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38 #ifndef GMX_GMXPREPROCESS_HACKBLOCK_H
39 #define GMX_GMXPREPROCESS_HACKBLOCK_H
41 #include "gromacs/fileio/pdbio.h"
42 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
43 #include "gromacs/gmxpreprocess/grompp-impl.h"
44 #include "gromacs/legacyheaders/typedefs.h"
45 #include "gromacs/topology/symtab.h"
47 /* Used for reading .rtp/.tdb */
48 /* ebtsBONDS must be the first, new types can be added to the end */
49 /* these *MUST* correspond to the arrays in hackblock.c */
51 ebtsBONDS, ebtsANGLES, ebtsPDIHS, ebtsIDIHS, ebtsEXCLS, ebtsCMAP, ebtsNR
53 extern const char *btsNames[ebtsNR];
54 extern const int btsNiatoms[ebtsNR];
56 /* if changing any of these structs, make sure that all of the
57 free/clear/copy/merge_t_* functions stay updated */
61 char *a[MAXATOMLIST]; /* atom names */
62 char *s; /* optional define string which gets copied from
63 .rtp/.tdb to .top and will be parsed by cpp
65 gmx_bool match; /* boolean to mark that the entry has been found */
69 int type; /* The type of bonded interaction */
70 int nb; /* number of bondeds */
71 t_rbonded *b; /* bondeds */
77 /* The base file name this rtp entry was read from */
84 /* Bonded interaction setup */
85 gmx_bool bKeepAllGeneratedDihedrals;
87 gmx_bool bGenerateHH14Interactions;
88 gmx_bool bRemoveDihedralIfWithImproper;
89 /* list of bonded interactions to add */
90 t_rbondeds rb[ebtsNR];
93 /* Block to hack residues */
95 int nr; /* Number of atoms to hack */
96 char *oname; /* Old name */
97 char *nname; /* New name */
98 /* the type of hack depends on the setting of oname and nname:
99 * if oname==NULL we're adding, must have tp>0 also!
100 * if oname!=NULL && nname==NULL we're deleting
101 * if oname!=NULL && nname!=NULL we're replacing
103 t_atom *atom; /* New atom data */
104 int cgnr; /* chargegroup number. if not read will be NOTSET */
105 int tp; /* Type of attachment (1..11) */
106 int nctl; /* How many control atoms there are */
107 char *a[4]; /* Control atoms i,j,k,l */
108 gmx_bool bAlreadyPresent;
110 rvec newx; /* calculated new position */
111 atom_id newi; /* new atom index number (after additions) */
115 char *name; /* Name of hack block (residue or terminus) */
116 char *filebase; /* The base file name this entry was read from */
117 int nhack; /* Number of atoms to hack */
118 int maxhack; /* used for efficient srenew-ing */
119 t_hack *hack; /* Hack list */
120 /* list of bonded interactions to add */
121 t_rbondeds rb[ebtsNR];
124 /* all libraries and other data to protonate a structure or trajectory */
126 gmx_bool bInit; /* true after init; set false by init_t_protonate */
127 /* force field name: */
132 t_hackblock *ah, *ntdb, *ctdb;
133 t_hackblock **sel_ntdb, **sel_ctdb;
136 /* residue indices (not numbers!) of the N and C termini */
138 gpp_atomtype_t atype;
139 /* protonated topology: */
141 /* unprotonated topology: */
149 char *newres1, *newres2;
154 t_specbond *get_specbonds(int *nspecbond);
155 void done_specbonds(int nsb, t_specbond sb[]);
157 void free_t_restp(int nrtp, t_restp **rtp);
158 void free_t_hack(int nh, t_hack **h);
159 void free_t_hackblock(int nhb, t_hackblock **hb);
160 /* free the whole datastructure */
162 void clear_t_hackblock(t_hackblock *hb);
163 void clear_t_hack(t_hack *hack);
166 gmx_bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[],
167 gmx_bool bMin, gmx_bool bPlus);
168 /* add s[].b[] to d[].b[]
169 * If bMin==TRUE, don't copy bondeds with atoms starting with '-'
170 * If bPlus==TRUE, don't copy bondeds with atoms starting with '+'
171 * Returns if bonds were removed at the termini.
174 void copy_t_restp(t_restp *s, t_restp *d);
175 void copy_t_hack(t_hack *s, t_hack *d);
176 void copy_t_hackblock(t_hackblock *s, t_hackblock *d);
177 /* make copy of whole datastructure */
179 void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d);
180 /* add s[] to *d[] */
182 void merge_hacks(t_hackblock *s, t_hackblock *d);
183 /* add s->hacks[] to d->hacks[] */
185 void merge_t_hackblock(t_hackblock *s, t_hackblock *d);
186 /* add s->hacks[] and s->rb[] to d*/
188 void dump_hb(FILE *out, int nres, t_hackblock hb[]);
189 /* print out whole datastructure */
191 void init_t_protonate(t_protonate *protonate);
192 /* initialize t_protein struct */