def get_new(self, position):
if self.current_object == "Fragment":
filename = context.get_share_filename('fragments/%s.cml' % self.current_fragment)
molecule = load_cml(filename)[0]
Frame = context.application.plugins.get_node("Frame")
new = Frame(name=self.current_fragment)
load_filter = context.application.plugins.get_load_filter('cml')
load_filter.load_molecule(new, molecule)
else:
NewClass = context.application.plugins.get_node(self.current_object)
new = NewClass()
if self.current_object == "Atom":
new.set_number(self.atom_number)
new.set_name(periodic[self.atom_number].symbol)
translation = Translation(position)
primitive.Transform(new, translation)
return new
def from_file(cls, filename):
"""Construct a molecule object read from the given file.
The file format is inferred from the extensions. Currently supported
formats are: ``*.cml``, ``*.fchk``, ``*.pdb``, ``*.sdf``, ``*.xyz``
If a file contains more than one molecule, only the first one is
read.
Argument:
| ``filename`` -- the name of the file containing the molecule
Example usage::
>>> mol = Molecule.from_file("foo.xyz")
"""
# TODO: many different API's to load files. brrr...
if filename.endswith(".cml"):
from molmod.io import load_cml
return load_cml(filename)[0]
elif filename.endswith(".fchk"):
from molmod.io import FCHKFile
fchk = FCHKFile(filename, field_labels=[])
return fchk.molecule
elif filename.endswith(".pdb"):
from molmod.io import load_pdb
return load_pdb(filename)
elif filename.endswith(".sdf"):
from molmod.io import SDFReader
return next(SDFReader(filename))
elif filename.endswith(".xyz"):
from molmod.io import XYZReader
xyz_reader = XYZReader(filename)
title, coordinates = next(xyz_reader)
return Molecule(xyz_reader.numbers,
coordinates,
title,
symbols=xyz_reader.symbols)
else:
raise ValueError("Could not determine file format for %s." %
filename)
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]
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]
def get_new(self, position):
if self.current_object == "Fragment":
filename = context.get_share_filename('fragments/%s.cml' %
self.current_fragment)
molecule = load_cml(filename)[0]
Frame = context.application.plugins.get_node("Frame")
new = Frame(name=self.current_fragment)
load_filter = context.application.plugins.get_load_filter('cml')
load_filter.load_molecule(new, molecule)
else:
NewClass = context.application.plugins.get_node(
self.current_object)
new = NewClass()
if self.current_object == "Atom":
new.set_number(self.atom_number)
new.set_name(periodic[self.atom_number].symbol)
translation = Translation(position)
primitive.Transform(new, translation)
return new
def from_file(cls, filename):
"""Construct a molecule object read from the given file.
The file format is inferred from the extensions. Currently supported
formats are: ``*.cml``, ``*.fchk``, ``*.pdb``, ``*.sdf``, ``*.xyz``
If a file contains more than one molecule, only the first one is
read.
Argument:
| ``filename`` -- the name of the file containing the molecule
Example usage::
>>> mol = Molecule.from_file("foo.xyz")
"""
# TODO: many different API's to load files. brrr...
if filename.endswith(".cml"):
from molmod.io import load_cml
return load_cml(filename)[0]
elif filename.endswith(".fchk"):
from molmod.io import FCHKFile
fchk = FCHKFile(filename, field_labels=[])
return fchk.molecule
elif filename.endswith(".pdb"):
from molmod.io import load_pdb
return load_pdb(filename)
elif filename.endswith(".sdf"):
from molmod.io import SDFReader
return SDFReader(filename).next()
elif filename.endswith(".xyz"):
from molmod.io import XYZReader
xyz_reader = XYZReader(filename)
title, coordinates = xyz_reader.next()
return Molecule(xyz_reader.numbers, coordinates, title, symbols=xyz_reader.symbols)
else:
raise ValueError("Could not determine file format for %s." % filename)