def addToModel(self,position=[0,0,0],parent=None):
if parent is None:
parent = context.application.model.universe
fragmentdir = context.get_share_filename('fragments')
filename = fragmentdir+'/'+self.name+'.cml'
from molmod.io.cml import load_cml
molecules = load_cml(filename)
molecule = molecules[0] #we only look at first molecule in the list
#load 'universe' from file trough cml load filter (stolen from models.py > file_open)
load_filter = context.application.plugins.get_load_filter('cml')
#create frame
Frame = context.application.plugins.get_node("Frame")
self.fragment_frame = Frame(name=self.name)
#fill frame with molecule
load_filter.load_molecule(self.fragment_frame,molecule)
#rotate frame?
rotation = numpy.array([[1,2,0],
[0,0,0],
[0,0,0]])
# self.fragment_frame.transformation.r[:] = rotation
print self.fragment_frame.transformation.r
#apply transformation to frame
self.fragment_frame.transformation.t[:] = position
#add to model (note: should add to parent frame, not universe)
primitive.Add(self.fragment_frame, parent)
def get_in_frame(self,position):
fragmentdir = context.get_share_filename('fragments')
filename = fragmentdir+'/'+self.name+'.cml'
from molmod.io.cml import load_cml
molecules = load_cml(filename)
molecule = molecules[0] #we only look at first molecule in the list
#load 'universe' from file trough cml load filter (stolen from models.py > file_open)
load_filter = context.application.plugins.get_load_filter('cml')
#create frame
Frame = context.application.plugins.get_node("Frame")
self.fragment_frame = Frame(name=self.name)
#fill frame with molecule
load_filter.load_molecule(self.fragment_frame,molecule)
#rotate frame?
rotation = numpy.array([[1,2,0],
[0,0,0],
[0,0,0]])
# self.fragment_frame.transformation.r[:] = rotation
print self.fragment_frame.transformation.r
#apply transformation to frame
self.fragment_frame.transformation.t[:] = position
return self.fragment_frame
def get_fragment(self, fragmentname):
fragmentdir = context.get_share_filename('fragments')
filename = fragmentdir+'/'+fragmentname+'.cml'
molecules = load_cml(filename)
molecule = molecules[0]
Frame = context.application.plugins.get_node("Frame")
fragment_frame = Frame(name=fragmentname)
load_filter = context.application.plugins.get_load_filter('cml')
load_filter.load_molecule(fragment_frame,molecule)
return fragment_frame
def __call__(self, f):
Universe = context.application.plugins.get_node("Universe")
universe = Universe()
Folder = context.application.plugins.get_node("Folder")
folder = Folder()
Frame = context.application.plugins.get_node("Frame")
molecules = load_cml(f)
if len(molecules) == 1:
molecule = molecules[0]
universe.name = molecule.title
self.load_molecule(universe, molecule)
else:
for molecule in molecules:
parent = Frame(name=molecule.title)
universe.add(parent)
self.load_molecule(parent, molecule)
return [universe, folder]