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	LennardJonesType.h [code]
	Parameters for a Lennard-Jones interaction.
file	LennardJonesTypedPairScore.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 or BinaryCIF 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.