Python Molecule.dropFrames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 dropFrames [as 别名]
def _writeInputsFunction(i, f, epoch, inputpath, coorname):
    regex = re.compile('(e\d+s\d+)_')
    frameNum = f.frame
    piece = f.piece
    if f.sim.parent is None:
        currSim = f.sim
    else:
        currSim = f.sim.parent

    traj = currSim.trajectory[piece]
    if currSim.input is None:
        raise NameError('Could not find input folder in simulation lists. Cannot create new simulations.')

    wuName = _simName(traj)
    res = regex.search(wuName)
    if res:  # If we are running on top of adaptive, use the first name part for the next sim name
        wuName = res.group(1)

    # create new job directory
    newName = 'e' + str(epoch) + 's' + str(i + 1) + '_' + wuName + 'p' + str(piece) + 'f' + str(frameNum)
    newDir = path.join(inputpath, newName, '')

    # copy previous input directory including input files
    copytree(currSim.input, newDir, symlinks=False, ignore=ignore_patterns('*.coor', '*.rst', '*.out', *_IGNORE_EXTENSIONS))

    # overwrite input file with new one. frameNum + 1 as catdcd does 1 based indexing

    mol = Molecule(currSim.molfile)  # Always read the mol file, otherwise it does not work if we need to save a PDB as coorname
    mol.read(traj)
    mol.dropFrames(keep=frameNum)  # Making sure only specific frame to write is kept
    mol.write(path.join(newDir, coorname))

# 需要导入模块: from htmd.molecule.molecule import Molecule [as 别名]
# 或者: from htmd.molecule.molecule.Molecule import dropFrames [as 别名]
    def _viewStatesNGL(self, states, statetype, protein, ligand, mols, numsamples, gui=False):
        from htmd.molecule.util 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.dropFrames(keep=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 dropFrames [as 别名]
        from pandas import DataFrame
        types = []
        indexes = []
        description = []
        for i in atomidx:
            types += ['SASA']
            indexes += [i]
            description += ['SASA of {} {} {}'.format(mol.resname[i], mol.resid[i], mol.name[i])]
        return DataFrame({'type': types, 'atomIndexes': indexes, 'description': description})


if __name__ == '__name__':
    from htmd.molecule.molecule import Molecule
    from htmd.home import home
    from os import path
    import numpy as np
    mol = Molecule(path.join(home(), 'data', 'metricdistance', 'filtered.pdb'))
    mol.read(path.join(home(), 'data', 'metricdistance', 'traj.xtc'))
    mol.dropFrames(keep=[0, 1])  # Keep only two frames cause it's super slow

    metr = MetricSasa(mode='atom')
    sasaA = metr.project(mol)
    metr = MetricSasa(mode='residue')
    sasaR = metr.project(mol)

    sasaA_ref = np.load(path.join(home(), 'data', 'test-metrics', 'metricsasa', 'sasaA.npy'))
    sasaR_ref = np.load(path.join(home(), 'data', 'test-metrics', 'metricsasa', 'sasaR.npy'))

    assert np.array_equal(sasaA, sasaA_ref)
    assert np.array_equal(sasaR, sasaR_ref)