Python Molecule.viewname方法代码示例

# 需要导入模块: from htmd.molecule.molecule import Molecule [as 别名]
# 或者: from htmd.molecule.molecule.Molecule import viewname [as 别名]

#.........这里部分代码省略.........
    --------
    >>> poses, scoring = dock(protein, ligand)
    >>> poses, scoring = dock(protein, ligand, center=[ 10., 5., 12. ], extent=[ 15., 15., 15. ] )

    """
    if np.size(protein.coords, 2) != 1 or np.size(ligand.coords, 2) != 1:
        raise NameError('Protein and ligand Molecules should be single frames')

    buffer = 10.  # Angstrom buffer around protein for whole-protein docking
    c_min = np.min(protein.coords, 0).reshape((1, 3))[0]
    c_max = np.max(protein.coords, 0).reshape((1, 3))[0]

    if center is None:
        center = (buffer + (c_max + c_min)) / 2
    if extent is None:
        extent = (c_max - c_min) + buffer

    # babel -i pdb protein.pdb  -o pdbqt protein.pdbqt -xr
    # babel -i pdb ligand.pdb   -o pdbqt ligand.pdbqt -xhn
    # vina --ligand ligand.pdbqt --receptor protein.pdbqt --center_x 0. --center_y 0. --center_z 0. --size_x 60. --size_y 60. --size_z 60 --exhaustiveness 10
    # babel -m -i pdbqt ligand_out.pdbqt -o pdb out_.pdb -xhn

    protein_pdb = tempname(suffix=".pdb")
    ligand_mol2 = tempname(suffix=".mol2")
    output_pdb = tempname(suffix="_.pdb")
    output_prefix = path.splitext(output_pdb)[0]

    protein_pdbqt = tempname(suffix=".pdbqt")
    ligand_pdbqt = tempname(suffix=".pdbqt")
    output_pdbqt = tempname(suffix=".pdbqt")

    protein.write(protein_pdb)
    lig2 = ligand.copy()
    lig2.atomtype = lig2.element  # babel does not understand mol2 atomtypes and requires elements instead
    lig2.write(ligand_mol2)

    # Dirty hack to remove the 'END' line from the PDBs since babel hates it
    with open(protein_pdb, 'r') as f:
        lines = f.readlines()
    with open(protein_pdb, 'w') as f:
        f.writelines(lines[:-1])
    # End of dirty hack

    try:
        if vinaexe is None:
            import platform
            suffix = ''
            if platform.system() == "Windows":
                suffix = '.exe'
            vinaexe = '{}-vina{}'.format(platform.system(), suffix)

        vinaexe = shutil.which(vinaexe, mode=os.X_OK)
        if not vinaexe:
            raise NameError('Could not find vina, or no execute permissions are given')
    except:
        raise NameError('Could not find vina, or no execute permissions are given')
    try:
        babelexe = shutil.which(babelexe, mode=os.X_OK)
        if babelexe is None:
            raise NameError('Could not find babel, or no execute permissions are given')
    except:
        raise NameError('Could not find babel, or no execute permissions are given')

    call([babelexe, '-i', 'pdb', protein_pdb, '-o', 'pdbqt', '-O', protein_pdbqt, '-xr'])
    if np.all(ligand.charge != 0):
        logger.info('Charges detected in ligand and will be used for docking.')
        call([babelexe, '-i', 'mol2', ligand_mol2, '-o', 'pdbqt', '-O', ligand_pdbqt, '-xn', '-xh'])
    else:
        logger.info('Charges were not defined for all atoms. Will guess charges anew using gasteiger method.')
        call([babelexe, '-i', 'mol2', ligand_mol2, '-o', 'pdbqt', '-O', ligand_pdbqt, '-xn', '-xh', '--partialcharge', 'gasteiger'])

    if not path.isfile(ligand_pdbqt):
        raise NameError('Ligand could not be converted to PDBQT')
    if not path.isfile(protein_pdbqt):
        raise NameError('Protein could not be converted to PDBQT')

    call([vinaexe, '--receptor', protein_pdbqt, '--ligand', ligand_pdbqt, '--out', output_pdbqt,
          '--center_x', str(center[0]), '--center_y', str(center[1]), '--center_z', str(center[2]),
          '--size_x', str(extent[0]), '--size_y', str(extent[1]), '--size_z', str(extent[2]), '--num_modes', str(numposes)])

    call([babelexe, '-m', '-i', 'pdbqt', output_pdbqt, '-o', 'pdb', '-O', output_pdb, '-xhn'])

    from natsort import natsorted
    outfiles = natsorted(glob('{}*.pdb'.format(output_prefix)))

    scoring = []
    poses = []
    for i, ligf in enumerate(outfiles):
        scoring.append(_parseScoring(ligf))
        l = Molecule(ligf)
        l.viewname = 'Pose {}'.format(i)
        poses.append(l)

    os.remove(protein_pdb)
    os.remove(ligand_mol2)
    os.remove(protein_pdbqt)
    os.remove(ligand_pdbqt)
    os.remove(output_pdbqt)

    return poses, np.array(scoring)