schrodinger.application.matsci.network_cg_mapping.translation module¶

Candidate translation generation and validation for atomic networks.

schrodinger.application.matsci.network_cg_mapping.translation.canonical_vector(vector, tolerance=1e-10)¶

Choose one direction for a Cartesian translation vector.

Parameters:

vector (numpy.ndarray) – Cartesian vector
tolerance (float) – Values no larger than this are treated as zero

Return type:

numpy.ndarray

Returns:

Vector with its first significant component positive

schrodinger.application.matsci.network_cg_mapping.translation.bond_order_key(bond_order)¶

Return the normalized bond order used for topology matching.

Parameters:: bond_order (float) – Atomic bond order
Return type:: float
Returns:: Bond order rounded for topology comparisons

schrodinger.application.matsci.network_cg_mapping.translation.find_translations(network, windings, position_tolerance=0.12, minimum_coverage=0.45, topology_coverage=0.85, max_candidates=96, max_anchors=48)¶

Return chemically and topologically validated network translations.

Parameters:

network (AtomicNetwork) – Atomic network to search
windings (collections.abc.Iterable) – Cycle windings in the input-PBC basis
position_tolerance (float) – Maximum Cartesian match error in angstroms
minimum_coverage (float) – Minimum fraction of atoms matched by a translation
topology_coverage (float) – Minimum fraction of matched bonds preserved
max_candidates (int) – Maximum translation candidates to validate
max_anchors (int) – Maximum sampled source atoms per matching key

Return type:

tuple(TranslationMatch)

Returns:

Chemically and topologically validated translations