IMP
2.0.1
The Integrative Modeling Platform
|
See IMP.domino Overview for more information.
Classes | |
class | Assignment |
Store a configuration of a subset. More... | |
class | AssignmentContainer |
class | AssignmentsTable |
class | BranchAndBoundAssignmentsTable |
class | BranchAndBoundSampler |
Sample best solutions using BranchAndBound. More... | |
class | CappedAssignmentContainer |
class | CompoundStates |
class | DependencyScoreState |
Add a dependency to the dependency graph. More... | |
class | DiscreteSampler |
A base class for discrete samplers in Domino2. More... | |
class | DisjointSetsSubsetFilterTable |
A base class. More... | |
class | DominoSampler |
Sample best solutions using Domino. More... | |
class | EqualitySubsetFilterTable |
Do not allow two particles to be in the same state. More... | |
class | EquivalenceAndExclusionSubsetFilterTable |
Define sets of equivalent and exclusive particles. More... | |
class | EquivalenceSubsetFilterTable |
Define sets of equivalent particles. More... | |
class | ExclusionSubsetFilterTable |
Do not allow two particles to be in the same state. More... | |
class | HeapAssignmentContainer |
class | IndexStates |
class | ListAssignmentContainer |
class | ListAssignmentsTable |
class | ListSubsetFilterTable |
Maintain an explicit list of what states each particle is allowed to have. More... | |
class | MinimumRestraintScoreSubsetFilterTable |
Filter a configuration of the subset using the Model thresholds. More... | |
class | NestedRigidBodyStates |
class | Order |
Store a persistent ordering for a subset based on the list. More... | |
class | PackedAssignmentContainer |
class | PairListSubsetFilterTable |
class | ParticlesAdaptor |
class | ParticleStates |
class | ParticleStatesTable |
class | PermutationStates |
class | ProbabilisticSubsetFilterTable |
class | RangeViewAssignmentContainer |
class | ReadAssignmentContainer |
class | ReadHDF5AssignmentContainer |
class | RecursiveAssignmentsTable |
class | RecursiveStates |
class | RestraintCache |
class | RestraintScoreSubsetFilterTable |
Filter a configuration of the subset using the Model thresholds. More... | |
class | RigidBodyStates |
class | SampleAssignmentContainer |
class | SimpleAssignmentsTable |
class | Slice |
Store a subset of a subset or assignment. More... | |
class | Subset |
Represent a subset of the particles being optimized. More... | |
class | SubsetFilter |
class | SubsetFilterTable |
class | WriteAssignmentContainer |
class | WriteHDF5AssignmentContainer |
class | XYZStates |
Functions | |
std::string | get_data_path (std::string file_name) |
Return the full path to installed data. More... | |
Subset | get_difference (const Subset &a, const Subset &b) |
double | get_distance_if_smaller_than (const Subset &s, const Assignment &a, const Assignment &b, ParticleStatesTable *pst, const statistics::Metrics &metrics, double max) |
algebra::VectorKD | get_embedding (const Subset &s, const Assignment &a, ParticleStatesTable *pst) |
Return an embedding for an assignment. | |
std::string | get_example_path (std::string file_name) |
Return the path to installed example data for this module. More... | |
Ints | get_index (const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded) |
Subset | get_intersection (const Subset &a, const Subset &b) |
SubsetGraph | get_junction_tree (const InteractionGraph &ig) |
Assignment | get_nearest_assignment (const Subset &s, const algebra::VectorKD &embedding, ParticleStatesTable *pst) |
Return the nearest assignment from an embedding. | |
ParticlesTemp | get_order (const Subset &s, const SubsetFilterTables &sft) |
Ints | get_partial_index (const ParticlesTemp &particles, const Subset &subset, const Subsets &excluded) |
ParticlePairsTemp | get_possible_interactions (const ParticlesTemp &ps, double max_distance, ParticleStatesTable *pst) |
SubsetGraph | get_restraint_graph (ScoringFunctionAdaptor rs, const ParticleStatesTable *pst) |
Slice | get_slice (Subset outer, Subset inner, const Subsets &excluded) |
Assignments | get_state_clusters (const Subset &subset, const Assignments &states, ParticleStatesTable *pst, double resolution) |
Subsets | get_subsets (const SubsetGraph &g) |
Gets all of the Subsets of a SubsetGraph. | |
Subset | get_union (const Subset &a, const Subset &b) |
void | load_leaf_assignments (const Subset &subset, AssignmentsTable *at, AssignmentContainer *ac) |
Fill in assignments for a leaf. | |
void | load_merged_assignments (const Subset &first_subset, AssignmentContainer *first, const Subset &second_subset, AssignmentContainer *second, const SubsetFilterTablesTemp &filters, AssignmentContainer *ret) |
Fill in assignments for an internal node. More... | |
void | load_merged_assignments_random_order (const Subset &first_subset, AssignmentContainer *first, const Subset &second_subset, AssignmentContainer *second, const SubsetFilterTablesTemp &filters, unsigned int maximum_tries, AssignmentContainer *ret) |
Sample from the merged assignments. More... | |
void | swap (Assignment &a, Assignment &b) |
void | swap (Slice &a, Slice &b) |
void | swap (Order &a, Order &b) |
void | swap (Subset &a, Subset &b) |
Debugging Junction Trees | |
typedef boost::graph | CliqueGraph |
InteractionGraph | get_triangulated (const InteractionGraph &input) |
CliqueGraph | get_clique_graph (const InteractionGraph &input) |
SubsetGraph | get_minimum_spanning_tree (const CliqueGraph &input) |
typedef boost::graph | MergeTree |
typedef MergeTree::VertexNameMap | MergeTreeConstVertexName |
typedef MergeTree::EdgeNameMap | MergeTreeConstEdgeName |
typedef boost::graph_traits < MergeTree > | MergeTreeTraits |
typedef MergeTree::vertex_descriptor | MergeTreeVertex |
typedef MergeTree::edge_descriptor | MergeTreeEdge |
SubsetGraphVertexIndex | get_vertex_index (const SubsetGraph &g) |
InteractionGraph | get_interaction_graph (ScoringFunctionAdaptor rs, const ParticleStatesTable *pst) |
InteractionGraph | get_interaction_graph (ScoringFunctionAdaptor rs, const ParticlesTemp &pst) |
display::Geometries | get_interaction_graph_geometry (const InteractionGraph &ig) |
display::Geometries | get_subset_graph_geometry (const SubsetGraph &ig) |
MergeTree | get_merge_tree (ScoringFunctionAdaptor input, const ParticleStatesTable *pst) |
MergeTree | get_merge_tree (const SubsetGraph &junction_tree) |
MergeTree | get_balanced_merge_tree (const SubsetGraph &junction_tree) |
bool | get_is_merge_tree (const MergeTree &tree, Subset all, bool verbose=true) |
Read and write merge trees | |
Merge trees can be written to an read from a text stream. As always, this requires a canonical particles list whose order is the same for the reading and writing. | |
void | write_merge_tree (const MergeTree &tree, const ParticlesTemp &ps, std::ostream &out) |
MergeTree | read_merge_tree (std::istream &input, const ParticlesTemp &ps) |
Debug tools | |
We provide a number of different functions for helpering optimize and understand domino-based sampling. These functions are expose part of the implementation and are liable to change without notice. | |
void | load_particle_states (const Subset &s, const Assignment &ss, const ParticleStatesTable *pst) |
RestraintsTemp | get_restraints (const Subset &s, const ParticleStatesTable *pst, const DependencyGraph &dg, RestraintSet *rs) |
typedef IMP::base::Vector<IMP::base::Pointer< AssignmentContainer > > IMP::domino::AssignmentContainers |
Store a set of objects.
Definition at line 59 of file assignment_containers.h.
typedef IMP::base::Vector< Assignment > IMP::domino::Assignments |
Pass or store a set of Assignment .
Definition at line 45 of file Assignment.h.
Store a set of objects.
Definition at line 45 of file assignment_tables.h.
typedef IMP::base::Vector<IMP::base::Pointer< BranchAndBoundSampler > > IMP::domino::BranchAndBoundSamplers |
Store a set of objects.
Definition at line 39 of file BranchAndBoundSampler.h.
typedef boost::graph IMP::domino::CliqueGraph |
See Graphs for more information.
Definition at line 62 of file subset_graphs.h.
Store a set of objects.
Definition at line 126 of file DiscreteSampler.h.
Store a set of objects.
Definition at line 128 of file DominoSampler.h.
typedef IMP::base::Vector<IMP::base::Pointer< EqualitySubsetFilterTable > > IMP::domino::EqualitySubsetFilterTables |
Store a set of objects.
Definition at line 238 of file subset_filters.h.
typedef IMP::base::Vector<IMP::base::Pointer< EquivalenceAndExclusionSubsetFilterTable > > IMP::domino::EquivalenceAndExclusionSubsetFilterTables |
Store a set of objects.
Definition at line 256 of file subset_filters.h.
typedef IMP::base::Vector<IMP::base::Pointer< EquivalenceSubsetFilterTable > > IMP::domino::EquivalenceSubsetFilterTables |
Store a set of objects.
Definition at line 249 of file subset_filters.h.
typedef IMP::base::Vector<IMP::base::Pointer< ExclusionSubsetFilterTable > > IMP::domino::ExclusionSubsetFilterTables |
Store a set of objects.
Definition at line 229 of file subset_filters.h.
typedef boost::graph IMP::domino::InteractionGraph |
An undirected graph with one vertex per particle of interest. Two particles are connected by an edge if a Restraint or ScoreState creates and interaction between the two particles.
See Graphs in IMP for more information.See Graphs in IMP for more information.
Definition at line 33 of file subset_graphs.h.
typedef IMP::base::Vector<IMP::base::Pointer< ListSubsetFilterTable > > IMP::domino::ListSubsetFilterTables |
Store a set of objects.
Definition at line 301 of file subset_filters.h.
typedef boost::graph IMP::domino::MergeTree |
A directed graph on subsets of vertices. Each vertex is named with an Subset.See Graphs in IMP for more information.
Definition at line 130 of file subset_graphs.h.
typedef IMP::base::Vector<IMP::base::Pointer< MinimumRestraintScoreSubsetFilterTable > > IMP::domino::MinimumRestraintScoreSubsetFilterTables |
Store a set of objects.
Definition at line 152 of file subset_filters.h.
typedef IMP::base::Vector< Order > IMP::domino::Orders |
typedef IMP::base::Vector<IMP::base::Pointer< PairListSubsetFilterTable > > IMP::domino::PairListSubsetFilterTables |
Store a set of objects.
Definition at line 326 of file subset_filters.h.
Store a set of objects.
Definition at line 63 of file particle_states.h.
typedef IMP::base::Vector<IMP::base::Pointer< ParticleStatesTable > > IMP::domino::ParticleStatesTables |
Store a set of objects.
Definition at line 114 of file particle_states.h.
typedef IMP::base::Vector<IMP::base::Pointer< RestraintScoreSubsetFilterTable > > IMP::domino::RestraintScoreSubsetFilterTables |
Store a set of objects.
Definition at line 127 of file subset_filters.h.
typedef IMP::base::Vector< Slice > IMP::domino::Slices |
Store a set of objects.
Definition at line 67 of file subset_filters.h.
Store a set of objects.
Definition at line 347 of file subset_filters.h.
typedef boost::graph IMP::domino::SubsetGraph |
An undirected graph on subsets of vertices. Each vertex is named with an Subset.See Graphs in IMP for more information.
Definition at line 24 of file subset_graphs.h.
typedef IMP::base::Vector< Subset > IMP::domino::Subsets |
MergeTree IMP::domino::get_balanced_merge_tree | ( | const SubsetGraph & | junction_tree | ) |
Compute the merge tree from a junction tree, attempting to keep it fairly balanced.
std::string IMP::domino::get_data_path | ( | std::string | file_name | ) |
Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data
directory of module "mymodule", do something like
This will ensure that the code works when IMP
is installed or used via the tools/imppy.sh
script.
double IMP::domino::get_distance_if_smaller_than | ( | const Subset & | s, |
const Assignment & | a, | ||
const Assignment & | b, | ||
ParticleStatesTable * | pst, | ||
const statistics::Metrics & | metrics, | ||
double | max | ||
) |
Return a distance between two assignments if they are less than a threshold. The distance returned is the l2 norm on the distances between each state as given by the corresponding metric. If no metric is passed, then the l2 norm on the embedding is used.
Definition at line 125 of file domino/utility.h.
std::string IMP::domino::get_example_path | ( | std::string | file_name | ) |
Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb
located in the examples
directory of the IMP::atom module, do
This will ensure that the code works when IMP
is installed or used via the tools/imppy.sh
script.
Ints IMP::domino::get_index | ( | const ParticlesTemp & | particles, |
const Subset & | subset, | ||
const Subsets & | excluded | ||
) |
If the passed particles are all contained in the Subset and are not contained any of the Subsets in excluded, then return a a list of indices given the location of each passed particle in the passed subset. That is
Otherwise return an empty list.
This function is designed to be used for implementing SubsetFilterTable classes.
InteractionGraph IMP::domino::get_interaction_graph | ( | ScoringFunctionAdaptor | rs, |
const ParticleStatesTable * | pst | ||
) |
Compute the interaction graph of the restraints and the specified particles. The dependency graph in the model is traversed to determine how the passed particles relate to the actual particles read as input by the model. For example, if particles contains a rigid body, then an restraint which uses a member of the rigid body will have an edge from the rigid body particle.
display::Geometries IMP::domino::get_interaction_graph_geometry | ( | const InteractionGraph & | ig | ) |
Assuming that all the particles have Cartesian coordinates, output edges corresponding to the edges in the interaction graph. The edges are named by the restraint which induces them.
SubsetGraph IMP::domino::get_junction_tree | ( | const InteractionGraph & | ig | ) |
Compute the exact junction tree for an interaction graph. The resulting graph has the junction tree properties
MergeTree IMP::domino::get_merge_tree | ( | ScoringFunctionAdaptor | input, |
const ParticleStatesTable * | pst | ||
) |
Compute the merge tree for a given restraint set and particle states table. An OptimizeRestraints object is created to improve the InteractionGraph used internally.
MergeTree IMP::domino::get_merge_tree | ( | const SubsetGraph & | junction_tree | ) |
Compute the merge tree from a junction tree.
ParticlesTemp IMP::domino::get_order | ( | const Subset & | s, |
const SubsetFilterTables & | sft | ||
) |
Return the order computed for the particles in the subset to be used for enumeration. This function is there in order to expose internal functionality for easier testing and should not be depended upon.
Ints IMP::domino::get_partial_index | ( | const ParticlesTemp & | particles, |
const Subset & | subset, | ||
const Subsets & | excluded | ||
) |
All of the passed particles are not contained in an ofthe Subsets in excluded, then return a a list of indices given the location of each passed particle in the passed subset or -1 if it is missing.
This function is designed to be used for implementing SubsetFilterTable classes.
ParticlePairsTemp IMP::domino::get_possible_interactions | ( | const ParticlesTemp & | ps, |
double | max_distance, | ||
ParticleStatesTable * | pst | ||
) |
Return the list of interactions implied by the passed balls given the allowed positions specified by the ParticleStatesTable.
SubsetGraph IMP::domino::get_restraint_graph | ( | ScoringFunctionAdaptor | rs, |
const ParticleStatesTable * | pst | ||
) |
The restraint graph is formed by having one node per restraint and an edge connecting two restraints if they share input particles. The associated Subsets are the set of input particles for the restraint, projected onto ps.
RestraintsTemp IMP::domino::get_restraints | ( | const Subset & | s, |
const ParticleStatesTable * | pst, | ||
const DependencyGraph & | dg, | ||
RestraintSet * | rs | ||
) |
Return a list of all restraints from rs that
Slice IMP::domino::get_slice | ( | Subset | outer, |
Subset | inner, | ||
const Subsets & | excluded | ||
) |
Assignments IMP::domino::get_state_clusters | ( | const Subset & | subset, |
const Assignments & | states, | ||
ParticleStatesTable * | pst, | ||
double | resolution | ||
) |
Return subset of the passed states which are representative. The states for each particle is clustered and then the passed states are reduced to only be on the centers of that clustering.
The XYZ coordinates are used for clustering, there is not currently a nice mechanism to vary this, but it should be figured out. Probably by subclasses statistics::Embedding to statistics::ParticleEmbedding which has a method which takes a particle.
display::Geometries IMP::domino::get_subset_graph_geometry | ( | const SubsetGraph & | ig | ) |
Display the subsets of a subset graph, superimposed on the 3D coordinates of the particles.
void IMP::domino::load_merged_assignments | ( | const Subset & | first_subset, |
AssignmentContainer * | first, | ||
const Subset & | second_subset, | ||
AssignmentContainer * | second, | ||
const SubsetFilterTablesTemp & | filters, | ||
AssignmentContainer * | ret | ||
) |
The passed assignments, the ordering for the children is that of the node indexes for the children.
void IMP::domino::load_merged_assignments_random_order | ( | const Subset & | first_subset, |
AssignmentContainer * | first, | ||
const Subset & | second_subset, | ||
AssignmentContainer * | second, | ||
const SubsetFilterTablesTemp & | filters, | ||
unsigned int | maximum_tries, | ||
AssignmentContainer * | ret | ||
) |
The passed assignments, the ordering for the children is that of the node indexes for the children.
It will try maximum_tries times to merge an assignment from the first set with a randomly chosen assignment from the second. Note that duplicate solutions may be present in the output and the output will never be guaranteed to be complete.
void IMP::domino::load_particle_states | ( | const Subset & | s, |
const Assignment & | ss, | ||
const ParticleStatesTable * | pst | ||
) |
Load the appropriate state for each particle in a Subset.