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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 /* Get the database entries for the nres residues in resinfo
79 * and store them in restp and hb.
82 void match_atomnames_with_rtp(t_restp restp
[], t_hackblock hb
[],
83 t_atoms
*pdba
, rvec
*x
,
85 /* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
86 * If renaming involves atoms added wrt to the rtp database,
87 * add these atoms to restp.
90 void print_top_comment(FILE *out
, const char *filename
, const char *ffdir
, gmx_bool bITP
);
92 void print_top_header(FILE *out
, const char *filename
, gmx_bool bITP
,
93 const char *ffdir
, real mHmult
);
95 void print_top_mols(FILE *out
,
96 const char *title
, const char *ffdir
, const char *water
,
97 int nincl
, char **incls
,
98 int nmol
, t_mols
*mols
);
100 void write_top(FILE *out
, char *pr
, char *molname
,
101 t_atoms
*at
, gmx_bool bRTPresname
,
102 int bts
[], t_params plist
[], t_excls excls
[],
103 gpp_atomtype_t atype
, int *cgnr
, int nrexcl
);
104 /* NOTE: nrexcl is not the size of *excl! */
107 void pdb2top(FILE *top_file
, char *posre_fn
, char *molname
,
108 t_atoms
*atoms
, rvec
**x
,
109 gpp_atomtype_t atype
, struct t_symtab
*tab
,
110 int nrtp
, t_restp rtp
[],
111 t_restp
*restp
, t_hackblock
*hb
,
112 gmx_bool bAllowMissing
,
113 gmx_bool bVsites
, gmx_bool bVsiteAromatics
,
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
);