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33 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
42 #include "hackblock.h"
44 /* this *MUST* correspond to array in pdb2top.c */
45 enum { ehisA
, ehisB
, ehisH
, ehis1
, ehisNR
};
46 extern const char *hh
[ehisNR
];
53 extern void choose_ff(const char *ffsel
,
54 char *forcefield
, int ff_maxlen
,
55 char *ffdir
, int ffdir_maxlen
);
56 /* Find force fields in the current and libdirs and choose an ff.
57 * If ffsel!=NULL: search for ffsel.
58 * If ffsel==NULL: interactive selection.
61 extern void choose_watermodel(const char *wmsel
,const char *ffdir
,
63 /* Choose, possibly interactively, which water model to include,
64 * based on the wmsel command line option choice and watermodels.dat
68 extern void get_hackblocks_rtp(t_hackblock
**hb
, t_restp
**restp
,
69 int nrtp
, t_restp rtp
[],
70 int nres
, t_resinfo
*resinfo
,
72 t_hackblock
**ntdb
, t_hackblock
**ctdb
,
74 /* Get the database entries for the nres residues in resinfo
75 * and store them in restp and hb.
78 extern void match_atomnames_with_rtp(t_restp restp
[],t_hackblock hb
[],
79 t_atoms
*pdba
,rvec
*x
,
81 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
82 * If renaming involves atoms added wrt to the rtp database,
83 * add these atoms to restp.
86 extern void pdb2top(FILE *top_file
, char *posre_fn
, char *molname
,
87 t_atoms
*atoms
,rvec
**x
,
88 gpp_atomtype_t atype
,t_symtab
*tab
,
89 int nrtp
, t_restp rtp
[],
90 t_restp
*restp
, t_hackblock
*hb
,
91 int nterpairs
, t_hackblock
**ntdb
, t_hackblock
**ctdb
,
92 int *rn
, int *rc
, bool bAllowMissing
,
93 bool bVsites
, bool bVsiteAromatics
,
94 const char *ff
, const char *ffdir
, bool bAddCWD
,
96 int nssbonds
, t_ssbond ssbonds
[],
97 real long_bond_dist
, real short_bond_dist
,
98 bool bDeuterate
, bool bChargeGroups
, bool bCmap
,
99 bool bRenumRes
,bool bRTPresname
);
100 /* Create a topology ! */
102 extern void print_sums(t_atoms
*atoms
, bool bSystem
);
105 #endif /* _pdb2top_h */