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