Enumerations
enum	AspartateStates : int { Deprot, Prot, Count }

enum	GlutamateStates : int { Deprot, Prot, Count }

enum	GlutamineStates : int { Deprot, Prot, Count }

enum	LysineStates : int { Deprot, Prot, Count }

enum	ArginineStates : int { Deprot, Prot, Count }

enum	ChainSeparationType : int { IdOrTer, IdAndTer, Ter, Id, Interactive, Count }

enum	VSitesType : int { None, Hydrogens, Aromatics, Count }

enum	WaterType : int { Select, None, Spc, SpcE, Tip3p, Tip4p, Tip5p, Tips3p, Count }

enum	MergeType : int { No, All, Interactive, Count }

Functions
const char *	res2bb_notermini (const std::string &name, gmx::ArrayRef< const RtpRename > rr)

const char *	enumValueToLongString (HistidineStates enumValue)

const char *	enumValueToString (AspartateStates enumValue)

const char *	enumValueToLongString (AspartateStates enumValue)

const char *	enumValueToString (GlutamateStates enumValue)

const char *	enumValueToLongString (GlutamateStates enumValue)

const char *	enumValueToString (GlutamineStates enumValue)

const char *	enumValueToLongString (GlutamineStates enumValue)

const char *	enumValueToString (LysineStates enumValue)

const char *	enumValueToLongString (LysineStates enumValue)

const char *	enumValueToString (ArginineStates enumValue)

const char *	enumValueToLongString (ArginineStates enumValue)

template<typename EnumType >
const char *	select_res (int resnr, const char *title, gmx::ArrayRef< const RtpRename > rr)

const char *	get_asptp (int resnr, gmx::ArrayRef< const RtpRename > rr)

const char *	get_glutp (int resnr, gmx::ArrayRef< const RtpRename > rr)

const char *	get_glntp (int resnr, gmx::ArrayRef< const RtpRename > rr)

const char *	get_lystp (int resnr, gmx::ArrayRef< const RtpRename > rr)

const char *	get_argtp (int resnr, gmx::ArrayRef< const RtpRename > rr)

const char *	get_histp (int resnr, gmx::ArrayRef< const RtpRename > rr)

void	read_rtprename (const char fname, FILE fp, std::vector< RtpRename > *rtprename)

std::string	search_resrename (gmx::ArrayRef< const RtpRename > rr, const char *name, bool bStart, bool bEnd, bool bCompareFFRTPname)

void	rename_resrtp (t_atoms pdba, int nterpairs, gmx::ArrayRef< const int > r_start, gmx::ArrayRef< const int > r_end, gmx::ArrayRef< const RtpRename > rr, t_symtab symtab, bool bVerbose, const gmx::MDLogger &logger)

void	pdbres_to_gmxrtp (t_atoms *pdba)

void	rename_pdbres (t_atoms pdba, const char oldnm, const char newnm, bool bFullCompare, t_symtab symtab)

void	renameResidue (const gmx::MDLogger &logger, t_atoms pdba, const char oldnm, const char newnm, bool bFullCompare, t_symtab symtab)
	Rename all residues named `oldnm` to `newnm`. More...

void	renameResidueInteractively (t_atoms pdba, const char oldnm, const char gettp(int, gmx::ArrayRef< const RtpRename >), bool bFullCompare, t_symtab symtab, gmx::ArrayRef< const RtpRename > rr)
	Rename all residues named `oldnm` according to the user's interactive choice. More...

void	check_occupancy (t_atoms atoms, const char filename, bool bVerbose, const gmx::MDLogger &logger)

void	write_posres (const char fn, t_atoms pdba, real fc)

int	read_pdball (const char inf, bool bOutput, const char outf, char *title, t_atoms atoms, rvec *x, PbcType pbcType, matrix box, bool bRemoveH, t_symtab symtab, const ResidueTypeMap &residueTypeMap, const char watres, AtomProperties *aps, bool bVerbose)

void	process_chain (const gmx::MDLogger &logger, t_atoms pdba, gmx::ArrayRef< gmx::RVec > x, bool bTrpU, bool bPheU, bool bTyrU, bool bLysMan, bool bAspMan, bool bGluMan, bool bHisMan, bool bArgMan, bool bGlnMan, real angle, real distance, t_symtab symtab, gmx::ArrayRef< const RtpRename > rr)

bool	pdbicomp (const t_pdbindex &a, const t_pdbindex &b)

std::vector< IndexGroup >	sort_pdbatoms (gmx::ArrayRef< const PreprocessResidue > restp_chain, int natoms, t_atoms pdbaptr, t_atoms newPdbAtoms, std::vector< gmx::RVec > *x)

int	remove_duplicate_atoms (t_atoms *pdba, gmx::ArrayRef< gmx::RVec > x, bool bVerbose, const gmx::MDLogger &logger)

void	checkResidueTypeSanity (t_atoms *pdba, int r0, int r1, const ResidueTypeMap &residueTypeMap)

void	find_nc_ter (t_atoms pdba, int r0, int r1, int r_start, int *r_end, const ResidueTypeMap &residueTypeMap, const gmx::MDLogger &logger)

void	modify_chain_numbers (t_atoms *pdba, ChainSeparationType chainSeparation, const gmx::MDLogger &logger)

bool	checkChainCyclicity (t_atoms pdba, rvec pdbx, int start_ter, int end_ter, gmx::ArrayRef< const PreprocessResidue > rtpFFDB, gmx::ArrayRef< const RtpRename > rr, real long_bond_dist_, real short_bond_dist_)

Variables
const gmx::EnumerationArray < ChainSeparationType, const char * >	c_chainSeparationTypeNames

const gmx::EnumerationArray < ChainSeparationType, const char * >	c_chainSeparationTypeNotificationMessages

const gmx::EnumerationArray < VSitesType, const char * >	c_vsitesTypeNames

const gmx::EnumerationArray < WaterType, const char * >	c_waterTypeNames

const gmx::EnumerationArray < MergeType, const char * >	c_mergeTypeNames

Function Documentation

void anonymous_namespace{pdb2gmx.cpp}::renameResidue	(	const gmx::MDLogger &	logger,
		t_atoms *	pdba,
		const char *	oldnm,
		const char *	newnm,
		bool	bFullCompare,
		t_symtab *	symtab
	)

Rename all residues named oldnm to newnm.

Search for residues for which the residue name from the input configuration file matches oldnm, and when found choose the rtp entry and name of newnm.

Todo:: Refactor this function to accept a lambda that accepts i and numMatchesFound but always produces newnm. Then remove renameResiduesInteractively by calling this method with suitable lambdas that capture its parameter rr and ignores numMatchesFound.

void anonymous_namespace{pdb2gmx.cpp}::renameResidueInteractively	(	t_atoms *	pdba,
		const char *	oldnm,
		const char *	gettpint, gmx::ArrayRef< const RtpRename >,
		bool	bFullCompare,
		t_symtab *	symtab,
		gmx::ArrayRef< const RtpRename >	rr
	)

Rename all residues named oldnm according to the user's interactive choice.

Search for residues for which the residue name from the input configuration file matches oldnm, and when found choose the rtp entry and name of the interactive choice from gettp.

Todo:: Remove this function, per todo in renameResidue.

Variable Documentation

const gmx::EnumerationArray<ChainSeparationType, const char*> anonymous_namespace{pdb2gmx.cpp}::c_chainSeparationTypeNames

Initial value:

= {
    { "id_or_ter", "id_and_ter", "ter", "id", "interactive" }
}

const gmx::EnumerationArray<ChainSeparationType, const char*> anonymous_namespace{pdb2gmx.cpp}::c_chainSeparationTypeNotificationMessages

Initial value:

= {
    { "Splitting chemical chains based on TER records or chain id changing.\n",
      "Splitting chemical chains based on TER records and chain id changing.\n",
      "Splitting chemical chains based on TER records only (ignoring chain id).\n",
      "Splitting chemical chains based on changing chain id only (ignoring TER records).\n",
      "Splitting chemical chains interactively.\n" }
}

const gmx::EnumerationArray<MergeType, const char*> anonymous_namespace{pdb2gmx.cpp}::c_mergeTypeNames

Initial value:

= {
    { "no", "all", "interactive" }
}

const gmx::EnumerationArray<VSitesType, const char*> anonymous_namespace{pdb2gmx.cpp}::c_vsitesTypeNames

Initial value:

= {
    { "none", "hydrogens", "aromatics" }
}

const gmx::EnumerationArray<WaterType, const char*> anonymous_namespace{pdb2gmx.cpp}::c_waterTypeNames

Initial value:

= {
    { "select", "none", "spc", "spce", "tip3p", "tip4p", "tip5p", "tips3p" }
}

Enumerations

Functions

Variables

Function Documentation

Variable Documentation