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