IMP Reference Guide
2.11.0
The Integrative Modeling Platform
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Files | |
file | alignment.h [code] |
Alignment of structures. | |
file | angle_decorators.h [code] |
Decorators for angles. | |
file | AngleSingletonScore.h [code] |
A score on the deviation of an angle from ideality. | |
file | atom/Atom.h [code] |
Simple atom decorator. | |
file | atom_config.h [code] |
file | atom_macros.h [code] |
Various important macros for implementing decorators. | |
file | BerendsenThermostatOptimizerState.h [code] |
Maintains temperature during molecular dynamics using a Berendsen thermostat. | |
file | bond_decorators.h [code] |
Contains decorators for a bond. | |
file | bond_graph.h [code] |
Represents a graph of the bonds within an atomic structure. | |
file | BondedPairFilter.h [code] |
A fake container for bonds. | |
file | BondEndpointsRefiner.h [code] |
Return the endpoints of a bond. | |
file | BondPairContainer.h [code] |
A fake container for bonds. | |
file | BondSingletonScore.h [code] |
A Score on the distance between a the two particles in a bond. | |
file | BrownianDynamics.h [code] |
Simple Brownian dynamics optimizer. | |
file | BrownianDynamicsTAMD.h [code] |
Simple molecular dynamics optimizer. | |
file | CAAngleRestraint.h [code] |
Angle restraint between three residues in CA-only representation. | |
file | CADihedralRestraint.h [code] |
Dihedral restraint between five residues in CA-only representation. | |
file | CenterOfMass.h [code] |
A decorator for particles with mass. | |
file | Chain.h [code] |
Store the chain ID. | |
file | Charged.h [code] |
A decorator for a point particle that has an electrostatic charge. | |
file | charmm_segment_topology.h [code] |
Classes for handling CHARMM-style topology of segments. | |
file | charmm_topology.h [code] |
Classes for handling CHARMM-style topology. | |
file | CHARMMAtom.h [code] |
A decorator for an atom that has a defined CHARMM type. | |
file | CHARMMParameters.h [code] |
access to CHARMM force field parameters | |
file | CHARMMStereochemistryRestraint.h [code] |
Class to maintain CHARMM stereochemistry. | |
file | atom/constants.h [code] |
Define the elements used in IMP . | |
file | Copy.h [code] |
A decorator for keeping track of copies of a molecule. | |
file | CoulombPairScore.h [code] |
Coulomb (electrostatic) score between a pair of particles. | |
file | CoverBond.h [code] |
Cover a bond with a sphere. | |
file | Diffusion.h [code] |
A decorator for a diffusing particle. | |
file | dihedrals.h [code] |
Helpers to extract dihedral information. | |
file | DihedralSingletonScore.h [code] |
A score on a dihedral angle. | |
file | atom/distance.h [code] |
distance metrics | |
file | Domain.h [code] |
A decorator for associating an atom::Hierarchy piece with a domain. | |
file | DopePairScore.h [code] |
Dope scoring. | |
file | element.h [code] |
Define the elements used in IMP . | |
file | estimates.h [code] |
Estimates of various physical quantities. | |
file | EzRestraint.h [code] |
Ez potential. A statistical scoring function for atom proteins. | |
file | force_fields.h [code] |
Define functions to add bonds and radii to atoms. | |
file | ForceFieldParameters.h [code] |
force field base class | |
file | Fragment.h [code] |
A decorator for associating a Hierarchy piece. | |
file | HelixRestraint.h [code] |
Class to maintain helix shape (dihedrals + elastic network) | |
file | atom/Hierarchy.h [code] |
Decorator for helping deal with a hierarchy of molecules. | |
file | hierarchy_tools.h [code] |
A set of useful functionality on IMP::atom::Hierarchy decorators. | |
file | ImproperSingletonScore.h [code] |
A score on the deviation of an improper angle from ideality. | |
file | LangevinThermostatOptimizerState.h [code] |
Maintains temperature during molecular dynamics using a Langevin thermostat. | |
file | LennardJones.h [code] |
A decorator for a particle that has a Lennard-Jones potential well. | |
file | LennardJonesPairScore.h [code] |
Lennard-Jones score between a pair of particles. | |
file | Mass.h [code] |
A decorator for particles with mass. | |
file | atom/mmcif.h [code] |
Functions to read PDBs in mmCIF format. | |
file | mol2.h [code] |
Functions to read mol2s. | |
file | atom/MolecularDynamics.h [code] |
Simple molecular dynamics optimizer. | |
file | Molecule.h [code] |
A decorator for Molecules. | |
file | OrientedSoapPairScore.h [code] |
Orientation-dependent SOAP scoring. | |
file | pdb.h [code] |
Functions to read PDBs. | |
file | protein_ligand_score.h [code] |
Functions to read mol2s. | |
file | atom/python_only.h [code] |
Functionality only available in Python. | |
file | RemoveRigidMotionOptimizerState.h [code] |
Remove rigid rotation and translation during molecular dynamics. | |
file | RemoveTranslationOptimizerState.h [code] |
Remove rigid translation during optimization. | |
file | Representation.h [code] |
A decorator for Representations. | |
file | Residue.h [code] |
A decorator for Residues. | |
file | SameResiduePairFilter.h [code] |
A Score on the distance between a pair of particles. | |
file | secondary_structure_reader.h [code] |
Functions to read PSIPRED/DSSP and encode as SSES. | |
file | SecondaryStructureResidue.h [code] |
A decorator for storing secondary structure probabilities. Copyright 2007-2019 IMP Inventors. All rights reserved. | |
file | Selection.h [code] |
Select a subset of a hierarchy. | |
file | Simulator.h [code] |
Simple molecular dynamics optimizer. | |
file | smoothing_functions.h [code] |
Classes to smooth nonbonded interactions. | |
file | SoapPairFilter.h [code] |
PairFilter for SOAP. | |
file | State.h [code] |
A decorator for States. | |
file | StereochemistryPairFilter.h [code] |
A filter that excludes bonds, angles and dihedrals. | |
file | StructureSource.h [code] |
Add a Structure ID and Chain ID. | |
file | TAMDCentroid.h [code] |
A decorator for a particle that is a centroid of TAMD simulations. | |
file | TAMDParticle.h [code] |
A decorator for a diffusing particle. | |
file | VelocityScalingOptimizerState.h [code] |
Maintains temperature during molecular dynamics by velocity scaling. | |