Python Molecule.bonds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 bonds [as 别名]
def build(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./', caps=None, ionize=True, saltconc=0,
          saltanion=None, saltcation=None, disulfide=None, tleap='tleap', execute=True):
    """ Builds a system for AMBER

    Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    ff : list of str
        A list of leaprc forcefield files. Default: ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    topo : list of str
        A list of topology `prepi` files.
    param : list of str
        A list of parameter `frcmod` files.
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps of that segment.
        e.g. caps['P'] = ['ACE', 'NME']. Default: will apply ACE and NME caps to proteins and no caps
        to the rest.
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration to add to the system after neutralization.
    saltanion : {'Cl-'}
        The anion type. Please use only AMBER ion atom names.
    saltcation : {'Na+', 'K+', 'Cs+'}
        The cation type. Please use only AMBER ion atom names.
    disulfide : np.ndarray
        If None it will guess disulfide bonds. Otherwise provide a 2D array where each row is a pair of atom indexes that makes a disulfide bond
    tleap : str
        Path to tleap executable used to build the system for AMBER
    execute : bool
        Disable building. Will only write out the input script needed by tleap. Does not include ionization.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> ffs = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    >>> molbuilt = amber.build(mol, ff=ffs, outdir='/tmp/build', saltconc=0.15)
    """
    # Remove pdb bonds!
    mol = mol.copy()
    mol.bonds = []
    if shutil.which(tleap) is None:
        raise NameError('Could not find executable: `' + tleap + '` in the PATH. Cannot build for AMBER.')
    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    _cleanOutDir(outdir)
    if ff is None:
        ff = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
    if topo is None:
        topo = []
    if param is None:
        param = []
    if caps is None:
        caps = _defaultCaps(mol)

    _missingSegID(mol)
    _checkMixedSegment(mol)

    logger.info('Converting CHARMM membranes to AMBER.')
    mol = _charmmLipid2Amber(mol)

    #_checkProteinGaps(mol)
    _applyCaps(mol, caps)

    f = open(path.join(outdir, 'tleap.in'), 'w')
    f.write('# tleap file generated by amber.build\n')

    # Printing out the forcefields
    for force in ff:
        f.write('source ' + force + '\n')
    f.write('\n')

    # Loading TIP3P water parameters
    f.write('# Loading ions and TIP3P water parameters\n')
    f.write('loadamberparams frcmod.ionsjc_tip3p\n\n')

    # Printing out topologies
    logger.info('Writing prepi files.')
    f.write('# Loading prepi topologies\n')
    for t in topo:
        shutil.copy(t, outdir)
        f.write('loadamberprep ' + path.basename(t) + '\n')
    f.write('\n')

    # Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
    logger.info('Writing PDB file for input to tleap.')
    pdbname = path.join(outdir, 'input.pdb')
    mol.write(pdbname)
    if not os.path.isfile(pdbname):
#.........这里部分代码省略.........

# 需要导入模块: from htmd.molecule.molecule import Molecule [as 别名]
# 或者: from htmd.molecule.molecule.Molecule import bonds [as 别名]
def build(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./build', caps=None, ionize=True, saltconc=0,
          saltanion=None, saltcation=None, disulfide=None, tleap=None, execute=True, atomtypes=None,
          offlibraries=None, gbsa=False, igb=2):
    """ Builds a system for AMBER

    Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.

    Parameters
    ----------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The Molecule object containing the system
    ff : list of str
        A list of leaprc forcefield files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available forcefield files.
        Default: :func:`amber.defaultFf <htmd.builder.amber.defaultFf>`
    topo : list of str
        A list of topology `prepi/prep/in` files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available topology files.
        Default: :func:`amber.defaultTopo <htmd.builder.amber.defaultTopo>`
    param : list of str
        A list of parameter `frcmod` files.
        Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available parameter files.
        Default: :func:`amber.defaultParam <htmd.builder.amber.defaultParam>`
    prefix : str
        The prefix for the generated pdb and psf files
    outdir : str
        The path to the output directory
        Default: './build'
    caps : dict
        A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment.
        e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. Default: will apply ACE and NME caps to every
        protein segment.
    ionize : bool
        Enable or disable ionization
    saltconc : float
        Salt concentration to add to the system after neutralization.
    saltanion : {'Cl-'}
        The anion type. Please use only AMBER ion atom names.
    saltcation : {'Na+', 'K+', 'Cs+'}
        The cation type. Please use only AMBER ion atom names.
    disulfide : list of pairs of atomselection strings
        If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of
        residues forming the disulfide bridge.
    tleap : str
        Path to tleap executable used to build the system for AMBER
    execute : bool
        Disable building. Will only write out the input script needed by tleap. Does not include ionization.
    atomtypes : list of triplets
        Custom atom types defined by the user as ('type', 'element', 'hybrid') triplets
        e.g. (('C1', 'C', 'sp2'), ('CI', 'C', 'sp3')). Check `addAtomTypes` in AmberTools docs.
    offlibraries : str or list
        A path or a list of paths to OFF library files. Check `loadOFF` in AmberTools docs.
    gbsa : bool
        Modify radii for GBSA implicit water model
    igb : int
        GB model. Select: 1 for mbondi, 2 and 5 for mbondi2, 7 for bondi and 8 for mbondi3.
        Check section 4. The Generalized Born/Surface Area Model of the AMBER manual.

    Returns
    -------
    molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The built system in a Molecule object

    Example
    -------
    >>> from htmd.ui import *  # doctest: +SKIP
    >>> mol = Molecule("3PTB")
    >>> molbuilt = amber.build(mol, outdir='/tmp/build')  # doctest: +SKIP
    >>> # More complex example
    >>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
    >>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu)  # doctest: +SKIP
    """
    # Remove pdb protein bonds as they can be regenerated by tleap. Keep non-protein bonds i.e. for ligands
    mol = mol.copy()
    _removeProteinBonds(mol)

    if tleap is None:
        tleap = _findTleap()
    else:
        if shutil.which(tleap) is None:
            raise NameError('Could not find executable: `{}` in the PATH. Cannot build for AMBER.'.format(tleap))

    if not os.path.isdir(outdir):
        os.makedirs(outdir)
    _cleanOutDir(outdir)
    if ff is None:
        ff = defaultFf()
    if topo is None:
        topo = defaultTopo()
    if param is None:
        param = defaultParam()
    if caps is None:
        caps = _defaultProteinCaps(mol)

    _missingSegID(mol)
    _checkMixedSegment(mol)

    mol = _charmmLipid2Amber(mol)

    _applyProteinCaps(mol, caps)
#.........这里部分代码省略.........