Added CHARMM neutral lysine, LYN, to residuetypes.dat.
[gromacs/adressmacs.git] / include / hackblock.h
blob8827987e5440e1f730acc77745d81e50ef68bd66
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36 #ifndef _hackblock_h
37 #define _hackblock_h
39 #include "typedefs.h"
40 #include "pdbio.h"
41 #include "grompp.h"
42 #include "gpp_atomtype.h"
44 #ifdef __cplusplus
45 extern "C" {
46 #endif
48 /* Used for reading .rtp/.tdb */
49 /* ebtsBONDS must be the first, new types can be added to the end */
50 /* these *MUST* correspond to the arrays in hackblock.c */
51 enum { ebtsBONDS, ebtsANGLES, ebtsPDIHS, ebtsIDIHS, ebtsEXCLS, ebtsCMAP, ebtsNR };
52 extern const char *btsNames[ebtsNR];
53 extern const int btsNiatoms[ebtsNR];
55 /* if changing any of these structs, make sure that all of the
56 free/clear/copy/merge_t_* functions stay updated */
58 /* BONDEDS */
59 typedef struct {
60 char *a[MAXATOMLIST]; /* atom names */
61 char *s; /* optional define string which gets copied from
62 .rtp/.tdb to .top and will be parsed by cpp
63 during grompp */
64 } t_rbonded;
66 typedef struct {
67 int type; /* The type of bonded interaction */
68 int nb; /* number of bondeds */
69 t_rbonded *b; /* bondeds */
70 } t_rbondeds;
72 /* RESIDUES (rtp) */
73 typedef struct {
74 char *resname;
75 /* The base file name this rtp entry was read from */
76 char *filebase;
77 /* atom data */
78 int natom;
79 t_atom *atom;
80 char ***atomname;
81 int *cgnr;
82 /* Bonded interaction setup */
83 gmx_bool bAlldih;
84 int nrexcl;
85 gmx_bool HH14;
86 gmx_bool bRemoveDih;
87 /* list of bonded interactions to add */
88 t_rbondeds rb[ebtsNR];
89 } t_restp;
91 /* Block to hack residues */
92 typedef struct {
93 int nr; /* Number of atoms to hack */
94 char *oname; /* Old name */
95 char *nname; /* New name */
96 /* the type of hack depends on the setting of oname and nname:
97 * if oname==NULL we're adding, must have tp>0 also!
98 * if oname!=NULL && nname==NULL we're deleting
99 * if oname!=NULL && nname!=NULL we're replacing
101 t_atom *atom; /* New atom data */
102 int cgnr; /* chargegroup number. if not read will be NOTSET */
103 int tp; /* Type of attachment (1..11) */
104 int nctl; /* How many control atoms there are */
105 char *a[4]; /* Control atoms i,j,k,l */
106 gmx_bool bAlreadyPresent;
107 gmx_bool bXSet;
108 rvec newx; /* calculated new position */
109 atom_id newi; /* new atom index number (after additions) */
110 } t_hack;
112 typedef struct {
113 char *name; /* Name of hack block (residue or terminus) */
114 char *filebase; /* The base file name this entry was read from */
115 int nhack; /* Number of atoms to hack */
116 int maxhack;/* used for efficient srenew-ing */
117 t_hack *hack; /* Hack list */
118 /* list of bonded interactions to add */
119 t_rbondeds rb[ebtsNR];
120 } t_hackblock;
122 /* all libraries and other data to protonate a structure or trajectory */
123 typedef struct {
124 gmx_bool bInit; /* true after init; set false by init_t_protonate */
125 /* force field name: */
126 char FF[10];
127 /* libarary data: */
128 int *nab;
129 t_hack **ab;
130 t_hackblock *ah, *ntdb, *ctdb;
131 t_hackblock **sel_ntdb, **sel_ctdb;
132 int nah;
133 t_symtab tab;
134 /* residue indices (not numbers!) of the N and C termini */
135 int *rN, *rC;
136 gpp_atomtype_t atype;
137 /* protonated topology: */
138 t_atoms *patoms;
139 /* unprotonated topology: */
140 t_atoms *upatoms;
142 } t_protonate;
144 typedef struct {
145 char *res1, *res2;
146 char *atom1,*atom2;
147 char *newres1,*newres2;
148 int nbond1,nbond2;
149 real length;
150 } t_specbond;
152 t_specbond *get_specbonds(int *nspecbond);
153 void done_specbonds(int nsb,t_specbond sb[]);
155 void free_t_restp(int nrtp, t_restp **rtp);
156 void free_t_hack(int nh, t_hack **h);
157 void free_t_hackblock(int nhb, t_hackblock **hb);
158 /* free the whole datastructure */
160 void clear_t_hackblock(t_hackblock *hb);
161 void clear_t_hack(t_hack *hack);
162 /* reset struct */
164 gmx_bool merge_t_bondeds(t_rbondeds s[], t_rbondeds d[],
165 gmx_bool bMin, gmx_bool bPlus);
166 /* add s[].b[] to d[].b[]
167 * If bMin==TRUE, don't copy bondeds with atoms starting with '-'
168 * If bPlus==TRUE, don't copy bondeds with atoms starting with '+'
169 * Returns if bonds were removed at the termini.
172 void copy_t_restp(t_restp *s, t_restp *d);
173 void copy_t_hack(t_hack *s, t_hack *d);
174 void copy_t_hackblock(t_hackblock *s, t_hackblock *d);
175 /* make copy of whole datastructure */
177 void merge_hacks_lo(int ns, t_hack *s, int *nd, t_hack **d);
178 /* add s[] to *d[] */
180 void merge_hacks(t_hackblock *s, t_hackblock *d);
181 /* add s->hacks[] to d->hacks[] */
183 void merge_t_hackblock(t_hackblock *s, t_hackblock *d);
184 /* add s->hacks[] and s->rb[] to d*/
186 void dump_hb(FILE *out, int nres, t_hackblock hb[]);
187 /* print out whole datastructure */
189 void init_t_protonate(t_protonate *protonate);
190 /* initialize t_protein struct */
192 #ifdef __cplusplus
194 #endif
196 #endif /* _hackblock_h */