stormm::topology::CharmmValenceTable Class Reference

Unguarded struct to assemble special "CHARMM" force field terms read from an Amber or other topology file. These include Urey-Bradley harmonic angle terms, CHARMM improper harmonic dihedrals, and CMAP terms. All descriptions follow from the eponymous member variables in an AtomGraph. More...

#include <atomgraph_refinement.h>

Public Member Functions
void	makeAtomAssignments ()
	Populate the atom assignments for this object. This can only be called once the Atom index arrays have been assigned.
	CharmmValenceTable ()
	The constructor simply allocates memory, if dimensions are available.
	CharmmValenceTable (int natom_in, int nubrd_in, int nimpr_in, int ncmap_in, const std::vector< int > &ubrd_i_atoms_in={}, const std::vector< int > &ubrd_k_atoms_in={}, const std::vector< int > &ubrd_param_idx_in={}, const std::vector< int > &impr_i_atoms_in={}, const std::vector< int > &impr_j_atoms_in={}, const std::vector< int > &impr_k_atoms_in={}, const std::vector< int > &impr_l_atoms_in={}, const std::vector< int > &impr_param_idx_in={}, const std::vector< int > &cmap_i_atoms_in={}, const std::vector< int > &cmap_j_atoms_in={}, const std::vector< int > &cmap_k_atoms_in={}, const std::vector< int > &cmap_l_atoms_in={}, const std::vector< int > &cmap_m_atoms_in={}, const std::vector< int > &cmap_param_idx_in={})

Public Attributes
int	total_ub_angles
int	total_impropers
int	total_cmaps
std::vector< int >	ubrd_i_atoms
std::vector< int >	ubrd_k_atoms
std::vector< int >	ubrd_param_idx
std::vector< int >	impr_i_atoms
std::vector< int >	impr_j_atoms
std::vector< int >	impr_k_atoms
std::vector< int >	impr_l_atoms
std::vector< int >	impr_param_idx
std::vector< int >	cmap_i_atoms
std::vector< int >	cmap_j_atoms
std::vector< int >	cmap_k_atoms
std::vector< int >	cmap_l_atoms
std::vector< int >	cmap_m_atoms
std::vector< int >	cmap_param_idx
std::vector< int >	ubrd_assigned_atoms
std::vector< int >	ubrd_assigned_index
std::vector< int >	ubrd_assigned_terms
std::vector< int >	ubrd_assigned_bounds
std::vector< int >	impr_assigned_atoms
std::vector< int >	impr_assigned_index
std::vector< int >	impr_assigned_terms
std::vector< int >	impr_assigned_bounds
std::vector< int >	cmap_assigned_atoms
std::vector< int >	cmap_assigned_index
std::vector< int >	cmap_assigned_terms
std::vector< int >	cmap_assigned_bounds

Detailed Description

Unguarded struct to assemble special "CHARMM" force field terms read from an Amber or other topology file. These include Urey-Bradley harmonic angle terms, CHARMM improper harmonic dihedrals, and CMAP terms. All descriptions follow from the eponymous member variables in an AtomGraph.

Constructor & Destructor Documentation

CharmmValenceTable()

stormm::topology::CharmmValenceTable::CharmmValenceTable

(

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The constructor simply allocates memory, if dimensions are available.

Overloaded:

• Create an empty object
• Create an object with pre-allocated memory for each type of CHARMM valence term

Parameters

natom_in	The number of atoms in the system (for bounds arrays)
nubrd_in	The number of Urey-Bradley harmonic angles terms to prepare for (atom indices will be filled if enough information is provided)
nimpr_in	The number of CHARMM improper dihedrals to prepare for (atom indices will be filled if enough information is provided)
ncmap_in	The number of CMAP terms to prepare for (atom indices will be filled if enough information is provided)

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The documentation for this class was generated from the following files:

• src/Topology/atomgraph_refinement.h
• src/Topology/atomgraph_refinement.cpp