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IMP Reference Guide  develop.49f026e7cd,2024/12/04
The Integrative Modeling Platform
Atom.h
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1 /**
2  * \file IMP/atom.h
3  * \brief Include all non-deprecated headers in IMP.atom.
4  *
5  * Copyright 2007-2024 IMP Inventors. All rights reserved.
6  */
7 
8 #ifndef IMP_ATOM_H
9 #define IMP_ATOM_H
11 #include <IMP/atom/Atom.h>
21 #include <IMP/atom/CHARMMAtom.h>
24 #include <IMP/atom/CenterOfMass.h>
25 #include <IMP/atom/Chain.h>
26 #include <IMP/atom/Charged.h>
27 #include <IMP/atom/Copy.h>
29 #include <IMP/atom/CoverBond.h>
30 #include <IMP/atom/Diffusion.h>
32 #include <IMP/atom/Domain.h>
33 #include <IMP/atom/DopePairScore.h>
34 #include <IMP/atom/EzRestraint.h>
36 #include <IMP/atom/Fragment.h>
38 #include <IMP/atom/Hierarchy.h>
41 #include <IMP/atom/LennardJones.h>
44 #include <IMP/atom/Mass.h>
46 #include <IMP/atom/Molecule.h>
51 #include <IMP/atom/Residue.h>
54 #include <IMP/atom/Selection.h>
55 #include <IMP/atom/Simulator.h>
57 #include <IMP/atom/State.h>
60 #include <IMP/atom/TAMDCentroid.h>
61 #include <IMP/atom/TAMDParticle.h>
63 #include <IMP/atom/alignment.h>
65 #include <IMP/atom/atom_macros.h>
67 #include <IMP/atom/bond_graph.h>
70 #include <IMP/atom/constants.h>
71 #include <IMP/atom/dihedrals.h>
72 #include <IMP/atom/distance.h>
73 #include <IMP/atom/element.h>
74 #include <IMP/atom/estimates.h>
75 #include <IMP/atom/force_fields.h>
77 #include <IMP/atom/mmcif.h>
78 #include <IMP/atom/mol2.h>
79 #include <IMP/atom/pdb.h>
81 #include <IMP/atom/python_only.h>
84 #endif /* IMP_ATOM_H */
A decorator for a diffusing particle.
Functions to read PDBs in mmCIF format.
A decorator for Representations.
Define the elements used in IMP.
A decorator for a diffusing particle.
A decorator for storing secondary structure probabilities.
Functionality only available in Python.
A decorator for particles with mass.
Functions to read PDBs.
A decorator for particles with mass.
Simple Brownian dynamics optimizer.
Filter out atoms that belong to the same residue.
Dihedral restraint between five residues in CA-only representation.
access to CHARMM force field parameters
Maintains temperature during molecular dynamics using a Langevin thermostat.
Remove rigid translation during optimization.
Ez potential. A statistical scoring function for atom proteins.
Remove rigid rotation and translation during molecular dynamics.
Simple molecular dynamics optimizer.
Lennard-Jones score between a pair of particles.
A score on the deviation of an angle from ideality.
A Score on the distance between a the two particles in a bond.
Simple atom decorator.
Coulomb (electrostatic) score between a pair of particles.
Maintains temperature during molecular dynamics using a Berendsen thermostat.
Functions to read PSIPRED/DSSP and encode as SSES.
Class to maintain helix shape (dihedrals + elastic network)
force field base class
Alignment of structures.
A decorator for an atom that has a defined CHARMM type.
Represents a graph of the bonds within an atomic structure.
Define various useful constants for atomic simulations.
A decorator for a particle that is a centroid of TAMD simulations.
Angle restraint between three residues in CA-only representation.
A decorator for Molecules.
Contains decorators for a bond.
A decorator for a particle that has a Lennard-Jones potential well.
Simple molecular dynamics optimizer.
Classes for handling CHARMM-style topology.
Decorator for helping deal with a hierarchy of molecules.
Return the endpoints of a bond.
A filter that excludes bonds, angles and dihedrals.
Define functions to add bonds and radii to atoms.
PairFilter for SOAP.
A decorator for associating an atom::Hierarchy piece with a domain.
Helpers to extract dihedral information.
A score on the deviation of an improper angle from ideality.
A decorator for Residues.
A score on a dihedral angle.
Dope scoring.
Fiser/Melo loop modeling statistical potential.
Store the chain ID.
Base class for "simulators", such as molecular dynamics.
A decorator for associating a Hierarchy piece.
A decorator for States.
Classes to smooth nonbonded interactions.
A decorator for a point particle that has an electrostatic charge.
Classes for handling CHARMM-style topology of segments.
Macros for maintaining molecular hierarchies.
Add a Structure ID and Chain ID.
distance metrics
Decorators for angles.
A decorator for keeping track of copies of a molecule.
Functions to score protein-ligand interactions.
Functions to read mol2s.
Orientation-dependent SOAP scoring.
A fake container for bonds.
A fake container for bonds.
Maintains temperature during molecular dynamics by velocity scaling.
A set of useful functionality on IMP::atom::Hierarchy decorators.
Select a subset of a hierarchy.
Cover a bond with a sphere.
Estimates of various physical quantities.
Class to maintain CHARMM stereochemistry.