stormm::topology::AtomGraph Class Reference

A struct to hold information relating to an Amber topology. This struct's member functions are limited to getters for its private data. Because the primary means of constructing a topology will be complex, i.e. meticulous parsing of a file or expansion of an existing topology based on some new information, the constructors will need to be buried within wrapper functions that perform such procedures. This struct contains all information contained within an Amber prmtop-format file, nothng more, as described on: More...

#include <atomgraph.h>

Public Member Functions
	AtomGraph ()
	The blank constructor makes a blank AtomGraph, which is used by the general- purpose file-based constructor to delegate initialization.
	~AtomGraph ()=default
	The default destructor is adequate.
	AtomGraph (const AtomGraph &original)
	The copy constructor takes a lot of tedium upon itself to prevent more complexity in working with AtomGraph objects downstream.
AtomGraph &	operator= (const AtomGraph &other)
	Copy constructor.
	AtomGraph (AtomGraph &&original)
	The move constructor makes prodigious use of std::move for each string and Hybrid member variable.
AtomGraph &	operator= (AtomGraph &&other)
	Move constructor.
void	buildFromPrmtop (const std::string &file_name, const ExceptionResponse policy=ExceptionResponse::WARN, double coulomb_constant_in=amber_ancient_bioq, double default_elec14_screening=amber_default_elec14_screen, double default_vdw14_screening=amber_default_vdw14_screen, double charge_rounding_tol=default_charge_rounding_tol, double charge_discretization=default_charge_precision_inc)
	Build an AtomGraph form a file. This is called by the general-purpose constructor or also by the developer after instantiating an empty object.
std::string	getTitle () const
	Get the title of the topology (may be blank).
std::string	getFileName () const
	Get the file name where a topology originated (may be blank, indicating that the topology was produced by some other means).
int	getAtomCount () const
	Get the number of atoms, using the topology's dedicated private variable rather than a list of input dimensions that was mostly stored for developers most familiar with Amber.
int	getResidueCount () const
	Get the number of residues.
int	getMoleculeCount () const
	Get the number of separate molecules in the system.
MoleculeKind	getMoleculeKind (int mol_index) const
	Get the kind of a specific molecule wihtin the topology.
int	getOrganicMoleculeCount () const
	Get the number of organic molecules in the system, based on the criteria of greater than or equal to eight total real atoms and at least one carbon atom.
int	getOrganicAtomCount () const
	Get the number of organic atoms in the system, based on the criteria of greater than or equal to eight total real atoms and at least one carbon atom.
int	getWaterResidueSize () const
	Get the number of particles (which may include virtual sites) in a single water molecule within the system.
int	getWaterResidueCount () const
	Get the number of water residues in the system.
int	getLargestResidueSize () const
	Get the number of separate molecules in the system.
int	getLastSoluteResidue () const
	Get the final solute residue, indexed according to C/C++ array indexing conventions.
int	getLastSoluteAtom () const
	Get the final solute atom, indexed according to C/C++ array indexing conventions.
int	getFirstSolventMolecule () const
	Get the first solvent molecule, indexed according to C/C++ array indexing conventions.
int	getFirstSolventAtom () const
	Get the first solvent atom, indexed according to C/C++ array indexing conventions.
int	getLargestMoleculeSize () const
	Get the largest molecule's size.
double	getTotalMass () const
	Get the total mass of all atoms in the topology (this is a computation, not a stored value).
int	getDegreesOfFreedom () const
	Get the number of degrees of freedom, without consideration to geometric constraints.
int	getConstrainedDegreesOfFreedom () const
	Get the number of degrees of freedom after geometric constraints have been applied.
std::vector< int >	getParticlesPerMolecule () const
	Get the sizes of all molecules in the system. Rather redundant with the molecule limits being accessible, but convenient.
int	getParticlesPerMolecule (int index) const
std::string	getFullAtomName (int index) const
	Get the full name (including the residue and structural residue number) of an atom, as a string.
std::vector< std::vector< char4 > >	getAtomTypeNameTable () const
	Get a table with the names of all unique atom types, arranged according to their Lennard-Jones indices as they appear in the topology (in ascending order).
int	getUreyBradleyTermCount () const
	Get the number of Urey-Bradley terms in the system.
int	getCharmmImprTermCount () const
	Get the number of CHARMM improper terms.
int	getCmapTermCount () const
	Get the number of CMAP terms (the number of CMAP parameter surfaces is different)
int	getUreyBradleyParameterCount () const
	Return the number of unique Urey-Bradley parameter sets.
int	getCharmmImprParameterCount () const
	Return the number of unique CHARMM improper parameter sets.
int	getCmapSurfaceCount () const
	Return the number of unique CMAP surfaces.
int	getCmapDimension (int index) const
	Return the dimension of a particular CMAP surface (all CMAPs are assumed to be square)
template<typename T>
UreyBradleyTerm< T >	getUreyBradleyTerm (int index) const
	Collect the atom indices and actual parameters to implement one of the system's Urey-Bradley terms. The special-purpose, unguarded struct that holds the result also provides the original parameter index, if of interest. This is for computing the potential energy and forces in the most straightforward manner possible, albeit slow.
template<typename T>
CharmmImprTerm< T >	getCharmmImprTerm (int index) const
	Collect the atom indices and actual parameters to implement one of the system's CHARMM improper terms. The special-pupose, unguarded struct that holds the result also provides the original parameter index, if of interest. This is for computing the potential energy and forces in the most straightforward manner possible, albeit slow.
template<typename T>
CmapTerm< T >	getCmapTerm (int index) const
	Collect the atom indices and a pointer to the surface to implement one of the system's CMAP terms. The special-purpose, unguarded struct that holds the result also provides the original parameter index, if of interest.
int	getBondTermCount () const
	Get the number of bond stretching terms in the system.
int	getAngleTermCount () const
	Get the number of angle bending terms in the system.
int	getDihedralTermCount () const
	Get the number of dihedral torsion terms in the system.
int	getBondParameterCount () const
	Return the number of unique bond stretching parameter sets.
int	getAngleParameterCount () const
	Return the number of unique bond angle bending parameter sets.
int	getDihedralParameterCount () const
	Return the number of unique dihedral parameter sets.
template<typename T>
BondTerm< T >	getBondTerm (int index) const
	Collect the atom indices and actual parameters for implement one of the system's harmonic bond stretching terms.
template<typename T>
AngleTerm< T >	getAngleTerm (int index) const
	Collect the atom indices and actual parameters for implement one of the system's harmonic bond angle bending terms.
template<typename T>
DihedralTerm< T >	getDihedralTerm (int index) const
	Collect the atom indices and actual parameters for implement one of the system's cosine-based dihedral torsion terms.
int	getVirtualSiteCount () const
	Get the number of virtual sites in the system.
int	getVirtualSiteParameterSetCount () const
	Get the number of unique virtual site frames in the system. For example, a system of 1024 TIP-4P waters would have one unique frame, applied to 1024 different groups of atoms.
int	getVirtualSiteIndex (int atom_index, ExceptionResponse policy=ExceptionResponse::DIE) const
	Get the virtual site index of an atom index. If the atom index is not a virtual site, this function will throw an error.
VirtualSiteKind	getVirtualSiteFrameType (int index) const
	Get the frame type of a particular virtual site.
int	getVirtualSiteFrameAtom (int index, int nfrm) const
	Get the general topology index of one of a virtual site's frame atoms.
template<typename T>
T	getVirtualSiteFrameDimension (int index, int ndim)
	Get the dimensions (could be length in A, could be scaling factor for a distance or cross product) of one virtual site's frame.
int	getChargeTypeCount () const
	Get the number of charge types in the system.
int	getLJTypeCount () const
	Get the number of atom types in the system.
int	getTotalExclusions () const
	Get the number of exclusions in the entire topology.
UnitCellType	getUnitCellType () const
	Get the simulation cell type (isolated boundary conditions, rectilinear, triclinic)
ImplicitSolventModel	getImplicitSolventModel () const
	Get the implicit solvent model type, i.e. some flavor of GB or NONE.
double	getDielectricConstant () const
	Get the dielectric constant (part of the implicit solvent setup)
double	getSaltConcentration () const
	Get the salt concentration (part of the implicit solvent setup)
double	getCoulombConstant () const
	Get the fundamental coulomb constant that this system uses in electrostatic calculations.
double	getElectrostatic14Screening () const
	Get the general 1:4 screening factor on electrostatic interactions.
double	getVanDerWaals14Screening () const
	Get the general 1:4 screening factor on van-der Waals interactions.
std::string	getPBRadiiSet () const
	Get the PB Radii set.
bool	usesShake () const
	Get the status of SHAKE and RATTLE constraints in the system.
bool	usesSettle () const
	Get the status of SETTLE rigid water constraints in the system.
std::string	getWaterResidueName () const
	Get the water residue name.
int	getRigidWaterCount () const
	Get the number of rigid waters in the system. This will check through the SETTLE groups and confirm the number that are, by their chemistry, water.
int	getRigidWaterAtomCount () const
	Get the number of atoms in a rigid water molecule of the system, if the system has rigid waters. This function will return zero if the system has no rigid waters.
int	getSettleGroupCount () const
	Get the number of SETTLE groups in the system.
int	getBondConstraintCount () const
	Get the number of bond constraints.
int	getConstraintGroupCount () const
	Get the total number of constrained groups.
std::vector< int >	getConstraintGroupAtoms (int index) const
	Get the atoms of a single constraint group.
int	getConstraintGroupTotalSize () const
	Get the total size of the constrained group atoms list.
int	getNonrigidParticleCount () const
	Get the number of non-rigid particles in the system.
std::vector< int >	getAtomExclusions (int index) const
	Get the exclusion list for a particular atom. This will concatenate 1:1, 1:2, 1:3, and 1:4 exclusions, without regard to which is which. To get a specific type of exclusion, use one of the getNonbondedXXExclusions() functions. All functions of this sort will return a complete list such that if exclusions for all atoms are considered in sequence, all exclusions will be double-counted.
std::vector< int >	getNonbonded11Exclusions (int index) const
	Get the 1:1 exclusions for a particular atom. This list will only be populated if the atom is a virtual site or has virtual sites that claim it as their parent.
std::vector< int >	getNonbonded12Exclusions (int index) const
	Get all 1:2 exclusions for a particular atom.
std::vector< int >	getNonbonded13Exclusions (int index) const
	Get all 1:3 exclusions for a particular atom.
std::vector< int >	getNonbonded14Exclusions (int index) const
	Get all 1:4 exclusions for a particular atom.
template<typename T>
T	getChargeParameter (int index) const
	Get the charge parameter for a specific atom. The quantity is derived from tables at the specified level of precision (float or double), and equals the value obtained from getPartialCharge<T>(index), although that function reaches into a separate array with a great deal of redundant information.
std::vector< char4 >	matchOverflowAtomName (const std::string &query) const
	Match a long atom name and return its key in the standard list of char4 atom names.
std::vector< char4 >	matchOverflowAtomType (const std::string &query) const
	Match a long atom type and return its key in the standard list of char4 atom types.
std::vector< char4 >	matchOverflowResidueName (const std::string &query) const
	Match a long residue name and return its key among the standard char4 residue names.
ValenceKit< double >	getDoublePrecisionValenceKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get an abstract for calculating valence terms in double precision.
ValenceKit< float >	getSinglePrecisionValenceKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a single-precision abstract for calculating valence terms.
NonbondedKit< double >	getDoublePrecisionNonbondedKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a double-precision abstract for calculating non-bonded energy and forces.
NonbondedKit< float >	getSinglePrecisionNonbondedKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a single-precision abstract for calculating non-bonded energy and forces.
ImplicitSolventKit< double >	getDoublePrecisionImplicitSolventKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a double-precision abstract for calculating implicit solvent energy and forces.
ImplicitSolventKit< float >	getSinglePrecisionImplicitSolventKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a single-precision abstract for calculating implicit solvent energy and forces.
ChemicalDetailsKit	getChemicalDetailsKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get an abstract of the chemical details of the system, such as atom name and type or residue names and limits.
VirtualSiteKit< double >	getDoublePrecisionVirtualSiteKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a double-precision abstract for placing virtual sites and transmitting their forces to frame atoms with mass.
VirtualSiteKit< float >	getSinglePrecisionVirtualSiteKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get a single-precision abstract for placing virtual sites and transmitting their forces to frame atoms with mass.
ConstraintKit< double >	getDoublePrecisionConstraintKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get an abstract for managing constraints based on double-precision parameters.
ConstraintKit< float >	getSinglePrecisionConstraintKit (HybridTargetLevel tier=HybridTargetLevel::HOST) const
	Get an abstract for managing constraints based on single-precision parameters. While the overall implementation for constraints cannot be implemented entirely in single precision, having the underlying parameters in this form is not, in principle, a drvier of energy drift. It will simply set the system into a slightly different geometry, which is probably still closer to the double-precision result than many cycles of SHAKE or RATTLE would get it anyway.
void	setSource (const std::string &new_source)
	Set the source file for the topology. Primary use is to impart a destination file for a topology to be written to disk, but can also be used to "disguise" one topology from another even if both are from the same original file.
void	setImplicitSolventModel (ImplicitSolventModel igb_in, double dielectric_in=80.0, double saltcon_in=0.0, AtomicRadiusSet radii_set=AtomicRadiusSet::NONE, ExceptionResponse policy=ExceptionResponse::WARN)
	Set the implicit solvent model. This will leverage a lot of hard-coded constants to fill out some allocated but otherwise blank arrays and impart one particular Generalized Born or other implicit solvent method.
void	printToFile (const std::string &output_file={}, TopologyKind output_style=TopologyKind::AMBER, PrintSituation expectation=PrintSituation::OPEN_NEW, ExceptionResponse pr_policy=ExceptionResponse::DIE) const
	Print out a topology in the specified format.
void	printAmberFormat (const std::string &output_file={}, PrintSituation expectation=PrintSituation::OPEN_NEW, ExceptionResponse pr_policy=ExceptionResponse::DIE) const
	Print the contents of the topology in the AMBER file format. Descriptions of input parameters follow from printToFile(), above.
	AtomGraph (const std::string &file_name, ExceptionResponse policy=ExceptionResponse::WARN, TopologyKind engine_format=TopologyKind::AMBER)
	The general-purpose constructor for file-based topology creation.
	AtomGraph (const std::string &file_name, ExceptionResponse policy, TopologyKind engine_format, double coulomb_constant_in, double default_elec14_screening, double default_vdw14_screening, double charge_rounding_tol, double charge_discretization, ApplyConstraints use_bond_constraints_in=ApplyConstraints::NO, ApplyConstraints use_settle_in=ApplyConstraints::NO)
	AtomGraph (const std::vector< AtomGraph * > &agv, const std::vector< int > &counts, MoleculeOrdering arrangement=MoleculeOrdering::REORDER_ALL, ExceptionResponse policy=ExceptionResponse::DIE)
	AtomGraph (const AtomGraph &ag_a, int n_a, const AtomGraph &ag_b, int n_b, MoleculeOrdering arrangement=MoleculeOrdering::REORDER_ALL, ExceptionResponse policy=ExceptionResponse::DIE)
	AtomGraph (const AtomGraph &ag_a, const AtomGraph &ag_b, int n_b, MoleculeOrdering arrangement=MoleculeOrdering::REORDER_ALL, ExceptionResponse policy=ExceptionResponse::DIE)
	AtomGraph (const AtomGraph &ag_a, const AtomGraph &ag_b, MoleculeOrdering arrangement=MoleculeOrdering::REORDER_ALL, ExceptionResponse policy=ExceptionResponse::DIE)
	AtomGraph (const AtomGraph &original, const std::vector< int > &atom_subset, ExceptionResponse policy=ExceptionResponse::DIE, double charge_rounding_tol=default_charge_rounding_tol, double charge_discretization=default_charge_precision_inc, ApplyConstraints use_bond_constraints_in=ApplyConstraints::NO, ApplyConstraints use_settle_in=ApplyConstraints::NO)
	AtomGraph (const AtomGraph &original, const std::vector< bool > &mask, ExceptionResponse policy=ExceptionResponse::DIE, double charge_rounding_tol=default_charge_rounding_tol, double charge_discretization=default_charge_precision_inc, ApplyConstraints use_bond_constraints_in=ApplyConstraints::NO, ApplyConstraints use_settle_in=ApplyConstraints::NO)
int	getDescriptor (TopologyDescriptor choice) const
	Get a descriptor from within the array of topology descriptors. If this topology were read from an Amber-format file, all descriptors are taken from the preamble in its first ~15 lines.
int	getDescriptor (SanderDescriptor choice) const
const Hybrid< int > &	getResidueLimits () const
	Get residue limits for the beginning and ends of up to N residues.
int2	getResidueLimits (int index) const
std::vector< int >	getResidueIndex () const
	Get the index (topology index, not natural / structure-informed residue number) of a particular residue.
int	getResidueIndex (int atom_index) const
std::vector< int >	getStructuralAtomNumber () const
	Get the (arbitrarily defined) atom numbers for atoms in the system. For example, a PDB file could ahve its own atom numbering scheme. This provides a way to transcribe that into the AtomGraph object.
std::vector< int >	getStructuralAtomNumber (int low_index, int high_index) const
int	getStructuralAtomNumber (int index) const
std::vector< int >	getResidueNumber () const
	Get the residue numbers for atoms in the system.
std::vector< int >	getResidueNumber (int low_index, int high_index) const
int	getResidueNumber (int index) const
std::vector< int >	getMoleculeLimits () const
	Get the molecule limits, indices into molecule_contents, for every molecule in the system. This allows that molecules not be contiguous in the topology atom indexing, but will be recoverable by molecule_contents.
int2	getMoleculeLimits (int index) const
std::vector< int >	getAtomicNumber () const
	Get the atomic numbers for atoms in the system.
std::vector< int >	getAtomicNumber (int low_index, int high_index) const
int	getAtomicNumber (int index) const
std::vector< bool >	getAtomMobility () const
	Get the mobile atom mask for the system, as a boolean vector translated from the bitmask stored internally.
std::vector< bool >	getAtomMobility (int low_index, int high_index) const
bool	getAtomMobility (int index) const
std::vector< uint >	getAtomMobilityMask () const
	Get the raw mobility bitmask over a particular range.
std::vector< uint >	getAtomMobilityMask (int low_index, int high_index) const
void	modifyAtomMobility (MobilitySetting movement)
	Change an atom's mobility in the topology.
void	modifyAtomMobility (int low_index, int high_index, MobilitySetting movement)
void	modifyAtomMobility (int index, MobilitySetting movement)
void	modifyAtomMobility (const std::vector< int > &mask, MobilitySetting movement)
std::vector< int >	getMoleculeMembership () const
	Get molecule membership for atoms within the system.
std::vector< int >	getMoleculeMembership (int low_index, int high_index) const
int	getMoleculeMembership (int index) const
std::vector< int >	getMoleculeContents () const
	Get the contents of a one or more molecules in the system.
std::vector< int >	getMoleculeContents (int index) const
template<typename T>
std::vector< T >	getPartialCharge () const
	Get the atomic partial charges of atoms in the system.
template<typename T>
std::vector< T >	getPartialCharge (int low_index, int high_index) const
template<typename T>
T	getPartialCharge (int index) const
template<typename T>
std::vector< T >	getAtomicMass (MassForm rep=MassForm::ORDINARY) const
	Get the masses of atoms in the system. The developer may also choose to take the pre-computed inverse masses (this can be useful when dealing with extra points, as inverses of zero-mass particles must also be set to zero by a conditional statement).
template<typename T>
std::vector< T >	getAtomicMass (int low_index, int high_index, MassForm rep=MassForm::ORDINARY) const
template<typename T>
T	getAtomicMass (int index, MassForm rep=MassForm::ORDINARY) const
const Hybrid< char4 > &	getAtomName () const
	Get the names of atoms in the system.
std::vector< char4 >	getAtomName (int low_index, int high_index) const
char4	getAtomName (int index) const
const Hybrid< char4 > &	getAtomType () const
	Get the types of atoms in the system.
std::vector< char4 >	getAtomType (int low_index, int high_index) const
char4	getAtomType (int index) const
const Hybrid< char4 > &	getResidueName () const
	Get the names of residues in the system.
char4	getResidueName (int index) const
std::vector< int >	findVirtualSites () const
	Get a list of the general topological indices of one or more virtual sites.
std::vector< int2 >	findVirtualSites (int low_index, int high_index) const
int	findVirtualSites (int index) const
std::vector< int >	getChargeIndex () const
	Get the charge type index of atoms in the system.
std::vector< int >	getChargeIndex (int low_index, int high_index) const
int	getChargeIndex (int index) const
std::vector< int >	getLennardJonesIndex () const
	Get the Lennard-Jones type index of atoms in the system.
std::vector< int >	getLennardJonesIndex (int low_index, int high_index) const
int	getLennardJonesIndex (int index) const
template<typename T>
T	getLennardJonesSigma (int index_a, int index_b) const
	Get the Lennard-Jones interaction sigma. The quantity is derived from tables at the specified level of precision (float or double), but computed in double precision based on that information before it is returned in the template data type.
template<typename T>
T	getLennardJonesSigma (int index_a) const
template<typename T>
std::vector< T >	getLennardJonesSigma () const
template<typename T>
T	getLennardJonesEpsilon (int index_a, int index_b) const
	Get the Lennard-Jones interaction epsilon value. The quantity is derived from tables at the specified level of precision (float or double), but computed in double precision based on that information before it is returned in the template data type.
template<typename T>
T	getLennardJonesEpsilon (int index_a) const
template<typename T>
std::vector< T >	getLennardJonesEpsilon () const
template<typename T>
std::vector< T >	getAtomPBRadius () const
	Get the Poisson-Boltzmann radius of a particular atom.
template<typename T>
std::vector< T >	getAtomPBRadius (int low_index, int high_index) const
template<typename T>
T	getAtomPBRadius (int index) const
template<typename T>
std::vector< T >	getGBScreeningFactor () const
	Get GB screening factors for one or more atoms.
template<typename T>
std::vector< T >	getGBScreeningFactor (int low_index, int high_index) const
template<typename T>
T	getGBScreeningFactor (int index) const
const AtomGraph *	getSelfPointer () const
	Get a pointer to the object itself.
AtomGraph *	getSelfPointer ()
void	setBondParameters (double new_keq, double new_leq, bool set_keq, bool set_leq, int parm_idx, ExceptionResponse policy=ExceptionResponse::SILENT)
	Alter the parameters for a bond parameter set. This will alter the parameters in the topology and all bond terms that use the parameters will then be altered. This function does not add or remove bond terms or parameter sets, nor does it change the mapping of bond terms to parameter sets.
void	setBondParameters (double new_keq, double new_leq, bool set_keq, bool set_leq, char4 type_a, char4 type_b, ExceptionResponse policy=ExceptionResponse::SILENT)
void	setAngleParameters (double new_keq, double new_teq, bool set_keq, bool set_teq, int parm_idx, ExceptionResponse policy=ExceptionResponse::SILENT)
	Alter the parameters for an angle parameter set. This will alter the parameters in the topology and all angle terms that use the parameters will then be use the new parameters. This function does not add or remove angle terms or parameter sets, nor does it change the mapping of angle terms to parameter sets.
void	setAngleParameters (double new_keq, double new_teq, bool set_keq, bool set_teq, char4 type_a, char4 type_b, char4 type_c, ExceptionResponse policy=ExceptionResponse::SILENT)
void	setDihedralParameters (double new_amplitude, double new_phase_angle, bool set_amplitude, bool set_phase_angle, int parm_idx, ExceptionResponse policy=ExceptionResponse::SILENT)
	Alter the parameters for a cosine-based dihedral angle parameter set. This will alter the parameters in the topology and all dihedral terms that use the parameters will then be use the new parameters. This function does not add or remove dihedral terms or parameter sets, nor does it change the mapping of dihedral terms to parameter sets.
void	setDihedralParameters (double new_amplitude, double new_phase_angle, bool set_amplitude, bool set_phase_angle, char4 type_a, char4 type_b, char4 type_c, char4 type_d, double periodicity, ExceptionResponse policy=ExceptionResponse::SILENT)
void	setUreyBradleyParameters (double new_keq, double new_leq, bool set_keq, bool set_leq, int parm_idx, ExceptionResponse policy=ExceptionResponse::SILENT)
	Alter the parameters for a Urey-Bradley parameter set.
void	setUreyBradleyParameters (double new_keq, double new_leq, bool set_keq, bool set_leq, char4 type_a, char4 type_b, char4 type_c, ExceptionResponse policy=ExceptionResponse::SILENT)
void	setCharmmImprParameters (double new_stiffness, double new_phase_angle, bool set_stiffness, bool set_phase_angle, int parm_idx, ExceptionResponse policy=ExceptionResponse::SILENT)
	Alter the characteristics of a CHARMM improper dihedral parameter set.
void	setCharmmImprParameters (double new_stiffness, double new_phase_angle, bool set_stiffness, bool set_phase_angle, char4 type_a, char4 type_b, char4 type_c, char4 type_d, ExceptionResponse policy=ExceptionResponse::SILENT)
void	setWaterResidueName (const char4 new_name)
	Set the name of the water residue.
void	setWaterResidueName (const std::string &new_name)

Friends
class	AtomGraphStage

Detailed Description

A struct to hold information relating to an Amber topology. This struct's member functions are limited to getters for its private data. Because the primary means of constructing a topology will be complex, i.e. meticulous parsing of a file or expansion of an existing topology based on some new information, the constructors will need to be buried within wrapper functions that perform such procedures. This struct contains all information contained within an Amber prmtop-format file, nothng more, as described on:

http://ambermd.org/FileFormats.php

The design is intended to be both performant as well as accessible to developers.

Constructor & Destructor Documentation

AtomGraph() [1/3]

stormm::topology::AtomGraph::AtomGraph	(	const std::string &	file_name,
		ExceptionResponse	policy = ExceptionResponse::WARN,
		TopologyKind	engine_format = TopologyKind::AMBER )

The general-purpose constructor for file-based topology creation.

Overloaded:

• Take just the file name, the exception response policy, and the kind of topology. APpropriate default values will be applied for each kind of topology.
• In addition, take specific values for Coulomb's constant, the general 1:4 screening parameters, and charge discretization.
• Extract a subset of the atoms from an existing AtomGraph and create a new AtomGraph from it. All parameters and terms from the original AtomGraph will be carried over, provided that the new AtomGraph contains all of the atoms that each term spans. Exclusions from the original AtomGraph will be inferred from the bonding pattern.
• Construct an AtomGraph from two existing objects and perhaps multipliers for both

Parameters

file_name	Name of the source file
policy	The alert level to raise if a problem is encountered
engine_format	Format of the topology file to read
coulomb_constant_in	Value of Coulomb's constant, in kcal-A/mol-e^2
default_elec14_screening	The 1:4 electrostatic scaling to apply in absense of any other indications
default_vdw14_screening	The 1:4 van-der Waals scaling to apply in absense of any other indications
charge_rounding_tol	The maximum tolerance at which to initiate charge rounding
charge_discretization	Increment with which to discretize charges
ag_a	The first of two topologies to combine
ag_b	The second of two topologies to combine

AtomGraph() [2/3]

stormm::topology::AtomGraph::AtomGraph

(

const AtomGraph &

original

)

The copy constructor takes a lot of tedium upon itself to prevent more complexity in working with AtomGraph objects downstream.

Parameters

original

The original AtomGraph. A deep copy of all data and repair of all pointers in the present object will be undertaken.

AtomGraph() [3/3]

stormm::topology::AtomGraph::AtomGraph

(

AtomGraph &&

original

)

The move constructor makes prodigious use of std::move for each string and Hybrid member variable.

Parameters

original

The original AtomGraph to move into this one. The std::move function handles movement of the underlying Hybrid objects.

Member Function Documentation

buildFromPrmtop()

void stormm::topology::AtomGraph::buildFromPrmtop	(	const std::string &	file_name,
		const ExceptionResponse	policy = ExceptionResponse::WARN,
		double	coulomb_constant_in = amber_ancient_bioq,
		double	default_elec14_screening = amber_default_elec14_screen,
		double	default_vdw14_screening = amber_default_vdw14_screen,
		double	charge_rounding_tol = default_charge_rounding_tol,
		double	charge_discretization = default_charge_precision_inc )

Build an AtomGraph form a file. This is called by the general-purpose constructor or also by the developer after instantiating an empty object.

Parameters

file_name	Name of the source file
policy	Indicates the alert level to raise if a problem is encountered

findVirtualSites()

std::vector< int > stormm::topology::AtomGraph::findVirtualSites

(

)

const

Get a list of the general topological indices of one or more virtual sites.

Overloaded:

• Get a list of all virtual sites, indexed by their order in the general topology
• Get virtual sites within a range, limits given by ordering in the general topology, results given as indices into the general topology (part x) plus indices into the array of virtual sites (part y). For the first case, "get all virtual sites," the index in the returned array of general topology atom indices serves as an implicit indicator of the index into the list of virtual sites.
• Get the topological index of one virtual site out of the list of virtual sites

Parameters

low_index	The start of a stretch of atoms in the general topology
high_index	The end of a stretch of atoms in the general topology
index	A specific virtual site index

getAngleTerm()

template<typename T>

AngleTerm< T > stormm::topology::AtomGraph::getAngleTerm

(

int

index

)

const

Collect the atom indices and actual parameters for implement one of the system's harmonic bond angle bending terms.

Parameters

index

The bond angle term to query, indexed according to the list of bond angle terms

getAtomExclusions()

std::vector< int > stormm::topology::AtomGraph::getAtomExclusions

(

int

index

)

const

Get the exclusion list for a particular atom. This will concatenate 1:1, 1:2, 1:3, and 1:4 exclusions, without regard to which is which. To get a specific type of exclusion, use one of the getNonbondedXXExclusions() functions. All functions of this sort will return a complete list such that if exclusions for all atoms are considered in sequence, all exclusions will be double-counted.

Parameters

index

The atom of interest

getAtomicMass()

template<typename T>

std::vector< T > stormm::topology::AtomGraph::getAtomicMass

(

MassForm

rep = MassForm::ORDINARY

)

const

Get the masses of atoms in the system. The developer may also choose to take the pre-computed inverse masses (this can be useful when dealing with extra points, as inverses of zero-mass particles must also be set to zero by a conditional statement).

Overloaded:

• Get masses of all atoms in the system, indexed from 0
• Get masses of a stretch of atoms in the system
• Get the mass of a particular atom

Parameters

rep	The representation of the mass to take: ORDINARY or INVERSE
low_index	The start of a stretch of atoms
high_index	The end of a stretch of atoms
index	A specific atom index

getAtomicNumber()

std::vector< int > stormm::topology::AtomGraph::getAtomicNumber

(

)

const

Get the atomic numbers for atoms in the system.

Overloaded:

• Get the atomic numbers of all atoms in the system, as a std::vector<int>
• Get the atomic numbers of a stretch of atoms in the system, as a std::vector<int>
• Get the atomic number of a specific atom

Parameters

low_index	Index of the first atom for which to read a Z number
high_index	Index of the last atom for which to read a Z number
index	Index of a specific atom

getAtomMobility()

std::vector< bool > stormm::topology::AtomGraph::getAtomMobility

(

)

const

Get the mobile atom mask for the system, as a boolean vector translated from the bitmask stored internally.

Overloaded:

• Get the mobility of all atoms in the system, as a std::vector<bool>
• Get the mobility of a stretch of atoms in the system
• Get the mobility of a particular atom

Parameters

low_index	Index of the first atom for which to read the mobility
high_index	Index of the last atom for which to read the mobility
index	Index of a specific atom

getAtomMobilityMask()

std::vector< uint > stormm::topology::AtomGraph::getAtomMobilityMask

(

)

const

Get the raw mobility bitmask over a particular range.

Overloaded:

• Get the mobility of all atoms in the system, as a std::vector<uint>
• Get the mobility of a stretch of atoms in the system

Parameters

low_index	Index of the first atom for which to read the mobility
high_index	Index of the last atom for which to read the mobility

getAtomName()

const Hybrid< char4 > & stormm::topology::AtomGraph::getAtomName

(

)

const

Get the names of atoms in the system.

Overloaded:

• Get names of all atoms in the system, indexed from 0
• Get names of a stretch of atoms in the system
• Get the name of a particular atom

Parameters

low_index	The start of a stretch of atoms
high_index	The end of a stretch of atoms
index	A specific atom index

getAtomPBRadius()

template<typename T>

std::vector< T > stormm::topology::AtomGraph::getAtomPBRadius

(

)

const

Get the Poisson-Boltzmann radius of a particular atom.

Overloaded:

• Get Poisson-Boltzmann radii of all atoms in the system, indexed from 0
• Get Poisson-Boltzmann radii for a stretch of atoms in the system
• Get the Poisson-Boltzmann radius of a particular atom

Parameters

low_index	The start of a stretch of atoms
high_index	The end of a stretch of atoms
index	A specific atom index

getAtomType()

const Hybrid< char4 > & stormm::topology::AtomGraph::getAtomType

(

)

const

Get the types of atoms in the system.

Overloaded:

• Get types of all atoms in the system, indexed from 0
• Get types of a stretch of atoms in the system
• Get the type of a particular atom

Parameters

low_index	The start of a stretch of atoms
high_index	The end of a stretch of atoms
index	A specific atom index

getBondTerm()

template<typename T>

BondTerm< T > stormm::topology::AtomGraph::getBondTerm

(

int

index

)

const

Collect the atom indices and actual parameters for implement one of the system's harmonic bond stretching terms.

Parameters

index

The bond term to query, indexed according to the list of bond terms

getChargeIndex()

std::vector< int > stormm::topology::AtomGraph::getChargeIndex

(

)

const

Get the charge type index of atoms in the system.

Overloaded:

• Get charge indices of all atoms in the system, indexed from 0
• Get charge indices of a stretch of atoms in the system
• Get the charge index of a particular atom

Parameters

low_index	The start of a stretch of atoms
high_index	The end of a stretch of atoms
index	A specific atom index

getCharmmImprTerm()

template<typename T>

CharmmImprTerm< T > stormm::topology::AtomGraph::getCharmmImprTerm

(

int

index

)

const

Collect the atom indices and actual parameters to implement one of the system's CHARMM improper terms. The special-pupose, unguarded struct that holds the result also provides the original parameter index, if of interest. This is for computing the potential energy and forces in the most straightforward manner possible, albeit slow.

Parameters

index

The CHARMM improper term to query, indexed according to the list of CHARMM improper terms (not the general atom list)

getChemicalDetailsKit()

ChemicalDetailsKit stormm::topology::AtomGraph::getChemicalDetailsKit

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get an abstract of the chemical details of the system, such as atom name and type or residue names and limits.

Parameters

tier	Indicator of whether pointers should target the CPU or the GPU layer

getCmapDimension()

int stormm::topology::AtomGraph::getCmapDimension

(

int

index

)

const

Return the dimension of a particular CMAP surface (all CMAPs are assumed to be square)

Parameters

index

The CMAP surface of interest (along the list of available CMAP surfaces, not the list of CMAP terms)

getCmapTerm()

template<typename T>

CmapTerm< T > stormm::topology::AtomGraph::getCmapTerm

(

int

index

)

const

Collect the atom indices and a pointer to the surface to implement one of the system's CMAP terms. The special-purpose, unguarded struct that holds the result also provides the original parameter index, if of interest.

Parameters

index

The CMAP term to query, indexed according to the list of CMAP terms (not the general atom list)

getConstraintGroupAtoms()

std::vector< int > stormm::topology::AtomGraph::getConstraintGroupAtoms

(

int

index

)

const

Get the atoms of a single constraint group.

Parameters

index

The index of the constraint group within the topology

getDescriptor()

int stormm::topology::AtomGraph::getDescriptor

(

TopologyDescriptor

choice

)

const

Get a descriptor from within the array of topology descriptors. If this topology were read from an Amber-format file, all descriptors are taken from the preamble in its first ~15 lines.

Overloaded:

• Take one of the longer, clarified enumerations from the TopologyDescriptor class
• Take one of the shorter enumerations pulled from the Amber sander program and the online documentation (http://ambermd.org/FileFormats.php)

Parameters

choice

Index of the descriptor in the list. Call this function using the enum classes TopologyDescriptors or SanderDescriptors (see above) for easy, annotated access.

getDihedralTerm()

template<typename T>

DihedralTerm< T > stormm::topology::AtomGraph::getDihedralTerm

(

int

index

)

const

Collect the atom indices and actual parameters for implement one of the system's cosine-based dihedral torsion terms.

Parameters

index

The dihedral term to query, indexed according to the list of dihedral terms

getDoublePrecisionConstraintKit()

ConstraintKit< double > stormm::topology::AtomGraph::getDoublePrecisionConstraintKit

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get an abstract for managing constraints based on double-precision parameters.

Parameters

tier	Indicator of whether pointers should target the CPU or the GPU layer

getDoublePrecisionImplicitSolventKit()

ImplicitSolventKit< double > stormm::topology::AtomGraph::getDoublePrecisionImplicitSolventKit

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get a double-precision abstract for calculating implicit solvent energy and forces.

Parameters

tier	Indicator of whether pointers should target the CPU or the GPU layer

getDoublePrecisionNonbondedKit()

NonbondedKit< double > stormm::topology::AtomGraph::getDoublePrecisionNonbondedKit

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get a double-precision abstract for calculating non-bonded energy and forces.

Parameters

tier	Indicator of whether pointers should target the CPU or the GPU layer

getDoublePrecisionValenceKit()

ValenceKit< double > stormm::topology::AtomGraph::getDoublePrecisionValenceKit

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get an abstract for calculating valence terms in double precision.

Parameters

tier	Indicator of whether pointers should target the CPU or the GPU layer

getDoublePrecisionVirtualSiteKit()

VirtualSiteKit< double > stormm::topology::AtomGraph::getDoublePrecisionVirtualSiteKit

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get a double-precision abstract for placing virtual sites and transmitting their forces to frame atoms with mass.

Parameters

tier	Indicator of whether pointers should target the CPU or the GPU layer

getFullAtomName()

std::string stormm::topology::AtomGraph::getFullAtomName

(

int

index

)

const

Get the full name (including the residue and structural residue number) of an atom, as a string.

Parameters

index

The topological index of the atom of interest

getGBScreeningFactor()

template<typename T>

std::vector< T > stormm::topology::AtomGraph::getGBScreeningFactor

(

)

const

Get GB screening factors for one or more atoms.

Overloaded:

• Get GB screening factors of all atoms in the system, indexed from 0
• Get GB screening factors for a stretch of atoms in the system
• Get the GB screening factor of a particular atom

Parameters

low_index	The start of a stretch of atoms
high_index	The end of a stretch of atoms
index	A specific atom index

getLennardJonesEpsilon()

template<typename T>

T stormm::topology::AtomGraph::getLennardJonesEpsilon	(	int	index_a,
		int	index_b ) const

Get the Lennard-Jones interaction epsilon value. The quantity is derived from tables at the specified level of precision (float or double), but computed in double precision based on that information before it is returned in the template data type.

Overloaded:

• Get a single atom's self-interaction epsilon
• Get the epsilon for a pair of atoms (may not obey combining rules, e.g. CHARMM NB-Fix)
• Get a table for the self-interaction epsilon values of all types present in the topology

Parameters

index_a	Index for the first atom
index_b	Index for the second atom

getLennardJonesIndex()

std::vector< int > stormm::topology::AtomGraph::getLennardJonesIndex

(

)

const

Get the Lennard-Jones type index of atoms in the system.

Overloaded:

• Get Lennard-Jones indices of all atoms in the system, indexed from 0
• Get Lennard-Jones indices of a stretch of atoms in the system
• Get the Lennard-Jones index of a particular atom

Parameters

low_index	The start of a stretch of atoms
high_index	The end of a stretch of atoms
index	A specific atom index

getLennardJonesSigma()

template<typename T>

T stormm::topology::AtomGraph::getLennardJonesSigma	(	int	index_a,
		int	index_b ) const

Get the Lennard-Jones interaction sigma. The quantity is derived from tables at the specified level of precision (float or double), but computed in double precision based on that information before it is returned in the template data type.

Overloaded:

• Get a single atom's self-interaction sigma
• Get the sigma for a pair of atoms (may not obey combining rules, e.g. CHARMM NB-Fix)
• Get a table for the self-interaction sigma values of all types present in the topology

Parameters

index_a	Index for the first atom
index_b	Index for the second atom

getMoleculeContents()

std::vector< int > stormm::topology::AtomGraph::getMoleculeContents

(

)

const

Get the contents of a one or more molecules in the system.

Overloaded:

• Get the contents of all molecules
• Get the contents of one particular molecule

Parameters

index

Index of a specific molecule

getMoleculeKind()

MoleculeKind stormm::topology::AtomGraph::getMoleculeKind

(

int

mol_index

)

const

Get the kind of a specific molecule wihtin the topology.

Parameters

mol_index

The index of the molecule of interesta

getMoleculeLimits()

std::vector< int > stormm::topology::AtomGraph::getMoleculeLimits

(

)

const

Get the molecule limits, indices into molecule_contents, for every molecule in the system. This allows that molecules not be contiguous in the topology atom indexing, but will be recoverable by molecule_contents.

Overloaded:

• Get all molecule limits as a std::vector<int>
• Get the initial and final indices of a specific molecule in molecule_contents as an int2

Parameters

index

Index of a specific molecule

getMoleculeMembership()

std::vector< int > stormm::topology::AtomGraph::getMoleculeMembership

(

)

const

Get molecule membership for atoms within the system.

Overloaded:

• Get the molecular membership of all atoms in the system, indexed from 0
• Get the molecular membership a stretch of atoms in the system
• Get the molecule index that a particular atom is part of

Parameters

low_index	Index of the first atom for which to read the mobility
high_index	Index of the last atom for which to read the mobility
index	Index of a specific atom

getNonbonded11Exclusions()

std::vector< int > stormm::topology::AtomGraph::getNonbonded11Exclusions

(

int

index

)

const

Get the 1:1 exclusions for a particular atom. This list will only be populated if the atom is a virtual site or has virtual sites that claim it as their parent.

Parameters

index

The atom of interest

getNonbonded12Exclusions()

std::vector< int > stormm::topology::AtomGraph::getNonbonded12Exclusions

(

int

index

)

const

Get all 1:2 exclusions for a particular atom.

Parameters

index

The atom of interest

getNonbonded13Exclusions()

std::vector< int > stormm::topology::AtomGraph::getNonbonded13Exclusions

(

int

index

)

const

Get all 1:3 exclusions for a particular atom.

Parameters

index

The atom of interest

getNonbonded14Exclusions()

std::vector< int > stormm::topology::AtomGraph::getNonbonded14Exclusions

(

int

index

)

const

Get all 1:4 exclusions for a particular atom.

Parameters

index

The atom of interest

getPartialCharge()

template<typename T>

std::vector< T > stormm::topology::AtomGraph::getPartialCharge

(

)

const

Get the atomic partial charges of atoms in the system.

Overloaded:

• Get partial charges of all atoms in the system, indexed from 0
• Get partial charges of a stretch of atoms in the system
• Get the partial charge of a particular atom

Parameters

low_index	The start of a stretch of atoms
high_index	The end of a stretch of atoms
index	A specific atom index

getParticlesPerMolecule()

std::vector< int > stormm::topology::AtomGraph::getParticlesPerMolecule

(

)

const

Get the sizes of all molecules in the system. Rather redundant with the molecule limits being accessible, but convenient.

Overloaded:

• Get the sizes of all molecules as a std::vector<int>
• Get the size of a single molecule

Parameters

index

Index of a specific residue

getResidueIndex()

std::vector< int > stormm::topology::AtomGraph::getResidueIndex

(

)

const

Get the index (topology index, not natural / structure-informed residue number) of a particular residue.

Overloaded:

• Get all residue indices as a std::vector<int>
• Get the residue index of a particular atom

Parameters

atom_index

Index of the atom in question

getResidueLimits()

const Hybrid< int > & stormm::topology::AtomGraph::getResidueLimits

(

)

const

Get residue limits for the beginning and ends of up to N residues.

Overloaded:

• Get all residue limits as a std::vector<int>
• Get the initial and final atom indices of a specific residue as an int2

Parameters

index

Index of a specific residue

getResidueName()

const Hybrid< char4 > & stormm::topology::AtomGraph::getResidueName

(

)

const

Get the names of residues in the system.

Overloaded:

• Get names of all residues in the system, indexed from 0
• Get the name of a particular residue

Parameters

index

A specific residue index

getResidueNumber()

std::vector< int > stormm::topology::AtomGraph::getResidueNumber

(

)

const

Get the residue numbers for atoms in the system.

Overloaded:

• Get the residue numbers of all atoms in the system, as a std::vector<int>
• Get the residue numbers of a stretch of atoms in the system, as a std::vector<int>
• Get the residue number of a specific atom

Parameters

low_index	Index of the first atom for which to read a residue number
high_index	Index of the last atom for which to read a residue number
index	Index of a specific atom

getSelfPointer()

const AtomGraph * stormm::topology::AtomGraph::getSelfPointer

(

)

const

Get a pointer to the object itself.

Overloaded:

• Get a const pointer to a const AtomGraph
• Get a non-const pointer to a mutable AtomGraph

getSinglePrecisionConstraintKit()

ConstraintKit< float > stormm::topology::AtomGraph::getSinglePrecisionConstraintKit

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get an abstract for managing constraints based on single-precision parameters. While the overall implementation for constraints cannot be implemented entirely in single precision, having the underlying parameters in this form is not, in principle, a drvier of energy drift. It will simply set the system into a slightly different geometry, which is probably still closer to the double-precision result than many cycles of SHAKE or RATTLE would get it anyway.

Parameters

tier	Indicator of whether pointers should target the CPU or the GPU layer

getSinglePrecisionImplicitSolventKit()

ImplicitSolventKit< float > stormm::topology::AtomGraph::getSinglePrecisionImplicitSolventKit

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get a single-precision abstract for calculating implicit solvent energy and forces.

Parameters

tier	Indicator of whether pointers should target the CPU or the GPU layer

getSinglePrecisionNonbondedKit()

NonbondedKit< float > stormm::topology::AtomGraph::getSinglePrecisionNonbondedKit

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get a single-precision abstract for calculating non-bonded energy and forces.

Parameters

tier	Indicator of whether pointers should target the CPU or the GPU layer

getSinglePrecisionValenceKit()

ValenceKit< float > stormm::topology::AtomGraph::getSinglePrecisionValenceKit

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get a single-precision abstract for calculating valence terms.

Parameters

tier	Indicator of whether pointers should target the CPU or the GPU layer

getSinglePrecisionVirtualSiteKit()

VirtualSiteKit< float > stormm::topology::AtomGraph::getSinglePrecisionVirtualSiteKit

(

HybridTargetLevel

tier = HybridTargetLevel::HOST

)

const

Get a single-precision abstract for placing virtual sites and transmitting their forces to frame atoms with mass.

Parameters

tier	Indicator of whether pointers should target the CPU or the GPU layer

getStructuralAtomNumber()

std::vector< int > stormm::topology::AtomGraph::getStructuralAtomNumber

(

)

const

Get the (arbitrarily defined) atom numbers for atoms in the system. For example, a PDB file could ahve its own atom numbering scheme. This provides a way to transcribe that into the AtomGraph object.

Overloaded:

• Get the structural atom numbers of all atoms in the system, as a std::vector<int>
• Get structural atom numbers of a stretch of atoms in the system, as a std::vector<int>
• Get the structural atom number of a specific atom

Parameters

low_index	Index of the first atom for which to read a residue number
high_index	Index of the last atom for which to read a residue number
index	Index of a specific atom

getUreyBradleyTerm()

template<typename T>

UreyBradleyTerm< T > stormm::topology::AtomGraph::getUreyBradleyTerm

(

int

index

)

const

Collect the atom indices and actual parameters to implement one of the system's Urey-Bradley terms. The special-purpose, unguarded struct that holds the result also provides the original parameter index, if of interest. This is for computing the potential energy and forces in the most straightforward manner possible, albeit slow.

Parameters

index

The Urey-Bradley term to query, indexed according to the list of Urey-Bradley terms (not the general atom list)

getVirtualSiteFrameAtom()

int stormm::topology::AtomGraph::getVirtualSiteFrameAtom	(	int	index,
		int	nfrm ) const

Get the general topology index of one of a virtual site's frame atoms.

Parameters

index	The virtual site of interest, indexed according to its place in the list of virtual sites (not the general topology atom list)
nfrm	The frame atom to pull out (values of 1:4 for one, two, three, or four-atom frames are acceptable)

getVirtualSiteFrameDimension()

template<typename T>

T stormm::topology::AtomGraph::getVirtualSiteFrameDimension	(	int	index,
		int	ndim )

Get the dimensions (could be length in A, could be scaling factor for a distance or cross product) of one virtual site's frame.

Parameters

index	The virtual site of interest, indexed according to its place in the list of virtual sites (not the general topology atom list)
ndim	The frame dimension to pull out (values of 1-3 for frames with one, two, or three details are acceptable)

getVirtualSiteFrameType()

VirtualSiteKind stormm::topology::AtomGraph::getVirtualSiteFrameType

(

int

index

)

const

Get the frame type of a particular virtual site.

Parameters

index

The virtual site of interest, indexed according to its place in the list of virtual sites (not the general topology atom list)

getVirtualSiteIndex()

int stormm::topology::AtomGraph::getVirtualSiteIndex	(	int	atom_index,
		ExceptionResponse	policy = ExceptionResponse::DIE ) const

Get the virtual site index of an atom index. If the atom index is not a virtual site, this function will throw an error.

Parameters

atom_index	Index of the atom in question
policy	Action to take if the atom turns out not to be a virtual site at all

matchOverflowAtomName()

std::vector< char4 > stormm::topology::AtomGraph::matchOverflowAtomName

(

const std::string &

query

)

const

Match a long atom name and return its key in the standard list of char4 atom names.

Parameters

query

The extended atom name to match

matchOverflowAtomType()

std::vector< char4 > stormm::topology::AtomGraph::matchOverflowAtomType

(

const std::string &

query

)

const

Match a long atom type and return its key in the standard list of char4 atom types.

Parameters

query

The extended atom type name to match

matchOverflowResidueName()

std::vector< char4 > stormm::topology::AtomGraph::matchOverflowResidueName

(

const std::string &

query

)

const

Match a long residue name and return its key among the standard char4 residue names.

Parameters

query

The extended residue name to match

modifyAtomMobility()

void stormm::topology::AtomGraph::modifyAtomMobility

(

MobilitySetting

movement

)

Change an atom's mobility in the topology.

Overloaded:

• Change all atoms to become mobile or not, or toggle mobility.
• Change a specific stretch of atoms to become mobile or not, or toggle mobility.
• Make a specific atom mobile or not, or toggle mobility.
• Make a scattered selection of atoms mask mobile or not, or toggle the mobility.

Parameters

movement	The desired atom mobility (OFF, ON, or TOGGLE)
low_index	The start of a stretch of atoms
high_index	The end of a stretch of atoms
index	A specific atom index

operator=() [1/2]

AtomGraph & stormm::topology::AtomGraph::operator=

(

AtomGraph &&

other

)

Move constructor.

Parameters

other

Another AtomGraph to form the basis for re-assigning members of this one

operator=() [2/2]

AtomGraph & stormm::topology::AtomGraph::operator=

(

const AtomGraph &

other

)

Copy constructor.

Parameters

other

Another AtomGraph to form the basis for re-assigning members of this one

printToFile()

void stormm::topology::AtomGraph::printToFile	(	const std::string &	output_file = {},
		TopologyKind	output_style = TopologyKind::AMBER,
		PrintSituation	expectation = PrintSituation::OPEN_NEW,
		ExceptionResponse	pr_policy = ExceptionResponse::DIE ) const

Print out a topology in the specified format.

Parameters

output_file	The name of the file to print. If an empty string is given, the source file will be scheduled for overwriting, pending a user-specifiable directive as to whether overwriting is enabled.
output_style	The format of topology to write, each format being readable by specific third-party molecular mechancis packages
expectation	Indicates what state the output file is expected to be found in, if such a file may be found to already exist at all
pr_policy	Specifies the course of action to take if errors are encountered

setAngleParameters()

void stormm::topology::AtomGraph::setAngleParameters	(	double	new_keq,
		double	new_teq,
		bool	set_keq,
		bool	set_teq,
		int	parm_idx,
		ExceptionResponse	policy = ExceptionResponse::SILENT )

Alter the parameters for an angle parameter set. This will alter the parameters in the topology and all angle terms that use the parameters will then be use the new parameters. This function does not add or remove angle terms or parameter sets, nor does it change the mapping of angle terms to parameter sets.

Overloaded:

• Accept the atom types for each atom in the angle
• Accept the parameter set index for the angle

Parameters

new_keq	The new stiffness constant to apply
new_teq	The new angular equilibrium constant to apply
set_keq	Whether to change the stiffness constant
set_teq	Whether to change the equilibrium
parm_idx	Index of the angle parameter set from within the topology's table (one cannot depend on this index to be consistent across topologies of different systems making use of the same force field)
type_a	Atom type of the first atom in the angle (this will be consistent across multiple topologies using the same force field)
type_b	Atom type of the second atom in the angle
type_c	Atom type of the third atom in the angle
policy	Behavior if an angle parameter set matching the index or atom types is not found in the topology

setBondParameters()

void stormm::topology::AtomGraph::setBondParameters	(	double	new_keq,
		double	new_leq,
		bool	set_keq,
		bool	set_leq,
		int	parm_idx,
		ExceptionResponse	policy = ExceptionResponse::SILENT )

Alter the parameters for a bond parameter set. This will alter the parameters in the topology and all bond terms that use the parameters will then be altered. This function does not add or remove bond terms or parameter sets, nor does it change the mapping of bond terms to parameter sets.

Overloaded:

• Accept the atom types for each atom in the bond
• Accept the parameter set index for the bond

Parameters

new_keq	The new stiffness constant to apply
new_leq	The new equilibrium constant to apply
set_keq	Whether to change the stiffness constant
set_leq	Whether to change the equilibrium
parm_idx	Index of the bond parameter set from within the topology's table (one cannot depend on this index to be consistent across topologies of different systems making use of the same force field)
type_a	Atom type of the first atom in the bond (this will be consistent across multiple topologies using the same force field)
type_b	Atom type of the second atom in the bond
policy	Behavior if a bond parameter set matching the index or atom types is not found in the topology

setCharmmImprParameters()

void stormm::topology::AtomGraph::setCharmmImprParameters	(	double	new_stiffness,
		double	new_phase_angle,
		bool	set_stiffness,
		bool	set_phase_angle,
		int	parm_idx,
		ExceptionResponse	policy = ExceptionResponse::SILENT )

Alter the characteristics of a CHARMM improper dihedral parameter set.

Overloaded:

• Accept the atom types for each atom in the CHARMM improper term
• Accept the parameter set index for the CHARMM improper term

Parameters

new_stiffness	The new stiffness constant to apply
new_phase_angle	The new phase angle constant to apply
set_stiffness	Whether to change the stiffness constant
set_phase_angle	Whether to change the equilibrium
parm_idx	Index of the CHARMM improper dihedral parameter set from within the topology's table (one cannot depend on this index to be consistent across topologies of different systems making use of the same force field)
type_a	Atom type of the first atom in the improper (this will be consistent across multiple topologies using the same force field)
type_b	Atom type of the second atom in the improper
type_c	Atom type of the third atom in the improper
type_d	Atom type of the fourth atom in the improper
policy	Behavior if a CHARMM improper dihedral parameter set matching the index or atom types and periodicity is not found in the topology

setDihedralParameters()

void stormm::topology::AtomGraph::setDihedralParameters	(	double	new_amplitude,
		double	new_phase_angle,
		bool	set_amplitude,
		bool	set_phase_angle,
		int	parm_idx,
		ExceptionResponse	policy = ExceptionResponse::SILENT )

Alter the parameters for a cosine-based dihedral angle parameter set. This will alter the parameters in the topology and all dihedral terms that use the parameters will then be use the new parameters. This function does not add or remove dihedral terms or parameter sets, nor does it change the mapping of dihedral terms to parameter sets.

Overloaded:

• Accept the atom types for each atom in the dihedral angle
• Accept the parameter set index for the dihedral angle

Parameters

new_amplitude	The new cosine series term amplitude constant to apply
new_phase_angle	The new phase angle to apply
set_amplitude	Whether to change the amplitude constant
set_phase_angle	Whether to change the equilibrium
parm_idx	Index of the dihedral angle parameter set from within the topology's table (one cannot depend on this index to be consistent across topologies of different systems making use of the same force field)
type_a	Atom type of the first atom in the dihedral (this will be consistent across multiple topologies using the same force field)
type_b	Atom type of the second atom in the dihedral
type_c	Atom type of the third atom in the dihedral
type_d	Atom type of the fourth atom in the dihedral
periodicity	Periodicity of the dihedral parameter set (this disambiguates dihedral parameters that apply on top of one another to the same four atom types)
policy	Behavior if a dihedral parameter set matching the index or atom types and periodicity is not found in the topology

setImplicitSolventModel()

void stormm::topology::AtomGraph::setImplicitSolventModel	(	ImplicitSolventModel	igb_in,
		double	dielectric_in = 80.0,
		double	saltcon_in = 0.0,
		AtomicRadiusSet	radii_set = AtomicRadiusSet::NONE,
		ExceptionResponse	policy = ExceptionResponse::WARN )

Set the implicit solvent model. This will leverage a lot of hard-coded constants to fill out some allocated but otherwise blank arrays and impart one particular Generalized Born or other implicit solvent method.

Parameters

igb_in	The implicit solvent model to impart onto the system
dielectric_in	The desired dielectric constant
saltcon_in	The intended salt concentration (affects the GB decay parameter Kappa)
radii_set	Radii to impart to the topology (this is often coupled to the choice of implicit solvent model, but for purposes of experimentation or new model development might be flexible)
policy	Indicator of what to do if the topology's PB radii to not meet the implicit solvent model requirements, or there is some other problem

setUreyBradleyParameters()

void stormm::topology::AtomGraph::setUreyBradleyParameters	(	double	new_keq,
		double	new_leq,
		bool	set_keq,
		bool	set_leq,
		int	parm_idx,
		ExceptionResponse	policy = ExceptionResponse::SILENT )

Alter the parameters for a Urey-Bradley parameter set.

Overloaded:

• Accept the atom types for each atom in the Urey-Bradley term
• Accept the parameter set index for the Urey-Bradley term

Parameters

new_keq	The new stiffness constant to apply
new_leq	The new equilibrium constant to apply
set_keq	Whether to change the stiffness constant
set_leq	Whether to change the equilibrium
parm_idx	Index of the bond parameter set from within the topology's table (one cannot depend on this index to be consistent across topologies of different systems making use of the same force field)
type_a	Atom type of the first atom in the Urey-Bradley term, the I atom (this will be consistent across multiple topologies using the same force field)
type_b	Atom type of the second atom in the Urey-Bradley term (the K atom)
policy	Behavior if a Urey-Bradley parameter set matching the index or atom types is not found in the topology

setWaterResidueName()

void stormm::topology::AtomGraph::setWaterResidueName

(

const char4

new_name

)

Set the name of the water residue.

Overloaded:

• Set the name based on a char4 (the native representation in the topology)
• Set the name based on up to four characters from a string

Parameters

new_name

The new water residue name to use

Friends And Related Symbol Documentation

AtomGraphStage

friend class AtomGraphStage

friend

Allow the AtomGraphStage to access private members directly to modify and guide construction of topologies used in STORMM's production calculations.

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

• src/Topology/atomgraph.h
• src/Topology/atomgraph_combination.cpp
• src/Topology/atomgraph_constructors.cpp
• src/Topology/atomgraph_detailers.cpp
• src/Topology/atomgraph_extraction.cpp
• src/Topology/atomgraph_getters.cpp
• src/Topology/atomgraph_miscellaneous.cpp
• src/Topology/atomgraph_setters.cpp
• src/Topology/atomgraph_writing.cpp