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IMP Reference Guide  develop.63b38c487d,2024/12/21
The Integrative Modeling Platform
version 20241221.develop.63b38c487d
npctransport.h
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1 /**
2  * \file IMP/npctransport.h
3  * \brief Include all non-deprecated headers in IMP.npctransport.
4  *
5  * Copyright 2007-2024 IMP Inventors. All rights reserved.
6  */
7 
8 #ifndef IMP_NPCTRANSPORT_H
9 #define IMP_NPCTRANSPORT_H
10 #include <IMP/npctransport/AnchorToCylindricalPorePairScore.h>
11 #include <IMP/npctransport/Avro2PBReader.h>
12 #include <IMP/npctransport/AvroDataFileData.h>
13 #include <IMP/npctransport/BipartitePairsStatisticsOptimizerState.h>
14 #include <IMP/npctransport/BodyStatisticsOptimizerState.h>
15 #include <IMP/npctransport/BrownianDynamicsTAMDWithSlabSupport.h>
16 #include <IMP/npctransport/ChainStatisticsOptimizerState.h>
17 #include <IMP/npctransport/ExcludeZRangeSingletonScore.h>
18 #include <IMP/npctransport/FGChain.h>
19 #include <IMP/npctransport/GlobalStatisticsOptimizerState.h>
20 #include <IMP/npctransport/HarmonicSpringSingletonScore.h>
21 #include <IMP/npctransport/Parameter.h>
22 #include <IMP/npctransport/ParticleFactory.h>
23 #include <IMP/npctransport/ParticleTransportStatisticsOptimizerState.h>
24 #include <IMP/npctransport/PoreRadiusSingletonScore.h>
25 #include <IMP/npctransport/RelaxingSpring.h>
26 #include <IMP/npctransport/Scoring.h>
27 #include <IMP/npctransport/SimulationData.h>
28 #include <IMP/npctransport/SitesGeometry.h>
29 #include <IMP/npctransport/SitesPairScore.h>
30 #include <IMP/npctransport/SitesPairScoreParameters.h>
31 #include <IMP/npctransport/SlabWithCylindricalPore.h>
32 #include <IMP/npctransport/SlabWithCylindricalPoreGeometry.h>
33 #include <IMP/npctransport/SlabWithCylindricalPorePairScore.h>
34 #include <IMP/npctransport/SlabWithPore.h>
35 #include <IMP/npctransport/SlabWithToroidalPore.h>
36 #include <IMP/npctransport/SlabWithToroidalPoreGeometry.h>
37 #include <IMP/npctransport/SlabWithToroidalPorePairScore.h>
38 #include <IMP/npctransport/Statistics.h>
39 #include <IMP/npctransport/Transporting.h>
40 #include <IMP/npctransport/ZBiasSingletonScore.h>
41 #include <IMP/npctransport/automatic_parameters.h>
42 #include <IMP/npctransport/avro.h>
43 #include <IMP/npctransport/enums.h>
44 #include <IMP/npctransport/functor_linear_distance_pair_scores.h>
45 #include <IMP/npctransport/functor_linear_distance_pair_scores_typedefs.h>
46 #include <IMP/npctransport/harmonic_distance_pair_scores.h>
47 #include <IMP/npctransport/initialize_positions.h>
48 #include <IMP/npctransport/io.h>
49 #include <IMP/npctransport/linear_distance_pair_scores.h>
50 #include <IMP/npctransport/main.h>
51 #include <IMP/npctransport/npctransport_proto.fwd.h>
52 #include <IMP/npctransport/protobuf.h>
53 #include <IMP/npctransport/randomize_particles.h>
54 #include <IMP/npctransport/rmf_links.h>
55 #include <IMP/npctransport/typedefs.h>
56 #include <IMP/npctransport/util.h>
57 #endif /* IMP_NPCTRANSPORT_H */
RelaxingSpring.h
a spring between two diffusing particles whose resting length is relaxing towards some equilibrium va...
SlabWithToroidalPorePairScore.h
a score for a slab with a toroidal pore
Transporting.h
A decorator for a transporting particle, so as to keep track of its directionality.
Scoring.h
scoring associated with a SimulationData object
ZBiasSingletonScore.h
score that biases particles to go down the Z axis
enums.h
useful enums and constants
initialize_positions.h
description
BodyStatisticsOptimizerState.h
Track the rotational correlation time of a rigid body particle.
Statistics.h
statistics and order parameters about the simulations that is associated with a SimulationData object...
SitesPairScore.h
A Score on the distance between a pair of particles.
protobuf.h
A Score on the distance between a pair of particles.
rmf_links.h
description
FGChain.h
creating TAMD chains
main.h
Helper functions for executable .cpp files.
Avro2PBReader.h
an iterator that reads npctransport protobuf output files one by one from a list of avro files (used ...
PoreRadiusSingletonScore.h
a score on the pore radius equilibrium value of a slab particle
Parameter.h
description
functor_linear_distance_pair_scores.h
A Score on the distance between a pair of particles.
SlabWithCylindricalPore.h
A decorator for a particle that's a slab with a cylindrical pore.
SlabWithPore.h
A decorator for a particle that's a slab with a cylindrical pore.
util.h
utility methods for npctransport
automatic_parameters.h
description
ParticleFactory.h
description
SitesGeometry.h
Geometry of sites on particle surfaces.
SimulationData.h
description
functor_linear_distance_pair_scores_typedefs.h
Typedefs for the functor scores on the distance between a pair of particles.
harmonic_distance_pair_scores.h
Harmonic scores on the distance between a pair of particles.
HarmonicSpringSingletonScore.h
Harmonic scores on the spring between a pair of particles. The spring resting length is dynamic Copyr...
typedefs.h
description
BrownianDynamicsTAMDWithSlabSupport.h
Simple molecular dynamics optimizer.
linear_distance_pair_scores.h
A Score on the distance between a pair of particles.
SlabWithToroidalPore.h
A decorator for a particle that's a slab with a toroidal pore.
io.h
description
SitesPairScoreParameters.h
A summary of useful information about rigid bodies and their transformation for eg, caching purposes for SitesPairScore.
AnchorToCylindricalPorePairScore.h
A chore for anchoring a bead to a pore.
randomize_particles.h
Randomizing particles in a bounding volume.
npctransport_proto.fwd.h
forward declaration of incomplete protobuf files for the main data structures used ...