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10 * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
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33 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
38 #include "visibility.h"
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 GMX_LIBGMXPREPROCESS_EXPORT
48 extern const char *hh
[ehisNR
];
55 GMX_LIBGMXPREPROCESS_EXPORT
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 GMX_LIBGMXPREPROCESS_EXPORT
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 GMX_LIBGMXPREPROCESS_EXPORT
73 void get_hackblocks_rtp(t_hackblock
**hb
, t_restp
**restp
,
74 int nrtp
, t_restp rtp
[],
75 int nres
, t_resinfo
*resinfo
,
77 t_hackblock
**ntdb
, t_hackblock
**ctdb
,
79 /* Get the database entries for the nres residues in resinfo
80 * and store them in restp and hb.
83 GMX_LIBGMXPREPROCESS_EXPORT
84 void match_atomnames_with_rtp(t_restp restp
[],t_hackblock hb
[],
85 t_atoms
*pdba
,rvec
*x
,
87 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
88 * If renaming involves atoms added wrt to the rtp database,
89 * add these atoms to restp.
92 GMX_LIBGMXPREPROCESS_EXPORT
93 void print_top_comment(FILE *out
,const char *filename
,const char *generator
,const char *ffdir
,gmx_bool bITP
);
95 GMX_LIBGMXPREPROCESS_EXPORT
96 void print_top_header(FILE *out
,const char *filename
,const char *title
,gmx_bool bITP
,
97 const char *ffdir
,real mHmult
);
99 GMX_LIBGMXPREPROCESS_EXPORT
100 void print_top_mols(FILE *out
,
101 const char *title
, const char *ffdir
, const char *water
,
102 int nincl
, char **incls
,
103 int nmol
, t_mols
*mols
);
105 GMX_LIBGMXPREPROCESS_EXPORT
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 GMX_LIBGMXPREPROCESS_EXPORT
114 void pdb2top(FILE *top_file
, char *posre_fn
, char *molname
,
115 t_atoms
*atoms
,rvec
**x
,
116 gpp_atomtype_t atype
,t_symtab
*tab
,
117 int nrtp
, t_restp rtp
[],
118 t_restp
*restp
, t_hackblock
*hb
,
119 int nterpairs
, t_hackblock
**ntdb
, t_hackblock
**ctdb
,
120 gmx_bool bAllowMissing
,
121 gmx_bool bVsites
, gmx_bool bVsiteAromatics
,
122 const char *ff
, const char *ffdir
,
124 int nssbonds
, t_ssbond ssbonds
[],
125 real long_bond_dist
, real short_bond_dist
,
126 gmx_bool bDeuterate
, gmx_bool bChargeGroups
, gmx_bool bCmap
,
127 gmx_bool bRenumRes
,gmx_bool bRTPresname
);
128 /* Create a topology ! */
130 GMX_LIBGMXPREPROCESS_EXPORT
131 void print_sums(t_atoms
*atoms
, gmx_bool bSystem
);
134 #endif /* _pdb2top_h */