gromacs-dev 4.6.5-1build1 / usr / include / gromacs / pdb2top.h

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#ifndef _pdb2top_h
#define _pdb2top_h
#include "visibility.h"
#include "typedefs.h"
#include "grompp.h"
#include "gpp_atomtype.h"
#include "toputil.h"
#include "hackblock.h"

/* this *MUST* correspond to array in pdb2top.c */
enum {
    ehisA, ehisB, ehisH, ehis1, ehisNR
};
GMX_LIBGMXPREPROCESS_EXPORT
extern const char *hh[ehisNR];

typedef struct {
    int   res1, res2;
    char *a1, *a2;
} t_ssbond;

GMX_LIBGMXPREPROCESS_EXPORT
void choose_ff(const char *ffsel,
               char *forcefield, int ff_maxlen,
               char *ffdir, int ffdir_maxlen);
/* Find force fields in the current and libdirs and choose an ff.
 * If ffsel!=NULL: search for ffsel.
 * If ffsel==NULL: interactive selection.
 */

GMX_LIBGMXPREPROCESS_EXPORT
void choose_watermodel(const char *wmsel, const char *ffdir,
                       char **watermodel);
/* Choose, possibly interactively, which water model to include,
 * based on the wmsel command line option choice and watermodels.dat
 * in ffdir.
 */

GMX_LIBGMXPREPROCESS_EXPORT
void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
                        int nrtp, t_restp rtp[],
                        int nres, t_resinfo *resinfo,
                        int nterpairs,
                        t_hackblock **ntdb, t_hackblock **ctdb,
                        int *rn, int *rc);
/* Get the database entries for the nres residues in resinfo
 * and store them in restp and hb.
 */

GMX_LIBGMXPREPROCESS_EXPORT
void match_atomnames_with_rtp(t_restp restp[], t_hackblock hb[],
                              t_atoms *pdba, rvec *x,
                              gmx_bool bVerbose);
/* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
 * If renaming involves atoms added wrt to the rtp database,
 * add these atoms to restp.
 */

GMX_LIBGMXPREPROCESS_EXPORT
void print_top_comment(FILE *out, const char *filename, const char *generator, const char *ffdir, gmx_bool bITP);

GMX_LIBGMXPREPROCESS_EXPORT
void print_top_header(FILE *out, const char *filename, const char *title, gmx_bool bITP,
                      const char *ffdir, real mHmult);

GMX_LIBGMXPREPROCESS_EXPORT
void print_top_mols(FILE *out,
                    const char *title, const char *ffdir, const char *water,
                    int nincl, char **incls,
                    int nmol, t_mols *mols);

GMX_LIBGMXPREPROCESS_EXPORT
void write_top(FILE *out, char *pr, char *molname,
               t_atoms *at, gmx_bool bRTPresname,
               int bts[], t_params plist[], t_excls excls[],
               gpp_atomtype_t atype, int *cgnr, int nrexcl);
/* NOTE: nrexcl is not the size of *excl! */


GMX_LIBGMXPREPROCESS_EXPORT
void pdb2top(FILE *top_file, char *posre_fn, char *molname,
             t_atoms *atoms, rvec **x,
             gpp_atomtype_t atype, t_symtab *tab,
             int nrtp, t_restp rtp[],
             t_restp *restp, t_hackblock *hb,
             int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
             gmx_bool bAllowMissing,
             gmx_bool bVsites, gmx_bool bVsiteAromatics,
             const char *ff, const char *ffdir,
             real mHmult,
             int nssbonds, t_ssbond ssbonds[],
             real long_bond_dist, real short_bond_dist,
             gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
             gmx_bool bRenumRes, gmx_bool bRTPresname);
/* Create a topology ! */

GMX_LIBGMXPREPROCESS_EXPORT
void print_sums(t_atoms *atoms, gmx_bool bSystem);


#endif  /* _pdb2top_h */