Python Topology.from_dataframe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 from_dataframe [as 別名]
def load_mol2(filename):
    """Load a TRIPOS mol2 file from disk.

    Parameters
    ----------
    filename : str
        Path to the prmtop file on disk.

    Returns
    -------
    traj : md.Trajectory
        The resulting topology, as an md.Topology object.

    Notes
    -----
    This function should work on GAFF and sybyl style MOL2 files, but has
    been primarily tested on GAFF mol2 files.
    This function does NOT accept multi-structure MOL2 files!!!
    The elements are guessed using GAFF atom types or via the atype string.

    Examples
    --------
    >>> traj = md.load_mol2('mysystem.mol2')
    """
    from mdtraj.core.trajectory import Trajectory
    from mdtraj.core.topology import Topology

    atoms, bonds = mol2_to_dataframes(filename)

    atoms_mdtraj = atoms[["name", "resName"]].copy()
    atoms_mdtraj["serial"] = atoms.index

    #Figure out 1 letter element names

    # IF this is a GAFF mol2, this line should work without issues
    atoms_mdtraj["element"] = atoms.atype.map(gaff_elements)
    # If this is a sybyl mol2, there should be NAN (null) values
    if atoms_mdtraj.element.isnull().any():
        # If this is a sybyl mol2, I think this works generally.
        atoms_mdtraj["element"] = atoms.atype.apply(lambda x: x.strip(".")[0])

    atoms_mdtraj["resSeq"] = np.ones(len(atoms), 'int')
    atoms_mdtraj["chainID"] = np.ones(len(atoms), 'int')

    if bonds is not None:
        bonds_mdtraj = bonds[["id0", "id1"]].values
        offset = bonds_mdtraj.min()  # Should this just be 1???
        bonds_mdtraj -= offset
    else:
        bonds_mdtraj = None

    top = Topology.from_dataframe(atoms_mdtraj, bonds_mdtraj)

    xyzlist = np.array([atoms[["x", "y", "z"]].values])
    xyzlist /= 10.0  # Convert from angstrom to nanometer

    traj = Trajectory(xyzlist, top)

    return traj

# 需要導入模塊: from mdtraj.core.topology import Topology [as 別名]
# 或者: from mdtraj.core.topology.Topology import from_dataframe [as 別名]
def load_mol2(filename):
    """Load a TRIPOS mol2 file from disk.

    Parameters
    ----------
    filename : str
        Path to the prmtop file on disk.

    Returns
    -------
    traj : md.Trajectory
        The resulting topology, as an md.Topology object.

    Notes
    -----
    This function should work on GAFF and sybyl style MOL2 files, but has
    been primarily tested on GAFF mol2 files.
    This function does NOT accept multi-structure MOL2 files!!!
    The elements are guessed using GAFF atom types or via the atype string.

    Examples
    --------
    >>> traj = md.load_mol2('mysystem.mol2')
    """
    from mdtraj.core.trajectory import Trajectory
    from mdtraj.core.topology import Topology, Single, Double, Triple, Aromatic, Amide

    atoms, bonds = mol2_to_dataframes(filename)

    atoms_mdtraj = atoms[["name", "resName"]].copy()
    atoms_mdtraj["serial"] = atoms.index

    #Figure out 1 letter element names

    # IF this is a GAFF mol2, this line should work without issues
    atoms_mdtraj["element"] = atoms.atype.map(gaff_elements)
    # If this is a sybyl mol2, there should be NAN (null) values
    if atoms_mdtraj.element.isnull().any():
        # If this is a sybyl mol2, I think this works generally.
        # Argument x is being passed as a list with only one element.
        def to_element(x):
            if isinstance(x, (list, tuple)):
                assert len(x) == 1
                x = x[0]

            if '.' in x:  # orbital-hybridizations in SYBL
                return x.split('.')[0]
            try:
                # check if we can convert the whole str to an Element,
                # if not, we only pass the first letter.
                from mdtraj.core.element import Element
                Element.getBySymbol(x)
            except KeyError:
                return to_element(x[0])
            return x
        atoms_mdtraj["element"] = atoms.atype.apply(to_element)

    atoms_mdtraj["resSeq"] = np.ones(len(atoms), 'int')
    atoms_mdtraj["chainID"] = np.ones(len(atoms), 'int')

    bond_type_map = {
        '1': Single,
        '2': Double,
        '3': Triple,
        'am': Amide,
        'ar': Aromatic
    }
    if bonds is not None:
        bonds_mdtraj = bonds[["id0", "id1"]].values
        offset = bonds_mdtraj.min()  # Should this just be 1???
        bonds_mdtraj -= offset
        # Create the bond augment information
        n_bonds = bonds_mdtraj.shape[0]
        bond_augment = np.zeros([n_bonds, 2], dtype=float)
        # Add bond type information
        bond_augment[:, 0] = [float(bond_type_map[str(bond_value)]) for bond_value in bonds["bond_type"].values]
        # Add Bond "order" information, this is not known from Mol2 files
        bond_augment[:, 1] = [0.0 for _ in range(n_bonds)]
        # Augment array, dtype is cast to minimal representation of float
        bonds_mdtraj = np.append(bonds_mdtraj, bond_augment, axis=-1)
    else:
        bonds_mdtraj = None

    top = Topology.from_dataframe(atoms_mdtraj, bonds_mdtraj)

    xyzlist = np.array([atoms[["x", "y", "z"]].values])
    xyzlist /= 10.0  # Convert from angstrom to nanometer

    traj = Trajectory(xyzlist, top)

    return traj