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IMP Reference Guide
2.20.0
The Integrative Modeling Platform
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Base functionality and abstract base classes for representation, scoring and sampling. More...
Base functionality and abstract base classes for representation, scoring and sampling.
Graphs in IMP are represented in C++ using the Boost.Graph. All graphs used in IMP are VertexAndEdgeListGraphs, have vertex_name properties, are BidirectionalGraphs if they are directed.
The Boost.Graph interface cannot be easily exported to Python so we instead provide a simple wrapper IMP::PythonDirectedGraph. There are methods to translate the graphs into various common python and other formats (eg graphviz).
As is conventional in C++, IMP classes are divided into broad, exclusive types
const&), never by pointer. Equality is defined based on the data stored in the value. Most value types in IMP are always valid, but a few, mostly geometric types (IMP::algebra::Vector3D) are designed for fast, low-level use and are left in an uninitialized state by their default constructorAll types in IMP, with a few documented exceptions, can be
The google perf tools can be used for cpu and memory profiling of IMP. They can be controlled from the command line in many IMP executables.
Author(s): Daniel Russel, Ben Webb
Maintainer: benmwebb
License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.
Publications:
Namespaces | |
| algebra | |
| General purpose algebraic and geometric methods that are expected to be used by a wide variety of IMP modules. | |
| atom | |
| Functionality for loading, creating, manipulating and scoring atomic structures. | |
| bayesianem | |
| Restraints for handling electron microscopy maps. | |
| benchmark | |
| Support for developing and analyzing benchmarks of IMP code. | |
| cgal | |
| Make CGAL functionality available to IMP. | |
| cnmultifit | |
| Generate cyclic atomic structures using cryo-electron microscopy data. | |
| container | |
| Various classes to hold sets of particles. | |
| core | |
| Basic functionality that is expected to be used by a wide variety of IMP users. | |
| display | |
| Output IMP model data in various file formats. | |
| domino | |
| Divide-and-conquer inferential optimization in discrete space. | |
| em | |
| Basic utilities for handling cryo-electron microscopy 3D density maps. | |
| em2d | |
| Restraints using electron microscopy 2D images (class averages). | |
| EMageFit | |
| Build assembly models consistent with EM images (class averages). | |
| example | |
| Example module. | |
| foxs | |
| Determine small angle X-ray (SAXS) profiles. | |
| gsl | |
| Several general purpose optimizers from the GNU Scientific Library (GSL). | |
| integrative_docking | |
| Pairwise docking incorporating additional data. | |
| isd | |
| Inferential scoring building on methods developed as part of the Inferential Structure Determination software (ISD). | |
| kinematics | |
| Functionality for dealing with kinematic mechanical structures. | |
| kmeans | |
| Interface to the GPL k-means clustering library | |
| misc | |
| Miscellaneous functionality that is not expected to be used by many IMP users. | |
| mmcif | |
| Support for output of models in mmCIF format. | |
| modeller | |
| Interface to the Modeller comparative modeling package. | |
| mpi | |
| Code that uses the MPI parallel library. | |
| multi_state | |
| Functionality for handling multi-state models. | |
| multifit | |
| Fitting atomic structures into a cryo-electron microscopy density map. | |
| npc | |
| Restraints designed for modeling the Nuclear Pore Complex (NPC) | |
| npctransport | |
| parallel | |
| Distribute IMP tasks to multiple processors or machines. | |
| pepdock | |
| Initial peptide docking. | |
| pmi | |
| Python classes to represent, score, sample and analyze models. | |
| pmi1 | |
| Legacy PMI1 module to represent, score, sample and analyze models. | |
| rmf | |
| Support for the RMF file format for storing hierarchical molecular data and markup. | |
| rotamer | |
| Sampling of sidechain rotamers. | |
| sampcon | |
| Sampling exhaustiveness protocol. | |
| saxs | |
| Support for small angle X-ray scattering (SAXS) data. | |
| saxs_merge | |
| A method for merging SAXS profiles using Gaussian processes. | |
| score_functor | |
| Composable functors to implement scores via compile-time composition. | |
| scratch | |
| A space to add temporary classes while experimenting without forcing you to create your own module. | |
| spb | |
| Classes, functions and executables for modeling of the Spindle Pole Body. | |
| statistics | |
| Code to compute statistical measures. | |
| symmetry | |
| Support for basic symmetry, such as periodic boundary conditions (PBC). | |
| test | |
| Support for running tests of IMP functionality. | |
Classes | |
| struct | AddBoolFlag |
| struct | AddFloatFlag |
| struct | AddIntFlag |
| struct | AddStringFlag |
| class | AdvancedFlag |
| Use this to add an advanced flag to the program. More... | |
| class | ArgumentParser |
| IMP-specific subclass of argparse.ArgumentParser. More... | |
| class | Array |
| A class to store a fixed array of same-typed values. More... | |
| class | AttributeOptimizer |
| Base class for optimizers that act on individual attributes. More... | |
| class | CommandDispatcher |
| Allow command line tools to easily implement multiple commands. More... | |
| class | Configuration |
| A class to store a configuration of a model. More... | |
| class | ConfigurationSet |
| A class to store a set of configurations of a model. More... | |
| class | Constraint |
| Implement a constraint on the Model. More... | |
| class | ConstVector |
| Store an array of values of the same type. More... | |
| class | Container |
| Abstract class for containers of particles. More... | |
| class | CreateLogContext |
| Create a new log context. More... | |
| class | Decorator |
| Interface to specialized Particle types (e.g. atoms) More... | |
| class | DerivativeAccumulator |
| Class for adding derivatives from restraints to the model. More... | |
| struct | EvaluationState |
| class | EventException |
| An exception that signifies some event occurred. More... | |
| class | Exception |
The general base class for IMP exceptions. More... | |
| class | Flag |
| struct | FloatIndex |
| A FloatIndex identifies an optimized attribute in a model. More... | |
| class | Index |
| A typed index. More... | |
| class | IndexException |
| An exception for a request for an invalid member of a container. More... | |
| class | IndexVector |
| Implements a vector tied to a particular index of type Index<Tag>. More... | |
| class | InputAdaptor |
| Convenience class to accept multiple input types. More... | |
| struct | InternalException |
| A general exception for an internal error in IMP. More... | |
| class | IOException |
| An input/output exception. More... | |
| class | Key |
| A base class for Keys. More... | |
| class | LRUCache |
| Implement a simple least recently used cache. More... | |
| class | Memoizer |
| Helper class for writing memoizers. More... | |
| class | Model |
| Class for storing model, its restraints, constraints, and particles. More... | |
| class | ModelException |
| An exception which is thrown when the Model has attributes with invalid values. More... | |
| class | ModelObject |
| Base class for objects in a Model that depend on other objects. More... | |
| class | NonCopyable |
| Base class for all objects that cannot be copied. More... | |
| class | Object |
Common base class for heavy weight IMP objects. More... | |
| class | Optimizer |
| Base class for all optimizers. More... | |
| class | OptimizerState |
| Shared optimizer state that is invoked upon commitment of new coordinates. More... | |
| class | PairContainer |
| A shared container for Pairs. More... | |
| class | PairContainerAdaptor |
| class | PairModifier |
| A base class for modifiers of ParticlePairsTemp. More... | |
| class | PairPredicate |
| Abstract predicate function. More... | |
| class | PairScore |
| Abstract class for scoring object(s) of type ParticleIndexPair. More... | |
| class | Particle |
| Class to handle individual particles of a Model object. More... | |
| class | ParticleAdaptor |
| class | ParticleIndexAdaptor |
| Take Decorator, Particle or ParticleIndex. More... | |
| class | ParticleIndexesAdaptor |
| Take Decorator, Particle or ParticleIndex. More... | |
| class | ParticleIndexPairsAdaptor |
| Take ParticlePairs or ParticleIndexPairs. More... | |
| class | ParticleInputs |
| Base class for objects that take particle arguments and read from them. More... | |
| class | ParticleOutputs |
| Base class for objects that take particle arguments and modify them. More... | |
| struct | Pointer |
| A smart pointer to a reference counted object. More... | |
| struct | PointerMember |
| A smart pointer to a ref-counted Object that is a class member. More... | |
| class | PythonDirectedGraph |
| class | QuadContainer |
| A shared container for Quads. More... | |
| class | QuadContainerAdaptor |
| class | QuadModifier |
| A base class for modifiers of ParticleQuadsTemp. More... | |
| class | QuadPredicate |
| Abstract predicate function. More... | |
| class | QuadScore |
| Abstract class for scoring object(s) of type ParticleIndexQuad. More... | |
| class | RAII |
| Temporarily change something; undo the change when this object is destroyed. More... | |
| class | Refiner |
| Abstract class to implement hierarchical methods. More... | |
| class | Restraint |
A restraint is a term in an IMP ScoringFunction. More... | |
| class | RestraintInfo |
| Report key:value information on restraints. More... | |
| class | RestraintsAdaptor |
| Provide a consistent interface for things that take Restraints as arguments. More... | |
| class | RestraintSet |
| Object used to hold a set of restraints. More... | |
| class | Sampler |
| Base class for all samplers. More... | |
| class | SaveToConfigurationSetOptimizerState |
| class | ScopedAddCacheAttribute |
| class | ScopedSetAttribute |
| class | ScoreAccumulator |
| Class for adding up scores during ScoringFunction evaluation. More... | |
| class | ScoreState |
| ScoreStates maintain invariants in the Model. More... | |
| class | ScoringFunction |
| Represents a scoring function on the model. More... | |
| class | ScoringFunctionAdaptor |
| class | SetCheckState |
| A class to change and restore check state. More... | |
| class | SetLogState |
| A class to change and restore log state. More... | |
| class | SetLogTarget |
| Temporarily set log target. More... | |
| class | SetNumberOfThreads |
| class | Showable |
Helper class to aid in output of IMP classes to streams. More... | |
| class | SingletonContainer |
| A shared container for Singletons. More... | |
| class | SingletonContainerAdaptor |
| class | SingletonModifier |
| A base class for modifiers of ParticlesTemp. More... | |
| class | SingletonPredicate |
| Abstract predicate function. More... | |
| class | SingletonScore |
| Abstract class for scoring object(s) of type ParticleIndex. More... | |
| class | SparseSymmetricPairMemoizer |
| class | TextInput |
| class | TextOutput |
| class | TripletContainer |
| A shared container for Triplets. More... | |
| class | TripletContainerAdaptor |
| class | TripletModifier |
| A base class for modifiers of ParticleTripletsTemp. More... | |
| class | TripletPredicate |
| Abstract predicate function. More... | |
| class | TripletScore |
| Abstract class for scoring object(s) of type ParticleIndexTriplet. More... | |
| class | TypeException |
An exception for an invalid type being passed to IMP. More... | |
| class | UnaryFunction |
| Abstract single variable functor class for score functions. More... | |
| struct | UncheckedWeakPointer |
| A weak pointer to an Object or RefCountedObject. More... | |
| class | Undecorator |
| class | UsageException |
An exception for an invalid usage of IMP. More... | |
| class | Value |
| Base class for a simple primitive-like type. More... | |
| class | ValueException |
An exception for an invalid value being passed to IMP. More... | |
| class | Vector |
A more IMP-like version of the std::vector. More... | |
| class | VersionInfo |
| Version and module information for Objects. More... | |
| struct | WarningContext |
| Warnings with the same key within the context are only output once. More... | |
| struct | WeakPointer |
| Smart pointer to Object-derived classes that does not refcount. More... | |
Enumerations | |
| enum | CheckLevel { DEFAULT_CHECK = -1, NONE = 0, USAGE = 1, USAGE_AND_INTERNAL = 2 } |
| Specify the level of runtime checks performed. More... | |
| enum | LogLevel { DEFAULT = -1, SILENT = 0, WARNING = 0 + 1, PROGRESS = 2, TERSE = 3, VERBOSE = 4, MEMORY = 5 } |
The log levels supported by IMP. More... | |
Functions | |
| def | allow_deprecated |
| Context manager to temporarily allow (or disallow) deprecated code. More... | |
| template<class Before , class After > | |
| Constraint * | create_constraint (Before *b, After *a, const typename Before::Argument &t, std::string name=std::string()) |
| ScoringFunctions | create_decomposition (ScoringFunction *sf) |
| Restraints | create_decomposition (const RestraintsTemp &rs) |
| Return the decomposition of a list of restraints. More... | |
| template<class Score > | |
| Restraint * | create_restraint (Score *s, const typename Score::Argument &t, std::string name=std::string()) |
| template<class Score > | |
| Restraint * | create_restraint (const Score *s, const typename Score::Argument &t, std::string name=std::string()) |
| template<class Score , class Container > | |
| Restraint * | create_restraint (const Score *s, Container *t, std::string name=std::string()) |
| template<class RestraintType > | |
| ScoringFunction * | create_scoring_function (RestraintType *rs, double weight=1.0, double max=NO_MAX, std::string name=std::string()) |
| Create a ScoringFunction on a single restraint. More... | |
| TextOutput | create_temporary_file (std::string prefix="imp_temp", std::string suffix="") |
| Create a temporary file. The path can be extracted from the TextOutput. More... | |
| std::string | create_temporary_file_name (std::string prefix="imp_temp", std::string suffix="") |
| Create a temporary file. More... | |
| def | deprecated_function |
| Python decorator to mark a function as deprecated. More... | |
| def | deprecated_method |
| Python decorator to mark a method as deprecated. More... | |
| def | deprecated_module |
| Mark a Python module as deprecated. More... | |
| def | deprecated_object |
| Python decorator to mark a class as deprecated. More... | |
| std::string | get_absolute_path (std::string file) |
| Convert a possibly relative path to an absolute path. More... | |
| template<class Tag > | |
| unsigned int | get_as_unsigned_int (Index< Tag > i) |
| std::string | get_copyright () |
| Get the IMP copyright notice. More... | |
| DependencyGraph | get_dependency_graph (Model *m) |
| ParticlesTemp | get_dependent_particles (ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index) |
| bool | get_deprecation_exceptions () |
| Get whether an exception is thrown when a deprecated method is used. More... | |
| ParticleIndexes | get_indexes (const ParticlesTemp &ps) |
| Get the indexes from a list of particles. More... | |
| ParticleIndexPairs | get_indexes (const ParticlePairsTemp &ps) |
| Get the indexes from a list of particle pairs. More... | |
| template<class Tag > | |
| Index< Tag > | get_invalid_index () |
| bool | get_is_quick_test () |
| Strings | get_live_object_names () |
| Return the names of all live objects. More... | |
| Objects | get_live_objects () |
| Return pointers to all live objects. More... | |
| TextOutput | get_log_target () |
| ParticlesTemp | get_particles (Model *m, const ParticleIndexes &ps) |
| Get the particles from a list of indexes. More... | |
| DependencyGraph | get_pruned_dependency_graph (Model *m) |
| double | get_random_double_uniform () |
| Return a uniformly distributed double number in range [0..1) More... | |
| double | get_random_double_uniform (double min, double max) |
| Return a uniformly distributed double number in range [min..max) More... | |
| float | get_random_float_uniform () |
| Return a uniformly distributed float number in range [0..1) More... | |
| float | get_random_float_uniform (float min, float max) |
| Return a uniformly distributed float number in range [min..max) More... | |
| template<typename RealType > | |
| void | get_random_numbers_normal (Vector< RealType > &v, unsigned int n, RealType mean=0.0, RealType stddev=1.0) |
| Fill the double array with random normally distributed values. More... | |
| template<typename RealType > | |
| void | get_random_numbers_uniform (Vector< RealType > &v, unsigned int n) |
| Fill the float array with random uniformly distributed values. More... | |
| boost::uint64_t | get_random_seed () |
| Return the initial random seed. More... | |
| std::string | get_relative_path (std::string base, std::string relative) |
| Return a path to a file relative to another file. More... | |
| ScoreStatesTemp | get_required_score_states (const ModelObjectsTemp &mos, ScoreStatesTemp exclude=ScoreStatesTemp()) |
| Compute the set of score states required by the passed ModelObjects. More... | |
| ScoreStatesTemp | get_required_score_states (ModelObject *p, const ModelObjectsTemp &all, const DependencyGraph &dg, const DependencyGraphVertexIndex &index) |
| std::string | get_unique_name (std::string templ) |
| Return a unique name produced from the string. More... | |
| ScoreStatesTemp | get_update_order (ScoreStatesTemp input) |
| ScoreStatesTemp | get_update_order (std::set< ScoreState * > input) |
| const algebra::Vector3D & | get_vector_geometry (Particle *p) |
| const algebra::Vector3D & | get_vector_geometry (Decorator d) |
| const algebra::Vector3D & | get_vector_geometry (WeakPointer< Particle > d) |
| const algebra::Vector3D & | get_vector_geometry (Pointer< Particle > d) |
| DependencyGraphVertexIndex | get_vertex_index (const DependencyGraph &g) |
| void | handle_use_deprecated (std::string message) |
| Break in this method in gdb to find deprecated uses at runtime. More... | |
| template<class T > | |
| std::size_t | hash_value (const T &t) |
| std::size_t | hash_value (double d) |
| std::size_t | hash_value (int d) |
| std::size_t | hash_value (bool d) |
| std::size_t | hash_value (const std::string &d) |
| template<class T > | |
| std::size_t | hash_value (const std::vector< T > &t) |
| template<class T > | |
| std::size_t | hash_value (const std::set< T > &t) |
| template<class T > | |
| bool | isinf (const T &a) |
| Return true if a number is infinite. More... | |
| template<class T > | |
| bool | isnan (const T &a) |
| Return true if a number is NaN. More... | |
| template<class Pred > | |
| internal::PredicateEquals < Pred, true > | make_predicate_equal (const Pred *p, Model *m, int value) |
| Return a functor that returns true when the predicate has a certain value. More... | |
| template<class Pred > | |
| internal::PredicateEquals < Pred, false > | make_predicate_not_equal (const Pred *p, Model *m, int value) |
| template<class O > | |
| O * | object_cast (Object *o) |
Up (or down) cast an IMP Object-derived class. More... | |
| std::ostream & | operator<< (std::ostream &out, const Showable &s) |
| template<class Tag , class Container , class T > | |
| void | resize_to_fit (Container &v, Index< Tag > i, const T &default_value=T()) |
| void | set_deprecation_exceptions (bool tf) |
| Toggle whether an exception is thrown when a deprecated method is used. More... | |
| void | set_deprecation_warnings (bool tf) |
| Toggle printing of warnings on using deprecated classes. More... | |
| void | set_log_target (TextOutput l) |
| Set the target for the log. More... | |
| void | set_show_leaked_objects (bool tf) |
| Set whether to complain about objects not being properly cleaned up. More... | |
| void | set_vector_geometry (Particle *p, const algebra::Vector3D &v) |
| void | set_vector_geometry (Decorator d, const algebra::Vector3D &v) |
| void | set_vector_geometry (WeakPointer< Particle > d, const algebra::Vector3D &v) |
| void | set_vector_geometry (Pointer< Particle > d, const algebra::Vector3D &v) |
| void | show_as_graphviz (const DependencyGraph &name, TextOutput out) |
| void | show_restraint_hierarchy (ScoringFunctionAdaptor rs, std::ostream &out=std::cout) |
| Print the hierarchy of restraints. More... | |
| template<class A > | |
| void | swap (ConstVector< A > &a, ConstVector< A > &b) |
| void | write_help (std::ostream &out=std::cerr) |
Variables | |
| const double | BAD_SCORE |
| const double | NO_MAX |
| Use this value when you want to turn off maximum for restraint evaluation. More... | |
| RandomNumberGenerator | random_number_generator |
| A shared non-GPU random number generator. More... | |
Attribute Keys | |
Each type of attribute has an associated type of key. The keys can be constructed from a string. Such construction can be expensive and so the resulting keys should be cached. | |
| typedef Key< 0 > | FloatKey |
| The type used to identify float attributes in the Particles. More... | |
| typedef IMP::Vector< FloatKey > | FloatKeys |
| typedef Key< 1 > | IntKey |
| The type used to identify int attributes in the Particles. More... | |
| typedef IMP::Vector< IntKey > | IntKeys |
| typedef Key< 2 > | StringKey |
| The type used to identify string attributes in the Particles. More... | |
| typedef IMP::Vector< StringKey > | StringKeys |
| typedef Key< 3 > | ParticleIndexKey |
| The type used to identify a particle attribute in the Particles. More... | |
| typedef IMP::Vector < ParticleIndexKey > | ParticleIndexKeys |
| typedef Key< 4 > | ObjectKey |
| The type used to identify an Object attribute. More... | |
| typedef IMP::Vector< ObjectKey > | ObjectKeys |
| typedef Key< 9 > | WeakObjectKey |
| The type used to identify a non-ref counted Object attribute. More... | |
| typedef IMP::Vector < WeakObjectKey > | WeakObjectKeys |
| typedef Key< 5 > | IntsKey |
| The type used to identify int attributes in the Particles. More... | |
| typedef IMP::Vector< IntsKey > | IntsKeys |
| typedef Key< 10 > | FloatsKey |
| The type used to identify float vector attributes in the Particles. More... | |
| typedef IMP::Vector< FloatsKey > | FloatsKeys |
| typedef Key< 6 > | ParticleIndexesKey |
| The type used to identify a particle attribute in the Particles. More... | |
| typedef IMP::Vector < ParticleIndexesKey > | ParticleIndexesKeys |
| typedef Key< 7 > | ObjectsKey |
| The type used to identify a particle attribute in the Particles. More... | |
| typedef IMP::Vector< ObjectsKey > | ObjectsKeys |
| typedef Key< 8 > | ModelKey |
| The type used to identify data stored directly in the model. More... | |
| typedef IMP::Vector< ModelKey > | ModelKeys |
| typedef Key< 11 > | TriggerKey |
| The type used to identify changed model properties. More... | |
| typedef IMP::Vector< TriggerKey > | TriggerKeys |
| typedef Key< 12 > | SparseStringKey |
| The type used to identify sparse string attributes in the Particles. More... | |
| typedef IMP::Vector < SparseStringKey > | SparseStringKeys |
| typedef Key< 13 > | SparseIntKey |
| The type used to identify sparse int attributes in the Particles. More... | |
| typedef IMP::Vector< SparseIntKey > | SparseIntKeys |
| typedef Key< 14 > | SparseFloatKey |
| The type used to identify sparse float attributes in the Particles. More... | |
| typedef IMP::Vector < SparseFloatKey > | SparseFloatKeys |
| typedef Key< 15 > | SparseParticleIndexKey |
| The type used to identify sparse particle attributes in the Particles. More... | |
| typedef IMP::Vector < SparseParticleIndexKey > | SparseParticleIndexKeys |
Error checking and reporting | |
By default Error handling is provided by IMP/exception.h, Use the | |
| void | set_check_level (CheckLevel tf) |
| Control runtime checks in the code. More... | |
| CheckLevel | get_check_level () |
| Get the current audit mode. More... | |
| void | handle_error (const char *msg) |
Flags | |
These methods add support for shared command line flags to In C++, you can also use the AddFloatFlag, AddStringFlag, AddBoolFlag and AddIntFlag classes to add flags statically. | |
| std::string | get_executable_name () |
| Return the name of the current executable. More... | |
| void | setup_from_argv (int argc, char **argv, std::string description) |
| Parse the command line flags and return the positional arguments. More... | |
| Strings | setup_from_argv_allowing_unknown (int argc, char **argv, std::string description) |
| Strings | setup_from_argv (int argc, char **argv, std::string description, std::string positional_description, int num_positional) |
| void | setup_from_argv (const Strings &argv, std::string description) |
| Strings | setup_from_argv (const Strings &argv, std::string description, std::string positional_description, int num_positional) |
| void | add_string_flag (std::string name, std::string default_value, std::string description) |
| std::string | get_string_flag (std::string name) |
| void | add_int_flag (std::string name, size_t default_value, std::string description) |
| size_t | get_int_flag (std::string name) |
| void | add_bool_flag (std::string name, std::string description) |
| bool | get_bool_flag (std::string name) |
| void | add_float_flag (std::string name, double default_value, std::string description) |
| double | get_float_flag (std::string name) |
Inputs and outputs | |
These methods recursively find all inputs or outputs of a given type. If you don't want recursive, use the non input/output variants. | |
| ParticlesTemp | get_input_particles (const ModelObjectsTemp &mos) |
| Return all the input particles for a given ModelObject. More... | |
| ContainersTemp | get_input_containers (const ModelObjectsTemp &mos) |
| Return all the input particles for a given ModelObject. More... | |
| ParticlesTemp | get_output_particles (const ModelObjectsTemp &mos) |
| Return all the output particles for a given ModelObject. More... | |
| ContainersTemp | get_output_containers (const ModelObjectsTemp &mos) |
| Return all the output particles for a given ModelObject. More... | |
Buffer I/O | |
Write/read the state of the particles to/from a buffer in memory.
| |
| Vector< char > | write_particles_to_buffer (const ParticlesTemp &particles, const FloatKeys &keys) |
| return a binary buffer with the data More... | |
| void | read_particles_from_buffer (const Vector< char > &buffer, const ParticlesTemp &particles, const FloatKeys &keys) |
| load found attributes into the particles More... | |
Standard module functions | |
All | |
| std::string | get_module_version () |
| Return the version of this module, as a string. More... | |
| std::string | get_module_name () |
| std::string | get_data_path (std::string file_name) |
| Return the full path to one of this module's data files. More... | |
| std::string | get_example_path (std::string file_name) |
| Return the full path to one of this module's example files. More... | |
Logging | |
Logging is provided by IMP/log.h. People implementing IMP::Object classes should also see IMP_OBJECT_LOG() and IMP::SetLogState. All logging is disabled when | |
| void | add_to_log (LogLevel level, std::string to_write) |
| Write a string to the log, for Python. More... | |
| void | set_log_level (LogLevel l) |
| Set the current global log level. More... | |
| void | set_log_timer (bool tb) |
| Set whether log messages are tagged with the current log time. More... | |
| void | reset_log_timer () |
| Reset the log timer. More... | |
| LogLevel | get_log_level () |
| Get the currently active global log level. More... | |
Create a progress bar in the terminal | |
| void | set_progress_display (std::string description, unsigned int steps) |
| Set up the progress bar with the passed description. More... | |
| void | add_to_progress_display (unsigned int step=1) |
| Set the current progress. More... | |
Python Only | |
| void | show_altgraph (Graph g) |
| networkx::DiGraph | get_networkx_graph (Graph g) |
| std::string | show_graphviz (Graph g) |
Gathering restraints | |
It is sometimes useful to extract all the non-RestraintSet restraints from a hierarchy involving RestraintSets mixed with Restraints. | |
| RestraintsTemp | get_restraints (const RestraintsTemp &rs) |
| template<class It > | |
| RestraintsTemp | get_restraints (It b, It e) |
Number of threads | |
| unsigned int | get_number_of_threads () |
| void | set_number_of_threads (unsigned int n) |
A vector of reference-counting object pointers.
Definition at line 112 of file AttributeOptimizer.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 112 of file AttributeOptimizer.h.
| typedef IMP::Vector<IMP::Pointer< Configuration > > IMP::Configurations |
A vector of reference-counting object pointers.
Definition at line 49 of file Configuration.h.
| typedef IMP::Vector<IMP::Pointer< ConfigurationSet > > IMP::ConfigurationSets |
A vector of reference-counting object pointers.
Definition at line 46 of file ConfigurationSet.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 46 of file ConfigurationSet.h.
| typedef IMP::Vector<IMP::WeakPointer< Configuration > > IMP::ConfigurationsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 49 of file Configuration.h.
| typedef IMP::Vector<IMP::Pointer< Constraint > > IMP::Constraints |
A vector of reference-counting object pointers.
Definition at line 63 of file Constraint.h.
| typedef IMP::Vector<IMP::WeakPointer< Constraint > > IMP::ConstraintsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 63 of file Constraint.h.
| typedef IMP::Vector<IMP::Pointer< Container > > IMP::Containers |
A vector of reference-counting object pointers.
Definition at line 117 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< Container > > IMP::ContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 118 of file base_types.h.
| typedef boost::graph IMP::DependencyGraph |
Directed graph on the interactions between the various objects in the model.
The vertices are named by the associated Object*. There is an edge from a to b, if a is an input to b. For example, there is an edge from a particle to a restraint if the restraint directly reads the particle.
See Dependencies for more information about dependencies.See Graphs in IMP for more information.
Definition at line 35 of file dependency_graph.h.
Pass or store a set of DerivativeAccumulator .
Definition at line 48 of file DerivativeAccumulator.h.
| typedef std::pair<double, double> IMP::DerivativePair |
| typedef IMP::Vector< DerivativePair > IMP::DerivativePairs |
| typedef IMP::Vector< DerivativePairs > IMP::DerivativePairss |
| typedef IMP::Vector< EvaluationState > IMP::EvaluationStates |
Pass or store a set of EvaluationState .
Definition at line 43 of file ScoreAccumulator.h.
| typedef double IMP::Float |
| typedef IMP::Vector< FloatIndex > IMP::FloatIndexes |
Pass or store a set of FloatIndex .
Definition at line 21 of file FloatIndex.h.
| typedef Key<0> IMP::FloatKey |
The type used to identify float attributes in the Particles.
Definition at line 32 of file base_types.h.
| typedef IMP::Vector< FloatKey > IMP::FloatKeys |
Pass or store a set of FloatKey .
Definition at line 33 of file base_types.h.
| typedef std::pair<double, double> IMP::FloatPair |
| typedef IMP::Vector< FloatPair > IMP::FloatPairs |
| typedef IMP::Vector< FloatPairs > IMP::FloatPairss |
| typedef std::pair<Float, Float> IMP::FloatRange |
| typedef IMP::Vector< FloatRange > IMP::FloatRanges |
| typedef IMP::Vector< FloatRanges > IMP::FloatRangess |
| typedef IMP::Vector< Float > IMP::Floats |
| typedef Key<10> IMP::FloatsKey |
The type used to identify float vector attributes in the Particles.
Definition at line 60 of file base_types.h.
| typedef IMP::Vector< FloatsKey > IMP::FloatsKeys |
Pass or store a set of FloatsKey .
Definition at line 61 of file base_types.h.
| typedef IMP::Vector< Floats > IMP::FloatsList |
| typedef IMP::Vector< FloatsList > IMP::FloatsLists |
| typedef IMP::Vector< Floats > IMP::Floatss |
| typedef Key<1> IMP::IntKey |
The type used to identify int attributes in the Particles.
Definition at line 36 of file base_types.h.
| typedef IMP::Vector< IntKey > IMP::IntKeys |
Pass or store a set of IntKey .
Definition at line 37 of file base_types.h.
| typedef IMP::Vector< IntPair > IMP::IntPairs |
| typedef IMP::Vector< IntPairs > IMP::IntPairss |
| typedef IMP::Vector< IntRange > IMP::IntRanges |
| typedef IMP::Vector< IntRanges > IMP::IntRangess |
| typedef IMP::Vector< Int > IMP::Ints |
| typedef Key<5> IMP::IntsKey |
The type used to identify int attributes in the Particles.
Definition at line 56 of file base_types.h.
| typedef IMP::Vector< IntsKey > IMP::IntsKeys |
Pass or store a set of IntsKey .
Definition at line 57 of file base_types.h.
| typedef IMP::Vector< Ints > IMP::IntsList |
| typedef IMP::Vector< IntsList > IMP::IntsLists |
| typedef IMP::Vector< Ints > IMP::Intss |
| typedef Key<8> IMP::ModelKey |
The type used to identify data stored directly in the model.
Definition at line 78 of file base_types.h.
| typedef IMP::Vector< ModelKey > IMP::ModelKeys |
Pass or store a set of ModelKey .
Definition at line 79 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< ModelObject > > IMP::ModelObjects |
A vector of reference-counting object pointers.
Definition at line 105 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< ModelObject > > IMP::ModelObjectsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 106 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< Model > > IMP::Models |
A vector of reference-counting object pointers.
Definition at line 109 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< Model > > IMP::ModelsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 110 of file base_types.h.
| typedef Key<4> IMP::ObjectKey |
The type used to identify an Object attribute.
Definition at line 48 of file base_types.h.
| typedef IMP::Vector< ObjectKey > IMP::ObjectKeys |
Pass or store a set of ObjectKey .
Definition at line 49 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< Object > > IMP::Objects |
| typedef Key<7> IMP::ObjectsKey |
The type used to identify a particle attribute in the Particles.
Definition at line 74 of file base_types.h.
| typedef IMP::Vector< ObjectsKey > IMP::ObjectsKeys |
Pass or store a set of ObjectsKey .
Definition at line 75 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< Object > > IMP::ObjectsTemp |
| typedef IMP::Vector<IMP::Pointer< Optimizer > > IMP::Optimizers |
A vector of reference-counting object pointers.
Definition at line 145 of file Optimizer.h.
| typedef IMP::Vector<IMP::Pointer< OptimizerState > > IMP::OptimizerStates |
A vector of reference-counting object pointers.
Definition at line 123 of file base_types.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 124 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< Optimizer > > IMP::OptimizersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 145 of file Optimizer.h.
| typedef IMP::Vector<IMP::Pointer< PairContainer > > IMP::PairContainers |
A vector of reference-counting object pointers.
Definition at line 127 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< PairContainer > > IMP::PairContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 128 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< PairModifier > > IMP::PairModifiers |
A vector of reference-counting object pointers.
Definition at line 154 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< PairModifier > > IMP::PairModifiersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 155 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< PairPredicate > > IMP::PairPredicates |
A vector of reference-counting object pointers.
Definition at line 145 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< PairPredicate > > IMP::PairPredicatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 146 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< PairScore > > IMP::PairScores |
A vector of reference-counting object pointers.
Definition at line 136 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< PairScore > > IMP::PairScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 137 of file base_types.h.
| typedef Index<ParticleIndexTag> IMP::ParticleIndex |
A unique identifier for a particle within a Model. Use it to identify particles when getting and setting attributes and constructing decorators.
See for example, Model attributes, Decorator, and Model::get_particle().
Definition at line 178 of file base_types.h.
| typedef Key<6> IMP::ParticleIndexesKey |
The type used to identify a particle attribute in the Particles.
Definition at line 64 of file base_types.h.
Pass or store a set of ParticleIndexesKey .
Definition at line 65 of file base_types.h.
| typedef Key<3> IMP::ParticleIndexKey |
The type used to identify a particle attribute in the Particles.
Definition at line 44 of file base_types.h.
| typedef IMP::Vector< ParticleIndexKey > IMP::ParticleIndexKeys |
Pass or store a set of ParticleIndexKey .
Definition at line 45 of file base_types.h.
| typedef IMP::Vector< ParticleIndexPair > IMP::ParticleIndexPairs |
Pass or store a set of ParticleIndexPair .
Definition at line 185 of file base_types.h.
| typedef IMP::Vector< ParticleIndexQuad > IMP::ParticleIndexQuads |
Pass or store a set of ParticleIndexQuad .
Definition at line 187 of file base_types.h.
Pass or store a set of ParticleIndexTriplet .
Definition at line 186 of file base_types.h.
| typedef Array<2, WeakPointer<Particle>, Particle*> IMP::ParticlePair |
An ordered pair of particles.
Definition at line 159 of file base_types.h.
| typedef IMP::Vector< ParticlePair > IMP::ParticlePairsTemp |
Pass or store a set of ParticlePair .
Definition at line 163 of file base_types.h.
| typedef Array<4, WeakPointer<Particle>, Particle*> IMP::ParticleQuad |
An ordered quad of particles.
Definition at line 168 of file base_types.h.
| typedef IMP::Vector< ParticleQuad > IMP::ParticleQuadsTemp |
Pass or store a set of ParticleQuad .
Definition at line 169 of file base_types.h.
| typedef Array<3, WeakPointer<Particle>, Particle*> IMP::ParticleTriplet |
An ordered triplet of particles.
Definition at line 165 of file base_types.h.
| typedef IMP::Vector< ParticleTriplet > IMP::ParticleTripletsTemp |
Pass or store a set of ParticleTriplet .
Definition at line 166 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< QuadContainer > > IMP::QuadContainers |
A vector of reference-counting object pointers.
Definition at line 131 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< QuadContainer > > IMP::QuadContainersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 132 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< QuadModifier > > IMP::QuadModifiers |
A vector of reference-counting object pointers.
Definition at line 158 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< QuadModifier > > IMP::QuadModifiersTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 159 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< QuadPredicate > > IMP::QuadPredicates |
A vector of reference-counting object pointers.
Definition at line 149 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< QuadPredicate > > IMP::QuadPredicatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 150 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< QuadScore > > IMP::QuadScores |
A vector of reference-counting object pointers.
Definition at line 140 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< QuadScore > > IMP::QuadScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 141 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< Refiner > > IMP::Refiners |
| typedef IMP::Vector<IMP::WeakPointer< Refiner > > IMP::RefinersTemp |
| typedef IMP::Vector<IMP::Pointer< Restraint > > IMP::Restraints |
A vector of reference-counting object pointers.
Definition at line 103 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< RestraintSet > > IMP::RestraintSets |
A vector of reference-counting object pointers.
Definition at line 111 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< RestraintSet > > IMP::RestraintSetsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 112 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< Restraint > > IMP::RestraintsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 104 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< Sampler > > IMP::Samplers |
| typedef IMP::Vector<IMP::WeakPointer< Sampler > > IMP::SamplersTemp |
| typedef IMP::Vector< ScoreAccumulator > IMP::ScoreAccumulators |
Pass or store a set of ScoreAccumulator .
Definition at line 144 of file ScoreAccumulator.h.
| typedef IMP::Vector<IMP::Pointer< ScoreState > > IMP::ScoreStates |
A vector of reference-counting object pointers.
Definition at line 113 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< ScoreState > > IMP::ScoreStatesTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 114 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< ScoringFunction > > IMP::ScoringFunctions |
A vector of reference-counting object pointers.
Definition at line 115 of file base_types.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 116 of file base_types.h.
| typedef IMP::Vector< SetCheckState > IMP::SetCheckStates |
Pass or store a set of SetCheckState .
Definition at line 53 of file SetCheckState.h.
| typedef IMP::Vector< SetLogState > IMP::SetLogStates |
Pass or store a set of SetLogState .
Definition at line 49 of file SetLogState.h.
A vector of reference-counting object pointers.
Definition at line 125 of file base_types.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 126 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< SingletonModifier > > IMP::SingletonModifiers |
A vector of reference-counting object pointers.
Definition at line 152 of file base_types.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 153 of file base_types.h.
A vector of reference-counting object pointers.
Definition at line 143 of file base_types.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 144 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< SingletonScore > > IMP::SingletonScores |
A vector of reference-counting object pointers.
Definition at line 134 of file base_types.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 135 of file base_types.h.
| typedef Key<14> IMP::SparseFloatKey |
The type used to identify sparse float attributes in the Particles.
Definition at line 94 of file base_types.h.
| typedef IMP::Vector< SparseFloatKey > IMP::SparseFloatKeys |
Pass or store a set of SparseFloatKey .
Definition at line 95 of file base_types.h.
| typedef Key<13> IMP::SparseIntKey |
The type used to identify sparse int attributes in the Particles.
Definition at line 90 of file base_types.h.
| typedef IMP::Vector< SparseIntKey > IMP::SparseIntKeys |
Pass or store a set of SparseIntKey .
Definition at line 91 of file base_types.h.
| typedef Key<15> IMP::SparseParticleIndexKey |
The type used to identify sparse particle attributes in the Particles.
Definition at line 98 of file base_types.h.
Pass or store a set of SparseParticleIndexKey .
Definition at line 99 of file base_types.h.
| typedef Key<12> IMP::SparseStringKey |
The type used to identify sparse string attributes in the Particles.
Definition at line 86 of file base_types.h.
| typedef IMP::Vector< SparseStringKey > IMP::SparseStringKeys |
Pass or store a set of SparseStringKey .
Definition at line 87 of file base_types.h.
| typedef std::string IMP::String |
| typedef Key<2> IMP::StringKey |
The type used to identify string attributes in the Particles.
Definition at line 40 of file base_types.h.
| typedef IMP::Vector< StringKey > IMP::StringKeys |
Pass or store a set of StringKey .
Definition at line 41 of file base_types.h.
| typedef IMP::Vector< String > IMP::Strings |
| typedef IMP::Vector< Strings > IMP::StringsList |
| typedef IMP::Vector< StringsList > IMP::StringsLists |
| typedef IMP::Vector< Strings > IMP::Stringss |
| typedef IMP::Vector< TextInput > IMP::TextInputs |
| typedef IMP::Vector< TextOutput > IMP::TextOutputs |
Pass or store a set of TextOutput .
| typedef Key<11> IMP::TriggerKey |
The type used to identify changed model properties.
Definition at line 82 of file base_types.h.
| typedef IMP::Vector< TriggerKey > IMP::TriggerKeys |
Pass or store a set of TriggerKey .
Definition at line 83 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< TripletContainer > > IMP::TripletContainers |
A vector of reference-counting object pointers.
Definition at line 129 of file base_types.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 130 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< TripletModifier > > IMP::TripletModifiers |
A vector of reference-counting object pointers.
Definition at line 156 of file base_types.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 157 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< TripletPredicate > > IMP::TripletPredicates |
A vector of reference-counting object pointers.
Definition at line 147 of file base_types.h.
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 148 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< TripletScore > > IMP::TripletScores |
A vector of reference-counting object pointers.
Definition at line 138 of file base_types.h.
| typedef IMP::Vector<IMP::WeakPointer< TripletScore > > IMP::TripletScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 139 of file base_types.h.
| typedef IMP::Vector<IMP::Pointer< UnaryFunction > > IMP::UnaryFunctions |
A vector of reference-counting object pointers.
Definition at line 65 of file UnaryFunction.h.
| typedef IMP::Vector<IMP::WeakPointer< UnaryFunction > > IMP::UnaryFunctionsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 65 of file UnaryFunction.h.
| typedef IMP::Vector<IMP::Pointer< Undecorator > > IMP::Undecorators |
A vector of reference-counting object pointers.
Definition at line 33 of file Undecorator.h.
| typedef IMP::Vector<IMP::WeakPointer< Undecorator > > IMP::UndecoratorsTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 33 of file Undecorator.h.
| typedef IMP::Vector< VersionInfo > IMP::VersionInfos |
Pass or store a set of VersionInfo .
Definition at line 54 of file VersionInfo.h.
| typedef Key<9> IMP::WeakObjectKey |
The type used to identify a non-ref counted Object attribute.
Definition at line 52 of file base_types.h.
| typedef IMP::Vector< WeakObjectKey > IMP::WeakObjectKeys |
Pass or store a set of WeakObjectKey .
Definition at line 53 of file base_types.h.
| enum IMP::CheckLevel |
Specify the level of runtime checks performed.
| Enumerator | |
|---|---|
| DEFAULT_CHECK |
Use the default check level (eg IMP::Object::set_check_level()). |
| NONE |
Perform no runtime checks. |
| USAGE |
Perform checks that |
| USAGE_AND_INTERNAL |
Check internal |
| enum IMP::LogLevel |
The log levels supported by IMP.
| Enumerator | |
|---|---|
| DEFAULT |
Use to specify that the global log level should be used (eg in IMP::Object::set_log_level()) |
| SILENT |
Do not output any text. |
| WARNING |
Output only warnings. |
| PROGRESS |
Output only progress meter style displays and occasional printouts when switching phases of work. |
| TERSE |
Output a line or two per evaluation call. |
| VERBOSE |
Produce copious output to allow someone to trace through the computation. |
| MEMORY |
Log memory allocations and frees. |
| void IMP::add_bool_flag | ( | std::string | name, |
| std::string | description | ||
| ) |
For Python use. Default is always false.
| void IMP::add_float_flag | ( | std::string | name, |
| double | default_value, | ||
| std::string | description | ||
| ) |
For Python use.
| void IMP::add_int_flag | ( | std::string | name, |
| size_t | default_value, | ||
| std::string | description | ||
| ) |
For Python use.
| void IMP::add_string_flag | ( | std::string | name, |
| std::string | default_value, | ||
| std::string | description | ||
| ) |
For Python use.
| void IMP::add_to_log | ( | LogLevel | level, |
| std::string | to_write | ||
| ) |
Write a string to the log, for Python.
| void IMP::add_to_progress_display | ( | unsigned int | step = 1 | ) |
Set the current progress.
When it equals the number of steps, the bar is done.
| def IMP.allow_deprecated | ( | allow = True | ) |
Context manager to temporarily allow (or disallow) deprecated code.
Definition at line 9562 of file __init__.py.
| Constraint* IMP::create_constraint | ( | Before * | b, |
| After * | a, | ||
| const typename Before::Argument & | t, | ||
| std::string | name = std::string() |
||
| ) |
| ScoringFunctions IMP::create_decomposition | ( | ScoringFunction * | sf | ) |
Return a list of ScoringFunction objects where each is as simple as possible and evaluating the sum (and anding the good score bits) is exactly like evaluating the one ScoringFunction.
| Restraints IMP::create_decomposition | ( | const RestraintsTemp & | rs | ) |
Return the decomposition of a list of restraints.
| Restraint* IMP::create_restraint | ( | Score * | s, |
| const typename Score::Argument & | t, | ||
| std::string | name = std::string() |
||
| ) |
| ScoringFunction* IMP::create_scoring_function | ( | RestraintType * | rs, |
| double | weight = 1.0, |
||
| double | max = NO_MAX, |
||
| std::string | name = std::string() |
||
| ) |
Create a ScoringFunction on a single restraint.
This can be faster than using a RestraintsScoringFunction.
| TextOutput IMP::create_temporary_file | ( | std::string | prefix = "imp_temp", |
| std::string | suffix = "" |
||
| ) |
Create a temporary file. The path can be extracted from the TextOutput.
If suffix is non-empty, there is some small chance of a collision on non-BSD systems as a unique temporary file is first created, and then a file with that suffix appended is created.
| std::string IMP::create_temporary_file_name | ( | std::string | prefix = "imp_temp", |
| std::string | suffix = "" |
||
| ) |
Create a temporary file.
If suffix is non-empty, there is some small chance of a collision on non-BSD systems as a unique temporary file is first created, and then a file with that suffix appended is created.
| def IMP.deprecated_function | ( | version, | |
| help_message | |||
| ) |
Python decorator to mark a function as deprecated.
Definition at line 9550 of file __init__.py.
| def IMP.deprecated_method | ( | version, | |
| help_message | |||
| ) |
Python decorator to mark a method as deprecated.
Definition at line 9538 of file __init__.py.
| def IMP.deprecated_module | ( | version, | |
| module, | |||
| help_message | |||
| ) |
Mark a Python module as deprecated.
module argument would normally be __name__. Definition at line 9515 of file __init__.py.
| def IMP.deprecated_object | ( | version, | |
| help_message | |||
| ) |
Python decorator to mark a class as deprecated.
Definition at line 9522 of file __init__.py.
| std::string IMP::get_absolute_path | ( | std::string | file | ) |
Convert a possibly relative path to an absolute path.
If the provided path is a relative path, add the current working directory to make it an absolute path.
| bool IMP::get_bool_flag | ( | std::string | name | ) |
For Python use.
| CheckLevel IMP::get_check_level | ( | ) |
Get the current audit mode.
Definition at line 80 of file exception.h.
| std::string IMP::get_copyright | ( | ) |
Get the IMP copyright notice.
| std::string IMP::get_data_path | ( | std::string | file_name | ) |
Return the full path to one of this module's data files.
To read the data file "data_library" that was placed in the data directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.
| DependencyGraph IMP::get_dependency_graph | ( | Model * | m | ) |
The dependency graph captures the interactions between Restraint, ScoreState and Particle objects. The graph has a directed edge if the source of the edge is an input for the target of the edge or the target of the edge is an output for the source. eg, there is an edge connecting a Container to the Restraint which gets its particles from the Container.
| bool IMP::get_deprecation_exceptions | ( | ) |
Get whether an exception is thrown when a deprecated method is used.
| std::string IMP::get_example_path | ( | std::string | file_name | ) |
Return the full path to one of this module's example files.
To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.
| std::string IMP::get_executable_name | ( | ) |
Return the name of the current executable.
| double IMP::get_float_flag | ( | std::string | name | ) |
For Python use.
| ParticleIndexes IMP::get_indexes | ( | const ParticlesTemp & | ps | ) |
Get the indexes from a list of particles.
| ParticleIndexPairs IMP::get_indexes | ( | const ParticlePairsTemp & | ps | ) |
Get the indexes from a list of particle pairs.
| ContainersTemp IMP::get_input_containers | ( | const ModelObjectsTemp & | mos | ) |
Return all the input particles for a given ModelObject.
| ParticlesTemp IMP::get_input_particles | ( | const ModelObjectsTemp & | mos | ) |
Return all the input particles for a given ModelObject.
| size_t IMP::get_int_flag | ( | std::string | name | ) |
For Python use.
| bool IMP::get_is_quick_test | ( | ) |
| Strings IMP::get_live_object_names | ( | ) |
Return the names of all live objects.
Use this to check for memory leaks.
| Objects IMP::get_live_objects | ( | ) |
Return pointers to all live objects.
Use this to check for memory leaks.
| LogLevel IMP::get_log_level | ( | ) |
Get the currently active global log level.
| std::string IMP::get_module_version | ( | ) |
Return the version of this module, as a string.
Definition at line 5 of file EMageFit/__init__.py.
| networkx::DiGraph IMP::get_networkx_graph | ( | Graph | g | ) |
Export an IMP graph to a networkx graph. The resulting graph can be analyzed and displayed, although the graph layout algorithms in networkx seem to be quite poor compared to graphviz.
On a Mac, such graphs can be displayed by
| unsigned int IMP::get_number_of_threads | ( | ) |
Get the current number of threads requested. The default is the number of cores/hardware threads in the machine if there is OpenMP support, or 1 otherwise.
| ContainersTemp IMP::get_output_containers | ( | const ModelObjectsTemp & | mos | ) |
Return all the output particles for a given ModelObject.
| ParticlesTemp IMP::get_output_particles | ( | const ModelObjectsTemp & | mos | ) |
Return all the output particles for a given ModelObject.
| ParticlesTemp IMP::get_particles | ( | Model * | m, |
| const ParticleIndexes & | ps | ||
| ) |
Get the particles from a list of indexes.
| DependencyGraph IMP::get_pruned_dependency_graph | ( | Model * | m | ) |
The pruned dependency graph merges all particles which have the same dependencies to produce a simpler graph.
| double IMP::get_random_double_uniform | ( | ) |
Return a uniformly distributed double number in range [0..1)
Definition at line 173 of file random_utils.h.
Here is the call graph for this function:| double IMP::get_random_double_uniform | ( | double | min, |
| double | max | ||
| ) |
Return a uniformly distributed double number in range [min..max)
Definition at line 194 of file random_utils.h.
| float IMP::get_random_float_uniform | ( | ) |
Return a uniformly distributed float number in range [0..1)
Definition at line 138 of file random_utils.h.
Here is the call graph for this function:| float IMP::get_random_float_uniform | ( | float | min, |
| float | max | ||
| ) |
Return a uniformly distributed float number in range [min..max)
Definition at line 160 of file random_utils.h.
| void IMP::get_random_numbers_normal | ( | Vector< RealType > & | v, |
| unsigned int | n, | ||
| RealType | mean = 0.0, |
||
| RealType | stddev = 1.0 |
||
| ) |
Fill the double array with random normally distributed values.
The pre-allocated array is filled with n double numbers with random normally distributed values with specified mean and standard deviation.
| v | vector array that will be resized to n |
| n | size of array |
| mean | mean of normal distribution |
| stddev | standard deviation |
Definition at line 48 of file random_utils.h.
| void IMP::get_random_numbers_uniform | ( | Vector< RealType > & | v, |
| unsigned int | n | ||
| ) |
Fill the float array with random uniformly distributed values.
Fill a pre-allocated array of n float numbers with random uniformly distributed values in the [0..1) range.
| v | vector array that will be resized to n |
| n | size of array |
Definition at line 90 of file random_utils.h.
| boost::uint64_t IMP::get_random_seed | ( | ) |
Return the initial random seed.
To set the seed or get random values, see IMP::random_number_generator.
| std::string IMP::get_relative_path | ( | std::string | base, |
| std::string | relative | ||
| ) |
Return a path to a file relative to another file.
For example if base is path/to/config.file and relative is data/image0.jpg then the return value would be path/to/data/image0.jpg. This function should be used when processing configuration files so that the meaning of the configuration file does not change if current working directory changes.
| ScoreStatesTemp IMP::get_required_score_states | ( | const ModelObjectsTemp & | mos, |
| ScoreStatesTemp | exclude = ScoreStatesTemp() |
||
| ) |
Compute the set of score states required by the passed ModelObjects.
This will compute dependencies if needed.
| std::string IMP::get_string_flag | ( | std::string | name | ) |
For Python use.
| std::string IMP::get_unique_name | ( | std::string | templ | ) |
Return a unique name produced from the string.
This is done by replacing %1% with a sequential number.
| ScoreStatesTemp IMP::get_update_order | ( | ScoreStatesTemp | input | ) |
Return an appropriate (topologically sorted) order to update the score states in.
| ScoreStatesTemp IMP::get_update_order | ( | std::set< ScoreState * > | input | ) |
Return an appropriate (topologically sorted) order to update the score states in.
| const algebra::Vector3D& IMP::get_vector_geometry | ( | Particle * | p | ) |
See generic geometry for more information.
Definition at line 147 of file XYZ.h.
Here is the call graph for this function:| void IMP::handle_error | ( | const char * | msg | ) |
This function is called whenever IMP detects an error. It can be useful to add a breakpoint in the function when using a debugger.
| void IMP::handle_use_deprecated | ( | std::string | message | ) |
Break in this method in gdb to find deprecated uses at runtime.
| bool IMP::isinf | ( | const T & | a | ) |
| bool IMP::isnan | ( | const T & | a | ) |
| internal::PredicateEquals<Pred, true> IMP::make_predicate_equal | ( | const Pred * | p, |
| Model * | m, | ||
| int | value | ||
| ) |
| internal::PredicateEquals<Pred, false> IMP::make_predicate_not_equal | ( | const Pred * | p, |
| Model * | m, | ||
| int | value | ||
| ) |
| O* IMP::object_cast | ( | Object * | o | ) |
Up (or down) cast an IMP Object-derived class.
If the cast does not succeed a ValueException will be thrown. Use a dynamic_cast if you prefer to have a nullptr returned.
Definition at line 23 of file object_cast.h.
| void IMP::read_particles_from_buffer | ( | const Vector< char > & | buffer, |
| const ParticlesTemp & | particles, | ||
| const FloatKeys & | keys | ||
| ) |
load found attributes into the particles
| void IMP::reset_log_timer | ( | ) |
Reset the log timer.
| void IMP::set_check_level | ( | CheckLevel | tf | ) |
Control runtime checks in the code.
The default level of checks is USAGE for release builds and USAGE_AND_INTERNAL for debug builds.
Definition at line 72 of file exception.h.
| void IMP::set_deprecation_exceptions | ( | bool | tf | ) |
Toggle whether an exception is thrown when a deprecated method is used.
| void IMP::set_deprecation_warnings | ( | bool | tf | ) |
Toggle printing of warnings on using deprecated classes.
If set to true (the default) a warning is printed every time a class marked as deprecated is used.
| void IMP::set_log_level | ( | LogLevel | l | ) |
Set the current global log level.
| void IMP::set_log_target | ( | TextOutput | l | ) |
Set the target for the log.
See TextOutput for options. Python users should use SetLogTarget instead.
| void IMP::set_log_timer | ( | bool | tb | ) |
Set whether log messages are tagged with the current log time.
| void IMP::set_number_of_threads | ( | unsigned int | n | ) |
Set the current number of threads to a number greater or equal to 1. Setting it to 1 disables multithreaded evaluation.
| void IMP::set_progress_display | ( | std::string | description, |
| unsigned int | steps | ||
| ) |
Set up the progress bar with the passed description.
| void IMP::set_show_leaked_objects | ( | bool | tf | ) |
Set whether to complain about objects not being properly cleaned up.
| void IMP::set_vector_geometry | ( | Particle * | p, |
| const algebra::Vector3D & | v | ||
| ) |
See generic geometry for more information.
Definition at line 151 of file XYZ.h.
Here is the call graph for this function:| void IMP::set_vector_geometry | ( | Decorator | d, |
| const algebra::Vector3D & | v | ||
| ) |
See generic geometry for more information.
Definition at line 159 of file XYZ.h.
Here is the call graph for this function:| void IMP::set_vector_geometry | ( | WeakPointer< Particle > | d, |
| const algebra::Vector3D & | v | ||
| ) |
See generic geometry for more information.
Definition at line 168 of file XYZ.h.
Here is the call graph for this function:| void IMP::set_vector_geometry | ( | Pointer< Particle > | d, |
| const algebra::Vector3D & | v | ||
| ) |
See generic geometry for more information.
Definition at line 177 of file XYZ.h.
Here is the call graph for this function:| void IMP::setup_from_argv | ( | int | argc, |
| char ** | argv, | ||
| std::string | description | ||
| ) |
Parse the command line flags and return the positional arguments.
| [in] | argc | argc |
| [in] | argv | argv |
| [in] | description | A message describing what the program does. |
| UsageException | if a problem with the command line was found. |
| Strings IMP::setup_from_argv | ( | int | argc, |
| char ** | argv, | ||
| std::string | description, | ||
| std::string | positional_description, | ||
| int | num_positional | ||
| ) |
Parse the command line flags and return the positional arguments.
| [in] | argc | argc |
| [in] | argv | argv |
| [in] | description | A message describing what the program does. |
| [in] | positional_description | A message describing the the positional arguments |
| [in] | num_positional | A positive integer to require that many positional arguments, or a negative integer to require at least that many. |
| UsageException | if a problem with the command line was found. |
| void IMP::setup_from_argv | ( | const Strings & | argv, |
| std::string | description | ||
| ) |
Parse the command line flags and return the positional arguments. For Python.
| [in] | argv | sys.argv |
| [in] | description | A message describing what the program does. |
| UsageException | if a problem with the command line was found. |
| Strings IMP::setup_from_argv | ( | const Strings & | argv, |
| std::string | description, | ||
| std::string | positional_description, | ||
| int | num_positional | ||
| ) |
Parse the command line flags and return the positional arguments. For Python.
| [in] | argv | sys.argv |
| [in] | description | A message describing what the program does. |
| [in] | positional_description | A message describing the positional arguments, eg "input.pdb output.pdb" |
| [in] | num_positional | A positive integer to require that many positional arguments, or a negative integer to require at least that many. |
| UsageException | if a problem with the command line was found. |
| Strings IMP::setup_from_argv_allowing_unknown | ( | int | argc, |
| char ** | argv, | ||
| std::string | description | ||
| ) |
Parse the command line flags and return the positional arguments returning unknown flags in a list. Use this version if some arguments are to be parsed by a different system.
| [in] | argc | argc |
| [in] | argv | argv |
| [in] | description | A message describing what the program does. |
| UsageException | if a problem with the command line was found. |
| void IMP::show_altgraph | ( | Graph | g | ) |
Use the Python altgraph package to graphically display a graph. Note that is requires X11 to be running (you can find it in your Utilities folder in MacOS) and the window produced is shockingly retro.
An alternative is to write the graph to a dot file
then turn it to pdf with dot
and finally view the pdf.
| std::string IMP::show_graphviz | ( | Graph | g | ) |
Generate a nice pdf of the graph and attempt to open the pdf. The name of the pdf will be returned in case the attempt to open it fails.
| void IMP::show_restraint_hierarchy | ( | ScoringFunctionAdaptor | rs, |
| std::ostream & | out = std::cout |
||
| ) |
Print the hierarchy of restraints.
The maximum accepted score (Restraint::get_maximum_score()) and the weight (Restraint::get_weight()) are printed for each restraint.
| void IMP::write_help | ( | std::ostream & | out = std::cerr | ) |
Prints out the help message, useful if you have extra error checking and the flags don't pass it.
| Vector<char> IMP::write_particles_to_buffer | ( | const ParticlesTemp & | particles, |
| const FloatKeys & | keys | ||
| ) |
return a binary buffer with the data
| const double IMP::BAD_SCORE |
Evaluation can return this value if limits are exceeded and it is a ScoringFunction::evaluate_if_below() or ScoringFunction::evaluate_if_good
| const double IMP::NO_MAX |
Use this value when you want to turn off maximum for restraint evaluation.
| RandomNumberGenerator IMP::random_number_generator |
A shared non-GPU random number generator.
The random number generator is seeded based on command line specified flag. Otherwise, the default seed is retrieved from among either boost::random_device, /dev/urandom, or the system clock, based on which method is available in this priority order.
To set the seed, call the seed method, which takes a single integer argument. This object is also callable, and returns a new random integer on each call.
This generator can be used by the Boost.Random distributions.