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44 #include "gromacs/listed-forces/bonded.h"
45 #include "gromacs/pbcutil/rmpbc.h"
46 #include "gromacs/utility/cstringutil.h"
47 #include "gromacs/utility/fatalerror.h"
48 #include "gromacs/utility/futil.h"
49 #include "gromacs/utility/smalloc.h"
51 static const char *pp_pat
[] = { "C", "N", "CA", "C", "N" };
52 #define NPP (sizeof(pp_pat)/sizeof(pp_pat[0]))
54 static int d_comp(const void *a
, const void *b
)
61 if (da
->ai
[1] < db
->ai
[1])
65 else if (da
->ai
[1] == db
->ai
[1])
67 return (da
->ai
[2] - db
->ai
[2]);
76 static void calc_dihs(t_xrama
*xr
)
79 rvec r_ij
, r_kj
, r_kl
, m
, n
;
82 gmx_rmpbc_t gpbc
= NULL
;
84 gpbc
= gmx_rmpbc_init(xr
->idef
, xr
->ePBC
, xr
->natoms
);
85 gmx_rmpbc(gpbc
, xr
->natoms
, xr
->box
, xr
->x
);
88 for (i
= 0; (i
< xr
->ndih
); i
++)
91 dd
->ang
= dih_angle(xr
->x
[dd
->ai
[0]], xr
->x
[dd
->ai
[1]],
92 xr
->x
[dd
->ai
[2]], xr
->x
[dd
->ai
[3]],
94 r_ij
, r_kj
, r_kl
, m
, n
, &sign
, &t1
, &t2
, &t3
);
98 gmx_bool
new_data(t_xrama
*xr
)
100 if (!read_next_x(xr
->oenv
, xr
->traj
, &xr
->t
, xr
->x
, xr
->box
))
110 static int find_atom(const char *find
, char ***names
, int start
, int nr
)
114 for (i
= start
; (i
< nr
); i
++)
116 if (std::strcmp(find
, *names
[i
]) == 0)
124 static void add_xr(t_xrama
*xr
, int ff
[5], const t_atoms
*atoms
)
129 srenew(xr
->dih
, xr
->ndih
+2);
130 for (i
= 0; (i
< 4); i
++)
132 xr
->dih
[xr
->ndih
].ai
[i
] = ff
[i
];
134 for (i
= 0; (i
< 4); i
++)
136 xr
->dih
[xr
->ndih
+1].ai
[i
] = ff
[i
+1];
140 srenew(xr
->pp
, xr
->npp
+1);
141 xr
->pp
[xr
->npp
].iphi
= xr
->ndih
-2;
142 xr
->pp
[xr
->npp
].ipsi
= xr
->ndih
-1;
143 xr
->pp
[xr
->npp
].bShow
= FALSE
;
144 sprintf(buf
, "%s-%d", *atoms
->resinfo
[atoms
->atom
[ff
[1]].resind
].name
,
145 atoms
->resinfo
[atoms
->atom
[ff
[1]].resind
].nr
);
146 xr
->pp
[xr
->npp
].label
= gmx_strdup(buf
);
150 static void get_dih(t_xrama
*xr
, const t_atoms
*atoms
)
156 for (i
= 0; (i
< atoms
->nr
); )
159 for (j
= 0; (j
< NPP
); j
++)
161 if ((ff
[j
] = find_atom(pp_pat
[j
], atoms
->atomname
, found
, atoms
->nr
)) == -1)
171 add_xr(xr
, ff
, atoms
);
174 fprintf(stderr
, "Found %d phi-psi combinations\n", xr
->npp
);
177 static void min_max(t_xrama
*xr
)
181 xr
->amin
= xr
->natoms
;
183 for (i
= 0; (i
< xr
->ndih
); i
++)
185 for (j
= 0; (j
< 4); j
++)
187 ai
= xr
->dih
[i
].ai
[j
];
192 else if (ai
> xr
->amax
)
200 static void get_dih_props(t_xrama
*xr
, const t_idef
*idef
, int mult
)
202 int i
, ft
, ftype
, nra
;
206 ia
= idef
->il
[F_PDIHS
].iatoms
;
207 for (i
= 0; (i
< idef
->il
[F_PDIHS
].nr
); )
210 ftype
= idef
->functype
[ft
];
211 nra
= interaction_function
[ftype
].nratoms
;
213 if (ftype
!= F_PDIHS
)
215 gmx_incons("ftype is not a dihedral");
220 if ((dd
= (t_dih
*)bsearch(&key
, xr
->dih
, xr
->ndih
, (size_t)sizeof(key
), d_comp
))
223 dd
->mult
= idef
->iparams
[ft
].pdihs
.mult
;
224 dd
->phi0
= idef
->iparams
[ft
].pdihs
.phiA
;
230 /* Fill in defaults for values not in the topology */
231 for (i
= 0; (i
< xr
->ndih
); i
++)
233 if (xr
->dih
[i
].mult
== 0)
236 "Dihedral around %d,%d not found in topology. Using mult=%d\n",
237 xr
->dih
[i
].ai
[1], xr
->dih
[i
].ai
[2], mult
);
238 xr
->dih
[i
].mult
= mult
;
239 xr
->dih
[i
].phi0
= 180;
246 t_topology
*init_rama(gmx_output_env_t
*oenv
, const char *infile
,
247 const char *topfile
, t_xrama
*xr
, int mult
)
252 top
= read_top(topfile
, &xr
->ePBC
);
254 /*get_dih2(xr,top->idef.functype,&(top->idef.bondeds),&(top->atoms));*/
255 get_dih(xr
, &(top
->atoms
));
256 get_dih_props(xr
, &(top
->idef
), mult
);
257 xr
->natoms
= read_first_x(oenv
, &xr
->traj
, infile
, &t
, &(xr
->x
), xr
->box
);
258 xr
->idef
= &(top
->idef
);