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33 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
41 #include "gpp_atomtype.h"
43 #include "hackblock.h"
45 /* this *MUST* correspond to array in pdb2top.c */
47 ehisA, ehisB, ehisH, ehis1, ehisNR
49 extern const char *hh[ehisNR];
56 void choose_ff(const char *ffsel,
57 char *forcefield, int ff_maxlen,
58 char *ffdir, int ffdir_maxlen);
59 /* Find force fields in the current and libdirs and choose an ff.
60 * If ffsel!=NULL: search for ffsel.
61 * If ffsel==NULL: interactive selection.
64 void choose_watermodel(const char *wmsel, const char *ffdir,
66 /* Choose, possibly interactively, which water model to include,
67 * based on the wmsel command line option choice and watermodels.dat
71 void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
72 int nrtp, t_restp rtp[],
73 int nres, t_resinfo *resinfo,
75 t_hackblock **ntdb, t_hackblock **ctdb,
77 /* Get the database entries for the nres residues in resinfo
78 * and store them in restp and hb.
81 void match_atomnames_with_rtp(t_restp restp[], t_hackblock hb[],
82 t_atoms *pdba, rvec *x,
84 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
85 * If renaming involves atoms added wrt to the rtp database,
86 * add these atoms to restp.
89 void print_top_comment(FILE *out, const char *filename, const char *generator, const char *ffdir, gmx_bool bITP);
91 void print_top_header(FILE *out, const char *filename, const char *title, gmx_bool bITP,
92 const char *ffdir, real mHmult);
94 void print_top_mols(FILE *out,
95 const char *title, const char *ffdir, const char *water,
96 int nincl, char **incls,
97 int nmol, t_mols *mols);
99 void write_top(FILE *out, char *pr, char *molname,
100 t_atoms *at, gmx_bool bRTPresname,
101 int bts[], t_params plist[], t_excls excls[],
102 gpp_atomtype_t atype, int *cgnr, int nrexcl);
103 /* NOTE: nrexcl is not the size of *excl! */
106 void pdb2top(FILE *top_file, char *posre_fn, char *molname,
107 t_atoms *atoms, rvec **x,
108 gpp_atomtype_t atype, t_symtab *tab,
109 int nrtp, t_restp rtp[],
110 t_restp *restp, t_hackblock *hb,
111 int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
112 gmx_bool bAllowMissing,
113 gmx_bool bVsites, gmx_bool bVsiteAromatics,
114 const char *ff, const char *ffdir,
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 ! */
122 void print_sums(t_atoms *atoms, gmx_bool bSystem);
125 #endif /* _pdb2top_h */