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33 * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
35 /* This file is completely threadsafe - keep it that way! */
46 #include "hackblock.h"
48 #include "gmx_fatal.h"
50 static void clear_atom_list(int i0, atom_id a[])
54 for (i = i0; i < MAXATOMLIST; i++)
60 static void clear_force_param(int i0, real c[])
64 for (i = i0; i < MAXFORCEPARAM; i++)
70 void add_param(t_params *ps, int ai, int aj, real *c, char *s)
74 if ((ai < 0) || (aj < 0))
76 gmx_fatal(FARGS, "Trying to add impossible atoms: ai=%d, aj=%d", ai, aj);
79 ps->param[ps->nr].AI = ai;
80 ps->param[ps->nr].AJ = aj;
81 clear_atom_list(2, ps->param[ps->nr].a);
84 clear_force_param(0, ps->param[ps->nr].c);
88 for (i = 0; (i < MAXFORCEPARAM); i++)
90 ps->param[ps->nr].c[i] = c[i];
93 set_p_string(&(ps->param[ps->nr]), s);
97 void add_imp_param(t_params *ps, int ai, int aj, int ak, int al, real c0, real c1,
101 ps->param[ps->nr].AI = ai;
102 ps->param[ps->nr].AJ = aj;
103 ps->param[ps->nr].AK = ak;
104 ps->param[ps->nr].AL = al;
105 clear_atom_list (4, ps->param[ps->nr].a);
106 ps->param[ps->nr].C0 = c0;
107 ps->param[ps->nr].C1 = c1;
108 clear_force_param(2, ps->param[ps->nr].c);
109 set_p_string(&(ps->param[ps->nr]), s);
113 void add_dih_param(t_params *ps, int ai, int aj, int ak, int al, real c0, real c1,
117 ps->param[ps->nr].AI = ai;
118 ps->param[ps->nr].AJ = aj;
119 ps->param[ps->nr].AK = ak;
120 ps->param[ps->nr].AL = al;
121 clear_atom_list (4, ps->param[ps->nr].a);
122 ps->param[ps->nr].C0 = c0;
123 ps->param[ps->nr].C1 = c1;
124 ps->param[ps->nr].C2 = c2;
125 clear_force_param(3, ps->param[ps->nr].c);
126 set_p_string(&(ps->param[ps->nr]), s);
130 void add_cmap_param(t_params *ps, int ai, int aj, int ak, int al, int am, char *s)
133 ps->param[ps->nr].AI = ai;
134 ps->param[ps->nr].AJ = aj;
135 ps->param[ps->nr].AK = ak;
136 ps->param[ps->nr].AL = al;
137 ps->param[ps->nr].AM = am;
138 clear_atom_list(5, ps->param[ps->nr].a);
139 clear_force_param(0, ps->param[ps->nr].c);
140 set_p_string(&(ps->param[ps->nr]), s);
144 void add_vsite2_atoms(t_params *ps, int ai, int aj, int ak)
147 ps->param[ps->nr].AI = ai;
148 ps->param[ps->nr].AJ = aj;
149 ps->param[ps->nr].AK = ak;
150 clear_atom_list (3, ps->param[ps->nr].a);
151 clear_force_param(0, ps->param[ps->nr].c);
152 set_p_string(&(ps->param[ps->nr]), "");
156 void add_vsite2_param(t_params *ps, int ai, int aj, int ak, real c0)
159 ps->param[ps->nr].AI = ai;
160 ps->param[ps->nr].AJ = aj;
161 ps->param[ps->nr].AK = ak;
162 clear_atom_list (3, ps->param[ps->nr].a);
163 ps->param[ps->nr].C0 = c0;
164 clear_force_param(1, ps->param[ps->nr].c);
165 set_p_string(&(ps->param[ps->nr]), "");
169 void add_vsite3_param(t_params *ps, int ai, int aj, int ak, int al,
173 ps->param[ps->nr].AI = ai;
174 ps->param[ps->nr].AJ = aj;
175 ps->param[ps->nr].AK = ak;
176 ps->param[ps->nr].AL = al;
177 clear_atom_list (4, ps->param[ps->nr].a);
178 ps->param[ps->nr].C0 = c0;
179 ps->param[ps->nr].C1 = c1;
180 clear_force_param(2, ps->param[ps->nr].c);
181 set_p_string(&(ps->param[ps->nr]), "");
185 void add_vsite3_atoms(t_params *ps, int ai, int aj, int ak, int al, gmx_bool bSwapParity)
188 ps->param[ps->nr].AI = ai;
189 ps->param[ps->nr].AJ = aj;
190 ps->param[ps->nr].AK = ak;
191 ps->param[ps->nr].AL = al;
192 clear_atom_list (4, ps->param[ps->nr].a);
193 clear_force_param(0, ps->param[ps->nr].c);
196 ps->param[ps->nr].C1 = -1;
198 set_p_string(&(ps->param[ps->nr]), "");
202 void add_vsite4_atoms(t_params *ps, int ai, int aj, int ak, int al, int am)
205 ps->param[ps->nr].AI = ai;
206 ps->param[ps->nr].AJ = aj;
207 ps->param[ps->nr].AK = ak;
208 ps->param[ps->nr].AL = al;
209 ps->param[ps->nr].AM = am;
210 clear_atom_list (5, ps->param[ps->nr].a);
211 clear_force_param(0, ps->param[ps->nr].c);
212 set_p_string(&(ps->param[ps->nr]), "");
216 int search_jtype(t_restp *rtp, char *name, gmx_bool bNterm)
218 int niter, iter, j, k, kmax, jmax, minstrlen;
219 char *rtpname, searchname[12];
221 strcpy(searchname, name);
223 /* Do a best match comparison */
224 /* for protein N-terminus, allow renaming of H1, H2 and H3 to H */
225 if (bNterm && (strlen(searchname) == 2) && (searchname[0] == 'H') &&
226 ( (searchname[1] == '1') || (searchname[1] == '2') ||
227 (searchname[1] == '3') ) )
237 for (iter = 0; (iter < niter && jmax == -1); iter++)
241 /* Try without the hydrogen number in the N-terminus */
242 searchname[1] = '\0';
244 for (j = 0; (j < rtp->natom); j++)
246 rtpname = *(rtp->atomname[j]);
247 if (gmx_strcasecmp(searchname, rtpname) == 0)
250 kmax = strlen(searchname);
253 if (iter == niter - 1)
255 minstrlen = min(strlen(searchname), strlen(rtpname));
256 for (k = 0; k < minstrlen; k++)
258 if (searchname[k] != rtpname[k])
273 gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s",
274 searchname, rtp->resname);
276 if (kmax != strlen(searchname))
278 gmx_fatal(FARGS, "Atom %s not found in rtp database in residue %s, "
279 "it looks a bit like %s",
280 searchname, rtp->resname, *(rtp->atomname[jmax]));