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38 #ifndef GMX_GMXPREPROCESS_HACKBLOCK_H
39 #define GMX_GMXPREPROCESS_HACKBLOCK_H
42 #include "../fileio/pdbio.h"
43 #include "grompp-impl.h"
44 #include "gpp_atomtype.h"
50 /* Used for reading .rtp/.tdb */
51 /* ebtsBONDS must be the first, new types can be added to the end */
52 /* these *MUST* correspond to the arrays in hackblock.c */
54 ebtsBONDS, ebtsANGLES, ebtsPDIHS, ebtsIDIHS, ebtsEXCLS, ebtsCMAP, ebtsNR
56 extern const char *btsNames[ebtsNR];
57 extern const int btsNiatoms[ebtsNR];
59 /* if changing any of these structs, make sure that all of the
60 free/clear/copy/merge_t_* functions stay updated */
64 char *a[MAXATOMLIST]; /* atom names */
65 char *s; /* optional define string which gets copied from
66 .rtp/.tdb to .top and will be parsed by cpp
71 int type; /* The type of bonded interaction */
72 int nb; /* number of bondeds */
73 t_rbonded *b; /* bondeds */
79 /* The base file name this rtp entry was read from */
86 /* Bonded interaction setup */
87 gmx_bool bKeepAllGeneratedDihedrals;
89 gmx_bool bGenerateHH14Interactions;
90 gmx_bool bRemoveDihedralIfWithImproper;
91 /* list of bonded interactions to add */
92 t_rbondeds rb[ebtsNR];
95 /* Block to hack residues */
97 int nr; /* Number of atoms to hack */
98 char *oname; /* Old name */
99 char *nname; /* New name */
100 /* the type of hack depends on the setting of oname and nname:
101 * if oname==NULL we're adding, must have tp>0 also!
102 * if oname!=NULL && nname==NULL we're deleting
103 * if oname!=NULL && nname!=NULL we're replacing
105 t_atom *atom; /* New atom data */
106 int cgnr; /* chargegroup number. if not read will be NOTSET */
107 int tp; /* Type of attachment (1..11) */
108 int nctl; /* How many control atoms there are */
109 char *a[4]; /* Control atoms i,j,k,l */
110 gmx_bool bAlreadyPresent;
112 rvec newx; /* calculated new position */
113 atom_id newi; /* new atom index number (after additions) */
117 char *name; /* Name of hack block (residue or terminus) */
118 char *filebase; /* The base file name this entry was read from */
119 int nhack; /* Number of atoms to hack */
120 int maxhack; /* used for efficient srenew-ing */
121 t_hack *hack; /* Hack list */
122 /* list of bonded interactions to add */
123 t_rbondeds rb[ebtsNR];
126 /* all libraries and other data to protonate a structure or trajectory */
128 gmx_bool bInit; /* true after init; set false by init_t_protonate */
129 /* force field name: */
134 t_hackblock *ah, *ntdb, *ctdb;
135 t_hackblock **sel_ntdb, **sel_ctdb;
138 /* residue indices (not numbers!) of the N and C termini */
140 gpp_atomtype_t atype;
141 /* protonated topology: */
143 /* unprotonated topology: */
151 char *newres1, *newres2;
156 t_specbond *get_specbonds(int *nspecbond);
157 void done_specbonds(int nsb, t_specbond sb[]);
159 void free_t_restp(int nrtp, t_restp **rtp);
160 void free_t_hack(int nh, t_hack **h);
161 void free_t_hackblock(int nhb, t_hackblock **hb);
162 /* free the whole datastructure */
164 void clear_t_hackblock(t_hackblock *hb);
165 void clear_t_hack(t_hack *hack);
168 gmx_bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[],
169 gmx_bool bMin, gmx_bool bPlus);
170 /* add s[].b[] to d[].b[]
171 * If bMin==TRUE, don't copy bondeds with atoms starting with '-'
172 * If bPlus==TRUE, don't copy bondeds with atoms starting with '+'
173 * Returns if bonds were removed at the termini.
176 void copy_t_restp(t_restp *s, t_restp *d);
177 void copy_t_hack(t_hack *s, t_hack *d);
178 void copy_t_hackblock(t_hackblock *s, t_hackblock *d);
179 /* make copy of whole datastructure */
181 void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d);
182 /* add s[] to *d[] */
184 void merge_hacks(t_hackblock *s, t_hackblock *d);
185 /* add s->hacks[] to d->hacks[] */
187 void merge_t_hackblock(t_hackblock *s, t_hackblock *d);
188 /* add s->hacks[] and s->rb[] to d*/
190 void dump_hb(FILE *out, int nres, t_hackblock hb[]);
191 /* print out whole datastructure */
193 void init_t_protonate(t_protonate *protonate);
194 /* initialize t_protein struct */