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.
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.
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)
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.
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.
Fiser/Melo loop modeling statistical potential.
Base class for "simulators", such as molecular dynamics.
A decorator for associating a Hierarchy piece.
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.
A decorator for keeping track of copies of a molecule.
Functions to score protein-ligand interactions.
Orientation-dependent SOAP scoring.
A fake container for bonds.
A fake container for bonds.
Maintains temperature during molecular dynamics by velocity scaling.
Select a subset of a hierarchy.
Cover a bond with a sphere.
Estimates of various physical quantities.
Class to maintain CHARMM stereochemistry.
