Public Member Functions
int	getAtomCount () const
	Get the number of atoms in the structure (the number of atoms per model).

int	getModelCount () const
	Get the number of models in the object.

bool	getFormalChargePrinting () const
	Get the object's current directive on whether to print formal charges to any output files.

CoordinateFrame	exportCoordinateFrame (int model_index, HybridFormat layout=default_hpc_format) const
	Produce a CoordinateFrame object from a specific model index.

PhaseSpace	exportPhaseSpace (int model_index, HybridFormat layout=default_hpc_format) const
	Produce a PhaseSpace object (with zero velocity and force components) based on the particle positions in a specific model index. Descriptions of input parameters follow from getCoordinateFrame(), above.

template<typename T>
CoordinateSeries< T >	getCoordinateSeries (const std::vector< int > model_sequence={}) const
	Produce a CoordinateSeries object based on the particle positions in a sequence of models.

void	writeToFile (const std::string &file_name, PrintSituation expectation, const std::vector< int > &model_indices={}) const
	Write the contents of the object to a PDB file.

void	setFormalChargePrinting (bool print_formal_charges_in=true)
	Set whether to print formal charges in any output files.


	Pdb (int atom_count_in=0, int model_count_in=1)
	The constructor can accept a file to read, arrays of data to compile, or a simple number of atoms for which to allocate space.

	Pdb (const std::string &file_name_in, int model_index=-1, const std::vector< char > &alternate_prefs={ ' ', 'A' })

	Pdb (const std::string &file_name_in, const std::vector< int > &model_indices, const std::vector< char > &alternate_prefs={ ' ', 'A' })

	Pdb (int atom_count_in, int model_count_in, const std::vector< double > &x_coordinates_in, const std::vector< double > &y_coordinates_in, const std::vector< double > &z_coordinates_in, const std::vector< char4 > &atom_names_in, const std::vector< char4 > &residue_names_in, const std::vector< char > &chain_names_in, const std::vector< double > &occupancies_in, const std::vector< double > &b_factors_in, const std::vector< char2 > &elements_in={}, const std::vector< int > &atom_numbers_in={}, const std::vector< int > &residue_numbers_in={}, const std::vector< int > &anisotropy_matrices_in={}, const std::vector< PdbAtomKind > &atom_classes_in={}, const std::vector< std::string > &header_in={}, const std::vector< std::string > &remark_in={}, const std::vector< std::string > &extras_in={})

	Pdb (const AtomGraph ag, const CoordinateFrame cf)

	Pdb (const AtomGraph &ag, const CoordinateFrame &cf)

	Pdb (const AtomGraph ag, const PhaseSpace ps)

	Pdb (const AtomGraph &ag, const PhaseSpace &ps)

template<typename T>
	Pdb (const AtomGraph ag, const CoordinateSeries< T > cf, const std::vector< int > &frames={})

template<typename T>
	Pdb (const AtomGraph &ag, const CoordinateSeries< T > &cf, const std::vector< int > &frames={})

template<typename T>
	Pdb (const AtomGraph ag, const CoordinateSeries< T > cs, int frame_number)

template<typename T>
	Pdb (const AtomGraph &ag, const CoordinateSeries< T > &cs, int frame_number)


void	loadTopologicalData (const AtomGraph *ag)
	Transcribe information from a topology into the object. This includes atom names, symbols, and formal charges. Atom classes will be assigned based on recognized amino acid names. Atom symbols for virtual sites will be listed as "VS", and all letters in atom symbols will be capitalized.

void	loadTopologicalData (const AtomGraph &ag)


template<typename T>
void	loadCoordinates (const T xcrd_in, const T ycrd_in, const T *zcrd_in, int model_index=0, double gpos_scale=1.0)
	Load coordinates into the object from various coordinate objects.

void	loadCoordinates (const llint xcrd_in, const llint ycrd_in, const llint zcrd_in, const int xcrd_ovrf, const int ycrd_ovrf, const int zcrd_ovrf, double gpos_scale=1.0, int model_index=0)

void	loadCoordinates (const CoordinateFrame *cf, int model_index=0)

void	loadCoordinates (const CoordinateFrame &cf, int model_index=0)

void	loadCoordinates (const PhaseSpace *ps, int model_index=0)

void	loadCoordinates (const PhaseSpace &ps, int model_index=0)

template<typename T>
void	loadCoordinates (const CoordinateSeries< T > *cs, const std::vector< int2 > &frame_mapping={})

template<typename T>
void	loadCoordinates (const CoordinateSeries< T > &cs, const std::vector< int2 > &frame_mapping={})

void	loadCoordinates (const PhaseSpaceSynthesis *poly_ps, int system_index, int model_index=0)

void	loadCoordinates (const PhaseSpaceSynthesis &poly_ps, int system_index, int model_index=0)

void	loadCoordinates (const Condensate *cdns, int system_index, int model_index=0)

void	loadCoordinates (const Condensate &cdns, int system_index, int model_index=0)

Constructor & Destructor Documentation

◆ Pdb()

stormm::structure::Pdb::Pdb	(	int	atom_count_in = 0,
		int	model_count_in = 1 )

The constructor can accept a file to read, arrays of data to compile, or a simple number of atoms for which to allocate space.

Parameters

atom_count_in	The anticipated number of atoms in each model entry
model_count_in	The anticipated number of models
file_name_in	Name of the input PDB file
model_index	Indicate a particular model of the PDB to use in constructing the object
alternate_prefs	List of symbols that will qualify for including an atom. White space is an option.
xcoordinates_in	Cartesian X coordinates of all particles, perhaps spanning multiple model entries. If multiple model entries are involved, the inputs for each separate model must be padded by the warp size.
ycoordinates_in	Cartesian Y coordinates of all particles
zcoordinates_in	Cartesian Z coordinates of all particles
atom_names_in	Names of atoms in each entry, common to all entries
res_names_in	Names of residues in each entry, listed atom by atom and common to all entries
chain_names_in	Names of each chain in the system, common to all entries
occupancies_in	The occupancies of each atom, unique to each entry
b_factors_in	Temperature factors indicating the spread of positions for each atom about some observed mean. Unique elements must be provided for each entry.
elements_in	IUPAC element symbols for each atom
ag	Topology providing atom-specific information for each model entry
cf	Coordinates for one system
ps	Coordinates for one system
cs	Coordinates for multiple copies of one system
frames	A list of frames associated with a CoordinateSeries (input cs)
frame_number	A specific frame associated with a CoordinateSeries

Member Function Documentation

◆ exportCoordinateFrame()

CoordinateFrame stormm::structure::Pdb::exportCoordinateFrame	(	int	model_index,
		HybridFormat	layout = default_hpc_format ) const

Produce a CoordinateFrame object from a specific model index.

Parameters

model_index	The model of interest (this will be checked against the actual number of models available)
layout	The memory (CPU host and GPU device) layout with which to create the resulting object

◆ getCoordinateSeries()

template<typename T>

CoordinateSeries< T > stormm::structure::Pdb::getCoordinateSeries ( const std::vector< int > model_sequence = {} ) const

Produce a CoordinateSeries object based on the particle positions in a sequence of models.

Parameters

model_sequence The sequence of models to impart to frames of the coordinate series. An empty vector indicates that all models should be imparted, in order.

◆ loadCoordinates()

template<typename T>

void stormm::structure::Pdb::loadCoordinates	(	const T *	xcrd_in,
		const T *	ycrd_in,
		const T *	zcrd_in,
		int	model_index = 0,
		double	gpos_scale = 1.0 )

Load coordinates into the object from various coordinate objects.

Overloaded:

Provide C-style arrays for each of the three Cartesian dimensions
Provide one of STORMM's typical coordinate objects, with a system index if necessary

Parameters

xcrd_in	Pointer to Cartesian X coordinates, in units of Angstroms. The order of atoms in these coordinates is expected to match that in the Pdb object.
ycrd_in	Pointer to Cartesian Y coordinates, in units of Angstroms
zcrd_in	Pointer to Cartesian Z coordinates, in units of Angstroms
xcrd_ovrf	Overflow bits for split fixed-precision Cartesian X coordinates
ycrd_ovrf	Overflow bits for split fixed-precision Cartesian Y coordinates
zcrd_ovrf	Overflow bits for split fixed-precision Cartesian Z coordinates
cf	A set of coordinates to draw from
ps	A set of coordinates to draw from. The POSITIONS aspect of this input will be taken, at whatever point in the coordinate cycle the object is currently at.
cs	A coordinate series to draw from (one frame, a collection of frames, or all frames in the series can be taken into the object). If all frames of the series are to be loaded and the series has more frames than the object has models, the loading will stop at the limit of the object.
poly_ps	A coordinate synthesis to draw from (a specific system within the synthesis must be specified)
cdns	An abridged coordinate synthesis to draw from (a specific system must be specified)
system_index	Index of the system to take from a coordinate synthesis
frame_index	Index of the frame to take from a coordinate series

◆ loadTopologicalData()

void stormm::structure::Pdb::loadTopologicalData ( const AtomGraph * ag )

Transcribe information from a topology into the object. This includes atom names, symbols, and formal charges. Atom classes will be assigned based on recognized amino acid names. Atom symbols for virtual sites will be listed as "VS", and all letters in atom symbols will be capitalized.

Overloaded:

Provide the topology by const pointer
Provide the topology by const reference

Parameters

ag	The topology containing information to transcribe

◆ setFormalChargePrinting()

void stormm::structure::Pdb::setFormalChargePrinting ( bool print_formal_charges_in = true )

Set whether to print formal charges in any output files.

Parameters

print_formal_charges_in The new setting to apply

◆ writeToFile()

void stormm::structure::Pdb::writeToFile	(	const std::string &	file_name,
		PrintSituation	expectation,
		const std::vector< int > &	model_indices = {} ) const

Write the contents of the object to a PDB file.

Parameters

file_name	Name of the file to write (likely to have a .pdb extension)
expectation	Directive as to what to do if the file already exists

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

src/MoleculeFormat/pdb.h
src/MoleculeFormat/pdb.cpp

Public Member Functions

Constructor & Destructor Documentation

◆ Pdb()

Member Function Documentation

◆ exportCoordinateFrame()

◆ getCoordinateSeries()

◆ loadCoordinates()

◆ loadTopologicalData()

◆ setFormalChargePrinting()

◆ writeToFile()