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38 #ifndef GMX_GMXPREPROCESS_HACKBLOCK_H
39 #define GMX_GMXPREPROCESS_HACKBLOCK_H
41 #include "gromacs/gmxpreprocess/gpp_atomtype.h"
42 #include "gromacs/gmxpreprocess/grompp-impl.h"
43 #include "gromacs/topology/symtab.h"
45 /* Used for reading .rtp/.tdb */
46 /* ebtsBONDS must be the first, new types can be added to the end */
47 /* these *MUST* correspond to the arrays in hackblock.c */
49 ebtsBONDS, ebtsANGLES, ebtsPDIHS, ebtsIDIHS, ebtsEXCLS, ebtsCMAP, ebtsNR
51 extern const char *btsNames[ebtsNR];
52 extern const int btsNiatoms[ebtsNR];
54 /* if changing any of these structs, make sure that all of the
55 free/clear/copy/merge_t_* functions stay updated */
59 char *a[MAXATOMLIST]; /* atom names */
60 char *s; /* optional define string which gets copied from
61 .rtp/.tdb to .top and will be parsed by cpp
63 bool match; /* boolean to mark that the entry has been found */
64 char* &ai() { return a[0]; }
65 char* &aj() { return a[1]; }
66 char* &ak() { return a[2]; }
67 char* &al() { return a[3]; }
68 char* &am() { return a[4]; }
72 int type; /* The type of bonded interaction */
73 int nb; /* number of bondeds */
74 t_rbonded *b; /* bondeds */
80 /* The base file name this rtp entry was read from */
87 /* Bonded interaction setup */
88 bool bKeepAllGeneratedDihedrals;
90 bool bGenerateHH14Interactions;
91 bool bRemoveDihedralIfWithImproper;
92 /* list of bonded interactions to add */
93 t_rbondeds rb[ebtsNR];
96 /* Block to hack residues */
98 int nr; /* Number of atoms to hack */
99 char *oname; /* Old name */
100 char *nname; /* New name */
101 /* the type of hack depends on the setting of oname and nname:
102 * if oname==NULL we're adding, must have tp>0 also!
103 * if oname!=NULL && nname==NULL we're deleting
104 * if oname!=NULL && nname!=NULL we're replacing
106 t_atom *atom; /* New atom data */
107 int cgnr; /* chargegroup number. if not read will be NOTSET */
108 int tp; /* Type of attachment (1..11) */
109 int nctl; /* How many control atoms there are */
110 char *a[4]; /* Control atoms i,j,k,l */
111 bool bAlreadyPresent;
113 rvec newx; /* calculated new position */
114 int newi; /* new atom index number (after additions) */
115 char* &ai() { return a[0]; }
116 char* &aj() { return a[1]; }
117 char* &ak() { return a[2]; }
118 char* &al() { return a[3]; }
122 char *name; /* Name of hack block (residue or terminus) */
123 char *filebase; /* The base file name this entry was read from */
124 int nhack; /* Number of atoms to hack */
125 int maxhack; /* used for efficient srenew-ing */
126 t_hack *hack; /* Hack list */
127 /* list of bonded interactions to add */
128 t_rbondeds rb[ebtsNR];
134 char *newres1, *newres2;
139 t_specbond *get_specbonds(int *nspecbond);
140 void done_specbonds(int nsb, t_specbond sb[]);
142 void free_t_restp(int nrtp, t_restp **rtp);
143 void free_t_hack(int nh, t_hack **h);
144 void free_t_hackblock(int nhb, t_hackblock **hb);
145 /* free the whole datastructure */
147 void clear_t_hackblock(t_hackblock *hb);
148 void clear_t_hack(t_hack *hack);
151 bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[],
152 bool bMin, bool bPlus);
153 /* add s[].b[] to d[].b[]
154 * If bMin==TRUE, don't copy bondeds with atoms starting with '-'
155 * If bPlus==TRUE, don't copy bondeds with atoms starting with '+'
156 * Returns if bonds were removed at the termini.
159 void copy_t_restp(t_restp *s, t_restp *d);
160 void copy_t_hack(t_hack *s, t_hack *d);
161 void copy_t_hackblock(t_hackblock *s, t_hackblock *d);
162 /* make copy of whole datastructure */
164 void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d);
165 /* add s[] to *d[] */
167 void merge_hacks(t_hackblock *s, t_hackblock *d);
168 /* add s->hacks[] to d->hacks[] */
170 void merge_t_hackblock(t_hackblock *s, t_hackblock *d);
171 /* add s->hacks[] and s->rb[] to d*/
173 void dump_hb(FILE *out, int nres, t_hackblock hb[]);
174 /* print out whole datastructure */