Beispiel #1
0
    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
Beispiel #2
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    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)
Beispiel #3
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    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]
Beispiel #4
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    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]
Beispiel #5
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    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
Beispiel #6
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    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)