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/*
*
* 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.
* Copyright (c) 2001-2004, The GROMACS development team,
* check out http://www.gromacs.org for more information.
* This program is free software; you can redistribute it and/or
* 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
*/
#ifndef _pdb2top_h
#define _pdb2top_h
#include "typedefs.h"
#include "grompp.h"
#include "gpp_atomtype.h"
#include "toputil.h"
#include "hackblock.h"
/* this *MUST* correspond to array in pdb2top.c */
enum { ehisA, ehisB, ehisH, ehis1, ehisNR };
extern const char *hh[ehisNR];
typedef struct {
int res1,res2;
char *a1,*a2;
} t_ssbond;
void choose_ff(const char *ffsel,
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);
/* 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);
/* 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);
/* 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_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);
/* 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);
/* Create a topology ! */
void print_sums(t_atoms *atoms, gmx_bool bSystem);
#endif /* _pdb2top_h */
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