\(\newcommand{\AA}{\text{Å}}\)

lmodea_k.CoordinateSpecification

class CoordinateSpecification

High-level container for all user-defined geometry specifications.

Stores:

• GroupSpec objects

• AtomCoordinate objects

• FeatureCoordinate objects

Maintains a consistent types string automatically.

__init__()

Methods

__init__()
add_atom_coordinate(coord)
add_feature_coordinate(coord)
add_group(group)
atom_coords_by_type(coord_type)
compute_cluster_dim([min_dim])	Determine the minimum cluster dimension needed to include all atoms referenced by Rl vectors in this specification.
coord_specs(cluster, coord_type)	Convert atom-based coordinates of a given type into cluster indices.
expand_auto_groups(cluster)	Complete groups specified with the @ seed syntax.
feature_coords_by_type(coord_type)
from_file(filepath)	Load a coordinate specification from a coords.in file.
inter_specs(cluster)	Return cluster indices for each group defining the intermolecular interaction coordinate, along with resolved axis vectors and human-readable axis names.
molecule_specs(cluster, coord_type)	Return parallel lists for molecule-level rigid-body coordinate builders:
ring_specs(cluster)	Return cluster indices and names for all ring (puckering) feature coordinates.
system_specs(cluster, coord_type)	Return resolved axis definitions for the unique system-level coordinate of the given type.

Attributes

atom_coordinates
feature_coordinates
groups