Gromacs
2021-beta2-UNCHECKED
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Functions | |
const char * | res2bb_notermini (const std::string &name, gmx::ArrayRef< const RtpRename > rr) |
const char * | select_res (int nr, int resnr, const char *name[], const char *expl[], 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 | rename_bb (t_atoms *pdba, const char *oldnm, const char *newnm, bool bFullCompare, t_symtab *symtab) |
void | rename_bbint (t_atoms *pdba, const char *oldnm, const char *gettp(int, gmx::ArrayRef< const RtpRename >), bool bFullCompare, t_symtab *symtab, gmx::ArrayRef< const RtpRename > rr) |
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, ResidueType *rt, const char *watres, AtomProperties *aps, bool bVerbose) |
void | process_chain (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) |
void | sort_pdbatoms (gmx::ArrayRef< const PreprocessResidue > restp_chain, int natoms, t_atoms **pdbaptr, t_atoms **newPdbAtoms, std::vector< gmx::RVec > *x, t_blocka *block, char ***gnames) |
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, ResidueType *rt) |
void | find_nc_ter (t_atoms *pdba, int r0, int r1, int *r_start, int *r_end, ResidueType *rt, 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 |
const gmx::EnumerationArray<ChainSeparationType, const char*> anonymous_namespace{pdb2gmx.cpp}::c_chainSeparationTypeNames |
const gmx::EnumerationArray<ChainSeparationType, const char*> anonymous_namespace{pdb2gmx.cpp}::c_chainSeparationTypeNotificationMessages |
const gmx::EnumerationArray<MergeType, const char*> anonymous_namespace{pdb2gmx.cpp}::c_mergeTypeNames |
const gmx::EnumerationArray<VSitesType, const char*> anonymous_namespace{pdb2gmx.cpp}::c_vsitesTypeNames |
const gmx::EnumerationArray<WaterType, const char*> anonymous_namespace{pdb2gmx.cpp}::c_waterTypeNames |