Python Topology.atom方法代碼示例

# 需要導入模塊: from mdtraj.core.topology import Topology [as 別名]
# 或者: from mdtraj.core.topology.Topology import atom [as 別名]
    def mutate(self, mut_res_idx, mut_new_resname):
        """Mutate residue

        Parameters 
        ----------
        mut_res_idx : int
            Index of residue to mutate.
        mut_new_resname : str
            Three-letter code of residue to mutate to.
        """

        assert (self.topology.residue(mut_res_idx).name != mut_new_resname), "mutating the residue to itself!"

        # Build new topology
        newTopology = Topology()
        for chain in self.topology.chains:
            newChain = newTopology.add_chain()
            for residue in chain._residues:
                res_idx = residue.index
                if res_idx == mut_res_idx:
                    # create mutated residue
                    self._add_mutated_residue(mut_new_resname, newTopology, newChain, res_idx, residue)
                else:
                    # copy old residue atoms directly
                    newResidue = newTopology.add_residue(residue.name, newChain, res_idx)
                    for atom in residue.atoms:
                        newTopology.add_atom(atom.name, 
                                    md.core.element.get_by_symbol(atom.element.symbol), 
                                    newResidue, serial=atom.index)

        # The bond connectivity should stay identical
        for atm1, atm2 in self.topology._bonds:
            new_atm1 = newTopology.atom(atm1.index)
            new_atm2 = newTopology.atom(atm2.index)
            newTopology.add_bond(new_atm1, new_atm2)

        self._prev_topology = self.topology.copy()
        self.topology = newTopology

# 需要導入模塊: from mdtraj.core.topology import Topology [as 別名]
# 或者: from mdtraj.core.topology.Topology import atom [as 別名]
def load_hoomdxml(filename, top=None):
    """Load a single conformation from an HOOMD-Blue XML file.

    For more information on this file format, see:
    http://codeblue.umich.edu/hoomd-blue/doc/page_xml_file_format.html
    Notably, all node names and attributes are in all lower case.
    HOOMD-Blue does not contain residue and chain information explicitly. 
    For this reason, chains will be found by looping over all the bonds and 
    finding what is bonded to what. 
    Each chain consisists of exactly one residue. 

    Parameters
    ----------
    filename : string
        The path on disk to the XML file

    Returns
    -------
    trajectory : md.Trajectory
        The resulting trajectory, as an md.Trajectory object, with corresponding 
        Topology.

    Notes
    -----
    This function requires the NetworkX python package.
    """
    from mdtraj.core.trajectory import Trajectory
    from mdtraj.core.topology import Topology
    topology = Topology()
    tree = cElementTree.parse(filename)
    config = tree.getroot().find('configuration')
    position = config.find('position')
    bond = config.find('bond')
    atom_type = config.find('type')  # MDTraj calls this "name"

    box = config.find('box')
    box.attrib = dict((key.lower(), val) for key, val in box.attrib.items())
    # be generous for case of box attributes
    lx = float(box.attrib['lx'])
    ly = float(box.attrib['ly'])
    lz = float(box.attrib['lz'])
    try:
        xy = float(box.attrib['xy'])
        xz = float(box.attrib['xz'])
        yz = float(box.attrib['yz'])
    except:
        xy = 0.0
        xz = 0.0
        yz = 0.0
    unitcell_vectors = np.array([[[lx,  xy*ly, xz*lz],
                                  [0.0, ly,    yz*lz],
                                  [0.0, 0.0,   lz   ]]])

    positions, types = [], {}
    for pos in position.text.splitlines()[1:]:
        positions.append((float(pos.split()[0]),
                          float(pos.split()[1]),
                          float(pos.split()[2])))

    for idx, atom_name in enumerate(atom_type.text.splitlines()[1:]):
        types[idx] = str(atom_name.split()[0])
    if len(types) != len(positions):
        raise ValueError('Different number of types and positions in xml file')

    # ignore the bond type
    bonds = [(int(b.split()[1]), int(b.split()[2])) for b in bond.text.splitlines()[1:]]
    chains = _find_chains(bonds)
    ions = [i for i in range(len(types)) if not _in_chain(chains, i)]

    # add chains, bonds and ions (each chain = 1 residue)
    for chain in chains:
        t_chain = topology.add_chain()
        t_residue = topology.add_residue('A', t_chain)
        for atom in chain:
            topology.add_atom(types[atom], 'U', t_residue)
    for ion in ions:
        t_chain = topology.add_chain()
        t_residue = topology.add_residue('A', t_chain)
        topology.add_atom(types[atom], 'U', t_residue)
    for bond in bonds:
        atom1, atom2 = bond[0], bond[1]
        topology.add_bond(topology.atom(atom1), topology.atom(atom2))

    traj = Trajectory(xyz=np.array(positions), topology=topology)
    traj.unitcell_vectors = unitcell_vectors

    return traj