/*
- *
+ *
* This source code is part of
- *
+ *
* G R O M A C S
- *
+ *
* GROningen MAchine for Chemical Simulations
- *
+ *
* VERSION 3.2.0
* Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
* Copyright (c) 1991-2000, University of Groningen, The Netherlands.
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
- *
+ *
* If you want to redistribute modifications, please consider that
* scientific software is very special. Version control is crucial -
* bugs must be traceable. We will be happy to consider code for
* inclusion in the official distribution, but derived work must not
* be called official GROMACS. Details are found in the README & COPYING
* files - if they are missing, get the official version at www.gromacs.org.
- *
+ *
* To help us fund GROMACS development, we humbly ask that you cite
* the papers on the package - you can find them in the top README file.
- *
+ *
* For more info, check our website at http://www.gromacs.org
- *
+ *
* And Hey:
* Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*/
#include "hackblock.h"
/* this *MUST* correspond to array in pdb2top.c */
-enum { ehisA, ehisB, ehisH, ehis1, ehisNR };
+enum {
+ ehisA, ehisB, ehisH, ehis1, ehisNR
+};
extern const char *hh[ehisNR];
typedef struct {
- int res1,res2;
- char *a1,*a2;
+ int res1, res2;
+ char *a1, *a2;
} t_ssbond;
void choose_ff(const char *ffsel,
- char *forcefield, int ff_maxlen,
- char *ffdir, int ffdir_maxlen);
+ char *forcefield, int ff_maxlen,
+ char *ffdir, int ffdir_maxlen);
/* Find force fields in the current and libdirs and choose an ff.
* If ffsel!=NULL: search for ffsel.
* If ffsel==NULL: interactive selection.
*/
-void choose_watermodel(const char *wmsel,const char *ffdir,
- char **watermodel);
+void choose_watermodel(const char *wmsel, const char *ffdir,
+ char **watermodel);
/* Choose, possibly interactively, which water model to include,
* based on the wmsel command line option choice and watermodels.dat
* in ffdir.
*/
-void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
- int nrtp, t_restp rtp[],
- int nres, t_resinfo *resinfo,
- int nterpairs,
- t_hackblock **ntdb, t_hackblock **ctdb,
- int *rn, int *rc);
+void get_hackblocks_rtp(t_hackblock **hb, t_restp **restp,
+ int nrtp, t_restp rtp[],
+ int nres, t_resinfo *resinfo,
+ int nterpairs,
+ t_hackblock **ntdb, t_hackblock **ctdb,
+ int *rn, int *rc);
/* Get the database entries for the nres residues in resinfo
* and store them in restp and hb.
*/
-void match_atomnames_with_rtp(t_restp restp[],t_hackblock hb[],
- t_atoms *pdba,rvec *x,
- gmx_bool bVerbose);
+void match_atomnames_with_rtp(t_restp restp[], t_hackblock hb[],
+ t_atoms *pdba, rvec *x,
+ gmx_bool bVerbose);
/* Check if atom in pdba need to be deleted of renamed due to tdb or hdb.
* If renaming involves atoms added wrt to the rtp database,
* add these atoms to restp.
*/
-void print_top_comment(FILE *out,const char *filename,const char *generator,const char *ffdir,gmx_bool bITP);
+void print_top_comment(FILE *out, const char *filename, const char *generator, const char *ffdir, gmx_bool bITP);
-void print_top_header(FILE *out,const char *filename,const char *title,gmx_bool bITP,
- const char *ffdir,real mHmult);
+void print_top_header(FILE *out, const char *filename, const char *title, gmx_bool bITP,
+ const char *ffdir, real mHmult);
void print_top_mols(FILE *out,
- const char *title, const char *ffdir, const char *water,
- int nincl, char **incls,
- int nmol, t_mols *mols);
-
-void write_top(FILE *out, char *pr,char *molname,
- t_atoms *at,gmx_bool bRTPresname,
- int bts[],t_params plist[],t_excls excls[],
- gpp_atomtype_t atype,int *cgnr, int nrexcl);
+ const char *title, const char *ffdir, const char *water,
+ int nincl, char **incls,
+ int nmol, t_mols *mols);
+
+void write_top(FILE *out, char *pr, char *molname,
+ t_atoms *at, gmx_bool bRTPresname,
+ int bts[], t_params plist[], t_excls excls[],
+ gpp_atomtype_t atype, int *cgnr, int nrexcl);
/* NOTE: nrexcl is not the size of *excl! */
void pdb2top(FILE *top_file, char *posre_fn, char *molname,
- t_atoms *atoms,rvec **x,
- gpp_atomtype_t atype,t_symtab *tab,
- int nrtp, t_restp rtp[],
- t_restp *restp, t_hackblock *hb,
- int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
- gmx_bool bAllowMissing,
- gmx_bool bVsites, gmx_bool bVsiteAromatics,
- const char *ff, const char *ffdir,
- real mHmult,
- int nssbonds, t_ssbond ssbonds[],
- real long_bond_dist, real short_bond_dist,
- gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
- gmx_bool bRenumRes,gmx_bool bRTPresname);
+ t_atoms *atoms, rvec **x,
+ gpp_atomtype_t atype, t_symtab *tab,
+ int nrtp, t_restp rtp[],
+ t_restp *restp, t_hackblock *hb,
+ int nterpairs, t_hackblock **ntdb, t_hackblock **ctdb,
+ gmx_bool bAllowMissing,
+ gmx_bool bVsites, gmx_bool bVsiteAromatics,
+ const char *ff, const char *ffdir,
+ real mHmult,
+ int nssbonds, t_ssbond ssbonds[],
+ real long_bond_dist, real short_bond_dist,
+ gmx_bool bDeuterate, gmx_bool bChargeGroups, gmx_bool bCmap,
+ gmx_bool bRenumRes, gmx_bool bRTPresname);
/* Create a topology ! */
void print_sums(t_atoms *atoms, gmx_bool bSystem);
-#endif /* _pdb2top_h */
+#endif /* _pdb2top_h */
biod.pnpi.spb.ru / alexxy / gromacs.git / blobdiff