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Enumerations | Functions | Variables
anonymous_namespace{pdb2gmx.cpp} Namespace Reference

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< IndexGroupsort_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" }
}