besmarts.core.assignments module

besmarts.core.assignments

Associates BESMARTS structures to data

There are two intepretations of the data. The first simpler model is the the graph_assignments, which contain (ic, data) pairs. The data is assumed to be a list of lists of independent samples, i.e. multiple conformers. This distinction means a “system” where there are two molecules interacting requires a list of graph assignments. These assignments are quite flexible and agnostic of the data. An additional layer is required to interpret data, which is provided, at least partially, to graph_db objects.

In constrast to the simple assignment objectives, the more complex graph_db system is explicitly designed to handle large systems with redundant graph information, e.g. a box of water where point triples use the same graph, and each triple exists in the same system and should be overlapping. See the documentation for graph_db for more information.

In general, most of the work is performed on assignments, and graph_db objects are designed to be a management system for the various types of data assigned to graphs, such as positions, gradients, and Hessians.

class besmarts.core.assignments.angle_assignment_float(selections)

Bases: structure_assignment_float

selections

topology

class besmarts.core.assignments.angle_assignment_float_matrix(selections)

Bases: structure_assignment_float

selections

topology

class besmarts.core.assignments.angle_assignment_str(selections)

Bases: structure_assignment_str

selections

topology

class besmarts.core.assignments.atom_assignment_float(selections)

Bases: structure_assignment_float

selections

topology

class besmarts.core.assignments.atom_assignment_str(selections)

Bases: structure_assignment_str

selections

topology

besmarts.core.assignments.b2matrix(pos, bonds=True, angles=True, torsions=True, outofplanes=True, pairs=True, remove1_3=False, linear_torsions=145.0)

besmarts.core.assignments.bmatrix(pos, bonds=True, angles=True, torsions=True, outofplanes=True, pairs=True, remove1_3=False, linear_torsions=145.0)

class besmarts.core.assignments.bond_assignment_float(selections)

Bases: structure_assignment_float

selections

topology

class besmarts.core.assignments.bond_assignment_float_matrix(selections)

Bases: structure_assignment_float

selections

topology

class besmarts.core.assignments.bond_assignment_str(selections)

Bases: structure_assignment_str

selections

topology

class besmarts.core.assignments.graph_assignment(smiles, assignments, graph)

Bases: smiles_assignment

Assign a subgraph selection some value.

copy()

graph: graph

selections: Dict[Sequence[int], Any]

smiles: str

besmarts.core.assignments.graph_assignment_copy(ga: graph_assignment) → graph_assignment

class besmarts.core.assignments.graph_assignment_float(graph, selections)

Bases: smiles_assignment

graph: str

selections: Dict[Sequence[int], List[float]]

class besmarts.core.assignments.graph_assignment_float_matrix(graphs, selections)

Bases: smiles_assignment

graph: List[graph]

selections: Dict[Sequence[int], List[float]]

besmarts.core.assignments.graph_assignment_geometry_angle_matrix(pos: List[graph_assignment_float], indices=None) → angle_assignment_float

besmarts.core.assignments.graph_assignment_geometry_angles(pos: graph_assignment_float, indices=None) → angle_assignment_float

besmarts.core.assignments.graph_assignment_geometry_bond_matrix(pos: List[graph_assignment_float], indices=None) → bond_assignment_float_matrix

besmarts.core.assignments.graph_assignment_geometry_bonds(pos: graph_assignment_float, indices=None) → bond_assignment_float

besmarts.core.assignments.graph_assignment_geometry_outofplane_matrix(pos: List[graph_assignment_float], indices=None) → outofplane_assignment_float_matrix

besmarts.core.assignments.graph_assignment_geometry_outofplanes(pos: graph_assignment_float, indices=None) → outofplane_assignment_float

besmarts.core.assignments.graph_assignment_geometry_pair_matrix(pos: List[graph_assignment_float], indices=None) → bond_assignment_float_matrix

besmarts.core.assignments.graph_assignment_geometry_pairs(pos: graph_assignment_float, indices=None) → bond_assignment_float

besmarts.core.assignments.graph_assignment_geometry_position(smiles, graph, confs)

besmarts.core.assignments.graph_assignment_geometry_torsion_matrix(pos: List[graph_assignment_float], indices=None) → torsion_assignment_float

besmarts.core.assignments.graph_assignment_geometry_torsions(pos: graph_assignment_float, indices=None) → torsion_assignment_float

besmarts.core.assignments.graph_assignment_jacobian2_angle_matrix(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian2_angles(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian2_bond_matrix(pos, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian2_bonds(pos, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian2_outofplane_matrix(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian2_outofplanes(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian2_pair_matrix(pos, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian2_pairs(pos, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian2_torsion_matrix(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian2_torsions(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_angle_matrix(pos: List[smiles_assignment_float], indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_angles(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_bond_matrix(pos, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_bonds(pos, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_distance_matrix(pos, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_distances(pos, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_outofplane_matrix(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_outofplanes(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_pair_matrix(pos, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_pairs(pos, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_torsion_matrix(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_jacobian_torsions(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.graph_assignment_matrix_angle_indices(pos)

besmarts.core.assignments.graph_assignment_matrix_bond_indices(pos)

besmarts.core.assignments.graph_assignment_matrix_outofplane_indices(pos)

besmarts.core.assignments.graph_assignment_matrix_pair_indices(pos)

besmarts.core.assignments.graph_assignment_matrix_torsion_indices(pos)

besmarts.core.assignments.graph_assignment_to_format_xyz(pos: graph_assignment, comment='') → List[str]

besmarts.core.assignments.graph_assignment_to_graph_db_graph(ga, topo)

besmarts.core.assignments.graph_assignment_to_graph_db_row(ga) → graph_db_row

class besmarts.core.assignments.graph_db

Bases: object

Holds a heterogeneous set of data associated to graphs

Here is the layout of a graph_db. Defined here are the smiles, graphs, and selections which are indexed by a graph id (gid). The entries use a different id (eid) which points to a graph_db_table object. This object holds several tables indexed by a table id (tid), which are similar to types of data. Examples of tables are positions and Hessians. Each table points to graphs, which use the same gid as those in the graphs member here. Each graph then points to “rows” indexed by rid, which are analogous to individual systems/snapshots/frames. Each row can points to “columns” indexed by cid, which are analogous to conformations in the same system. Finally, each cid points to selection id (sid) and data id pairs (xid). The (sid, xid) pairs are similar to a graph assignment, except in this case the data is always a flat array and xid is the index in that array.

The structures have a corresponding member to traverse deeper; however, the simple array notation is supported. This means that rather than

gdb.entries[eid].tables[tid].graphs[gid].rows[rid].columns[cid].selections[sid].data[xid]

one can simply write

gdb[eid][tid][gid][rid][cid][sid][xid] -> float

TODO: most of the development has been on single molecules in gas phase. As such, some functions assume this and may not handle multigraph, multi conformation data gracefully.

entries: Dict[int, graph_db_entry]

graphs: Dict[int, graph]

selections: Dict[int, graph_db_selection]

smiles: Dict[int, str]

besmarts.core.assignments.graph_db_add_graph(gdb: graph_db, smi, g) → int

besmarts.core.assignments.graph_db_add_multi_molecule(gdb: graph_db, gde: graph_db_entry, positions: List[graph_assignment], gradients: List[graph_assignment] = None, hessian: List[graph_assignment] = None, energy: List[float] = None)

besmarts.core.assignments.graph_db_add_single_molecule_list(gdb: graph_db, positions: List[graph_assignment], gradients: List[graph_assignment] = None, hessian: List[graph_assignment] = None, energy: List[float] = None)

besmarts.core.assignments.graph_db_add_single_molecule_state(gdb: graph_db, positions: graph_assignment, gradients: graph_assignment = None, hessian: graph_assignment = None, energy: float = None, tables=None) → Tuple[int, int]

A simple function to add a SMILES and positions to a gdb dataset

Assumes multiple confs are in the same state (columns)

Call this again for different systems

class besmarts.core.assignments.graph_db_address(*, eid=None, tid=None, gid=None, rid=None, cid=None, sid=None, xid=None)

Bases: object

A query for information in a graph_db.

class besmarts.core.assignments.graph_db_column

Bases: object

selections: Dict[int, List]

class besmarts.core.assignments.graph_db_entry

Bases: object

Data associated with a set of graphs

tables: Dict[int, graph_db_table]

besmarts.core.assignments.graph_db_entry_add_table(gde, tid, topo, gids)

besmarts.core.assignments.graph_db_get(GDB: graph_db, addr: graph_db_address) → graph_db

besmarts.core.assignments.graph_db_get_entries(GDB: graph_db, eids: List[int]) → graph_db

besmarts.core.assignments.graph_db_get_graphs(db)

class besmarts.core.assignments.graph_db_graph

Bases: object

rows: Dict[int, graph_db_row]

besmarts.core.assignments.graph_db_graph_to_graph_assignment(gdb, eid, tid, gid=None, rid=None, cid=None) → graph_assignment

besmarts.core.assignments.graph_db_iter_values(db)

class besmarts.core.assignments.graph_db_row

Bases: object

columns: Dict[int, graph_db_column]

class besmarts.core.assignments.graph_db_selection

Bases: object

coords: Dict[int, Sequence[int]]

besmarts.core.assignments.graph_db_set_gradient(gdb, eid, gradient: List[float])

besmarts.core.assignments.graph_db_set_positions(gdb, eid, gid, sel, rid=None) → int

class besmarts.core.assignments.graph_db_table(top)

Bases: object

Holds the data for a db of graphs that all share the same topology.

graphs: Dict[int, graph_db_graph]

topology: structure_topology

values

besmarts.core.assignments.graph_db_table_get_row_ids(gdt)

besmarts.core.assignments.make_structure_assignment_type(name)

class besmarts.core.assignments.outofplane_assignment_float(selections)

Bases: structure_assignment_float

selections

topology

class besmarts.core.assignments.outofplane_assignment_float_matrix(selections)

Bases: structure_assignment_float

selections

topology

class besmarts.core.assignments.outofplane_assignment_str(selections)

Bases: structure_assignment_str

selections

topology

class besmarts.core.assignments.pair_assignment_float(selections)

Bases: structure_assignment_float

selections

topology

class besmarts.core.assignments.pair_assignment_float_matrix(selections)

Bases: structure_assignment_float

selections

topology

besmarts.core.assignments.parse_xyz(xyzdata: str) → Tuple[List[str], List[List[Tuple[float, float, float]]]]

class besmarts.core.assignments.smarts_assignment

Bases: object

selections

smarts

class besmarts.core.assignments.smarts_assignment_float

Bases: smarts_assignment

selections

smarts

class besmarts.core.assignments.smarts_assignment_str

Bases: smarts_assignment

selections

smarts

class besmarts.core.assignments.smarts_hierarchy_assignment

Bases: object

assign(shier: smarts_hierarchy, gcd: graph_codec, smi: List[str], selections) → smiles_assignment_group

assign_angles(shier: smarts_hierarchy, gcd: graph_codec, smi: List[str]) → smiles_assignment_group

assign_atoms(shier: smarts_hierarchy, gcd: graph_codec, smi: List[str]) → smiles_assignment_group

assign_bonds(shier: smarts_hierarchy, gcd: graph_codec, smi: List[str]) → smiles_assignment_group

assign_outofplanes(shier: smarts_hierarchy, gcd: graph_codec, smi: List[str]) → smiles_assignment_group

assign_torsions(shier: smarts_hierarchy, gcd: graph_codec, smi: List[str]) → smiles_assignment_group

class besmarts.core.assignments.smiles_assignment(smiles, selections)

Bases: object

compute(idx: Sequence[int])

copy()

selections

smiles

besmarts.core.assignments.smiles_assignment_copy(sa: smiles_assignment) → smiles_assignment

class besmarts.core.assignments.smiles_assignment_float(smiles, selections)

Bases: smiles_assignment

selections: Dict[Sequence[int], List[float]]

smiles: str

besmarts.core.assignments.smiles_assignment_geometry_angle_matrix(pos: List[smiles_assignment_float], indices) → angle_assignment_float

besmarts.core.assignments.smiles_assignment_geometry_angles(pos: smiles_assignment_float, indices) → angle_assignment_float

besmarts.core.assignments.smiles_assignment_geometry_distance_matrix(pos: smiles_assignment_float, indices) → bond_assignment_float_matrix

besmarts.core.assignments.smiles_assignment_geometry_distances(pos: smiles_assignment_float, indices) → bond_assignment_float

besmarts.core.assignments.smiles_assignment_geometry_outofplane_matrix(pos: List[smiles_assignment_float], indices=None) → smiles_assignment

besmarts.core.assignments.smiles_assignment_geometry_outofplanes(pos: smiles_assignment_float, indices=None) → smiles_assignment

besmarts.core.assignments.smiles_assignment_geometry_torsion_matrix(pos: List[smiles_assignment_float], indices=None) → torsion_assignment_float_matrix

besmarts.core.assignments.smiles_assignment_geometry_torsion_matrix_nonlinear(pos: List[smiles_assignment_float], indices=None, angle_degrees=145.0) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_geometry_torsions(pos: smiles_assignment_float, indices=None) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_geometry_torsions_nonlinear(pos: smiles_assignment_float, indices=None, angle_degrees=145.0) → smiles_assignment_float

class besmarts.core.assignments.smiles_assignment_group(assignments, topo)

Bases: object

copy()

besmarts.core.assignments.smiles_assignment_group_angles(assignments: List[smiles_assignment])

besmarts.core.assignments.smiles_assignment_group_atoms(assignments: List[smiles_assignment])

besmarts.core.assignments.smiles_assignment_group_bonds(assignments: List[smiles_assignment])

besmarts.core.assignments.smiles_assignment_group_concatenate(A: smiles_assignment_group, B: smiles_assignment_group)

besmarts.core.assignments.smiles_assignment_group_copy(sag: smiles_assignment_group) → smiles_assignment_group

besmarts.core.assignments.smiles_assignment_group_outofplanes(assignments: List[smiles_assignment])

besmarts.core.assignments.smiles_assignment_group_pairs(assignments: List[smiles_assignment])

besmarts.core.assignments.smiles_assignment_group_to_graph_db_entry(sag, aid, gcd) → graph_db_entry

besmarts.core.assignments.smiles_assignment_group_to_structure_assignment_group(smag: smiles_assignment_group, gcd: graph_codec) → structure_assignment_group

besmarts.core.assignments.smiles_assignment_group_torsions(assignments: List[smiles_assignment])

besmarts.core.assignments.smiles_assignment_jacobian2_angle_matrix(pos: smiles_assignment_float, indices) → angle_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian2_angles(pos: smiles_assignment_float, indices) → angle_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian2_distance_matrix(pos, indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian2_distances(pos, indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian2_outofplane_matrix(pos: smiles_assignment_float, indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian2_outofplanes(pos: smiles_assignment_float, indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian2_torsion_matrix(pos: smiles_assignment_float, indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian2_torsions(pos: smiles_assignment_float, indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian_angle_matrix(pos: List[smiles_assignment_float], indices) → angle_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian_angles(pos: smiles_assignment_float, indices) → angle_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian_distance_matrix(pos, indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian_distances(pos, indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian_outofplane_matrix(pos: List[smiles_assignment_float], indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian_outofplanes(pos: smiles_assignment_float, indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian_torsion_matrix(pos: List[smiles_assignment_float], indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_jacobian_torsions(pos: smiles_assignment_float, indices) → smiles_assignment_float

besmarts.core.assignments.smiles_assignment_to_graph_assignment(smas: smiles_assignment, gcd) → graph_assignment

class besmarts.core.assignments.structure_assignment_float(topology, selections)

Bases: object

selections

topology

class besmarts.core.assignments.structure_assignment_group(assignments, topo)

Bases: smiles_assignment_group

A group of assignments that share the same topology.

assignments: List[graph_assignment]

copy()

topology: structure_topology

besmarts.core.assignments.structure_assignment_group_copy(stuag: structure_assignment_group)

class besmarts.core.assignments.structure_assignment_str

Bases: object

selections

topology

class besmarts.core.assignments.topology_assignment_group

Bases: object

class besmarts.core.assignments.torsion_assignment_float(selections)

Bases: structure_assignment_float

selections

topology

class besmarts.core.assignments.torsion_assignment_float_matrix(selections)

Bases: structure_assignment_float

selections

topology

class besmarts.core.assignments.torsion_assignment_str(selections)

Bases: structure_assignment_str

selections

topology

besmarts.core.assignments.xyz_to_graph_assignment(gcd, smi, xyzdata: str, indices=None) → graph_assignment