Python Molecule.appendFrames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 appendFrames [as 别名]
    def sampleRegion(self, point=None, radius=None, limits=None, nsamples=20, singlemol=False):
        """ Samples conformations from a region in the projected space.

        Parameters
        ----------
        point : list or np.ndarray
            A point in the projected space. Undefined dimensions should have None value.
        radius : float
            The radius in around the point in which to sample conformations.
        limits : np.ndarray
            A (2, ndim) dimensional array containing the min (1st row) and max (2nd row) limits for each dimension.
            None values will be interpreted as no limit in that dimension, or min/max value.
        nsamples : int
            The number of conformations to sample.
        singlemol : bool
            If True it will return all samples within a single Molecule instead of a list of Molecules.

        Returns
        -------
        absFrames : list
            A list of the absolute frame indexes sampled
        relFrames : list of tuples
            A list of (trajNum, frameNum) tuples sampled
        mols : Molecule or list of Molecules
            The conformations stored in a Molecule or a list of Molecules

        Examples
        --------
        >>> # Working with 4 dimensional data for example
        >>> abs, rel, mols = data.sampleRegion(point=(0.5, 3, None, None), radius=0.1)  # Point undefined in dim 3, 4
        >>> minlims = [-1, None, None, 4]  # No min limit for 2, 3 dim
        >>> maxlims = [2,     3, None, 7]  # No max limit for 3 dim
        >>> abs, rel, mols = data.sampleRegion(limits=np.array([minlims, maxlims]))
        """
        from scipy.spatial.distance import cdist
        datconcat = np.concatenate(self.dat)
        numdim = datconcat.shape[1]
        if point is not None:
            if radius is None:
                raise RuntimeError('You must define a radius with a point.')
            point = np.array(point)
            if len(point) != numdim:
                raise RuntimeError(
                    'Argument `point` should be same dimensionality as your data ({} dimensions)'.format(numdim))
            keepdim = np.array([p is not None for p in point])
            dists = cdist(datconcat[:, keepdim], [point[keepdim]])
            confs = np.where(dists < radius)[0]
        elif limits is not None:
            if limits.shape != (2, numdim):
                raise RuntimeError('Argument `limits` should be of shape (2, {})'.format(numdim))
            mask = np.ones(datconcat.shape[0], dtype=bool)
            for i in range(numdim):
                if limits[0, i] is not None:
                    mask &= datconcat[:, i] > limits[0, i]
                if limits[1, i] is not None:
                    mask &= datconcat[:, i] < limits[1, i]
            confs = np.where(mask)[0]

        if len(confs) > nsamples:
            confs = np.random.choice(confs, nsamples, replace=False)
        sims = self.abs2sim(confs)

        from htmd.molecule.molecule import Molecule
        if singlemol:
            mol = Molecule(sims[0])
            for i in range(1, len(sims)):
                m = Molecule(sims[i])
                mol.appendFrames(m)
        else:
            mol = []
            for s in sims:
                mol.append(Molecule(s))
        return confs, self.abs2rel(confs), mol