module.Line(p2, p2 - bond_vector, material=material2))
else:
objects.append(
module.Cylinder(p1,
p1 + bond_vector,
radius,
material=material1))
objects.append(
module.Cylinder(p2,
p2 - bond_vector,
radius,
material=material2))
return objects
Database.registerInstanceClass(Bond.blueprintclass, Bond)
#
# Bond angles
#
class BondAngle(object):
"""
Bond angle
A bond angle is the angle between two bonds that share a common atom.
It is defined by two bond objects (attributes b1 and b2) and an atom
object (the common atom, attribute ca).
"""
def __init__(self, b1, b2, ca):
self.b1 = b1 # bond 1
ChemicalObject.writeXML(self, file, memo, toplevel)
if toplevel:
return ['<molecule ref="%s"/>' % name]
else:
return None
def getXMLAtomOrder(self):
if self.type is None:
atoms = []
for molecule in self.molecules:
atoms.extend(molecule.getXMLAtomOrder())
return atoms
else:
return ChemicalObject.getXMLAtomOrder(self)
Database.registerInstanceClass(Atom.blueprintclass, Atom)
Database.registerInstanceClass(Group.blueprintclass, Group)
Database.registerInstanceClass(Molecule.blueprintclass, Molecule)
Database.registerInstanceClass(Crystal.blueprintclass, Crystal)
Database.registerInstanceClass(Complex.blueprintclass, Complex)
class AtomCluster(CompositeChemicalObject, ChemicalObject):
"""
An agglomeration of atoms
An atom cluster acts like a molecule without any bonds or atom
properties. It can be used to represent a group of atoms that
are known to form a chemical unit but whose chemical properties
are not sufficiently known to define a molecule.
if toplevel:
return ['<molecule ref="%s"/>' % name]
else:
return None
def getXMLAtomOrder(self):
if self.type is None:
atoms = []
for molecule in self.molecules:
atoms.extend(molecule.getXMLAtomOrder())
return atoms
else:
return ChemicalObject.getXMLAtomOrder(self)
Database.registerInstanceClass(Atom.blueprintclass, Atom)
Database.registerInstanceClass(Group.blueprintclass, Group)
Database.registerInstanceClass(Molecule.blueprintclass, Molecule)
Database.registerInstanceClass(Crystal.blueprintclass, Crystal)
Database.registerInstanceClass(Complex.blueprintclass, Complex)
class AtomCluster(CompositeChemicalObject, ChemicalObject):
"""
An agglomeration of atoms
An atom cluster acts like a molecule without any bonds or atom
properties. It can be used to represent a group of atoms that
are known to form a chemical unit but whose chemical properties
are not sufficiently known to define a molecule.
"""
objects.append(module.Cylinder(p1, p2, radius,
material = material1))
else:
if radius is None:
objects.append(module.Line(p1, p1+bond_vector,
material = material1))
objects.append(module.Line(p2, p2-bond_vector,
material = material2))
else:
objects.append(module.Cylinder(p1, p1+bond_vector, radius,
material = material1))
objects.append(module.Cylinder(p2, p2-bond_vector, radius,
material = material2))
return objects
Database.registerInstanceClass(Bond.blueprintclass, Bond)
#
# Bond angles
#
class BondAngle(object):
"""
Bond angle
A bond angle is the angle between two bonds that share a common atom.
It is defined by two bond objects (attributes b1 and b2) and an atom
object (the common atom, attribute ca).
"""
def __init__(self, b1, b2, ca):