mmtbx.geometry package

Submodules

mmtbx.geometry.altloc module

class mmtbx.geometry.altloc.Aggregator(indexer)

Bases: object

Queries the indexer and returns altloc-correct neighbours

property entities
process_altloc(data, coordinates, identifier)
process_regular(data, coordinates)
class mmtbx.geometry.altloc.Alternate(identifier)

Bases: object

An object assigned with an altloc identifier

class mmtbx.geometry.altloc.Description(data, coordinates, altid)

Bases: object

An internal format to allow processing with the visitor pattern

accept(processor)
mmtbx.geometry.altloc.Empty(data, coordinates, processor)

An object without an altloc identifier

class mmtbx.geometry.altloc.Indexer(factory)

Bases: object

Indexer that takes into account altloc

add(altloc)
class mmtbx.geometry.altloc.Inserter(indexer)

Bases: object

Fills up an indexer with data

process_altloc(data, coordinates, identifier)
process_regular(data, coordinates)
mmtbx.geometry.altloc.altid_for(atom)

mmtbx.geometry.asa module

class mmtbx.geometry.asa.AccessibleSurfaceAreas(values, unit)

Bases: object

Result of a series of calculations

property areas
property points
class mmtbx.geometry.asa.AccessibleSurfaceResult(count, radius_sq)

Bases: object

Result of the calculation

property surface
class mmtbx.geometry.asa.CompositeCheckerBuilder(indexer, description)

Bases: object

Finds neighbours for a sphere

class mmtbx.geometry.asa.SeparateCheckerBuilder(indexer, description)

Bases: object

Finds neighbours for a sphere

static append_neighbours(indexer, sphere, centre, checker)
process_altloc(data, coordinates, identifier)
process_regular(data, coordinates)
mmtbx.geometry.asa.altloc_averaged_calculation(indexer, sampling, description)

For atoms with altloc identifier, use empty altloc + atom with same altloc. For atoms with empty altloc, run a calculation for each know altloc and average the results.

mmtbx.geometry.asa.calculate(atoms, calculation=<function simple_surface_calculation>, indexer_selector=<function get_optimal_indexer_for>, probe=1.4, precision=960)
mmtbx.geometry.asa.coordinate_adaptor(array, transformation=<function identity>)
mmtbx.geometry.asa.create_and_populate_indexer(factory, descriptions)
mmtbx.geometry.asa.create_description(index, atom, radius)
mmtbx.geometry.asa.get_hash_indexer_for(descriptions)
mmtbx.geometry.asa.get_linear_indexer_for(descriptions)
mmtbx.geometry.asa.get_optimal_indexer_for(descriptions)
mmtbx.geometry.asa.get_voxelizer_for(descriptions, step=7)
mmtbx.geometry.asa.identity(value)
mmtbx.geometry.asa.radius_adaptor(array, transformation=<function identity>)
mmtbx.geometry.asa.simple_surface_calculation(indexer, sampling, description)

Calculates ASA by not worrying about altlocs

mmtbx.geometry.clash module

class mmtbx.geometry.clash.ASUContent(case, ifactory=<function hash_indexer_for>)

Bases: object

Contains the asymmetric unit

add(sequence)
clashing_with(sphere, tolerance)
descriptor_for(sphere)
class mmtbx.geometry.clash.AtomDescriptor(model, sphere)

Bases: object

A descriptor that allows looking up the original object is necessary

property atom
class mmtbx.geometry.clash.Case(symmetry, vdw_radius_for, max_radius, margin)

Bases: object

Calculation parameters that are transferable

asu_mapping_for(atoms)
classmethod create(symmetry, models, vdw_radius_for, margin=1.0)
radius_for(atom)
sphere_model_group_for(model)
voxelizer()
class mmtbx.geometry.clash.ClashCalculation(tolerance=0.5)

Bases: object

Calculates clashpoints

class mmtbx.geometry.clash.ClashCollection(points)

Bases: object

All clashes in a model

pairs()
class mmtbx.geometry.clash.ClashCountCalculation(tolerance=0.5)

Bases: object

Calculates number of clashes

class mmtbx.geometry.clash.ClashPoint(centre, others)

Bases: object

Clashes with a central atom

count()
pairs()
class mmtbx.geometry.clash.ClashingPair(left, right)

Bases: object

Clashing atom pair

atom_pair()
frozenset()
is_self_clash()
class mmtbx.geometry.clash.DistanceCalculation(cell)

Bases: object

Calculates clash distance for atom pair

class mmtbx.geometry.clash.ElementAccumulator

Bases: object

Collects all elements in a list

class mmtbx.geometry.clash.Model(root)

Bases: object

A model, providing fast access to atoms by memory_id

atoms()
elements()
class mmtbx.geometry.clash.ReducingAccumulator(initial, operation)

Bases: object

Sums up the elements as they come in

class mmtbx.geometry.clash.SphereModel(model, spheres)

Bases: object

Sphere representation of a model

descriptors()
class mmtbx.geometry.clash.SphereModelGroup(model, group)

Bases: object

Partitioned sphere model

group()
class mmtbx.geometry.clash.SymmetryEquivalent(atom, symop)

Bases: object

A potential symmetry equivalent of an atom

property atom_group
property chain
property molecule
property residue_group
property root
mmtbx.geometry.clash.altloc_strategy_from_atom(atom)
mmtbx.geometry.clash.calculate(roots, symmetry, vdw_table, ifactory=<function hash_indexer_for>, margin=1.0, calculation=None, accumulator=None)
mmtbx.geometry.clash.calculate_contents(roots, symmetry, vdw_radius_for, ifactory, margin)
mmtbx.geometry.clash.element_of(atom)
mmtbx.geometry.clash.hash_indexer_for(params)
mmtbx.geometry.clash.linear_indexer_for(params)
mmtbx.geometry.clash.to_xray_structure(atoms, symmetry)

A utility function to convert atoms into cctbx.xray.structure

mmtbx.geometry.indexing module

class mmtbx.geometry.indexing.composite_predicate(conditions)

Bases: object

Layer several conditions

class mmtbx.geometry.indexing.containment_predicate(selection, getter, relation)

Bases: object

Simple predicate to evaluate whether the object is in a predefined set

static exclude(obj, selection)
classmethod exclusion(selection, getter)
static include(obj, selection)
classmethod inclusion(selection, getter)
mmtbx.geometry.indexing.direct(obj)
mmtbx.geometry.indexing.filter(range, predicate)
class mmtbx.geometry.indexing.identity_predicate(element, getter)

Bases: object

Simple predicate to evaluate whether the object is identical to something

class mmtbx.geometry.indexing.overlap_predicate(centre, distance, getter=<function direct>)

Bases: object

Simple predicate to evaluate actual distance

class mmtbx.geometry.indexing.structure_indexer(indexer, datagen, maxdist)

Bases: object

Indexes iotbx.pdb.hierarchy objects

add_atoms_in(obj)
composite_distance_predicate(predicates, centre)
static coordinate_of(obj)
static data_of(obj)
classmethod exclude_predicate(selection)
classmethod hash(base, maxdist, datagen=<function structure_indexer.<lambda>>, subdivision=1, safescale=1.01)
classmethod identity_predicate(element)
classmethod include_predicate(selection)
interaction_counts_with(obj, predicates=[])
interaction_ranges_with(obj, predicates=[])
interactions_with(obj, predicates=[])
overlap_predicate(centre)
simple_distance_predicate(predicates, centre)

mmtbx.geometry.primitive module

mmtbx.geometry.shared_types module

mmtbx.geometry.shared_types.calculate_base_for_coordinates(xyzs)

mmtbx.geometry.sphere_surface_sampling module

mmtbx.geometry.topology module

class mmtbx.geometry.topology.Atom(**kwargs)

Bases: object

Match results by identity

class mmtbx.geometry.topology.Compound(graph)

Bases: object

A graph-based 2D-representation of a compound

add_atom(atom)
add_bond(left, right, order=1)
property atom_for
property atoms
property bonds
connected_segment_from(atom)
connected_segments()
classmethod create(vertex_type='vector', edge_type='set')
property descriptors
distances_from(atom)
classmethod from_structure(atoms, tolerance=0.1, vertex_type='vector', edge_type='set')
subset(atoms)
class mmtbx.geometry.topology.GreedyMatch(molecule1, molecule2, prematched=[], vertex_equality=None, edge_equality=None, maxsol=0)

Bases: object

Geometry and label-based correspondence matching using the Greedy algorithm

count()
length()
remapped()
class mmtbx.geometry.topology.McGregorMatch(molecule1, molecule2, is_valid, maxsteps=500, vertex_equality=None, edge_equality=None)

Bases: object

Geometry and label-based correspondence matching using the McGregor algorithm

length()
remapped()
class mmtbx.geometry.topology.Molecule(vertex_type='vector', edge_type='set')

Bases: object

A graph-based 3D-description of a molecule

add(atom, xyz)
property atoms
property descriptor_for
size()
class mmtbx.geometry.topology.RascalMatch(molecule1, molecule2, prematched=[], vertex_equality=None, edge_equality=None)

Bases: object

Geometry and label-based correspondence matching using the Rascal algorithm

count()
length()
remapped()

mmtbx.geometry.volume module

Module contents