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IMP Reference Guide  develop.33c691def1,2022/08/08
The Integrative Modeling Platform
atom Directory Reference
+ Directory dependency graph for atom:

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]
 Macros for maintaining molecular hierarchies.
 
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 various useful constants for atomic simulations.
 
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  LoopStatisticalPairScore.h [code]
 Fiser/Melo loop modeling statistical potential.
 
file  Mass.h [code]
 A decorator for particles with mass.
 
file  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 score protein-ligand interactions.
 
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]
 Filter out atoms that belong to the same residue.
 
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.
 
file  Selection.h [code]
 Select a subset of a hierarchy.
 
file  Simulator.h [code]
 Base class for "simulators", such as molecular dynamics.
 
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.