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38 #ifndef GMX_GMXPREPROCESS_PDB2TOP_H
39 #define GMX_GMXPREPROCESS_PDB2TOP_H
42 #include "grompp-impl.h"
43 #include "gpp_atomtype.h"
45 #include "hackblock.h"
52 /* this *MUST* correspond to array in pdb2top.c */
54 ehisA, ehisB, ehisH, ehis1, ehisNR
56 extern const char *hh[ehisNR];
63 void choose_ff(const char *ffsel,
64 char *forcefield, int ff_maxlen,
65 char *ffdir, int ffdir_maxlen);
66 /* Find force fields in the current and libdirs and choose an ff.
67 * If ffsel!=NULL: search for ffsel.
68 * If ffsel==NULL: interactive selection.
71 void choose_watermodel(const char *wmsel, const char *ffdir,
73 /* Choose, possibly interactively, which water model to include,
74 * based on the wmsel command line option choice and watermodels.dat
78 void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
79 int nrtp, t_restp rtp[],
80 int nres, t_resinfo *resinfo,
82 t_hackblock **ntdb, t_hackblock **ctdb,
84 /* Get the database entries for the nres residues in resinfo
85 * and store them in restp and hb.
88 void match_atomnames_with_rtp(t_restp restp[], t_hackblock hb[],
89 t_atoms *pdba, rvec *x,
91 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
92 * If renaming involves atoms added wrt to the rtp database,
93 * add these atoms to restp.
96 void print_top_comment(FILE *out, const char *filename, const char *ffdir, gmx_bool bITP);
98 void print_top_header(FILE *out, const char *filename, gmx_bool bITP,
99 const char *ffdir, real mHmult);
101 void print_top_mols(FILE *out,
102 const char *title, const char *ffdir, const char *water,
103 int nincl, char **incls,
104 int nmol, t_mols *mols);
106 void write_top(FILE *out, char *pr, char *molname,
107 t_atoms *at, gmx_bool bRTPresname,
108 int bts[], t_params plist[], t_excls excls[],
109 gpp_atomtype_t atype, int *cgnr, int nrexcl);
110 /* NOTE: nrexcl is not the size of *excl! */
113 void pdb2top(FILE *top_file, char *posre_fn, char *molname,
114 t_atoms *atoms, rvec **x,
115 gpp_atomtype_t atype, t_symtab *tab,
116 int nrtp, t_restp rtp[],
117 t_restp *restp, t_hackblock *hb,
118 gmx_bool bAllowMissing,
119 gmx_bool bVsites, gmx_bool bVsiteAromatics,
122 int nssbonds, t_ssbond ssbonds[],
123 real long_bond_dist, real short_bond_dist,
124 gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
125 gmx_bool bRenumRes, gmx_bool bRTPresname);
126 /* Create a topology ! */
128 void print_sums(t_atoms *atoms, gmx_bool bSystem);