1 /****************************************************************************
2 * MeshLab o o *
3 * An extendible mesh processor o o *
4 * _ O _ *
5 * Copyright(C) 2005, 2006 \/)\/ *
6 * Visual Computing Lab /\/| *
7 * ISTI - Italian National Research Council | *
8 * \ *
9 * All rights reserved. *
10 * *
11 * This program is free software; you can redistribute it and/or modify *
12 * it under the terms of the GNU General Public License as published by *
13 * the Free Software Foundation; either version 2 of the License, or *
14 * (at your option) any later version. *
15 * *
16 * This program is distributed in the hope that it will be useful, *
17 * but WITHOUT ANY WARRANTY; without even the implied warranty of *
18 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
19 * GNU General Public License (http://www.gnu.org/licenses/gpl.txt) *
20 * for more details. *
21 * *
22 ****************************************************************************/
23
24 #include <Qt>
25
26 #include "io_pdb.h"
27
28 #include <wrap/io_trimesh/import_ply.h>
29
30 #include <wrap/io_trimesh/export_ply.h>
31 #include <wrap/io_trimesh/export.h>
32
33
34 #include <vcg/complex/append.h>
35 #include <vcg/complex/algorithms/create/platonic.h>
36 #include <vcg/complex/algorithms/create/marching_cubes.h>
37 #include <vcg/complex/algorithms/create/mc_trivial_walker.h>
38
39 #include <QMessageBox>
40 #include <QFileDialog>
41
42 using namespace std;
43 using namespace vcg;
44 typedef vcg::SimpleVoxel<MESHLAB_SCALAR> SimpleVoxelm;
45 // initialize importing parameters
initPreOpenParameter(const QString & formatName,const QString &,RichParameterSet & parlst)46 void PDBIOPlugin::initPreOpenParameter(const QString &formatName, const QString &/*filename*/, RichParameterSet &parlst)
47 {
48 if (formatName.toUpper() == tr("PDB"))
49 {
50 parlst.addParam(new RichBool("usecolors",true,"Use Atoms colors","Atoms are colored according to atomic type"));
51 parlst.addParam(new RichBool("justpoints",false,"SURFACE: Atoms as Points","Atoms are created as points, no surface is built. Overrides all subsequential surface parameters"));
52 parlst.addParam(new RichBool("justspheres",true,"SURFACE: Atoms as Spheres","Atoms are created as intersecting spheres, no interpolation surface is built. Overrides all subsequential surface parameters"));
53 parlst.addParam(new RichBool("interpspheres",false,"SURFACE: Atoms as Jointed Spheres","Atoms are created as spheres, joining surface is built. Overrides all subsequential surface parameters"));
54 parlst.addParam(new RichBool("metaballs",false,"SURFACE: Atoms as Metaballs","Atoms are created as blobby interpolation surface, refer to BLINN Metaballs article. Overrides all subsequential surface parameters"));
55 parlst.addParam(new RichFloat("voxelsize",0.25,"Surface Resolution","is used by Jointed Spheres and Metaball"));
56 parlst.addParam(new RichFloat("blobby",2.0,"Blobbyness factor","is used by Metaball"));
57 /*
58 parlst.addParam(new RichInt("meshindex",0,"Index of Range Map to be Imported","PTX files may contain more than one range map. 0 is the first range map. If the number if higher than the actual mesh number, the import will fail");
59 parlst.addParam(new RichBool("anglecull",true,"Cull faces by angle","short");
60 parlst.addParam(new RichFloat("angle",85.0,"Angle limit for face culling","short");
61 parlst.addParam(new RichBool("usecolor",true,"import color","Read color from PTX, if color is not present, uses reflectance instead");
62 parlst.addParam(new RichBool("pointcull",true,"delete unsampled points","Deletes unsampled points in the grid that are normally located in [0,0,0]");
63 parlst.addParam(new RichBool("pointsonly",false,"Keep only points","Just import points, without triangulation");
64 parlst.addParam(new RichBool("switchside",false,"Swap rows/columns","On some PTX, the rows and columns number are switched over");
65 parlst.addParam(new RichBool("flipfaces",false,"Flip all faces","Flip the orientation of all the triangles");
66 */
67 }
68 }
69
open(const QString & formatName,const QString & fileName,MeshModel & m,int & mask,const RichParameterSet & parlst,CallBackPos * cb,QWidget *)70 bool PDBIOPlugin::open(const QString &formatName, const QString &fileName, MeshModel &m, int& mask, const RichParameterSet &parlst, CallBackPos *cb, QWidget * /*parent*/)
71 {
72 //bool normalsUpdated = false;
73
74 // initializing mask
75 mask = 0;
76
77 // initializing progress bar status
78 if (cb != NULL) (*cb)(0, "Loading...");
79
80 QString errorMsgFormat = "Error encountered while loading file:\n\"%1\"\n\nError details: %2";
81
82 //string filename = fileName.toUtf8().data();
83 string filename = QFile::encodeName(fileName).constData ();
84
85 if (formatName.toUpper() == tr("PDB"))
86 {
87
88 mask |= vcg::tri::io::Mask::IOM_VERTCOLOR;
89 m.Enable(mask);
90
91 return parsePDB(qUtf8Printable(fileName), m.cm, parlst, cb);
92
93
94 /*
95 tri::io::ImporterPTX<CMeshO>::Info importparams;
96
97 importparams.meshnum = parlst.getInt("meshindex");
98 importparams.anglecull =parlst.getBool("anglecull");
99 importparams.angle = parlst.getFloat("angle");
100 importparams.savecolor = parlst.getBool("usecolor");
101 importparams.pointcull = parlst.getBool("pointcull");
102 importparams.pointsonly = parlst.getBool("pointsonly");
103 importparams.switchside = parlst.getBool("switchside");
104 importparams.flipfaces = parlst.getBool("flipfaces");
105
106 // if color, add to mesh
107 if(importparams.savecolor)
108 importparams.mask |= tri::io::Mask::IOM_VERTCOLOR;
109
110 // reflectance is stored in quality
111 importparams.mask |= tri::io::Mask::IOM_VERTQUALITY;
112
113 m.Enable(importparams.mask);
114
115 int result = tri::io::ImporterPTX<CMeshO>::Open(m.cm, filename.c_str(), importparams, cb);
116 if (result == 1)
117 {
118 errorMessage = errorMsgFormat.arg(fileName, tri::io::ImporterPTX<CMeshO>::ErrorMsg(result));
119 return false;
120 }
121
122 // update mask
123 mask = importparams.mask;
124 */
125 }
126 else
127 {
128 assert(0); // Unknown File type
129 return false;
130 }
131
132 if (cb != NULL) (*cb)(99, "Done");
133
134 return true;
135 }
136
save(const QString &,const QString &,MeshModel &,const int,const RichParameterSet &,CallBackPos *,QWidget *)137 bool PDBIOPlugin::save(const QString & /*formatName*/,const QString & /*fileName*/, MeshModel & /*m*/, const int /*mask*/, const RichParameterSet & /*par*/, CallBackPos * /*cb*/, QWidget * /*parent*/)
138 {
139 assert(0);
140 return false;
141 }
142
143 /*
144 returns the list of the file's type which can be imported
145 */
importFormats() const146 QList<MeshIOInterface::Format> PDBIOPlugin::importFormats() const
147 {
148 QList<Format> formatList;
149 formatList << Format("Protein Data Bank" , tr("PDB"));
150
151 return formatList;
152 }
153
154 /*
155 returns the list of the file's type which can be exported
156 */
exportFormats() const157 QList<MeshIOInterface::Format> PDBIOPlugin::exportFormats() const
158 {
159 QList<Format> formatList;
160 // formatList << Format("Stanford Polygon File Format" , tr("PLY"));
161
162 return formatList;
163 }
164
165 /*
166 returns the mask on the basis of the file's type.
167 otherwise it returns 0 if the file format is unknown
168 */
GetExportMaskCapability(QString &,int & capability,int & defaultBits) const169 void PDBIOPlugin::GetExportMaskCapability(QString & /*format*/, int &capability, int &defaultBits) const
170 {
171 capability=defaultBits=0;
172 return;
173 }
174
initOpenParameter(const QString &,MeshModel &,RichParameterSet &)175 void PDBIOPlugin::initOpenParameter(const QString & /*format*/, MeshModel &/*m*/, RichParameterSet & /*par*/)
176 {
177 /*
178 if(format.toUpper() == tr("STL"))
179 par.addBool("Unify",true, "Unify Duplicated Vertices",
180 "The STL format is not an vertex-indexed format. Each triangle is composed by independent vertices, so, usually, duplicated vertices should be unified");
181 */
182 }
initSaveParameter(const QString &,MeshModel &,RichParameterSet &)183 void PDBIOPlugin::initSaveParameter(const QString & /*format*/, MeshModel &/*m*/, RichParameterSet & /*par*/)
184 {
185 /*
186 if(format.toUpper() == tr("STL") || format.toUpper() == tr("PLY"))
187 par.addBool("Binary",true, "Binary encoding",
188 "Save the mesh using a binary encoding. If false the mesh is saved in a plain, readable ascii format");
189 */
190 }
applyOpenParameter(const QString &,MeshModel &,const RichParameterSet &)191 void PDBIOPlugin::applyOpenParameter(const QString & /*format*/, MeshModel & /*m*/, const RichParameterSet & /*par*/)
192 {
193 /*
194 if(format.toUpper() == tr("STL"))
195 if(par.getBool("Unify"))
196 tri::Clean<CMeshO>::RemoveDuplicateVertex(m.cm);
197 */
198 }
199
MESHLAB_PLUGIN_NAME_EXPORTER(PDBIOPlugin)200 MESHLAB_PLUGIN_NAME_EXPORTER(PDBIOPlugin)
201
202
203 //---------- PDB READER -----------//
204 bool PDBIOPlugin::parsePDB(const std::string &filename, CMeshO &m, const RichParameterSet &parlst, CallBackPos *cb)
205 {
206 size_t atomNumber=0;
207 bool surfacecreated = false;
208
209 FILE *fp = fopen(filename.c_str(), "rb");
210 if (!fp) {
211 return false;
212 }
213
214 //-- clear all molecule data
215 atomDetails.clear();
216 atomPos.clear();
217 atomCol.clear();
218 atomRad.clear();
219
220 //-- read all lines, if the line contains ATOM, then store the details for parsing
221 char buf[82];
222 buf[81]=0;
223
224 while(1)
225 {
226 if(! fgets(buf,81,fp)) break;
227 string st(buf);
228 if (strcmp( st.substr(0,6).c_str(), "ATOM ") == 0 )
229 {
230 atomDetails.push_back(st);
231 atomNumber++;
232 }
233 }
234
235 // updating progress bar status
236 char msgbuf[256];
237 sprintf(msgbuf,"Read %zu atoms...",atomNumber);
238 if (cb != NULL) (*cb)(10, "Loading...");
239
240 //-- atoms parsing
241 for(size_t atomIndex=0; atomIndex<atomDetails.size(); atomIndex++)
242 {
243 Point3m currAtomPos;
244 Color4b currAtomCol;
245 float currAtomRad;
246
247 // position
248 mysscanf(atomDetails[atomIndex].substr( 31, 38).c_str(), &(currAtomPos.X()));
249 mysscanf(atomDetails[atomIndex].substr( 39, 46).c_str(), &(currAtomPos.Y()));
250 mysscanf(atomDetails[atomIndex].substr( 47, 54).c_str(), &(currAtomPos.Z()));
251 atomPos.push_back(currAtomPos);
252
253 // color
254 currAtomCol=getAtomColor(atomDetails[atomIndex].substr(13, 4).c_str());
255 atomCol.push_back(currAtomCol);
256
257 // radius
258 currAtomRad=getAtomRadius(atomDetails[atomIndex].substr(13, 4).c_str()); // Van der Waals radii
259 atomRad.push_back(currAtomRad);
260 }
261
262 // build mesh
263
264 if(parlst.getBool("justpoints") && !surfacecreated) // pointcloud
265 {
266 tri::Allocator<CMeshO>::AddVertices(m,atomNumber);
267
268 for (size_t atomIndex = 0; atomIndex < atomNumber; ++atomIndex)
269 {
270 m.vert[atomIndex].P()=atomPos[atomIndex];
271 m.vert[atomIndex].C()=atomCol[atomIndex];
272 }
273
274 surfacecreated = true;
275 }
276
277 if(parlst.getBool("justspheres") && !surfacecreated) // spheres
278 {
279 CMeshO tmpmesh;
280 tmpmesh.face.EnableFFAdjacency();
281 vcg::tri::UpdateTopology<CMeshO>::FaceFace(tmpmesh);
282
283 for (size_t atomIndex = 0; atomIndex < atomNumber; ++atomIndex)
284 {
285 tmpmesh.Clear();
286 vcg::tri::Sphere<CMeshO>(tmpmesh,1);
287
288 // scale, move and apply color
289 for(int vi=0; vi<tmpmesh.vn; vi++)
290 {
291 tmpmesh.vert[vi].P().X() = (tmpmesh.vert[vi].P().X() * atomRad[atomIndex]) + atomPos[atomIndex].X();
292 tmpmesh.vert[vi].P().Y() = (tmpmesh.vert[vi].P().Y() * atomRad[atomIndex]) + atomPos[atomIndex].Y();
293 tmpmesh.vert[vi].P().Z() = (tmpmesh.vert[vi].P().Z() * atomRad[atomIndex]) + atomPos[atomIndex].Z();
294
295 tmpmesh.vert[vi].C() = atomCol[atomIndex];
296 }
297
298 tri::Append<CMeshO,CMeshO>::Mesh(m,tmpmesh);
299 }
300 tmpmesh.Clear();
301
302 surfacecreated = true;
303 }
304
305 if(parlst.getBool("interpspheres") && !surfacecreated) // jointed spheres marching cube
306 {
307 SimpleVolume<SimpleVoxelm> volume;
308
309 typedef vcg::tri::TrivialWalker<CMeshO, SimpleVolume<SimpleVoxelm> > MyWalker;
310 typedef vcg::tri::MarchingCubes<CMeshO, MyWalker> MyMarchingCubes;
311 MyWalker walker;
312
313 Box3m rbb;
314 // calculating an enlarged bbox
315 rbb.min[0]=rbb.min[1]=rbb.min[2]= 100000;
316 rbb.max[0]=rbb.max[1]=rbb.max[2]=-100000;
317 for (size_t atomIndex = 0; atomIndex < atomNumber; ++atomIndex)
318 {
319 if(atomPos[atomIndex].X() < rbb.min[0]) rbb.min[0]=atomPos[atomIndex].X();
320 if(atomPos[atomIndex].X() > rbb.max[0]) rbb.max[0]=atomPos[atomIndex].X();
321 if(atomPos[atomIndex].Y() < rbb.min[1]) rbb.min[1]=atomPos[atomIndex].Y();
322 if(atomPos[atomIndex].Y() > rbb.max[1]) rbb.max[1]=atomPos[atomIndex].Y();
323 if(atomPos[atomIndex].Z() < rbb.min[2]) rbb.min[2]=atomPos[atomIndex].Z();
324 if(atomPos[atomIndex].Z() > rbb.max[2]) rbb.max[2]=atomPos[atomIndex].Z();
325 }
326 rbb.min[0]-=5; rbb.min[1]-=5; rbb.min[2]-=5;
327 rbb.max[0]+=5; rbb.max[1]+=5; rbb.max[2]+=5;
328
329 // defining resolution
330 double step = parlst.getFloat("voxelsize");
331 Point3i siz= Point3i::Construct((rbb.max-rbb.min)*(1.0/step));
332
333 volume.Init(siz,rbb);
334 float xpos,ypos,zpos;
335 for(double i=0;i<siz[0];i++)
336 for(double j=0;j<siz[1];j++)
337 for(double k=0;k<siz[2];k++)
338 {
339 xpos = rbb.min[0]+step*i;
340 ypos = rbb.min[1]+step*j;
341 zpos = rbb.min[2]+step*k;
342
343 volume.Val(i,j,k)=10000;
344 for (size_t atomIndex = 0; atomIndex < atomNumber; ++atomIndex)
345 {
346 if(! (fabs(xpos-atomPos[atomIndex].X())>3.0f) )
347 if(! (fabs(ypos-atomPos[atomIndex].Y())>3.0f) )
348 if(! (fabs(zpos-atomPos[atomIndex].Z())>3.0f) )
349 {
350 float val = pow((double)(xpos-atomPos[atomIndex].X()),2.0) +
351 pow((double)(ypos-atomPos[atomIndex].Y()),2.0) +
352 pow((double)(zpos-atomPos[atomIndex].Z()),2.0) - atomRad[atomIndex];
353 if(val < volume.Val(i,j,k))
354 volume.Val(i,j,k) = val;
355 }
356 }
357 }
358
359 // MARCHING CUBES
360 MyMarchingCubes mc(m, walker);
361 walker.BuildMesh<MyMarchingCubes>(m, volume, mc, 0);
362 Matrix44m tr; tr.SetIdentity(); tr.SetTranslate(rbb.min[0],rbb.min[1],rbb.min[2]);
363 Matrix44m sc; sc.SetIdentity(); sc.SetScale(step,step,step);
364 tr=tr*sc;
365
366 tri::UpdatePosition<CMeshO>::Matrix(m,tr);
367 tri::UpdateNormal<CMeshO>::PerVertexNormalizedPerFace(m);
368 tri::UpdateBounding<CMeshO>::Box(m); // updates bounding box
369
370 surfacecreated = true;
371 }
372
373
374 if(parlst.getBool("metaballs") && !surfacecreated) // metaballs marching cube
375 {
376 SimpleVolume<SimpleVoxelm> volume;
377
378 typedef vcg::tri::TrivialWalker<CMeshO, SimpleVolume<SimpleVoxelm> > MyWalker;
379 typedef vcg::tri::MarchingCubes<CMeshO, MyWalker> MyMarchingCubes;
380 MyWalker walker;
381
382 Box3m rbb;
383 // calculating an enlarged bbox
384 rbb.min[0]=rbb.min[1]=rbb.min[2]= 100000;
385 rbb.max[0]=rbb.max[1]=rbb.max[2]=-100000;
386 for (size_t atomIndex = 0; atomIndex < atomNumber; ++atomIndex)
387 {
388 if(atomPos[atomIndex].X() < rbb.min[0]) rbb.min[0]=atomPos[atomIndex].X();
389 if(atomPos[atomIndex].X() > rbb.max[0]) rbb.max[0]=atomPos[atomIndex].X();
390 if(atomPos[atomIndex].Y() < rbb.min[1]) rbb.min[1]=atomPos[atomIndex].Y();
391 if(atomPos[atomIndex].Y() > rbb.max[1]) rbb.max[1]=atomPos[atomIndex].Y();
392 if(atomPos[atomIndex].Z() < rbb.min[2]) rbb.min[2]=atomPos[atomIndex].Z();
393 if(atomPos[atomIndex].Z() > rbb.max[2]) rbb.max[2]=atomPos[atomIndex].Z();
394 }
395 rbb.min[0]-=5; rbb.min[1]-=5; rbb.min[2]-=5;
396 rbb.max[0]+=5; rbb.max[1]+=5; rbb.max[2]+=5;
397
398 // defining resolution
399 double step = parlst.getFloat("voxelsize");
400 float blobby = -parlst.getFloat("blobby");
401 Point3i siz= Point3i::Construct((rbb.max-rbb.min)*(1.0/step));
402
403
404 // Log("Filling a Volume of %i %i %i",siz[0],siz[1],siz[2]);
405 volume.Init(siz,rbb);
406 float xpos,ypos,zpos;
407 for(double i=0;i<siz[0];i++)
408 for(double j=0;j<siz[1];j++)
409 for(double k=0;k<siz[2];k++)
410 {
411 xpos = rbb.min[0]+step*i;
412 ypos = rbb.min[1]+step*j;
413 zpos = rbb.min[2]+step*k;
414
415 volume.Val(i,j,k)=0.0;
416 for (size_t atomIndex = 0; atomIndex < atomNumber; ++atomIndex)
417 {
418 if(! (fabs(xpos-atomPos[atomIndex].X())>5.0f) )
419 if(! (fabs(ypos-atomPos[atomIndex].Y())>5.0f) )
420 if(! (fabs(zpos-atomPos[atomIndex].Z())>5.0f) )
421 {
422 float r2 = (pow((double)(xpos-atomPos[atomIndex].X()),2.0) +
423 pow((double)(ypos-atomPos[atomIndex].Y()),2.0) +
424 pow((double)(zpos-atomPos[atomIndex].Z()),2.0));
425 float val = exp((blobby/atomRad[atomIndex])*r2 - blobby);
426
427 volume.Val(i,j,k) += val;
428 }
429 }
430 }
431
432 // MARCHING CUBES
433 MyMarchingCubes mc(m, walker);
434 walker.BuildMesh<MyMarchingCubes>(m, volume, mc, 1);
435 Matrix44m tr; tr.SetIdentity(); tr.SetTranslate(rbb.min[0],rbb.min[1],rbb.min[2]);
436 Matrix44m sc; sc.SetIdentity(); sc.SetScale(step,step,step);
437 tr=tr*sc;
438
439 //tri::io::ExporterPLY<CMeshO>::Save(m,"./pippo.ply");
440
441 tri::UpdatePosition<CMeshO>::Matrix(m,tr);
442 tri::Clean<CMeshO>::FlipMesh(m);
443 tri::UpdateNormal<CMeshO>::PerVertexNormalizedPerFace(m);
444 tri::UpdateBounding<CMeshO>::Box(m); // updates bounding box
445
446 //------------------------------------------------
447
448 double ww;
449 double rr;
450 double gg;
451 double bb;
452 for(int vind=0; vind<m.vn ; vind++)
453 {
454 xpos = m.vert[vind].P().X();
455 ypos = m.vert[vind].P().Y();
456 zpos = m.vert[vind].P().Z();
457 ww=rr=gg=bb=0;
458
459 for (size_t atomIndex = 0; atomIndex < atomNumber; ++atomIndex)
460 {
461 if(! (fabs(xpos-atomPos[atomIndex].X())>5.0f) )
462 {
463 if(! (fabs(ypos-atomPos[atomIndex].Y())>5.0f) )
464 {
465 if(! (fabs(zpos-atomPos[atomIndex].Z())>5.0f) )
466 {
467 float r2 = (pow((double)(xpos-atomPos[atomIndex].X()),2.0) +
468 pow((double)(ypos-atomPos[atomIndex].Y()),2.0) +
469 pow((double)(zpos-atomPos[atomIndex].Z()),2.0));
470 r2 = r2 / atomRad[atomIndex];
471 r2 = min(2.0f,r2);
472
473 ww += r2;
474 rr += r2 * atomCol[atomIndex].X();
475 gg += r2 * atomCol[atomIndex].Y();
476 bb += r2 * atomCol[atomIndex].Z();
477
478 }
479 }
480 }
481
482 m.vert[vind].C().X() = rr/ww;
483 m.vert[vind].C().Y() = gg/ww;
484 m.vert[vind].C().Z() = bb/ww;
485 }
486
487
488 }
489
490 //------------------------------------------------
491
492 surfacecreated = true;
493 }
494
495
496 //-- ending all
497 if (cb != NULL) (*cb)(99, "Done");
498
499 //-- finish by clearing all molecule data
500 atomDetails.clear();
501 atomPos.clear();
502 atomCol.clear();
503 atomRad.clear();
504
505 // closing file
506 fclose(fp);
507
508 return surfacecreated;
509 }
510
511
512 //-- helper function... parses + and - values with space
mysscanf(const char * st,float * f)513 void PDBIOPlugin::mysscanf(const char* st, float *f)
514 {
515 if (!sscanf( st, "%f", f)) {
516 if (sscanf( st, " - %f", f))
517 *f=-*f;
518 else *f=0.0;
519 };
520 }
521
mysscanf(const char * st,double * f)522 void PDBIOPlugin::mysscanf(const char* st, double *f)
523 {
524 if (!sscanf( st, "%lf", f)) {
525 if (sscanf( st, " - %lf", f))
526 *f=-*f;
527 else *f=0.0;
528 };
529 }
530
531
532 //-- returns the correct radius for each atom type
getAtomRadius(const char * atomicElementCharP)533 float PDBIOPlugin::getAtomRadius(const char* atomicElementCharP)
534 {
535 static std::map<std::string,float> E2R;
536 if(E2R.size()==0)
537 {
538 // according to http://www.imb-jena.de/ImgLibDoc/glossary/IMAGE_VDWR.html
539 //E2R["H"]= 1.20f;
540 //E2R["C"]= 1.70f;
541 //E2R["N"]= 1.55f;
542 //E2R["O"]= 1.52f;
543 //E2R["F"]= 1.47f;
544 //E2R["P"]= 1.80f;
545 //E2R["S"]= 1.80f;
546 //E2R["CL"]= 1.89f;
547
548 /// according to http://www.umass.edu/microbio/rasmol/rasbonds.htm
549 E2R["H"]= 1.100f;
550 E2R["C"]= 1.400f;//1.548f;
551 E2R["N"]= 1.400f;
552 E2R["O"]= 1.348f;
553 E2R["P"]= 1.880f;
554 E2R["S"]= 1.808f;
555 E2R["CA"]= 1.948f;
556 E2R["FE"]= 1.948f;
557 E2R["ZN"]= 1.148f;
558 E2R["CD"]= 1.748f;
559 E2R["I"]= 1.748f;
560 }
561 std::string ss0,ss1;
562 string atomicElement(atomicElementCharP);
563 ss0=atomicElement.substr(0,1);
564 ss1=atomicElement.substr(0,2);
565 float rad=E2R[ss1];
566 if(rad==0) rad = E2R[ss0];
567 if(rad==0) rad=1;
568 return rad;
569 }
570
getAtomColor(const char * atomicElementCharP)571 vcg::Color4b PDBIOPlugin::getAtomColor(const char* atomicElementCharP)
572 {
573 string atomicElement(atomicElementCharP);
574 static std::map<std::string,vcg::Color4b> E2C;
575
576 if(E2C.size()==0)
577 {
578 E2C["H"] = vcg::Color4b(255,255,255,255) /* 0xFFFFFF */ ;
579 E2C["HE"]= vcg::Color4b(217,255,255,255) /* 0xD9FFFF */ ;
580 E2C["LI"]= vcg::Color4b(204,128,255,255) /* 0xCC80FF */ ;
581 E2C["BE"]= vcg::Color4b(194,255, 0,255) /* 0xC2FF00 */ ;
582 E2C["B"] = vcg::Color4b(255,181,181,255) /* 0xFFB5B5 */ ;
583 E2C["C"] = vcg::Color4b(144,144,144,255) /* 0x909090 */ ;
584 E2C["N"] = vcg::Color4b( 48, 80,248,255) /* 0x3050F8 */ ;
585 E2C["O"] = vcg::Color4b(255, 13, 13,255) /* 0xFF0D0D */ ;
586 E2C["F"] = vcg::Color4b(144,224, 80,255) /* 0x90E050 */ ;
587 E2C["NE"]= vcg::Color4b(179,227,245,255) /* 0xB3E3F5 */ ;
588 E2C["NA"]= vcg::Color4b(171, 92,242,255) /* 0xAB5CF2 */ ;
589 E2C["MG"]= vcg::Color4b(138,255, 0,255) /* 0x8AFF00 */ ;
590 E2C["AL"]= vcg::Color4b(191,166,166,255) /* 0xBFA6A6 */ ;
591 E2C["SI"]= vcg::Color4b(240,200,160,255) /* 0xF0C8A0 */ ;
592 E2C["P"] = vcg::Color4b(255,128, 0,255) /* 0xFF8000 */ ;
593 E2C["S"] = vcg::Color4b(255,255, 48,255) /* 0xFFFF30 */ ;
594 E2C["CL"]= vcg::Color4b( 31,240, 31,255) /* 0x1FF01F */ ;
595 E2C["AR"]= vcg::Color4b(128,209,227,255) /* 0x80D1E3 */ ;
596 E2C["K"] = vcg::Color4b(143, 64,212,255) /* 0x8F40D4 */ ;
597 E2C["CA"]= vcg::Color4b( 61,255, 0,255) /* 0x3DFF00 */ ;
598 E2C["SC"]= vcg::Color4b(230,230,230,255) /* 0xE6E6E6 */ ;
599 E2C["TI"]= vcg::Color4b(191,194,199,255) /* 0xBFC2C7 */ ;
600 E2C["V"] = vcg::Color4b(166,166,171,255) /* 0xA6A6AB */ ;
601 E2C["CR"]= vcg::Color4b(138,153,199,255) /* 0x8A99C7 */ ;
602 E2C["MN"]= vcg::Color4b(156,122,199,255) /* 0x9C7AC7 */ ;
603 E2C["FE"]= vcg::Color4b(224,102, 51,255) /* 0xE06633 */ ;
604 E2C["CO"]= vcg::Color4b(240,144,160,255) /* 0xF090A0 */ ;
605 E2C["NI"]= vcg::Color4b( 80,208, 80,255) /* 0x50D050 */ ;
606 E2C["CU"]= vcg::Color4b(200,128, 51,255) /* 0xC88033 */ ;
607 E2C["ZN"]= vcg::Color4b(125,128,176,255) /* 0x7D80B0 */ ;
608 E2C["GA"]= vcg::Color4b(194,143,143,255) /* 0xC28F8F */ ;
609 E2C["GE"]= vcg::Color4b(102,143,143,255) /* 0x668F8F */ ;
610 E2C["AS"]= vcg::Color4b(189,128,227,255) /* 0xBD80E3 */ ;
611 E2C["SE"]= vcg::Color4b(255,161, 0,255) /* 0xFFA100 */ ;
612 E2C["BR"]= vcg::Color4b(166, 41, 41,255) /* 0xA62929 */ ;
613 E2C["KR"]= vcg::Color4b( 92,184,209,255) /* 0x5CB8D1 */ ;
614 E2C["RB"]= vcg::Color4b(112, 46,176,255) /* 0x702EB0 */ ;
615 E2C["SR"]= vcg::Color4b( 0,255, 0,255) /* 0x00FF00 */ ;
616 E2C["Y"] = vcg::Color4b(148,255,255,255) /* 0x94FFFF */ ;
617 E2C["ZR"]= vcg::Color4b(148,224,224,255) /* 0x94E0E0 */ ;
618 E2C["NB"]= vcg::Color4b(115,194,201,255) /* 0x73C2C9 */ ;
619 E2C["MO"]= vcg::Color4b( 84,181,181,255) /* 0x54B5B5 */ ;
620 E2C["TC"]= vcg::Color4b( 59,158,158,255) /* 0x3B9E9E */ ;
621 E2C["RU"]= vcg::Color4b( 36,143,143,255) /* 0x248F8F */ ;
622 E2C["RH"]= vcg::Color4b( 10,125,140,255) /* 0x0A7D8C */ ;
623 E2C["PD"]= vcg::Color4b( 0,105,133,255) /* 0x006985 */ ;
624 E2C["AG"]= vcg::Color4b(192,192,192,255) /* 0xC0C0C0 */ ;
625 E2C["CD"]= vcg::Color4b(255,217,143,255) /* 0xFFD98F */ ;
626 E2C["IN"]= vcg::Color4b(166,117,115,255) /* 0xA67573 */ ;
627 E2C["SN"]= vcg::Color4b(102,128,128,255) /* 0x668080 */ ;
628 E2C["SB"]= vcg::Color4b(158, 99,181,255) /* 0x9E63B5 */ ;
629 E2C["TE"]= vcg::Color4b(212,122, 0,255) /* 0xD47A00 */ ;
630 E2C["I"] = vcg::Color4b(148, 0,148,255) /* 0x940094 */ ;
631 E2C["XE"]= vcg::Color4b( 66,158,176,255) /* 0x429EB0 */ ;
632 E2C["CS"]= vcg::Color4b( 87, 23,143,255) /* 0x57178F */ ;
633 E2C["BA"]= vcg::Color4b( 0,201, 0,255) /* 0x00C900 */ ;
634 E2C["LA"]= vcg::Color4b(112,212,255,255) /* 0x70D4FF */ ;
635 E2C["CE"]= vcg::Color4b(255,255,199,255) /* 0xFFFFC7 */ ;
636 E2C["PR"]= vcg::Color4b(217,255,199,255) /* 0xD9FFC7 */ ;
637 E2C["ND"]= vcg::Color4b(199,255,199,255) /* 0xC7FFC7 */ ;
638 E2C["PM"]= vcg::Color4b(163,255,199,255) /* 0xA3FFC7 */ ;
639 E2C["SM"]= vcg::Color4b(143,255,199,255) /* 0x8FFFC7 */ ;
640 E2C["EU"]= vcg::Color4b( 97,255,199,255) /* 0x61FFC7 */ ;
641 E2C["GD"]= vcg::Color4b( 69,255,199,255) /* 0x45FFC7 */ ;
642 E2C["TB"]= vcg::Color4b( 48,255,199,255) /* 0x30FFC7 */ ;
643 E2C["DY"]= vcg::Color4b( 31,255,199,255) /* 0x1FFFC7 */ ;
644 E2C["HO"]= vcg::Color4b( 0,255,156,255) /* 0x00FF9C */ ;
645 E2C["ER"]= vcg::Color4b( 0,230,117,255) /* 0x00E675 */ ;
646 E2C["TM"]= vcg::Color4b( 0,212, 82,255) /* 0x00D452 */ ;
647 E2C["YB"]= vcg::Color4b( 0,191, 56,255) /* 0x00BF38 */ ;
648 E2C["LU"]= vcg::Color4b( 0,171, 36,255) /* 0x00AB24 */ ;
649 E2C["HF"]= vcg::Color4b( 77,194,255,255) /* 0x4DC2FF */ ;
650 E2C["TA"]= vcg::Color4b( 77,166,255,255) /* 0x4DA6FF */ ;
651 E2C["W"] = vcg::Color4b( 33,148,214,255) /* 0x2194D6 */ ;
652 E2C["RE"]= vcg::Color4b( 38,125,171,255) /* 0x267DAB */ ;
653 E2C["OS"]= vcg::Color4b( 38,102,150,255) /* 0x266696 */ ;
654 E2C["IR"]= vcg::Color4b( 23, 84,135,255) /* 0x175487 */ ;
655 E2C["PT"]= vcg::Color4b(208,208,224,255) /* 0xD0D0E0 */ ;
656 E2C["AU"]= vcg::Color4b(255,209, 35,255) /* 0xFFD123 */ ;
657 E2C["HG"]= vcg::Color4b(184,184,208,255) /* 0xB8B8D0 */ ;
658 E2C["TL"]= vcg::Color4b(166, 84, 77,255) /* 0xA6544D */ ;
659 E2C["PB"]= vcg::Color4b( 87, 89, 97,255) /* 0x575961 */ ;
660 E2C["BI"]= vcg::Color4b(158, 79,181,255) /* 0x9E4FB5 */ ;
661 E2C["PO"]= vcg::Color4b(171, 92, 0,255) /* 0xAB5C00 */ ;
662 E2C["AT"]= vcg::Color4b(117, 79, 69,255) /* 0x754F45 */ ;
663 E2C["RN"]= vcg::Color4b( 66,130,150,255) /* 0x428296 */ ;
664 E2C["FR"]= vcg::Color4b( 66, 0,102,255) /* 0x420066 */ ;
665 E2C["RA"]= vcg::Color4b( 0,125, 0,255) /* 0x007D00 */ ;
666 E2C["AC"]= vcg::Color4b(112,171,250,255) /* 0x70ABFA */ ;
667 E2C["TH"]= vcg::Color4b( 0,186,255,255) /* 0x00BAFF */ ;
668 E2C["PA"]= vcg::Color4b( 0,161,255,255) /* 0x00A1FF */ ;
669 E2C["U"] = vcg::Color4b( 0,143,255,255) /* 0x008FFF */ ;
670 E2C["NP"]= vcg::Color4b( 0,128,255,255) /* 0x0080FF */ ;
671 E2C["PU"]= vcg::Color4b( 0,107,255,255) /* 0x006BFF */ ;
672 E2C["AM"]= vcg::Color4b( 84, 92,242,255) /* 0x545CF2 */ ;
673 E2C["CM"]= vcg::Color4b(120, 92,227,255) /* 0x785CE3 */ ;
674 E2C["BK"]= vcg::Color4b(138, 79,227,255) /* 0x8A4FE3 */ ;
675 E2C["CF"]= vcg::Color4b(161, 54,212,255) /* 0xA136D4 */ ;
676 E2C["ES"]= vcg::Color4b(179, 31,212,255) /* 0xB31FD4 */ ;
677 E2C["FM"]= vcg::Color4b(179, 31,186,255) /* 0xB31FBA */ ;
678 E2C["MD"]= vcg::Color4b(179, 13,166,255) /* 0xB30DA6 */ ;
679 E2C["NO"]= vcg::Color4b(189, 13,135,255) /* 0xBD0D87 */ ;
680 E2C["LR"]= vcg::Color4b(199, 0,102,255) /* 0xC70066 */ ;
681 E2C["RF"]= vcg::Color4b(204, 0, 89,255) /* 0xCC0059 */ ;
682 E2C["DB"]= vcg::Color4b(209, 0, 79,255) /* 0xD1004F */ ;
683 E2C["SG"]= vcg::Color4b(217, 0, 69,255) /* 0xD90045 */ ;
684 E2C["BH"]= vcg::Color4b(224, 0, 56,255) /* 0xE00038 */ ;
685 E2C["HS"]= vcg::Color4b(230, 0, 46,255) /* 0xE6002E */ ;
686 E2C["MT"]= vcg::Color4b(235, 0, 38,255) /* 0xEB0026 */ ;
687 }
688
689 std::string ss0,ss1,ss2;
690 std::min(atomicElement.length(),atomicElement.find_first_of(' '));
691 ss0=atomicElement.substr(0,1);
692 vcg::Color4b color=vcg::Color4b::Black;
693 color=E2C[ss0];
694 if((color.Red==0) && (color.Green==0) && (color.Blue==0))
695 {
696 ss1=atomicElement.substr(0,2);
697 color = E2C[ss1];
698 }
699
700 return color;
701 }
702