Python Molecule.remove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 remove [as 别名]
    def _viewStatesNGL(self, states, statetype, protein, ligand, mols, numsamples):
        if states is None:
            states = range(self.macronum)
        if isinstance(states, int):
            states = [states]
        if mols is None:
            mols = self.getStates(states, statetype, numsamples=min(numsamples, 15))
        colors = [0, 1, 3, 4, 5, 6, 7, 9]
        if protein is None and ligand is None:
            raise NameError('Please provide either the "protein" or "ligand" parameter for viewStates.')
        if protein:
            mol = Molecule()
        if ligand:
            mol = mols[0].copy()
            mol.remove(ligand, _logger=False)
            mol.coords = np.atleast_3d(mol.coords[:, :, 0])
            mol.reps.add(sel='protein', style='NewCartoon', color='Secondary Structure')
        for i, s in enumerate(states):
            if protein:
                mol.reps.add(sel='segid ST{}'.format(s), style='NewCartoon', color='Index')
            if ligand:
                mol.reps.add(sel='segid ST{}'.format(s), style='Licorice', color=colors[np.mod(i, len(colors))])
                mols[i].filter(ligand, _logger=False)

            mols[i].set('segid', 'ST{}'.format(s))
            tmpcoo = mols[i].coords
            for j in range(mols[i].numFrames):
                mols[i].coords = np.atleast_3d(tmpcoo[:, :, j])
                mol.append(mols[i])

        w = mol.view(viewer='ngl')
        self._nglButtons(w, statetype, states)
        return w

# 需要导入模块: from htmd.molecule.molecule import Molecule [as 别名]
# 或者: from htmd.molecule.molecule.Molecule import remove [as 别名]
def tileMembrane(memb, xmin, ymin, xmax, ymax, buffer=1.5):
    """ Tile a membrane in the X and Y dimensions to reach a specific size.

    Parameters
    ----------
    memb
    xmin
    ymin
    xmax
    ymax
    buffer

    Returns
    -------
    megamemb :
        A big membrane Molecule
    """
    from htmd.progress.progress import ProgressBar
    memb = memb.copy()
    memb.resid = sequenceID(memb.resid)

    minmemb = np.min(memb.get('coords', 'water'), axis=0).flatten()

    size = np.max(memb.get('coords', 'water'), axis=0) - np.min(memb.get('coords', 'water'), axis=0)
    size = size.flatten()
    xreps = int(np.ceil((xmax - xmin) / size[0]))
    yreps = int(np.ceil((ymax - ymin) / size[1]))

    logger.info('Replicating Membrane {}x{}'.format(xreps, yreps))

    from htmd.molecule.molecule import Molecule
    megamemb = Molecule()
    bar = ProgressBar(xreps * yreps, description='Replicating Membrane')
    k = 0
    for x in range(xreps):
        for y in range(yreps):
            tmpmemb = memb.copy()
            xpos = xmin + x * (size[0] + buffer)
            ypos = ymin + y * (size[1] + buffer)

            tmpmemb.moveBy([-float(minmemb[0]) + xpos, -float(minmemb[1]) + ypos, 0])
            tmpmemb.remove('same resid as (x > {} or y > {})'.format(xmax, ymax), _logger=False)
            tmpmemb.set('segid', 'M{}'.format(k))

            megamemb.append(tmpmemb)
            k += 1
            bar.progress()
    bar.stop()
    # Membranes don't tile perfectly. Need to remove waters that clash with lipids of other tiles
    # Some clashes will still occur between periodic images however
    megamemb.remove('same fragment as water and within 1.5 of not water', _logger=False)
    return megamemb

# 需要导入模块: from htmd.molecule.molecule import Molecule [as 别名]
# 或者: from htmd.molecule.molecule.Molecule import remove [as 别名]
    def _viewStatesNGL(self, states, statetype, protein, ligand, mols, numsamples, gui=False):
        from htmd.builder.builder import sequenceID
        if states is None:
            states = range(self.macronum)
        if isinstance(states, int):
            states = [states]
        if mols is None:
            mols = self.getStates(states, statetype, numsamples=min(numsamples, 15))
        colors = [0, 1, 3, 4, 5, 6, 7, 9]
        hexcolors = {0: '#0000ff', 1: '#ff0000', 2: '#333333', 3: '#ff6600', 4: '#ffff00', 5: '#4c4d00', 6: '#b2b2cc',
                     7: '#33cc33', 8: '#ffffff', 9: '#ff3399', 10: '#33ccff'}
        if protein is None and ligand is None:
            raise NameError('Please provide either the "protein" or "ligand" parameter for viewStates.')
        k = 0
        from nglview import NGLWidget, HTMDTrajectory
        view = NGLWidget(gui=gui)
        ref = mols[0].copy()
        for i, s in enumerate(states):
            if protein:
                mol = Molecule()
            if ligand:
                mol = ref.copy()
                mol.remove(ligand, _logger=False)
                mol.coords = np.atleast_3d(mol.coords[:, :, 0])
                mols[i].filter(ligand, _logger=False)
            mols[i].set('chain', '{}'.format(s))
            tmpcoo = mols[i].coords
            for j in range(mols[i].numFrames):
                mols[i].coords = np.atleast_3d(tmpcoo[:, :, j])
                if ligand:
                    mols[i].set('segid', sequenceID(mols[i].resid)+k)
                    k = int(mols[i].segid[-1])
                mol.append(mols[i])
            view.add_trajectory(HTMDTrajectory(mol))
            # Setting up representations
            if ligand:
                view[i].add_cartoon('protein', color='sstruc')
                view[i].add_hyperball(':{}'.format(s), color=hexcolors[np.mod(i, len(hexcolors))])
            if protein:
                view[i].add_cartoon('protein', color='residueindex')

        self._nglButtons(view, statetype, states)
        return view

# 需要导入模块: from htmd.molecule.molecule import Molecule [as 别名]
# 或者: from htmd.molecule.molecule.Molecule import remove [as 别名]
def tileMembrane(memb, xmin, ymin, xmax, ymax, buffer=1.5):
    """ Tile a membrane in the X and Y dimensions to reach a specific size.

    Parameters
    ----------
    memb : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        The membrane to be tiled
    xmin : float
        Minimum x coordinate
    ymin : float
        Minimum y coordinate
    xmax : float
        Maximum x coordinate
    ymax : float
        Maximum y coordinate
    buffer : float
        Buffer distance between tiles

    Returns
    -------
    megamemb :
        A big membrane Molecule
    """
    from tqdm import tqdm
    memb = memb.copy()
    memb.resid = sequenceID((memb.resid, memb.insertion, memb.chain, memb.segid))

    minmemb = np.min(memb.get('coords', 'water'), axis=0).flatten()

    size = np.max(memb.get('coords', 'water'), axis=0) - np.min(memb.get('coords', 'water'), axis=0)
    size = size.flatten()
    xreps = int(np.ceil((xmax - xmin) / size[0]))
    yreps = int(np.ceil((ymax - ymin) / size[1]))

    logger.info('Replicating Membrane {}x{}'.format(xreps, yreps))

    from htmd.molecule.molecule import Molecule
    megamemb = Molecule()
    bar = tqdm(total=xreps * yreps, desc='Replicating Membrane')
    k = 0
    for x in range(xreps):
        for y in range(yreps):
            tmpmemb = memb.copy()
            xpos = xmin + x * (size[0] + buffer)
            ypos = ymin + y * (size[1] + buffer)

            tmpmemb.moveBy([-float(minmemb[0]) + xpos, -float(minmemb[1]) + ypos, 0])
            tmpmemb.remove('same resid as (x > {} or y > {})'.format(xmax, ymax), _logger=False)
            if tmpmemb.numAtoms == 0:
                continue

            tmpmemb.set('segid', 'M{}'.format(k), sel='not water')
            tmpmemb.set('segid', 'MW{}'.format(k), sel='water')

            megamemb.append(tmpmemb)
            k += 1
            bar.update(1)
    bar.close()

    # Membranes don't tile perfectly. Need to remove waters that clash with lipids of other tiles
    # Some clashes will still occur between periodic images however
    megamemb.remove('same resid as water and within 1.5 of not water', _logger=False)
    return megamemb