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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 _hackblock_h
#define _hackblock_h
#include "typedefs.h"
#include "pdbio.h"
#include "grompp.h"
#include "gpp_atomtype.h"
#ifdef __cplusplus
extern "C" {
#endif
/* Used for reading .rtp/.tdb */
/* ebtsBONDS must be the first, new types can be added to the end */
/* these *MUST* correspond to the arrays in hackblock.c */
enum { ebtsBONDS, ebtsANGLES, ebtsPDIHS, ebtsIDIHS, ebtsEXCLS, ebtsCMAP, ebtsNR };
extern const char *btsNames[ebtsNR];
extern const int btsNiatoms[ebtsNR];
/* if changing any of these structs, make sure that all of the
free/clear/copy/merge_t_* functions stay updated */
/* BONDEDS */
typedef struct {
char *a[MAXATOMLIST]; /* atom names */
char *s; /* optional define string which gets copied from
.rtp/.tdb to .top and will be parsed by cpp
during grompp */
} t_rbonded;
typedef struct {
int type; /* The type of bonded interaction */
int nb; /* number of bondeds */
t_rbonded *b; /* bondeds */
} t_rbondeds;
/* RESIDUES (rtp) */
typedef struct {
char *resname;
/* The base file name this rtp entry was read from */
char *filebase;
/* atom data */
int natom;
t_atom *atom;
char ***atomname;
int *cgnr;
/* Bonded interaction setup */
gmx_bool bAlldih;
int nrexcl;
gmx_bool HH14;
gmx_bool bRemoveDih;
/* list of bonded interactions to add */
t_rbondeds rb[ebtsNR];
} t_restp;
/* Block to hack residues */
typedef struct {
int nr; /* Number of atoms to hack */
char *oname; /* Old name */
char *nname; /* New name */
/* the type of hack depends on the setting of oname and nname:
* if oname==NULL we're adding, must have tp>0 also!
* if oname!=NULL && nname==NULL we're deleting
* if oname!=NULL && nname!=NULL we're replacing
*/
t_atom *atom; /* New atom data */
int cgnr; /* chargegroup number. if not read will be NOTSET */
int tp; /* Type of attachment (1..11) */
int nctl; /* How many control atoms there are */
char *a[4]; /* Control atoms i,j,k,l */
gmx_bool bAlreadyPresent;
gmx_bool bXSet;
rvec newx; /* calculated new position */
atom_id newi; /* new atom index number (after additions) */
} t_hack;
typedef struct {
char *name; /* Name of hack block (residue or terminus) */
char *filebase; /* The base file name this entry was read from */
int nhack; /* Number of atoms to hack */
int maxhack;/* used for efficient srenew-ing */
t_hack *hack; /* Hack list */
/* list of bonded interactions to add */
t_rbondeds rb[ebtsNR];
} t_hackblock;
/* all libraries and other data to protonate a structure or trajectory */
typedef struct {
gmx_bool bInit; /* true after init; set false by init_t_protonate */
/* force field name: */
char FF[10];
/* libarary data: */
int *nab;
t_hack **ab;
t_hackblock *ah, *ntdb, *ctdb;
t_hackblock **sel_ntdb, **sel_ctdb;
int nah;
t_symtab tab;
/* residue indices (not numbers!) of the N and C termini */
int *rN, *rC;
gpp_atomtype_t atype;
/* protonated topology: */
t_atoms *patoms;
/* unprotonated topology: */
t_atoms *upatoms;
} t_protonate;
typedef struct {
char *res1, *res2;
char *atom1,*atom2;
char *newres1,*newres2;
int nbond1,nbond2;
real length;
} t_specbond;
t_specbond *get_specbonds(int *nspecbond);
void done_specbonds(int nsb,t_specbond sb[]);
void free_t_restp(int nrtp, t_restp **rtp);
void free_t_hack(int nh, t_hack **h);
void free_t_hackblock(int nhb, t_hackblock **hb);
/* free the whole datastructure */
void clear_t_hackblock(t_hackblock *hb);
void clear_t_hack(t_hack *hack);
/* reset struct */
gmx_bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[],
gmx_bool bMin, gmx_bool bPlus);
/* add s[].b[] to d[].b[]
* If bMin==TRUE, don't copy bondeds with atoms starting with '-'
* If bPlus==TRUE, don't copy bondeds with atoms starting with '+'
* Returns if bonds were removed at the termini.
*/
void copy_t_restp(t_restp *s, t_restp *d);
void copy_t_hack(t_hack *s, t_hack *d);
void copy_t_hackblock(t_hackblock *s, t_hackblock *d);
/* make copy of whole datastructure */
void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d);
/* add s[] to *d[] */
void merge_hacks(t_hackblock *s, t_hackblock *d);
/* add s->hacks[] to d->hacks[] */
void merge_t_hackblock(t_hackblock *s, t_hackblock *d);
/* add s->hacks[] and s->rb[] to d*/
void dump_hb(FILE *out, int nres, t_hackblock hb[]);
/* print out whole datastructure */
void init_t_protonate(t_protonate *protonate);
/* initialize t_protein struct */
#ifdef __cplusplus
}
#endif
#endif /* _hackblock_h */
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