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 _select_correct_text( self, texts):
"""returns the right text according to the lang attribute"""
if not texts:
return ''
for text in texts:
lang = text.getAttribute( "lang") or "en"
if lang == Store.lang:
return dom_ext.getAllTextFromElement( text)
# if nothing found, return the first one
return dom_ext.getAllTextFromElement( texts[0])
def read_from_dom( self, doc):
top = doc.getElementsByTagName( "bkchem-prefs")[0]
for child in dom_extensions.childNodesWithoutEmptySpaces( top):
name = child.nodeName
itype = child.getAttribute( 'type') or unicode
if itype in ("ListType", "TupleType", "DictType"):
value = eval( dom_extensions.getAllTextFromElement( child))
else:
itype = types.__dict__[ itype]
try:
value = itype( dom_extensions.getAllTextFromElement( child))
except:
print >> sys.stderr, "Preference manager: ignoring value %s of type %s" % (dom_extensions.getAllTextFromElement( child), itype)
break
self.add_preference( name, value)
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 text(self):
"""Unmarked plain-text representing the object.
Taken from xml_ftext and the markup is stripped.
"""
doc = dom.parseString(ftext.ftext.sanitize_text(self.xml_ftext))
return dom_extensions.getAllTextFromElement(doc)
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 text(self):
"""Unmarked plain-text representing the object.
Taken from xml_ftext and the markup is stripped.
"""
doc = dom.parseString( ftext.ftext.sanitize_text(self.xml_ftext))
return dom_extensions.getAllTextFromElement(doc)
def _read_bond(self, bo):
b = bond(self.paper)
b.order = gtml_to_bkchem_bond_order_remap.index(
dom_ext.getAllTextFromElement(xpath.Evaluate("bond", bo)[0]))
ids = [i.nodeValue for i in xpath.Evaluate("end/@idref", bo)]
b.atoms = [self._atom_id_remap[i] for i in ids]
return b
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)
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_bond(self, bo):
b = bond(self.paper)
b.order = gtml_to_bkchem_bond_order_remap.index(dom_ext.getAllTextFromElement(xpath.Evaluate("bond", bo)[0]))
ids = [i.nodeValue for i in xpath.Evaluate("end/@idref", bo)]
b.atoms = [self._atom_id_remap[i] for i in ids]
return b
def _get_text(self):
doc = dom.parseString(ftext.ftext.sanitize_text(self.xml_ftext))
return dom_extensions.getAllTextFromElement(doc)
def get_molecules( self, file_name):
doc = dom.parse( file_name)
molecules = []
# read colors
colors=[]
for elem7 in doc.getElementsByTagName("color"):
red=(float(elem7.getAttribute("r"))*255)
green=(float(elem7.getAttribute("g"))*255)
blue=(float(elem7.getAttribute("b"))*255)
colors.append("#%02x%02x%02x" % (red,green,blue))
# read fonts
fonts={}
for elem8 in doc.getElementsByTagName("font"):
family=str(elem8.getAttribute("name"))
fonts[int(elem8.getAttribute("id"))]=family
# read molecules
for elem1 in doc.getElementsByTagName("fragment"):
if elem1.parentNode.nodeName=="page":
mol = molecule( paper=self.paper)
atom_id_to_atom = {}
atom_id_to_text = {}
for elem2 in elem1.childNodes:
# atom
if elem2.nodeName=="n":
font = ""
Size = 12
text = "C"
color1="#000000"
for elem3 in elem2.childNodes:
if elem3.nodeName=="t":
if elem3.hasAttribute("color"):
color1=colors[int(elem3.getAttribute("color"))-2]
text = ""
for elem4 in elem3.childNodes:
if elem4.nodeName=="s":
if elem3.hasAttribute("color"):
color1=colors[int(elem3.getAttribute("color"))-2]
for Id, Font in fonts.items():
if Id==int(elem4.getAttribute("font")):
font=Font
Size= int(elem4.getAttribute("size"))
text += dom_ext.getAllTextFromElement( elem4).strip()
position = elem2.getAttribute("p").split()
assert len( position) == 2
# we must postpone symbol assignment until we know the valency of the atoms
atom_id_to_text[ elem2.getAttribute('id')] = text
atom = mol.create_vertex()
atom.line_color = color1
atom.font_family = font
atom.font_size = Size
atom.x = float( position[0])
atom.y = float( position[1])
mol.add_vertex( atom)
atom_id_to_atom[ elem2.getAttribute('id')] = atom
# bond
#{"v BKChemu bond.type":"v ChemDraw hodnota atributu Display elementu b"}
bondType2={"WedgeBegin":"w",
"WedgedHashBegin":"h",
"Wavy":"a",
"Bold":"b",
"Dash":"d"
}
if elem2.nodeName=="b":
if elem2.hasAttribute("color"):
color2 = colors[(int(elem2.getAttribute("color"))-2)]
else:
color2="#000000"
order = 1
if elem2.hasAttribute("Order"):
order = int( elem2.getAttribute("Order"))
bond = mol.create_edge()
if elem2.hasAttribute("Display"):
display = elem2.getAttribute("Display").strip()
for bondC, bondB in bondType2.items():
if bondC ==display:
bond.type = bondB
bond.line_color = color2
bond.order = order
atom1 = atom_id_to_atom[ elem2.getAttribute("B")]
atom2 = atom_id_to_atom[ elem2.getAttribute("E")]
mol.add_edge( atom1, atom2, bond)
# here we reassign the symbols
for id, atom in atom_id_to_atom.items():
text = atom_id_to_text[ id]
v = mol.create_vertex_according_to_text( atom, text)
atom.copy_settings( v)
mol.replace_vertices( atom, v)
atom.delete()
# finally we add the molecule to the list of molecules for output
molecules.append( mol)
# read texts
textik={2:"i",
1:"b",
32:"sub",
64:"sup"}
for elem5 in doc.getElementsByTagName("t"):
if elem5.parentNode.nodeName=="page":
position = map( float, elem5.getAttribute("p").split())
assert len( position) == 2
celyText=""
for elem51 in elem5.childNodes:
if elem51.nodeName=="s":
for elem52 in elem51.childNodes:
if isinstance( elem52, dom.Text):
rodice=[]
text100=elem52.data
if elem51.hasAttribute("face"):
Face01=int(elem51.getAttribute("face"))
for face, parent in textik.items():
for i in range(9):
if not Face01&2**i==0:
if face==Face01&2**i:
rodice.append(parent)
for rodic in rodice:
text100 = "<%s>%s</%s>" % (rodic,text100,rodic)
celyText += text100
if elem5.hasAttribute("color"):
color3=colors[(int(elem5.getAttribute("color"))-2)]
else:
color3="#000000"
font_id = elem51.getAttribute("font")
if font_id != "":
font=fonts[int(font_id)]
#text = dom_ext.getAllTextFromElement(elem51)
#print celyText
text = celyText
t = text_class( self.paper, position, text=text)
t.line_color = color3
#print elem51
if elem51.hasAttribute("size"):
t.font_size = int( elem51.getAttribute("size"))
if font:
t.font_family = font
molecules.append(t)
# read graphics - plus
for elem6 in doc.getElementsByTagName("graphic"):
if elem6.getAttribute("GraphicType")=="Symbol" and elem6.getAttribute("SymbolType")=="Plus":
position = map( float, elem6.getAttribute("BoundingBox").split())
position2=[position[0],position[1]]
assert len(position2) == 2
if elem6.hasAttribute("color"):
color4=colors[(int(elem6.getAttribute("color"))-2)]
else:
color4="#000000"
pl = plus(self.paper, position2)
pl.line_color = color4
molecules.append(pl)
sipka=[]
#for elem71 in doc.getElementsByTagName("graphic"):
#if elem71.getAttribute("GraphicType")=="Line":
for elem7 in doc.getElementsByTagName("arrow"):
sipka.insert(0,elem7.getAttribute('Head3D') )
sipka.insert(1,elem7.getAttribute('Tail3D') )
if elem7.hasAttribute("color"):
sipka.insert(0,colors[(int(elem7.getAttribute("color"))-2)])
point1 = map( float, sipka[1].split())
point2 = map( float, sipka[2].split())
arr = arrow( self.paper, points=[point2[0:2],point1[0:2]], fill=sipka[0])
arr.line_color=sipka[0]
molecules.append( arr)
sipka=[]
return molecules
def get_molecules(self, file_name):
doc = dom.parse(file_name)
molecules = []
# read colors
colors = []
for elem7 in doc.getElementsByTagName("color"):
red = (float(elem7.getAttribute("r")) * 255)
green = (float(elem7.getAttribute("g")) * 255)
blue = (float(elem7.getAttribute("b")) * 255)
colors.append("#%02x%02x%02x" % (red, green, blue))
# read fonts
fonts = {}
for elem8 in doc.getElementsByTagName("font"):
family = str(elem8.getAttribute("name"))
fonts[int(elem8.getAttribute("id"))] = family
# read molecules
for elem1 in doc.getElementsByTagName("fragment"):
if elem1.parentNode.nodeName == "page":
mol = molecule(paper=self.paper)
atom_id_to_atom = {}
atom_id_to_text = {}
for elem2 in elem1.childNodes:
# atom
if elem2.nodeName == "n":
font = ""
Size = 12
text = "C"
color1 = "#000000"
for elem3 in elem2.childNodes:
if elem3.nodeName == "t":
if elem3.hasAttribute("color"):
color1 = colors[
int(elem3.getAttribute("color")) - 2]
text = ""
for elem4 in elem3.childNodes:
if elem4.nodeName == "s":
if elem3.hasAttribute("color"):
color1 = colors[int(
elem3.getAttribute("color")) -
2]
for Id, Font in fonts.items():
if Id == int(
elem4.getAttribute(
"font")):
font = Font
Size = int(elem4.getAttribute("size"))
text += dom_ext.getAllTextFromElement(
elem4).strip()
position = elem2.getAttribute("p").split()
assert len(position) == 2
# we must postpone symbol assignment until we know the valency of the atoms
atom_id_to_text[elem2.getAttribute('id')] = text
atom = mol.create_vertex()
atom.line_color = color1
atom.font_family = font
atom.font_size = Size
atom.x = float(position[0])
atom.y = float(position[1])
mol.add_vertex(atom)
atom_id_to_atom[elem2.getAttribute('id')] = atom
# bond
#{"v BKChemu bond.type":"v ChemDraw hodnota atributu Display elementu b"}
bondType2 = {
"WedgeBegin": "w",
"WedgedHashBegin": "h",
"Wavy": "a",
"Bold": "b",
"Dash": "d"
}
if elem2.nodeName == "b":
if elem2.hasAttribute("color"):
color2 = colors[(int(elem2.getAttribute("color")) -
2)]
else:
color2 = "#000000"
order = 1
if elem2.hasAttribute("Order"):
order = int(elem2.getAttribute("Order"))
bond = mol.create_edge()
if elem2.hasAttribute("Display"):
display = elem2.getAttribute("Display").strip()
for bondC, bondB in bondType2.items():
if bondC == display:
bond.type = bondB
bond.line_color = color2
bond.order = order
atom1 = atom_id_to_atom[elem2.getAttribute("B")]
atom2 = atom_id_to_atom[elem2.getAttribute("E")]
mol.add_edge(atom1, atom2, bond)
# here we reassign the symbols
for id, atom in atom_id_to_atom.items():
text = atom_id_to_text[id]
v = mol.create_vertex_according_to_text(atom, text)
atom.copy_settings(v)
mol.replace_vertices(atom, v)
atom.delete()
# finally we add the molecule to the list of molecules for output
molecules.append(mol)
# read texts
textik = {2: "i", 1: "b", 32: "sub", 64: "sup"}
for elem5 in doc.getElementsByTagName("t"):
if elem5.parentNode.nodeName == "page":
position = map(float, elem5.getAttribute("p").split())
assert len(position) == 2
celyText = ""
for elem51 in elem5.childNodes:
if elem51.nodeName == "s":
for elem52 in elem51.childNodes:
if isinstance(elem52, dom.Text):
rodice = []
text100 = elem52.data
if elem51.hasAttribute("face"):
Face01 = int(elem51.getAttribute("face"))
for face, parent in textik.items():
for i in range(9):
if not Face01 & 2**i == 0:
if face == Face01 & 2**i:
rodice.append(parent)
for rodic in rodice:
text100 = "<%s>%s</%s>" % (rodic, text100,
rodic)
celyText += text100
if elem5.hasAttribute("color"):
color3 = colors[(int(elem5.getAttribute("color")) -
2)]
else:
color3 = "#000000"
font_id = elem51.getAttribute("font")
if font_id != "":
font = fonts[int(font_id)]
#text = dom_ext.getAllTextFromElement(elem51)
#print celyText
text = celyText
t = text_class(self.paper, position, text=text)
t.line_color = color3
#print elem51
if elem51.hasAttribute("size"):
t.font_size = int(elem51.getAttribute("size"))
if font:
t.font_family = font
molecules.append(t)
# read graphics - plus
for elem6 in doc.getElementsByTagName("graphic"):
if elem6.getAttribute(
"GraphicType") == "Symbol" and elem6.getAttribute(
"SymbolType") == "Plus":
position = map(float,
elem6.getAttribute("BoundingBox").split())
position2 = [position[0], position[1]]
assert len(position2) == 2
if elem6.hasAttribute("color"):
color4 = colors[(int(elem6.getAttribute("color")) - 2)]
else:
color4 = "#000000"
pl = plus(self.paper, position2)
pl.line_color = color4
molecules.append(pl)
sipka = []
#for elem71 in doc.getElementsByTagName("graphic"):
#if elem71.getAttribute("GraphicType")=="Line":
for elem7 in doc.getElementsByTagName("arrow"):
sipka.insert(0, elem7.getAttribute('Head3D'))
sipka.insert(1, elem7.getAttribute('Tail3D'))
if elem7.hasAttribute("color"):
sipka.insert(0, colors[(int(elem7.getAttribute("color")) - 2)])
point1 = map(float, sipka[1].split())
point2 = map(float, sipka[2].split())
arr = arrow(self.paper,
points=[point2[0:2], point1[0:2]],
fill=sipka[0])
arr.line_color = sipka[0]
molecules.append(arr)
sipka = []
return molecules
def _get_text( self): doc = dom.parseString( ftext.ftext.sanitize_text( self.xml_ftext)) return dom_extensions.getAllTextFromElement( doc)
