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 {
  50     ehisA, ehisB, ehisH, ehis1, ehisNR
  51 };
  52 GMX_LIBGMXPREPROCESS_EXPORT
  53 extern const char *hh[ehisNR];
  54
  55 typedef struct {
  56     int   res1, res2;
  57     char *a1, *a2;
  58 } t_ssbond;
  59
  60 GMX_LIBGMXPREPROCESS_EXPORT
  61 void choose_ff(const char *ffsel,
  62                char *forcefield, int ff_maxlen,
  63                char *ffdir, int ffdir_maxlen);
  64 /* Find force fields in the current and libdirs and choose an ff.
  65  * If ffsel!=NULL: search for ffsel.
  66  * If ffsel==NULL: interactive selection.
  67  */
  68
  69 GMX_LIBGMXPREPROCESS_EXPORT
  70 void choose_watermodel(const char *wmsel, const char *ffdir,
  71                        char **watermodel);
  72 /* Choose, possibly interactively, which water model to include,
  73  * based on the wmsel command line option choice and watermodels.dat
  74  * in ffdir.
  75  */
  76
  77 GMX_LIBGMXPREPROCESS_EXPORT
  78 void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
  79                         int nrtp, t_restp rtp[],
  80                         int nres, t_resinfo *resinfo,
  81                         int nterpairs,
  82                         t_hackblock **ntdb, t_hackblock **ctdb,
  83                         int *rn, int *rc);
  84 /* Get the database entries for the nres residues in resinfo
  85  * and store them in restp and hb.
  86  */
  87
  88 GMX_LIBGMXPREPROCESS_EXPORT
  89 void match_atomnames_with_rtp(t_restp restp[], t_hackblock hb[],
  90                               t_atoms *pdba, rvec *x,
  91                               gmx_bool bVerbose);
  92 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
  93  * If renaming involves atoms added wrt to the rtp database,
  94  * add these atoms to restp.
  95  */
  96
  97 GMX_LIBGMXPREPROCESS_EXPORT
  98 void print_top_comment(FILE *out, const char *filename, const char *generator, const char *ffdir, gmx_bool bITP);
  99
 100 GMX_LIBGMXPREPROCESS_EXPORT
 101 void print_top_header(FILE *out, const char *filename, const char *title, gmx_bool bITP,
 102                       const char *ffdir, real mHmult);
 103
 104 GMX_LIBGMXPREPROCESS_EXPORT
 105 void print_top_mols(FILE *out,
 106                     const char *title, const char *ffdir, const char *water,
 107                     int nincl, char **incls,
 108                     int nmol, t_mols *mols);
 109
 110 GMX_LIBGMXPREPROCESS_EXPORT
 111 void write_top(FILE *out, char *pr, char *molname,
 112                t_atoms *at, gmx_bool bRTPresname,
 113                int bts[], t_params plist[], t_excls excls[],
 114                gpp_atomtype_t atype, int *cgnr, int nrexcl);
 115 /* NOTE: nrexcl is not the size of *excl! */
 116
 117
 118 GMX_LIBGMXPREPROCESS_EXPORT
 119 void pdb2top(FILE *top_file, char *posre_fn, char *molname,
 120              t_atoms *atoms, rvec **x,
 121              gpp_atomtype_t atype, t_symtab *tab,
 122              int nrtp, t_restp rtp[],
 123              t_restp *restp, t_hackblock *hb,
 124              int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
 125              gmx_bool bAllowMissing,
 126              gmx_bool bVsites, gmx_bool bVsiteAromatics,
 127              const char *ff, const char *ffdir,
 128              real mHmult,
 129              int nssbonds, t_ssbond ssbonds[],
 130              real long_bond_dist, real short_bond_dist,
 131              gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
 132              gmx_bool bRenumRes, gmx_bool bRTPresname);
 133 /* Create a topology ! */
 134
 135 GMX_LIBGMXPREPROCESS_EXPORT
 136 void print_sums(t_atoms *atoms, gmx_bool bSystem);
 137
 138
 139 #endif  /* _pdb2top_h */