def _parse_pairwise_input(indices1, indices2, MDlogger, fname=''):
r"""For input of pairwise type (distances, inverse distances, contacts) checks the
type of input the user gave and reformats it so that :py:func:`DistanceFeature`,
:py:func:`InverseDistanceFeature`, and ContactFeature can work.
In case the input isn't already a list of distances, this function will:
- sort the indices1 array
- check for duplicates within the indices1 array
- sort the indices2 array
- check for duplicates within the indices2 array
- check for duplicates between the indices1 and indices2 array
- if indices2 is None, produce a list of pairs of indices in indices1, or
- if indices2 is not None, produce a list of pairs of (i,j) where i comes from indices1, and j from indices2
"""
if is_iterable_of_int(indices1):
MDlogger.warning(
'The 1D arrays input for %s have been sorted, and '
'index duplicates have been eliminated.\n'
'Check the output of describe() to see the actual order of the features'
% fname)
# Eliminate duplicates and sort
indices1 = np.unique(indices1)
# Intra-group distances
if indices2 is None:
atom_pairs = combinations(indices1, 2)
# Inter-group distances
elif is_iterable_of_int(indices2):
# Eliminate duplicates and sort
indices2 = np.unique(indices2)
# Eliminate duplicates between indices1 and indices1
uniqs = np.in1d(indices2, indices1, invert=True)
indices2 = indices2[uniqs]
atom_pairs = product(indices1, indices2)
else:
atom_pairs = indices1
return atom_pairs
def _parse_groupwise_input(group_definitions, group_pairs, MDlogger, mname=''):
r"""For input of group type (add_group_mindist), prepare the array of pairs of indices
and groups so that :py:func:`MinDistanceFeature` can work
This function will:
- check the input types
- sort the 1D arrays of each entry of group_definitions
- check for duplicates within each group_definition
- produce the list of pairs for all needed distances
- produce a list that maps each entry in the pairlist to a given group of distances
Returns
--------
parsed_group_definitions: list
List of of 1D arrays containing sorted, unique atom indices
parsed_group_pairs: numpy.ndarray
(N,2)-numpy array containing pairs of indices that represent pairs
of groups for which the inter-group distance-pairs will be generated
distance_pairs: numpy.ndarray
(M,2)-numpy array with all the distance-pairs needed (regardless of their group)
group_membership: numpy.ndarray
(N,2)-numpy array mapping each pair in distance_pairs to their associated group pair
"""
assert isinstance(group_definitions, list), "group_definitions has to be of type list, not %s"%type(group_definitions)
# Handle the special case of just one group
if len(group_definitions) == 1:
group_pairs = np.array([0,0], ndmin=2)
# Sort the elements within each group
parsed_group_definitions = []
for igroup in group_definitions:
assert np.ndim(igroup) == 1, "The elements of the groups definition have to be of dim 1, not %u"%np.ndim(igroup)
parsed_group_definitions.append(np.unique(igroup))
# Check for group duplicates
for ii, igroup in enumerate(parsed_group_definitions[:-1]):
for jj, jgroup in enumerate(parsed_group_definitions[ii+1:]):
if len(igroup) == len(jgroup):
assert not np.allclose(igroup, jgroup), "Some group definitions appear to be duplicated, e.g %u and %u"%(ii,ii+jj+1)
# Create and/or check the pair-list
if is_string(group_pairs):
if group_pairs == 'all':
parsed_group_pairs = combinations(np.arange(len(group_definitions)), 2)
else:
assert isinstance(group_pairs, np.ndarray)
assert group_pairs.shape[1] == 2
assert group_pairs.max() <= len(parsed_group_definitions), "Cannot ask for group nr. %u if group_definitions only " \
"contains %u groups"%(group_pairs.max(), len(parsed_group_definitions))
assert group_pairs.min() >= 0, "Group pairs contains negative group indices"
parsed_group_pairs = np.zeros_like(group_pairs, dtype='int')
for ii, ipair in enumerate(group_pairs):
if ipair[0] == ipair[1]:
MDlogger.warning("%s will compute the mindist of group %u with itself. Is this wanted? "%(mname, ipair[0]))
parsed_group_pairs[ii, :] = np.sort(ipair)
# Create the large list of distances that will be computed, and an array containing group identfiers
# of the distances that actually characterize a pair of groups
distance_pairs = []
group_membership = np.zeros_like(parsed_group_pairs)
b = 0
for ii, pair in enumerate(parsed_group_pairs):
if pair[0] != pair[1]:
distance_pairs.append(product(parsed_group_definitions[pair[0]],
parsed_group_definitions[pair[1]]))
else:
parsed = parsed_group_definitions[pair[0]]
distance_pairs.append(combinations(parsed, 2))
group_membership[ii, :] = [b, b + len(distance_pairs[ii])]
b += len(distance_pairs[ii])
return parsed_group_definitions, parsed_group_pairs, np.vstack(distance_pairs), group_membership