Introduce Capped distances to evaluate the indices of pairs within a fixed radius

package/CHANGELOG

@@ -14,12 +14,14 @@ The rules for this file:
 
 ------------------------------------------------------------------------------
 ??/??/18 tylerjereddy, richardjgowers, palnabarun, orbeckst, kain88-de, zemanj,
-         VOD555, davidercruz, jbarnoud
+         VOD555, davidercruz, jbarnoud, ayushsuhane
 
   * 0.18.1
 
 Enhancements
 
+  * Added lib.distances.capped_distance function to quickly calculate all distances
+    up to a given maximum distance (PR #1941)
   * Added a rotation coordinate transformation (PR #1937)
   * Added a box centering trajectory transformation (PR #1946)
   * Added a on-the-fly trajectory transformations API and a coordinate translation

package/MDAnalysis/lib/distances.py

@@ -72,6 +72,7 @@
 from .mdamath import triclinic_vectors, triclinic_box
 
 
+
 # hack to select backend with backend=<backend> kwarg. Note that
 # the cython parallel code (prange) in parallel.distances is
 # independent from the OpenMP code
@@ -396,6 +397,215 @@ def self_distance_array(reference, box=None, result=None, backend="serial"):
     return distances
 
 
+def capped_distance(reference, configuration, max_cutoff, min_cutoff=None, box=None, method=None):
+    """Calculates the pairs and distance within a specified distance
+
+    If a *box* is supplied, then a minimum image convention is used
+    to evaluate the distances.
+
+    An automatic guessing of optimized method to calculate the distances is
+    included in the function. An optional keyword for the method is also
+    provided. Users can override the method with this functionality.
+    Currently pkdtree and bruteforce are implemented.
+
+
+    Parameters
+    -----------
+    reference : array
+        reference coordinates array with shape ``reference.shape = (3,)``
+        or ``reference.shape = (len(reference), 3)``
+    configuration : array
+        Configuration coordinate array with shape ``reference.shape = (3,)``
+        or ``reference.shape = (len(reference), 3)``
+    max_cutoff : float
+        Maximum cutoff distance between the reference and configuration
+    min_cutoff : (optional) float
+        Minimum cutoff distance between reference and configuration [None]
+    box : (optional) array or None
+        The dimensions, if provided, must be provided in the same
+        The unitcell dimesions for this system format as returned
+        by :attr:`MDAnalysis.coordinates.base.Timestep.dimensions`:
+        ``[lx,ly, lz, alpha, beta, gamma]``. Minimum image convention
+        is applied if the box is provided [None]
+    method : (optional) 'bruteforce' or 'pkdtree' or 'None'
+        Keyword to override the automatic guessing of method built-in
+        in the function [None]
+
+    Returns
+    -------
+    pairs : array
+        Pair of indices, one from each reference and configuration such that
+        distance between them is  within the ``max_cutoff`` and ``min_cutoff``
+        pairs[i,j] contains the indices i from reference coordinates, and
+        j from configuration
+    distances : array
+        Distances corresponding to each pair of indices.
+        d[k] corresponding to the pairs[i,j] gives the distance between
+        i-th and j-th coordinate in reference and configuration respectively
+
+        .. code-block:: python
+
+            pairs, distances = capped_distances(reference, coordinates, max_cutoff)
+            for indx, [a,b] in enumerate(pairs):
+                coord1 = reference[a]
+                coord2 = configuration[b]
+                distance = distances[indx]
+
+    Note
+    -----
+    Currently only supports brute force and Periodic KDtree
+
+    .. SeeAlso:: :func:'MDAnalysis.lib.distances.distance_array'
+    .. SeeAlso:: :func:'MDAnalysis.lib.pkdtree.PeriodicKDTree'
+
+    """
+
+    if box is not None:
+        boxtype = _box_check(box)
+        # Convert [A,B,C,alpha,beta,gamma] to [[A],[B],[C]]
+        if (boxtype == 'tri_box'):
+            box = triclinic_vectors(box)
+        if (boxtype == 'tri_vecs_bad'):
+            box = triclinic_vectors(triclinic_box(box[0], box[1], box[2]))
+    method = _determine_method(reference, configuration,
+                                   max_cutoff, min_cutoff=min_cutoff,
+                                   box=box, method=method)
+    pairs, dist = method(reference, configuration, max_cutoff,
+                         min_cutoff=min_cutoff, box=box)
+
+    return np.asarray(pairs), np.asarray(dist)
+
+
+def _determine_method(reference, configuration, max_cutoff, min_cutoff=None, box=None, method=None):
+    """
+    Switch between different methods based on the the optimized time.
+    All the rules to select the method based on the input can be
+    incorporated here.
+
+    Returns
+    -------
+    Function object based on the rules and specified method
+    Currently implemented methods are
+    bruteforce : returns ``_bruteforce_capped``
+    PKDtree : return ``_pkdtree_capped`
+
+    """
+    methods = {'bruteforce': _bruteforce_capped,
+            'pkdtree': _pkdtree_capped}
+
+    if method is not None:
+        return methods[method]
+
+    if len(reference) > 5000 and len(configuration) > 5000:
+        if box is None and reference.shape[0] != 3 and configuration.shape[0] != 3:
+            min_dim = np.array([reference.min(axis=0),
+                               configuration.min(axis=0)])
+            max_dim = np.array([reference.max(axis=0),
+                               configuration.max(axis=0)])
+            size = max_dim.max(axis=0) - min_dim.min(axis=0)
+        elif box is not None:
+            if box.shape[0] == 6:
+                size = box[:3]
+            else:
+                size = box.max(axis=0) - box.min(axis=0)
+
+        if (np.any(size < 10.0*max_cutoff) and
+                   len(reference) > 100000 and
+                   len(configuration) > 100000):
+            return methods['bruteforce']
+        else:
+            return methods['pkdtree']
+    return methods['bruteforce']
+
+
+def _bruteforce_capped(reference, configuration, max_cutoff, min_cutoff=None, box=None):
+    """
+    Using naive distance calulations, returns a list
+    containing the indices with one from each
+    reference and configuration arrays, such that the distance between
+    them is less than the specified cutoff distance
+    """
+    pairs, distance = [], []
+
+    reference = np.asarray(reference, dtype=np.float32)
+    configuration = np.asarray(configuration, dtype=np.float32)
+
+    if reference.shape == (3, ):
+        reference = reference[None, :]
+    if configuration.shape == (3, ):
+        configuration = configuration[None, :]
+
+    _check_array(reference, 'reference')
+    _check_array(configuration, 'configuration')
+
+    for i, coords in enumerate(reference):
+        dist = distance_array(coords[None, :], configuration, box=box)[0]
+        if min_cutoff is not None:
+            idx = np.where((dist <= max_cutoff) & (dist > min_cutoff))[0]
+        else:
+            idx = np.where((dist <= max_cutoff))[0]
+        for j in idx:
+            pairs.append((i, j))
+            distance.append(dist[j])
+    return pairs, distance
+
+
+def _pkdtree_capped(reference, configuration, max_cutoff, min_cutoff=None, box=None):
+    """ Capped Distance evaluations using KDtree.
+
+    Uses minimum image convention if *box* is specified
+
+    Returns:
+    --------
+    pairs : list
+        List of atom indices which are within the specified cutoff distance.
+        pairs `(i, j)` corresponds to i-th particle in reference and
+        j-th particle in configuration
+    distance : list
+        Distance between two atoms corresponding to the (i, j) indices
+        in pairs.
+
+    """
+    from .pkdtree import PeriodicKDTree
+    from Bio.KDTree import KDTree
+
+    pairs, distances = [], []
+
+    reference = np.asarray(reference, dtype=np.float32)
+    configuration = np.asarray(configuration, dtype=np.float32)
+
+    if reference.shape == (3, ):
+        reference = reference[None, :]
+    if configuration.shape == (3, ):
+        configuration = configuration[None, :]
+
+    _check_array(reference, 'reference')
+    _check_array(configuration, 'configuration')
+
+    # Build The KDTree
+    if box is not None:
+        kdtree = PeriodicKDTree(box, bucket_size=10)
+    else:
+        kdtree = KDTree(dim=3, bucket_size=10)
+
+    kdtree.set_coords(configuration)
+    # Search for every query point
+    for idx, centers in enumerate(reference):
+        kdtree.search(centers, max_cutoff)
+        indices = kdtree.get_indices()
+        dist = distance_array(centers.reshape((1, 3)),
+                              configuration[indices], box=box)[0]
+        if min_cutoff is not None:
+            mask = np.where(dist > min_cutoff)[0]
+            dist = dist[mask]
+            indices = [indices[mask[i]] for i in range(len(mask))]
+        if len(indices) != 0:
+            for num, j in enumerate(indices):
+                pairs.append((idx, j))
+                distances.append(dist[num])
+    return pairs, distances
+
+
 def transform_RtoS(inputcoords, box, backend="serial"):
     """Transform an array of coordinates from real space to S space (aka lambda space)
 

testsuite/MDAnalysisTests/lib/test_distances.py

@@ -25,8 +25,12 @@
 import numpy as np
 from numpy.testing import assert_equal, assert_almost_equal
 
+import itertools
+
 import MDAnalysis as mda
 
+from MDAnalysis.lib.mdamath import triclinic_vectors
+
 @pytest.mark.parametrize('coord_dtype', (np.float32, np.float64))
 def test_transform_StoR_pass(coord_dtype):
     box = np.array([10, 7, 3, 45, 60, 90], dtype=np.float32)
@@ -39,6 +43,57 @@ def test_transform_StoR_pass(coord_dtype):
     assert_equal(original_r, test_r)
 
 
+def test_capped_distance_noresults():
+    point1 = np.array([0.1, 0.1, 0.1], dtype=np.float32)
+    point2 = np.array([0.95, 0.1, 0.1], dtype=np.float32)
+
+    pairs, distances = mda.lib.distances.capped_distance(point1,
+                                                        point2,
+                                                        max_cutoff=0.2)
+
+    assert_equal(len(pairs), 0)
+
+
+boxes_1 = (np.array([1, 2, 3, 90, 90, 90], dtype=np.float32),  # ortho
+           np.array([1, 2, 3, 30, 45, 60], dtype=np.float32),  # tri_box
+           triclinic_vectors(  # tri_vecs
+           np.array([1, 2, 3, 90, 90, 45], dtype=np.float32)),
+           np.array([[0.5, 0.9, 1.9],  # tri_vecs_bad
+                     [2.0, 0.4, 0.1],
+                     [0.0, 0.6, 0.5]], dtype=np.float32))
+
+query_1 = (np.array([0.1, 0.1, 0.1], dtype=np.float32),
+           np.array([[0.1, 0.1, 0.1],
+                     [0.2, 0.1, 0.1]], dtype=np.float32))
+
+method_1 = ('bruteforce', 'pkdtree')
+
+@pytest.mark.parametrize('box', boxes_1)
+@pytest.mark.parametrize('query', query_1)
+@pytest.mark.parametrize('method', method_1)
+def test_capped_distance_checkbrute(box, query, method):
+    np.random.seed(90003)
+    points = (np.random.uniform(low=0, high=1.0,
+                        size=(100, 3))*(boxes_1[0][:3])).astype(np.float32)
+    max_cutoff = 0.3
+    # capped distance should be able to handle array of vectors
+    # as well as single vectors.
+    pairs, dist = mda.lib.distances.capped_distance(query,
+                                                    points,
+                                                    max_cutoff,
+                                                    box=box,
+                                                    method=method)
+    if(query.shape[0] == 3):
+        distances = mda.lib.distances.distance_array(query[None, :],
+                                                     points, box=box)
+    else:
+        distances = mda.lib.distances.distance_array(query,
+                                                     points, box=box)
+    indices = np.where(distances < max_cutoff)
+
+    assert_equal(pairs[:, 1], indices[1])
+
+
 # different boxlengths to shift a coordinate
 shifts = [
     ((0, 0, 0), (0, 0, 0), (0, 0, 0), (0, 0, 0)), # no shifting