resall.h File Reference

#include <cstdio>
#include <filesystem>
#include <string>
#include <vector>
#include "gromacs/utility/arrayref.h"

Include dependency graph for resall.h:

Description

Methods to get residue information during preprocessing.

Functions
std::string	searchResidueDatabase (const std::string &key, gmx::ArrayRef< const PreprocessResidue > rtpDBEntry, const gmx::MDLogger &logger)
	Search for an entry in the rtp database. More...
gmx::ArrayRef< const PreprocessResidue > ::const_iterator	getDatabaseEntry (const std::string &rtpname, gmx::ArrayRef< const PreprocessResidue > rtpDBEntry)
	Returns matching entry in database. More...
PreprocessingAtomTypes	read_atype (const std::filesystem::path &ffdir)
	Read atom types into database. More...
void	readResidueDatabase (const std::filesystem::path &resdb, std::vector< PreprocessResidue > *rtpDBEntry, PreprocessingAtomTypes *atype, t_symtab *tab, const gmx::MDLogger &logger, bool bAllowOverrideRTP)
	Read in database, append to exisiting. More...
void	print_resall (FILE *out, gmx::ArrayRef< const PreprocessResidue > rtpDBEntry, const PreprocessingAtomTypes &atype)
	Print out database. More...

Function Documentation

gmx::ArrayRef<const PreprocessResidue>::const_iterator getDatabaseEntry	(	const std::string &	rtpname,
		gmx::ArrayRef< const PreprocessResidue >	rtpDBEntry
	)

Returns matching entry in database.

Parameters

[in]	rtpname	Name of the entry looked for.
[in]	rtpDBEntry	Database to search.

Exceptions

If	the name can not be found in the database.

void print_resall	(	FILE *	out,
		gmx::ArrayRef< const PreprocessResidue >	rtpDBEntry,
		const PreprocessingAtomTypes &	atype
	)

Print out database.

Parameters

[in]	out	File to write to.
[in]	rtpDBEntry	Database to write out.
[in]	atype	Atom type information.

PreprocessingAtomTypes read_atype

(

const std::filesystem::path &

ffdir

)

Read atom types into database.

Parameters

[in]

ffdir

Force field directory.

Returns

Atom type database.

void readResidueDatabase	(	const std::filesystem::path &	resdb,
		std::vector< PreprocessResidue > *	rtpDBEntry,
		PreprocessingAtomTypes *	atype,
		t_symtab *	tab,
		const gmx::MDLogger &	logger,
		bool	bAllowOverrideRTP
	)

Read in database, append to exisiting.

Parameters

[in]	resdb	Name of database file.
[in,out]	rtpDBEntry	Database to populate.
[in,out]	atype	Atomtype information.
[in,out]	tab	Symbol table for names.
[in]	logger	MDLogger interface.
[in]	bAllowOverrideRTP	If entries can be overwritten in the database.

std::string searchResidueDatabase	(	const std::string &	key,
		gmx::ArrayRef< const PreprocessResidue >	rtpDBEntry,
		const gmx::MDLogger &	logger
	)

Search for an entry in the rtp database.

A mismatch of one character is allowed, if there is only one nearly matching entry in the database, a warning will be generated.

Parameters

[in]	key	The atomname to search for.
[in]	rtpDBEntry	Database with residue information.
[in]	logger	Logging object.

Returns

The rtp residue name.