_hydrogens == "True":
show_hydrogens = 1
self.show_hydrogens = int( show_hydrogens)
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_atom(self, at, mol):
a = atom(self.paper, molecule=mol)
a.set_name(
dom_ext.getAllTextFromElement(
dom_ext.getFirstChildNamed(at, "symbol")))
coords = dom_ext.getFirstChildNamed(at, "coordinates")
a.x = float(
dom_ext.getAllTextFromElement(
dom_ext.getFirstChildNamed(coords, "x")))
a.y = float(
dom_ext.getAllTextFromElement(
dom_ext.getFirstChildNamed(coords, "y")))
a.z = float(
dom_ext.getAllTextFromElement(
dom_ext.getFirstChildNamed(coords, "z")))
a.show_hydrogens = int(a.name != 'C')
# charge
chel = dom_ext.getFirstChildNamed(at, "charge")
if chel:
a.charge = int(dom_ext.getAllTextFromElement(chel))
# multiplicity
radical = dom_ext.getFirstChildNamed(at, "radical")
if radical:
a.multiplicity = 1 + int(dom_ext.getAllTextFromElement(radical))
# remap of ids
self._atom_id_remap[at.getAttribute('id')] = a
return a
def _read_atom(self, at, mol):
a = atom(self.paper, molecule=mol)
a.set_name(dom_ext.getAllTextFromElement(dom_ext.getFirstChildNamed(at, "symbol")))
coords = dom_ext.getFirstChildNamed(at, "coordinates")
a.x = float(dom_ext.getAllTextFromElement(dom_ext.getFirstChildNamed(coords, "x")))
a.y = float(dom_ext.getAllTextFromElement(dom_ext.getFirstChildNamed(coords, "y")))
a.z = float(dom_ext.getAllTextFromElement(dom_ext.getFirstChildNamed(coords, "z")))
a.show_hydrogens = int(a.name != "C")
# charge
chel = dom_ext.getFirstChildNamed(at, "charge")
if chel:
a.charge = int(dom_ext.getAllTextFromElement(chel))
# multiplicity
radical = dom_ext.getFirstChildNamed(at, "radical")
if radical:
a.multiplicity = 1 + int(dom_ext.getAllTextFromElement(radical))
# remap of ids
self._atom_id_remap[at.getAttribute("id")] = a
return a
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)