src/gromacs/gmxpreprocess/pdb2top.h

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  37
  38 #ifndef GMX_GMXPREPROCESS_PDB2TOP_H
  39 #define GMX_GMXPREPROCESS_PDB2TOP_H
  40
  41 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
  42 #include "gromacs/gmxpreprocess/grompp-impl.h"
  43 #include "gromacs/gmxpreprocess/hackblock.h"
  44 #include "gromacs/gmxpreprocess/toputil.h"
  45
  46 /* this *MUST* correspond to array in pdb2top.c */
  47 enum {
  48     ehisA, ehisB, ehisH, ehis1, ehisNR
  49 };
  50 extern const char *hh[ehisNR];
  51
  52 typedef struct {
  53     int   res1, res2;
  54     char *a1, *a2;
  55 } t_ssbond;
  56
  57 void choose_ff(const char *ffsel,
  58                char *forcefield, int ff_maxlen,
  59                char *ffdir, int ffdir_maxlen);
  60 /* Find force fields in the current and libdirs and choose an ff.
  61  * If ffsel!=NULL: search for ffsel.
  62  * If ffsel==NULL: interactive selection.
  63  */
  64
  65 void choose_watermodel(const char *wmsel, const char *ffdir,
  66                        char **watermodel);
  67 /* Choose, possibly interactively, which water model to include,
  68  * based on the wmsel command line option choice and watermodels.dat
  69  * in ffdir.
  70  */
  71
  72 void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
  73                         int nrtp, t_restp rtp[],
  74                         int nres, t_resinfo *resinfo,
  75                         int nterpairs,
  76                         t_hackblock **ntdb, t_hackblock **ctdb,
  77                         int *rn, int *rc);
  78 /* Get the database entries for the nres residues in resinfo
  79  * and store them in restp and hb.
  80  */
  81
  82 void match_atomnames_with_rtp(t_restp restp[], t_hackblock hb[],
  83                               t_atoms *pdba, rvec *x,
  84                               gmx_bool bVerbose);
  85 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
  86  * If renaming involves atoms added wrt to the rtp database,
  87  * add these atoms to restp.
  88  */
  89
  90 void print_top_comment(FILE *out, const char *filename, const char *ffdir, gmx_bool bITP);
  91
  92 void print_top_header(FILE *out, const char *filename, gmx_bool bITP,
  93                       const char *ffdir, real mHmult);
  94
  95 void print_top_mols(FILE *out,
  96                     const char *title, const char *ffdir, const char *water,
  97                     int nincl, char **incls,
  98                     int nmol, t_mols *mols);
  99
 100 void write_top(FILE *out, char *pr, char *molname,
 101                t_atoms *at, gmx_bool bRTPresname,
 102                int bts[], t_params plist[], t_excls excls[],
 103                gpp_atomtype_t atype, int *cgnr, int nrexcl);
 104 /* NOTE: nrexcl is not the size of *excl! */
 105
 106
 107 void pdb2top(FILE *top_file, char *posre_fn, char *molname,
 108              t_atoms *atoms, rvec **x,
 109              gpp_atomtype_t atype, struct t_symtab *tab,
 110              int nrtp, t_restp rtp[],
 111              t_restp *restp, t_hackblock *hb,
 112              gmx_bool bAllowMissing,
 113              gmx_bool bVsites, gmx_bool bVsiteAromatics,
 114              const char *ffdir,
 115              real mHmult,
 116              int nssbonds, t_ssbond ssbonds[],
 117              real long_bond_dist, real short_bond_dist,
 118              gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
 119              gmx_bool bRenumRes, gmx_bool bRTPresname);
 120 /* Create a topology ! */
 121
 122 void print_sums(t_atoms *atoms, gmx_bool bSystem);
 123
 124 #endif