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33 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
35 /* This file is completely threadsafe - keep it that way! */
45 #include "hackblock.h"
47 #include "gmx_fatal.h"
49 static void clear_atom_list(int i0, atom_id a[])
53 for (i=i0; i < MAXATOMLIST; i++)
57 static void clear_force_param(int i0, real c[])
61 for (i=i0; i < MAXFORCEPARAM; i++)
65 void add_param(t_params *ps,int ai,int aj, real *c, char *s)
69 if ((ai < 0) || (aj < 0))
70 gmx_fatal(FARGS,"Trying to add impossible atoms: ai=%d, aj=%d",ai,aj);
72 ps->param[ps->nr].AI=ai;
73 ps->param[ps->nr].AJ=aj;
74 clear_atom_list(2, ps->param[ps->nr].a);
76 clear_force_param(0, ps->param[ps->nr].c);
78 for(i=0; (i < MAXFORCEPARAM); i++)
79 ps->param[ps->nr].c[i]=c[i];
80 set_p_string(&(ps->param[ps->nr]),s);
84 void add_imp_param(t_params *ps,int ai,int aj,int ak,int al,real c0, real c1,
88 ps->param[ps->nr].AI=ai;
89 ps->param[ps->nr].AJ=aj;
90 ps->param[ps->nr].AK=ak;
91 ps->param[ps->nr].AL=al;
92 clear_atom_list (4, ps->param[ps->nr].a);
93 ps->param[ps->nr].C0=c0;
94 ps->param[ps->nr].C1=c1;
95 clear_force_param(2, ps->param[ps->nr].c);
96 set_p_string(&(ps->param[ps->nr]),s);
100 void add_dih_param(t_params *ps,int ai,int aj,int ak,int al,real c0, real c1,
104 ps->param[ps->nr].AI=ai;
105 ps->param[ps->nr].AJ=aj;
106 ps->param[ps->nr].AK=ak;
107 ps->param[ps->nr].AL=al;
108 clear_atom_list (4, ps->param[ps->nr].a);
109 ps->param[ps->nr].C0=c0;
110 ps->param[ps->nr].C1=c1;
111 ps->param[ps->nr].C2=c2;
112 clear_force_param(3, ps->param[ps->nr].c);
113 set_p_string(&(ps->param[ps->nr]),s);
117 void add_cmap_param(t_params *ps, int ai, int aj, int ak, int al, int am, char *s)
120 ps->param[ps->nr].AI=ai;
121 ps->param[ps->nr].AJ=aj;
122 ps->param[ps->nr].AK=ak;
123 ps->param[ps->nr].AL=al;
124 ps->param[ps->nr].AM=am;
125 clear_atom_list(5,ps->param[ps->nr].a);
126 clear_force_param(0,ps->param[ps->nr].c);
127 set_p_string(&(ps->param[ps->nr]),s);
131 void add_vsite2_atoms(t_params *ps,int ai,int aj,int ak)
134 ps->param[ps->nr].AI=ai;
135 ps->param[ps->nr].AJ=aj;
136 ps->param[ps->nr].AK=ak;
137 clear_atom_list (3, ps->param[ps->nr].a);
138 clear_force_param(0, ps->param[ps->nr].c);
139 set_p_string(&(ps->param[ps->nr]),"");
143 void add_vsite2_param(t_params *ps,int ai,int aj,int ak,real c0)
146 ps->param[ps->nr].AI=ai;
147 ps->param[ps->nr].AJ=aj;
148 ps->param[ps->nr].AK=ak;
149 clear_atom_list (3, ps->param[ps->nr].a);
150 ps->param[ps->nr].C0=c0;
151 clear_force_param(1, ps->param[ps->nr].c);
152 set_p_string(&(ps->param[ps->nr]),"");
156 void add_vsite3_param(t_params *ps,int ai,int aj,int ak,int al,
160 ps->param[ps->nr].AI=ai;
161 ps->param[ps->nr].AJ=aj;
162 ps->param[ps->nr].AK=ak;
163 ps->param[ps->nr].AL=al;
164 clear_atom_list (4, ps->param[ps->nr].a);
165 ps->param[ps->nr].C0=c0;
166 ps->param[ps->nr].C1=c1;
167 clear_force_param(2, ps->param[ps->nr].c);
168 set_p_string(&(ps->param[ps->nr]),"");
172 void add_vsite3_atoms(t_params *ps,int ai,int aj,int ak,int al, bool bSwapParity)
175 ps->param[ps->nr].AI=ai;
176 ps->param[ps->nr].AJ=aj;
177 ps->param[ps->nr].AK=ak;
178 ps->param[ps->nr].AL=al;
179 clear_atom_list (4, ps->param[ps->nr].a);
180 clear_force_param(0, ps->param[ps->nr].c);
182 ps->param[ps->nr].C1=-1;
183 set_p_string(&(ps->param[ps->nr]),"");
187 void add_vsite4_atoms(t_params *ps,int ai,int aj,int ak,int al,int am)
190 ps->param[ps->nr].AI=ai;
191 ps->param[ps->nr].AJ=aj;
192 ps->param[ps->nr].AK=ak;
193 ps->param[ps->nr].AL=al;
194 ps->param[ps->nr].AM=am;
195 clear_atom_list (5, ps->param[ps->nr].a);
196 clear_force_param(0, ps->param[ps->nr].c);
197 set_p_string(&(ps->param[ps->nr]),"");
201 int search_jtype(t_restp *rtp,char *name,bool bNterm)
203 int niter,iter,j,k,kmax,jmax,minstrlen;
204 char *rtpname,searchname[12];
206 strcpy(searchname,name);
208 /* Do a best match comparison */
209 /* for protein N-terminus, allow renaming of H1, H2 and H3 to H */
210 if ( bNterm && (strlen(searchname)==2) && (searchname[0] == 'H') &&
211 ( (searchname[1] == '1') || (searchname[1] == '2') ||
212 (searchname[1] == '3') ) ) {
219 for(iter=0; (iter<niter && jmax==-1); iter++) {
221 /* Try without the hydrogen number in the N-terminus */
222 searchname[1] = '\0';
224 for(j=0; (j<rtp->natom); j++) {
225 rtpname=*(rtp->atomname[j]);
226 if (gmx_strcasecmp(searchname,rtpname) == 0) {
228 kmax=strlen(searchname);
231 if (iter == niter - 1) {
232 minstrlen = min(strlen(searchname), strlen(rtpname));
233 for(k=0; k < minstrlen; k++)
234 if (searchname[k] != rtpname[k])
244 gmx_fatal(FARGS,"Atom %s not found in rtp database in residue %s",
245 searchname,rtp->resname);
246 if (kmax != strlen(searchname))
247 gmx_fatal(FARGS,"Atom %s not found in rtp database in residue %s, "
248 "it looks a bit like %s",
249 searchname,rtp->resname,*(rtp->atomname[jmax]));