2 * This file is part of the GROMACS molecular simulation package.
4 * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
5 * Copyright (c) 2001-2004, The GROMACS development team.
6 * Copyright (c) 2013,2014, by the GROMACS development team, led by
7 * Mark Abraham, David van der Spoel, Berk Hess, and Erik Lindahl,
8 * and including many others, as listed in the AUTHORS file in the
9 * top-level source directory and at http://www.gromacs.org.
11 * GROMACS is free software; you can redistribute it and/or
12 * modify it under the terms of the GNU Lesser General Public License
13 * as published by the Free Software Foundation; either version 2.1
14 * of the License, or (at your option) any later version.
16 * GROMACS is distributed in the hope that it will be useful,
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
19 * Lesser General Public License for more details.
21 * You should have received a copy of the GNU Lesser General Public
22 * License along with GROMACS; if not, see
23 * http://www.gnu.org/licenses, or write to the Free Software Foundation,
24 * Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
26 * If you want to redistribute modifications to GROMACS, please
27 * consider that scientific software is very special. Version
28 * control is crucial - bugs must be traceable. We will be happy to
29 * consider code for inclusion in the official distribution, but
30 * derived work must not be called official GROMACS. Details are found
31 * in the README & COPYING files - if they are missing, get the
32 * official version at http://www.gromacs.org.
34 * To help us fund GROMACS development, we humbly ask that you cite
35 * the research papers on the package. Check out http://www.gromacs.org.
38 #ifndef GMX_GMXPREPROCESS_HACKBLOCK_H
39 #define GMX_GMXPREPROCESS_HACKBLOCK_H
42 #include "gromacs/fileio/pdbio.h"
43 #include "grompp-impl.h"
44 #include "gpp_atomtype.h"
45 #include "gromacs/topology/symtab.h"
51 /* Used for reading .rtp/.tdb */
52 /* ebtsBONDS must be the first, new types can be added to the end */
53 /* these *MUST* correspond to the arrays in hackblock.c */
55 ebtsBONDS, ebtsANGLES, ebtsPDIHS, ebtsIDIHS, ebtsEXCLS, ebtsCMAP, ebtsNR
57 extern const char *btsNames[ebtsNR];
58 extern const int btsNiatoms[ebtsNR];
60 /* if changing any of these structs, make sure that all of the
61 free/clear/copy/merge_t_* functions stay updated */
65 char *a[MAXATOMLIST]; /* atom names */
66 char *s; /* optional define string which gets copied from
67 .rtp/.tdb to .top and will be parsed by cpp
69 gmx_bool match; /* boolean to mark that the entry has been found */
73 int type; /* The type of bonded interaction */
74 int nb; /* number of bondeds */
75 t_rbonded *b; /* bondeds */
81 /* The base file name this rtp entry was read from */
88 /* Bonded interaction setup */
89 gmx_bool bKeepAllGeneratedDihedrals;
91 gmx_bool bGenerateHH14Interactions;
92 gmx_bool bRemoveDihedralIfWithImproper;
93 /* list of bonded interactions to add */
94 t_rbondeds rb[ebtsNR];
97 /* Block to hack residues */
99 int nr; /* Number of atoms to hack */
100 char *oname; /* Old name */
101 char *nname; /* New name */
102 /* the type of hack depends on the setting of oname and nname:
103 * if oname==NULL we're adding, must have tp>0 also!
104 * if oname!=NULL && nname==NULL we're deleting
105 * if oname!=NULL && nname!=NULL we're replacing
107 t_atom *atom; /* New atom data */
108 int cgnr; /* chargegroup number. if not read will be NOTSET */
109 int tp; /* Type of attachment (1..11) */
110 int nctl; /* How many control atoms there are */
111 char *a[4]; /* Control atoms i,j,k,l */
112 gmx_bool bAlreadyPresent;
114 rvec newx; /* calculated new position */
115 atom_id newi; /* new atom index number (after additions) */
119 char *name; /* Name of hack block (residue or terminus) */
120 char *filebase; /* The base file name this entry was read from */
121 int nhack; /* Number of atoms to hack */
122 int maxhack; /* used for efficient srenew-ing */
123 t_hack *hack; /* Hack list */
124 /* list of bonded interactions to add */
125 t_rbondeds rb[ebtsNR];
128 /* all libraries and other data to protonate a structure or trajectory */
130 gmx_bool bInit; /* true after init; set false by init_t_protonate */
131 /* force field name: */
136 t_hackblock *ah, *ntdb, *ctdb;
137 t_hackblock **sel_ntdb, **sel_ctdb;
140 /* residue indices (not numbers!) of the N and C termini */
142 gpp_atomtype_t atype;
143 /* protonated topology: */
145 /* unprotonated topology: */
153 char *newres1, *newres2;
158 t_specbond *get_specbonds(int *nspecbond);
159 void done_specbonds(int nsb, t_specbond sb[]);
161 void free_t_restp(int nrtp, t_restp **rtp);
162 void free_t_hack(int nh, t_hack **h);
163 void free_t_hackblock(int nhb, t_hackblock **hb);
164 /* free the whole datastructure */
166 void clear_t_hackblock(t_hackblock *hb);
167 void clear_t_hack(t_hack *hack);
170 gmx_bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[],
171 gmx_bool bMin, gmx_bool bPlus);
172 /* add s[].b[] to d[].b[]
173 * If bMin==TRUE, don't copy bondeds with atoms starting with '-'
174 * If bPlus==TRUE, don't copy bondeds with atoms starting with '+'
175 * Returns if bonds were removed at the termini.
178 void copy_t_restp(t_restp *s, t_restp *d);
179 void copy_t_hack(t_hack *s, t_hack *d);
180 void copy_t_hackblock(t_hackblock *s, t_hackblock *d);
181 /* make copy of whole datastructure */
183 void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d);
184 /* add s[] to *d[] */
186 void merge_hacks(t_hackblock *s, t_hackblock *d);
187 /* add s->hacks[] to d->hacks[] */
189 void merge_t_hackblock(t_hackblock *s, t_hackblock *d);
190 /* add s->hacks[] and s->rb[] to d*/
192 void dump_hb(FILE *out, int nres, t_hackblock hb[]);
193 /* print out whole datastructure */
195 void init_t_protonate(t_protonate *protonate);
196 /* initialize t_protein struct */