Python Molecule.box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 box [as 别名]
    def viewStates(self, protein=None, ligand=None, nsamples=20):
        from htmd.projections.metric import _singleMolfile
        from htmd.molecule.molecule import Molecule
        from htmd.vmdviewer import getCurrentViewer
        (single, molfile) = _singleMolfile(self.data.simlist)
        if not single:
            raise RuntimeError('Can''t visualize states without unique molfile')

        viewer = getCurrentViewer()
        colors = [0, 1, 3, 4, 5, 6, 7, 9]

        print('Active set includes macrostates: {}'.format(self.hmm.active_set))

        # dtraj = np.vstack(self.hmm.discrete_trajectories_full)
        res = self.hmm.sample_by_observation_probabilities(nsamples)
        refmol = Molecule(molfile)

        for i, s in enumerate(self.hmm.active_set):
            mol = Molecule(molfile)
            mol.coords = []
            mol.box = []
            # idx = np.where(dtraj == i)[0]
            # samples = np.random.choice(idx, 20)
            # frames = self.data.abs2sim(samples)

            frames = self.data.rel2sim(res[i])
            for f in frames:
                mol._readTraj(f.sim.trajectory[f.piece], frames=[f.frame], append=True)
            mol.wrap('protein')
            mol.align('protein', refmol=refmol)
            viewer.loadMol(mol, name='hmm macro ' + str(s))
            if ligand is not None:
                viewer.rep('ligand', sel=ligand, color=colors[np.mod(i, len(colors))])
            if protein is not None:
                viewer.rep('protein')
            viewer.send('start_sscache')

# 需要导入模块: from htmd.molecule.molecule import Molecule [as 别名]
# 或者: from htmd.molecule.molecule.Molecule import box [as 别名]
def reconstructAdaptiveTraj(simlist, trajID):
    """ Reconstructs a long trajectory out of short adaptive runs.

    Parameters
    ----------
    simlist : numpy.ndarray of :class:`Sim <htmd.simlist.Sim>` objects
        A simulation list generated by the :func:`simlist <htmd.simlist.simlist>` function
    trajID : int
        The id of the trajectory from which to start going back.

    Returns
    -------
    mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
        A Molecule object containing the reconstructed trajectory
    chain : np.ndarray
        The simulation IDs of all simulations involved
    pathlist : np.ndarray of str
        The names of all simulations involved.

    Examples
    --------
    >>> mol, chain, pathlist = reconstructAdaptiveTraj(data.simlist, 52)
    """

    sim = None
    for s in simlist:
        if s.simid == trajID:
            sim = s
            break
    if sim is None:
        raise NameError('Could not find sim with ID {} in the simlist.'.format(trajID))

    pathlist = []
    pathlist.append(sim.trajectory[0])
    chain = []
    chain.append((sim, -1, -1))

    epo = None
    while epo != 1:
        [sim, piece, frame, epo] = _findprevioustraj(simlist, _simName(sim.trajectory[0]))
        pathlist.append(sim.trajectory[piece])
        chain.append((sim, piece, frame))
    pathlist = pathlist[::-1]
    chain = chain[::-1]

    mol = Molecule(sim.molfile)
    mol.coords = np.zeros((mol.numAtoms, 3, 0), dtype=np.float32)
    mol.fileloc = []
    mol.box = np.zeros((3, 0))
    for i, c in enumerate(chain):
        tmpmol = Molecule(sim.molfile)
        tmpmol.read(c[0].trajectory)
        endpiece = c[1]
        fileloc = np.vstack(tmpmol.fileloc)
        filenames = fileloc[:, 0]
        pieces = np.unique(filenames)
        firstpieceframe = np.where(filenames == pieces[endpiece])[0][0]
        endFrame = firstpieceframe + c[2]
        if endFrame != -1:
            tmpmol.coords = tmpmol.coords[:, :, 0:endFrame + 1]  # Adding the actual respawned frame (+1) since the respawned sim doesn't include it in the xtc
            tmpmol.fileloc = tmpmol.fileloc[0:endFrame + 1]
            tmpmol.box = tmpmol.box[:, 0:endFrame + 1]
        mol.coords = np.concatenate((mol.coords, tmpmol.coords), axis=2)
        mol.box = np.concatenate((mol.box, tmpmol.box), axis=1)
        mol.fileloc += tmpmol.fileloc
    #mol.fileloc[:, 1] = range(np.size(mol.fileloc, 0))

    return mol, chain, pathlist

# 需要导入模块: from htmd.molecule.molecule import Molecule [as 别名]
# 或者: from htmd.molecule.molecule.Molecule import box [as 别名]
    if ext not in _WRITERS:
        _WRITERS[ext] = MDTRAJwrite


if __name__ == '__main__':
    from htmd.home import home
    from htmd.molecule.molecule import Molecule, mol_equal
    from htmd.util import tempname
    import numpy as np
    import os
    testfolder = home(dataDir='metricdistance')
    mol = Molecule(os.path.join(testfolder, 'filtered.pdb'))
    mol.coords = np.tile(mol.coords, (1, 1, 2))
    mol.filter('protein and resid 1 to 20')
    mol.boxangles = np.ones((3, 2), dtype=np.float32) * 90
    mol.box = np.ones((3, 2), dtype=np.float32) * 15
    mol.step = np.arange(2)
    mol.time = np.arange(2) * 1E5

    for ext in _WRITERS:
        tmp = tempname(suffix='.'+ext)
        mol.write(tmp)
        print('Can write {} files'.format(ext))


    # from difflib import Differ
    # d = Differ()
    #
    # with open(tmp, 'rb') as f1, open(a, 'rb') as f2:
    #     res = d.compare([x.decode('utf8') for x in f1.readlines()], [x.decode('utf8') for x in f2.readlines()])
    #