include/pdb2top.h

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  38
  39 #ifndef _pdb2top_h
  40 #define _pdb2top_h
  41 #include "visibility.h"
  42 #include "typedefs.h"
  43 #include "grompp.h"
  44 #include "gpp_atomtype.h"
  45 #include "toputil.h"
  46 #include "hackblock.h"
  47
  48 /* this *MUST* correspond to array in pdb2top.c */
  49 enum { ehisA, ehisB, ehisH, ehis1, ehisNR };
  50 GMX_LIBGMXPREPROCESS_EXPORT
  51 extern const char *hh[ehisNR];
  52
  53 typedef struct {
  54   int  res1,res2;
  55   char *a1,*a2;
  56 } t_ssbond;
  57
  58 GMX_LIBGMXPREPROCESS_EXPORT
  59 void choose_ff(const char *ffsel,
  60                       char *forcefield, int ff_maxlen,
  61                       char *ffdir, int ffdir_maxlen);
  62 /* Find force fields in the current and libdirs and choose an ff.
  63  * If ffsel!=NULL: search for ffsel.
  64  * If ffsel==NULL: interactive selection.
  65  */
  66
  67 GMX_LIBGMXPREPROCESS_EXPORT
  68 void choose_watermodel(const char *wmsel,const char *ffdir,
  69                               char **watermodel);
  70 /* Choose, possibly interactively, which water model to include,
  71  * based on the wmsel command line option choice and watermodels.dat
  72  * in ffdir.
  73  */
  74
  75 GMX_LIBGMXPREPROCESS_EXPORT
  76 void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
  77                                int nrtp, t_restp rtp[],
  78                                int nres, t_resinfo *resinfo,
  79                                int nterpairs,
  80                                t_hackblock **ntdb, t_hackblock **ctdb,
  81                                int *rn, int *rc);
  82 /* Get the database entries for the nres residues in resinfo
  83  * and store them in restp and hb.
  84  */
  85
  86 GMX_LIBGMXPREPROCESS_EXPORT
  87 void match_atomnames_with_rtp(t_restp restp[],t_hackblock hb[],
  88                                      t_atoms *pdba,rvec *x,
  89                                      gmx_bool bVerbose);
  90 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
  91  * If renaming involves atoms added wrt to the rtp database,
  92  * add these atoms to restp.
  93  */
  94
  95 GMX_LIBGMXPREPROCESS_EXPORT
  96 void print_top_comment(FILE *out,const char *filename,const char *generator,const char *ffdir,gmx_bool bITP);
  97
  98 GMX_LIBGMXPREPROCESS_EXPORT
  99 void print_top_header(FILE *out,const char *filename,const char *title,gmx_bool bITP,
 100                              const char *ffdir,real mHmult);
 101
 102 GMX_LIBGMXPREPROCESS_EXPORT
 103 void print_top_mols(FILE *out,
 104                            const char *title, const char *ffdir, const char *water,
 105                            int nincl, char **incls,
 106                            int nmol, t_mols *mols);
 107
 108 GMX_LIBGMXPREPROCESS_EXPORT
 109 void write_top(FILE *out, char *pr,char *molname,
 110                       t_atoms *at,gmx_bool bRTPresname,
 111                       int bts[],t_params plist[],t_excls excls[],
 112                       gpp_atomtype_t atype,int *cgnr, int nrexcl);
 113 /* NOTE: nrexcl is not the size of *excl! */
 114
 115
 116 GMX_LIBGMXPREPROCESS_EXPORT
 117 void pdb2top(FILE *top_file, char *posre_fn, char *molname,
 118                     t_atoms *atoms,rvec **x,
 119                     gpp_atomtype_t atype,t_symtab *tab,
 120                     int nrtp, t_restp rtp[],
 121                     t_restp *restp, t_hackblock *hb,
 122                     int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
 123                     gmx_bool bAllowMissing,
 124                     gmx_bool bVsites, gmx_bool bVsiteAromatics,
 125                     const char *ff, const char *ffdir,
 126                     real mHmult,
 127                     int nssbonds, t_ssbond ssbonds[],
 128                     real long_bond_dist, real short_bond_dist,
 129                     gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
 130                     gmx_bool bRenumRes,gmx_bool bRTPresname);
 131 /* Create a topology ! */
 132
 133 GMX_LIBGMXPREPROCESS_EXPORT
 134 void print_sums(t_atoms *atoms, gmx_bool bSystem);
 135
 136
 137 #endif  /* _pdb2top_h */