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47 #include "gromacs/commandline/pargs.h"
48 #include "gromacs/fileio/writeps.h"
49 #include "gromacs/gmxana/gmx_ana.h"
50 #include "gromacs/gmxana/gstat.h"
51 #include "gromacs/math/vec.h"
52 #include "gromacs/utility/arraysize.h"
53 #include "gromacs/utility/cstringutil.h"
54 #include "gromacs/utility/fatalerror.h"
55 #include "gromacs/utility/futil.h"
56 #include "gromacs/utility/smalloc.h"
57 #include "gromacs/utility/strdb.h"
59 static gmx_bool
* bPhobics(int nres
, char* resnm
[])
65 nb
= get_lines("phbres.dat", &cb
);
68 for (i
= 0; (i
< nres
); i
++)
70 if (search_str(nb
, cb
, resnm
[i
]) != -1)
78 static void wheel(const char* fn
, int nres
, char* resnm
[], int r0
, real rot0
, char* title
)
80 const real fontsize
= 16;
81 const real gray
= 0.9;
82 const real fontasp
= 0.6;
83 const real fontwidth
= fontsize
* fontasp
;
86 real ring
, inner
, outer
;
95 for (i
= 0; (i
< nres
); i
++)
98 sl
= std::strlen(resnm
[i
]);
99 sign
= resnm
[i
][sl
- 1];
100 if ((sign
== '+') || (sign
== '-'))
102 resnm
[i
][sl
- 1] = '\0';
104 sprintf(rnms
[i
], "%s-%d", resnm
[i
], i
+ r0
);
105 if ((sign
== '+') || (sign
== '-'))
107 sl
= std::strlen(rnms
[i
]);
109 rnms
[i
][sl
+ 1] = '\0';
112 slen
= std::max(slen
, static_cast<int>(std::strlen(rnms
[i
])));
114 ring
= (2 + slen
) * fontwidth
;
115 outer
= inner
+ ring
;
116 box
= inner
* 1.5 + (1 + int{ nres
/ 18 }) * ring
;
118 bPh
= bPhobics(nres
, resnm
);
120 t_psdata out
= ps_open(fn
, 0, 0, 2.0 * box
, 2.0 * box
);
124 ps_font(&out
, efontHELV
, 1.5 * fontsize
);
125 ps_translate(&out
, xc
, yc
);
128 ps_ctext(&out
, 0, -fontsize
* 1.5 / 2.0, title
, eXCenter
);
130 ps_font(&out
, efontHELV
, fontsize
);
131 ps_rotate(&out
, rot0
);
132 for (i
= 0; (i
< nres
);)
136 ps_color(&out
, gray
, gray
, gray
);
137 ps_fillarcslice(&out
, 0, 0, inner
, outer
, -10, 10);
138 ps_color(&out
, 0, 0, 0);
140 ps_arcslice(&out
, 0, 0, inner
, outer
, -10, 10);
142 ps_ctext(&out
, inner
+ fontwidth
, -fontsize
/ 2.0, rnms
[i
], eXLeft
);
143 ps_rotate(&out
, -100);
155 static void wheel2(const char* fn
, int nres
, char* resnm
[], real rot0
, char* title
)
157 const real fontsize
= 14;
158 const real gray
= 0.9;
159 const real fontasp
= 0.45;
161 const real fontwidth
= fontsize
* fontasp
;
164 real ring
, inner
, outer
;
169 for (i
= 0; (i
< nres
); i
++)
171 slen
= std::max(slen
, static_cast<int>(strlen(resnm
[i
])));
173 fprintf(stderr
, "slen = %d\n", slen
);
174 ring
= slen
* fontwidth
;
175 outer
= inner
+ ring
;
176 box
= (1 + gmx::exactDiv(nres
, 2 * angle
)) * outer
;
178 t_psdata out
= ps_open(fn
, 0, 0, 2.0 * box
, 2.0 * box
);
182 ps_font(&out
, efontHELV
, 1.5 * fontsize
);
183 ps_translate(&out
, xc
, yc
);
184 ps_color(&out
, 0, 0, 0);
187 ps_ctext(&out
, 0, -fontsize
* 1.5 / 2.0, title
, eXCenter
);
189 ps_font(&out
, efontHELV
, fontsize
);
191 ps_rotate(&out
, rot0
);
192 for (i
= 0; (i
< nres
);)
196 ps_color(&out
, gray
, gray
, 1.0);
197 ps_fillarcslice(&out
, 0, 0, inner
, outer
, -angle
, angle
);
198 ps_color(&out
, 0, 0, 0);
200 ps_arcslice(&out
, 0, 0, inner
, outer
, -angle
, angle
);
202 ps_ctext(&out
, inner
+ fontwidth
, -fontsize
/ 2.0, resnm
[i
], eXLeft
);
203 ps_rotate(&out
, -2 * angle
);
206 if ((i
% (2 * angle
)) == 0)
215 int gmx_wheel(int argc
, char* argv
[])
217 const char* desc
[] = {
218 "[THISMODULE] plots a helical wheel representation of your sequence.",
219 "The input sequence is in the [REF].dat[ref] file where the first line contains",
220 "the number of residues and each consecutive line contains a residue "
223 gmx_output_env_t
* oenv
;
224 static real rot0
= 0;
225 static gmx_bool bNum
= TRUE
;
226 static char* title
= nullptr;
228 t_pargs pa
[] = { { "-r0", FALSE
, etINT
, { &r0
}, "The first residue number in the sequence" },
233 "Rotate around an angle initially (90 degrees makes sense)" },
238 "Plot a title in the center of the wheel (must be shorter than 10 "
239 "characters, or it will overwrite the wheel)" },
240 { "-nn", FALSE
, etBOOL
, { &bNum
}, "Toggle numbers" } };
241 t_filenm fnm
[] = { { efDAT
, "-f", nullptr, ffREAD
}, { efEPS
, "-o", nullptr, ffWRITE
} };
242 #define NFILE asize(fnm)
247 if (!parse_common_args(&argc
, argv
, 0, NFILE
, fnm
, asize(pa
), pa
, asize(desc
), desc
, 0, nullptr, &oenv
))
252 for (i
= 1; (i
< argc
); i
++)
254 if (std::strcmp(argv
[i
], "-r0") == 0)
256 r0
= std::strtol(argv
[++i
], nullptr, 10);
257 fprintf(stderr
, "First residue is %d\n", r0
);
259 else if (std::strcmp(argv
[i
], "-rot0") == 0)
261 rot0
= strtod(argv
[++i
], nullptr);
262 fprintf(stderr
, "Initial rotation is %g\n", rot0
);
264 else if (std::strcmp(argv
[i
], "-T") == 0)
266 title
= gmx_strdup(argv
[++i
]);
267 fprintf(stderr
, "Title will be '%s'\n", title
);
269 else if (std::strcmp(argv
[i
], "-nn") == 0)
272 fprintf(stderr
, "No residue numbers\n");
276 gmx_fatal(FARGS
, "Incorrect usage of option %s", argv
[i
]);
280 nres
= get_lines(ftp2fn(efDAT
, NFILE
, fnm
), &resnm
);
283 wheel(ftp2fn(efEPS
, NFILE
, fnm
), nres
, resnm
, r0
, rot0
, title
);
287 wheel2(ftp2fn(efEPS
, NFILE
, fnm
), nres
, resnm
, rot0
, title
);