diff --git a/src/meshlabplugins/io_pdb/io_pdb.cpp b/src/meshlabplugins/io_pdb/io_pdb.cpp new file mode 100644 index 000000000..cc56783d9 --- /dev/null +++ b/src/meshlabplugins/io_pdb/io_pdb.cpp @@ -0,0 +1,700 @@ +/**************************************************************************** +* MeshLab o o * +* An extendible mesh processor o o * +* _ O _ * +* Copyright(C) 2005, 2006 \/)\/ * +* Visual Computing Lab /\/| * +* ISTI - Italian National Research Council | * +* \ * +* All rights reserved. * +* * +* This program is free software; you can redistribute it and/or modify * +* it under the terms of the GNU General Public License as published by * +* the Free Software Foundation; either version 2 of the License, or * +* (at your option) any later version. * +* * +* This program is distributed in the hope that it will be useful, * +* but WITHOUT ANY WARRANTY; without even the implied warranty of * +* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * +* GNU General Public License (http://www.gnu.org/licenses/gpl.txt) * +* for more details. * +* * +****************************************************************************/ + +#include +#include + +#include "io_pdb.h" + +#include + +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +// debug, to be removed +#include + +#include +#include +#include + +#include +#include + +using namespace std; +using namespace vcg; + +// initialize importing parameters +void PDBIOPlugin::initPreOpenParameter(const QString &formatName, const QString &/*filename*/, FilterParameterSet &parlst) +{ + if (formatName.toUpper() == tr("PDB")) + { + parlst.addBool("usecolors",true,"Use Atoms colors","Atoms are colored according to atomic type"); + parlst.addBool("justpoints",false,"SURFACE: Atoms as Points","Atoms are created as points, no surface is built. Overrides all subsequential surface parameters"); + parlst.addBool("justspheres",true,"SURFACE: Atoms as Spheres","Atoms are created as intersecting spheres, no interpolation surface is built. Overrides all subsequential surface parameters"); + parlst.addBool("interpspheres",false,"SURFACE: Atoms as Jointed Spheres","Atoms are created as spheres, joining surface is built. Overrides all subsequential surface parameters"); + parlst.addBool("metaballs",false,"SURFACE: Atoms as Metaballs","Atoms are created as blobby interpolation surface, refer to BLINN Metaballs article. Overrides all subsequential surface parameters"); + parlst.addFloat("voxelsize",0.25,"Surface Resolution","is used by Jointed Spheres and Metaball"); + parlst.addFloat("blobby",2.0,"Blobbyness factor","is used by Metaball"); + /* + parlst.addInt("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"); + parlst.addBool("anglecull",true,"Cull faces by angle","short"); + parlst.addFloat("angle",85.0,"Angle limit for face culling","short"); + parlst.addBool("usecolor",true,"import color","Read color from PTX, if color is not present, uses reflectance instead"); + parlst.addBool("pointcull",true,"delete unsampled points","Deletes unsampled points in the grid that are normally located in [0,0,0]"); + parlst.addBool("pointsonly",false,"Keep only points","Just import points, without triangulation"); + parlst.addBool("switchside",false,"Swap rows/columns","On some PTX, the rows and columns number are switched over"); + parlst.addBool("flipfaces",false,"Flip all faces","Flip the orientation of all the triangles"); + */ + } +} + +bool PDBIOPlugin::open(const QString &formatName, const QString &fileName, MeshModel &m, int& mask, const FilterParameterSet &parlst, CallBackPos *cb, QWidget * /*parent*/) +{ + bool normalsUpdated = false; + + // initializing mask + mask = 0; + + // initializing progress bar status + if (cb != NULL) (*cb)(0, "Loading..."); + + QString errorMsgFormat = "Error encountered while loading file:\n\"%1\"\n\nError details: %2"; + + //string filename = fileName.toUtf8().data(); + string filename = QFile::encodeName(fileName).constData (); + + if (formatName.toUpper() == tr("PDB")) + { + + mask |= vcg::tri::io::Mask::IOM_VERTCOLOR; + m.Enable(mask); + + return parsePDB(qPrintable(fileName), m.cm, parlst, cb); + + + /* + tri::io::ImporterPTX::Info importparams; + + importparams.meshnum = parlst.getInt("meshindex"); + importparams.anglecull =parlst.getBool("anglecull"); + importparams.angle = parlst.getFloat("angle"); + importparams.savecolor = parlst.getBool("usecolor"); + importparams.pointcull = parlst.getBool("pointcull"); + importparams.pointsonly = parlst.getBool("pointsonly"); + importparams.switchside = parlst.getBool("switchside"); + importparams.flipfaces = parlst.getBool("flipfaces"); + + // if color, add to mesh + if(importparams.savecolor) + importparams.mask |= tri::io::Mask::IOM_VERTCOLOR; + + // reflectance is stored in quality + importparams.mask |= tri::io::Mask::IOM_VERTQUALITY; + + m.Enable(importparams.mask); + + int result = tri::io::ImporterPTX::Open(m.cm, filename.c_str(), importparams, cb); + if (result == 1) + { + errorMessage = errorMsgFormat.arg(fileName, tri::io::ImporterPTX::ErrorMsg(result)); + return false; + } + + // update mask + mask = importparams.mask; + */ + } + else + { + assert(0); // Unknown File type + return false; + } + + if (cb != NULL) (*cb)(99, "Done"); + + return true; +} + +bool PDBIOPlugin::save(const QString &formatName,const QString &fileName, MeshModel &m, const int mask, const FilterParameterSet & par, CallBackPos *cb, QWidget */*parent*/) +{ + assert(0); + return false; +} + +/* + returns the list of the file's type which can be imported +*/ +QList PDBIOPlugin::importFormats() const +{ + QList formatList; + formatList << Format("Protein Data Bank" , tr("PDB")); + + return formatList; +} + +/* + returns the list of the file's type which can be exported +*/ +QList PDBIOPlugin::exportFormats() const +{ + QList formatList; +// formatList << Format("Stanford Polygon File Format" , tr("PLY")); + + return formatList; +} + +/* + returns the mask on the basis of the file's type. + otherwise it returns 0 if the file format is unknown +*/ +void PDBIOPlugin::GetExportMaskCapability(QString &format, int &capability, int &defaultBits) const +{ + capability=defaultBits=0; + return; +} + +void PDBIOPlugin::initOpenParameter(const QString &format, MeshModel &/*m*/, FilterParameterSet &par) +{ + /* + if(format.toUpper() == tr("STL")) + par.addBool("Unify",true, "Unify Duplicated Vertices", + "The STL format is not an vertex-indexed format. Each triangle is composed by independent vertices, so, usually, duplicated vertices should be unified"); + */ +} +void PDBIOPlugin::initSaveParameter(const QString &format, MeshModel &/*m*/, FilterParameterSet &par) +{ + /* + if(format.toUpper() == tr("STL") || format.toUpper() == tr("PLY")) + par.addBool("Binary",true, "Binary encoding", + "Save the mesh using a binary encoding. If false the mesh is saved in a plain, readable ascii format"); + */ +} +void PDBIOPlugin::applyOpenParameter(const QString &format, MeshModel &m, const FilterParameterSet &par) +{ + /* + if(format.toUpper() == tr("STL")) + if(par.getBool("Unify")) + tri::Clean::RemoveDuplicateVertex(m.cm); + */ +} + +Q_EXPORT_PLUGIN(PDBIOPlugin) + + +//---------- PDB READER -----------// +bool PDBIOPlugin::parsePDB(const std::string &filename, CMeshO &m, const FilterParameterSet &parlst, CallBackPos *cb) +{ + int atomNumber=0; + int atomIndex; + bool surfacecreated = false; + + FILE *fp = fopen(filename.c_str(), "rb"); + if (!fp) { + return false; + } + + //-- clear all molecule data + atomDetails.clear(); + atomPos.clear(); + atomCol.clear(); + atomRad.clear(); + + //-- read all lines, if the line contains ATOM, then store the details for parsing + char buf[82]; + buf[81]=0; + + while(1) + { + if(! fgets(buf,81,fp)) break; + string st(buf); + if (strcmp( st.substr(0,6).c_str(), "ATOM ") == 0 ) + { + atomDetails.push_back(st); + atomNumber++; + } + } + + // updating progress bar status + char msgbuf[256]; + sprintf(msgbuf,"Read %i atoms...",atomNumber); + if (cb != NULL) (*cb)(10, "Loading..."); + + //-- atoms parsing + for(atomIndex=0; atomIndex::AddVertices(m,atomNumber); + + for (atomIndex = 0; atomIndex < atomNumber; ++atomIndex) + { + m.vert[atomIndex].P()=atomPos[atomIndex]; + m.vert[atomIndex].C()=atomCol[atomIndex]; + } + + surfacecreated = true; + } + + if(parlst.getBool("justspheres") && !surfacecreated) // spheres + { + CMeshO tmpmesh; + tmpmesh.face.EnableFFAdjacency(); + vcg::tri::UpdateTopology::FaceFace(tmpmesh); + + for ( atomIndex = 0; atomIndex < atomNumber; ++atomIndex) + { + tmpmesh.Clear(); + vcg::tri::Sphere(tmpmesh,1); + + // scale, move and apply color + for(int vi=0; vi::Mesh(m,tmpmesh); + } + tmpmesh.Clear(); + + surfacecreated = true; + } + + if(parlst.getBool("interpspheres") && !surfacecreated) // jointed spheres marching cube + { + SimpleVolume volume; + + typedef vcg::tri::TrivialWalker > MyWalker; + typedef vcg::tri::MarchingCubes MyMarchingCubes; + MyWalker walker; + + Box3d rbb; + // calculating an enlarged bbox + rbb.min[0]=rbb.min[1]=rbb.min[2]= 100000; + rbb.max[0]=rbb.max[1]=rbb.max[2]=-100000; + for (atomIndex = 0; atomIndex < atomNumber; ++atomIndex) + { + if(atomPos[atomIndex].X() < rbb.min[0]) rbb.min[0]=atomPos[atomIndex].X(); + if(atomPos[atomIndex].X() > rbb.max[0]) rbb.max[0]=atomPos[atomIndex].X(); + if(atomPos[atomIndex].Y() < rbb.min[1]) rbb.min[1]=atomPos[atomIndex].Y(); + if(atomPos[atomIndex].Y() > rbb.max[1]) rbb.max[1]=atomPos[atomIndex].Y(); + if(atomPos[atomIndex].Z() < rbb.min[2]) rbb.min[2]=atomPos[atomIndex].Z(); + if(atomPos[atomIndex].Z() > rbb.max[2]) rbb.max[2]=atomPos[atomIndex].Z(); + } + rbb.min[0]-=5; rbb.min[1]-=5; rbb.min[2]-=5; + rbb.max[0]+=5; rbb.max[1]+=5; rbb.max[2]+=5; + + // defining resolution + double step = parlst.getFloat("voxelsize"); + Point3i siz= Point3i::Construct((rbb.max-rbb.min)*(1.0/step)); + + volume.Init(siz); + float xpos,ypos,zpos; + for(double i=0;i3) ) + if(! (abs(ypos-atomPos[atomIndex].Y())>3) ) + if(! (abs(zpos-atomPos[atomIndex].Z())>3) ) + { + float val = pow((double)(xpos-atomPos[atomIndex].X()),2.0) + + pow((double)(ypos-atomPos[atomIndex].Y()),2.0) + + pow((double)(zpos-atomPos[atomIndex].Z()),2.0) - atomRad[atomIndex]; + if(val < volume.Val(i,j,k)) + volume.Val(i,j,k) = val; + } + } + } + + // MARCHING CUBES + MyMarchingCubes mc(m, walker); + walker.BuildMesh(m, volume, mc, 0); + Matrix44f tr; tr.SetIdentity(); tr.SetTranslate(rbb.min[0],rbb.min[1],rbb.min[2]); + Matrix44f sc; sc.SetIdentity(); sc.SetScale(step,step,step); + tr=tr*sc; + + tri::UpdatePosition::Matrix(m,tr); + tri::UpdateNormals::PerVertexNormalizedPerFace(m); + tri::UpdateBounding::Box(m); // updates bounding box + + surfacecreated = true; + } + + + if(parlst.getBool("metaballs") && !surfacecreated) // metaballs marching cube + { + SimpleVolume volume; + + typedef vcg::tri::TrivialWalker > MyWalker; + typedef vcg::tri::MarchingCubes MyMarchingCubes; + MyWalker walker; + + Box3d rbb; + // calculating an enlarged bbox + rbb.min[0]=rbb.min[1]=rbb.min[2]= 100000; + rbb.max[0]=rbb.max[1]=rbb.max[2]=-100000; + for (atomIndex = 0; atomIndex < atomNumber; ++atomIndex) + { + if(atomPos[atomIndex].X() < rbb.min[0]) rbb.min[0]=atomPos[atomIndex].X(); + if(atomPos[atomIndex].X() > rbb.max[0]) rbb.max[0]=atomPos[atomIndex].X(); + if(atomPos[atomIndex].Y() < rbb.min[1]) rbb.min[1]=atomPos[atomIndex].Y(); + if(atomPos[atomIndex].Y() > rbb.max[1]) rbb.max[1]=atomPos[atomIndex].Y(); + if(atomPos[atomIndex].Z() < rbb.min[2]) rbb.min[2]=atomPos[atomIndex].Z(); + if(atomPos[atomIndex].Z() > rbb.max[2]) rbb.max[2]=atomPos[atomIndex].Z(); + } + rbb.min[0]-=5; rbb.min[1]-=5; rbb.min[2]-=5; + rbb.max[0]+=5; rbb.max[1]+=5; rbb.max[2]+=5; + + // defining resolution + double step = parlst.getFloat("voxelsize"); + float blobby = -parlst.getFloat("blobby"); + Point3i siz= Point3i::Construct((rbb.max-rbb.min)*(1.0/step)); + + +// Log("Filling a Volume of %i %i %i",siz[0],siz[1],siz[2]); + volume.Init(siz); + float xpos,ypos,zpos; + for(double i=0;i5) ) + if(! (abs(ypos-atomPos[atomIndex].Y())>5) ) + if(! (abs(zpos-atomPos[atomIndex].Z())>5) ) + { + float r2 = (pow((double)(xpos-atomPos[atomIndex].X()),2.0) + + pow((double)(ypos-atomPos[atomIndex].Y()),2.0) + + pow((double)(zpos-atomPos[atomIndex].Z()),2.0)); + float val = exp((blobby/atomRad[atomIndex])*r2 - blobby); + + volume.Val(i,j,k) += val; + } + } + } + + // MARCHING CUBES + MyMarchingCubes mc(m, walker); + walker.BuildMesh(m, volume, mc, 1); + Matrix44f tr; tr.SetIdentity(); tr.SetTranslate(rbb.min[0],rbb.min[1],rbb.min[2]); + Matrix44f sc; sc.SetIdentity(); sc.SetScale(step,step,step); + tr=tr*sc; + + //tri::io::ExporterPLY::Save(m,"./pippo.ply"); + + tri::UpdatePosition::Matrix(m,tr); + tri::Clean::FlipMesh(m); + tri::UpdateNormals::PerVertexNormalizedPerFace(m); + tri::UpdateBounding::Box(m); // updates bounding box + + + //------------------------------------------------ + + double ww; + double rr; + double gg; + double bb; + for(int vind=0; vind5) ) + if(! (abs(ypos-atomPos[atomIndex].Y())>5) ) + if(! (abs(zpos-atomPos[atomIndex].Z())>5) ) + { + float r2 = (pow((double)(xpos-atomPos[atomIndex].X()),2.0) + + pow((double)(ypos-atomPos[atomIndex].Y()),2.0) + + pow((double)(zpos-atomPos[atomIndex].Z()),2.0)); + r2 = r2 / atomRad[atomIndex]; + r2 = min(2.0f,r2); + + ww += r2; + rr += r2 * atomCol[atomIndex].X(); + gg += r2 * atomCol[atomIndex].Y(); + bb += r2 * atomCol[atomIndex].Z(); + + } + + m.vert[vind].C().X() = rr/ww; + m.vert[vind].C().Y() = gg/ww; + m.vert[vind].C().Z() = bb/ww; + } + + + } + + //------------------------------------------------ + + surfacecreated = true; + } + + + //-- ending all + if (cb != NULL) (*cb)(99, "Done"); + + //-- finish by clearing all molecule data + atomDetails.clear(); + atomPos.clear(); + atomCol.clear(); + atomRad.clear(); + + // closing file + fclose(fp); + + return surfacecreated; +} + + +//-- helper function... parses + and - values with space +void PDBIOPlugin::mysscanf(const char* st, const char* format, float *f) +{ + if (!sscanf( st, "%f", f)) { + if (sscanf( st, " - %f", f)) + *f=-*f; + else *f=0.0; + }; +} + + +//-- returns the correct radius for each atom type +float PDBIOPlugin::getAtomRadius(const char* atomicElementCharP) +{ + static std::map E2R; + if(E2R.size()==0) + { + // according to http://www.imb-jena.de/ImgLibDoc/glossary/IMAGE_VDWR.html + //E2R["H"]= 1.20f; + //E2R["C"]= 1.70f; + //E2R["N"]= 1.55f; + //E2R["O"]= 1.52f; + //E2R["F"]= 1.47f; + //E2R["P"]= 1.80f; + //E2R["S"]= 1.80f; + //E2R["CL"]= 1.89f; + + /// according to http://www.umass.edu/microbio/rasmol/rasbonds.htm + E2R["H"]= 1.100f; + E2R["C"]= 1.400f;//1.548f; + E2R["N"]= 1.400f; + E2R["O"]= 1.348f; + E2R["P"]= 1.880f; + E2R["S"]= 1.808f; + E2R["CA"]= 1.948f; + E2R["FE"]= 1.948f; + E2R["ZN"]= 1.148f; + E2R["CD"]= 1.748f; + E2R["I"]= 1.748f; + } + std::string ss0,ss1; + string atomicElement(atomicElementCharP); + ss0=atomicElement.substr(0,1); + ss1=atomicElement.substr(0,2); + float rad=E2R[ss1]; + if(rad==0) rad = E2R[ss0]; + if(rad==0) rad=1; + return rad; +} + +vcg::Color4b PDBIOPlugin::getAtomColor(const char* atomicElementCharP) +{ + string atomicElement(atomicElementCharP); + static std::map E2C; + + if(E2C.size()==0) + { + E2C["H"] = vcg::Color4b(255,255,255,255) /* 0xFFFFFF */ ; + E2C["HE"]= vcg::Color4b(217,255,255,255) /* 0xD9FFFF */ ; + E2C["LI"]= vcg::Color4b(204,128,255,255) /* 0xCC80FF */ ; + E2C["BE"]= vcg::Color4b(194,255, 0,255) /* 0xC2FF00 */ ; + E2C["B"] = vcg::Color4b(255,181,181,255) /* 0xFFB5B5 */ ; + E2C["C"] = vcg::Color4b(144,144,144,255) /* 0x909090 */ ; + E2C["N"] = vcg::Color4b( 48, 80,248,255) /* 0x3050F8 */ ; + E2C["O"] = vcg::Color4b(255, 13, 13,255) /* 0xFF0D0D */ ; + E2C["F"] = vcg::Color4b(144,224, 80,255) /* 0x90E050 */ ; + E2C["NE"]= vcg::Color4b(179,227,245,255) /* 0xB3E3F5 */ ; + E2C["NA"]= vcg::Color4b(171, 92,242,255) /* 0xAB5CF2 */ ; + E2C["MG"]= vcg::Color4b(138,255, 0,255) /* 0x8AFF00 */ ; + E2C["AL"]= vcg::Color4b(191,166,166,255) /* 0xBFA6A6 */ ; + E2C["SI"]= vcg::Color4b(240,200,160,255) /* 0xF0C8A0 */ ; + E2C["P"] = vcg::Color4b(255,128, 0,255) /* 0xFF8000 */ ; + E2C["S"] = vcg::Color4b(255,255, 48,255) /* 0xFFFF30 */ ; + E2C["CL"]= vcg::Color4b( 31,240, 31,255) /* 0x1FF01F */ ; + E2C["AR"]= vcg::Color4b(128,209,227,255) /* 0x80D1E3 */ ; + E2C["K"] = vcg::Color4b(143, 64,212,255) /* 0x8F40D4 */ ; + E2C["CA"]= vcg::Color4b( 61,255, 0,255) /* 0x3DFF00 */ ; + E2C["SC"]= vcg::Color4b(230,230,230,255) /* 0xE6E6E6 */ ; + E2C["TI"]= vcg::Color4b(191,194,199,255) /* 0xBFC2C7 */ ; + E2C["V"] = vcg::Color4b(166,166,171,255) /* 0xA6A6AB */ ; + E2C["CR"]= vcg::Color4b(138,153,199,255) /* 0x8A99C7 */ ; + E2C["MN"]= vcg::Color4b(156,122,199,255) /* 0x9C7AC7 */ ; + E2C["FE"]= vcg::Color4b(224,102, 51,255) /* 0xE06633 */ ; + E2C["CO"]= vcg::Color4b(240,144,160,255) /* 0xF090A0 */ ; + E2C["NI"]= vcg::Color4b( 80,208, 80,255) /* 0x50D050 */ ; + E2C["CU"]= vcg::Color4b(200,128, 51,255) /* 0xC88033 */ ; + E2C["ZN"]= vcg::Color4b(125,128,176,255) /* 0x7D80B0 */ ; + E2C["GA"]= vcg::Color4b(194,143,143,255) /* 0xC28F8F */ ; + E2C["GE"]= vcg::Color4b(102,143,143,255) /* 0x668F8F */ ; + E2C["AS"]= vcg::Color4b(189,128,227,255) /* 0xBD80E3 */ ; + E2C["SE"]= vcg::Color4b(255,161, 0,255) /* 0xFFA100 */ ; + E2C["BR"]= vcg::Color4b(166, 41, 41,255) /* 0xA62929 */ ; + E2C["KR"]= vcg::Color4b( 92,184,209,255) /* 0x5CB8D1 */ ; + E2C["RB"]= vcg::Color4b(112, 46,176,255) /* 0x702EB0 */ ; + E2C["SR"]= vcg::Color4b( 0,255, 0,255) /* 0x00FF00 */ ; + E2C["Y"] = vcg::Color4b(148,255,255,255) /* 0x94FFFF */ ; + E2C["ZR"]= vcg::Color4b(148,224,224,255) /* 0x94E0E0 */ ; + E2C["NB"]= vcg::Color4b(115,194,201,255) /* 0x73C2C9 */ ; + E2C["MO"]= vcg::Color4b( 84,181,181,255) /* 0x54B5B5 */ ; + E2C["TC"]= vcg::Color4b( 59,158,158,255) /* 0x3B9E9E */ ; + E2C["RU"]= vcg::Color4b( 36,143,143,255) /* 0x248F8F */ ; + E2C["RH"]= vcg::Color4b( 10,125,140,255) /* 0x0A7D8C */ ; + E2C["PD"]= vcg::Color4b( 0,105,133,255) /* 0x006985 */ ; + E2C["AG"]= vcg::Color4b(192,192,192,255) /* 0xC0C0C0 */ ; + E2C["CD"]= vcg::Color4b(255,217,143,255) /* 0xFFD98F */ ; + E2C["IN"]= vcg::Color4b(166,117,115,255) /* 0xA67573 */ ; + E2C["SN"]= vcg::Color4b(102,128,128,255) /* 0x668080 */ ; + E2C["SB"]= vcg::Color4b(158, 99,181,255) /* 0x9E63B5 */ ; + E2C["TE"]= vcg::Color4b(212,122, 0,255) /* 0xD47A00 */ ; + E2C["I"] = vcg::Color4b(148, 0,148,255) /* 0x940094 */ ; + E2C["XE"]= vcg::Color4b( 66,158,176,255) /* 0x429EB0 */ ; + E2C["CS"]= vcg::Color4b( 87, 23,143,255) /* 0x57178F */ ; + E2C["BA"]= vcg::Color4b( 0,201, 0,255) /* 0x00C900 */ ; + E2C["LA"]= vcg::Color4b(112,212,255,255) /* 0x70D4FF */ ; + E2C["CE"]= vcg::Color4b(255,255,199,255) /* 0xFFFFC7 */ ; + E2C["PR"]= vcg::Color4b(217,255,199,255) /* 0xD9FFC7 */ ; + E2C["ND"]= vcg::Color4b(199,255,199,255) /* 0xC7FFC7 */ ; + E2C["PM"]= vcg::Color4b(163,255,199,255) /* 0xA3FFC7 */ ; + E2C["SM"]= vcg::Color4b(143,255,199,255) /* 0x8FFFC7 */ ; + E2C["EU"]= vcg::Color4b( 97,255,199,255) /* 0x61FFC7 */ ; + E2C["GD"]= vcg::Color4b( 69,255,199,255) /* 0x45FFC7 */ ; + E2C["TB"]= vcg::Color4b( 48,255,199,255) /* 0x30FFC7 */ ; + E2C["DY"]= vcg::Color4b( 31,255,199,255) /* 0x1FFFC7 */ ; + E2C["HO"]= vcg::Color4b( 0,255,156,255) /* 0x00FF9C */ ; + E2C["ER"]= vcg::Color4b( 0,230,117,255) /* 0x00E675 */ ; + E2C["TM"]= vcg::Color4b( 0,212, 82,255) /* 0x00D452 */ ; + E2C["YB"]= vcg::Color4b( 0,191, 56,255) /* 0x00BF38 */ ; + E2C["LU"]= vcg::Color4b( 0,171, 36,255) /* 0x00AB24 */ ; + E2C["HF"]= vcg::Color4b( 77,194,255,255) /* 0x4DC2FF */ ; + E2C["TA"]= vcg::Color4b( 77,166,255,255) /* 0x4DA6FF */ ; + E2C["W"] = vcg::Color4b( 33,148,214,255) /* 0x2194D6 */ ; + E2C["RE"]= vcg::Color4b( 38,125,171,255) /* 0x267DAB */ ; + E2C["OS"]= vcg::Color4b( 38,102,150,255) /* 0x266696 */ ; + E2C["IR"]= vcg::Color4b( 23, 84,135,255) /* 0x175487 */ ; + E2C["PT"]= vcg::Color4b(208,208,224,255) /* 0xD0D0E0 */ ; + E2C["AU"]= vcg::Color4b(255,209, 35,255) /* 0xFFD123 */ ; + E2C["HG"]= vcg::Color4b(184,184,208,255) /* 0xB8B8D0 */ ; + E2C["TL"]= vcg::Color4b(166, 84, 77,255) /* 0xA6544D */ ; + E2C["PB"]= vcg::Color4b( 87, 89, 97,255) /* 0x575961 */ ; + E2C["BI"]= vcg::Color4b(158, 79,181,255) /* 0x9E4FB5 */ ; + E2C["PO"]= vcg::Color4b(171, 92, 0,255) /* 0xAB5C00 */ ; + E2C["AT"]= vcg::Color4b(117, 79, 69,255) /* 0x754F45 */ ; + E2C["RN"]= vcg::Color4b( 66,130,150,255) /* 0x428296 */ ; + E2C["FR"]= vcg::Color4b( 66, 0,102,255) /* 0x420066 */ ; + E2C["RA"]= vcg::Color4b( 0,125, 0,255) /* 0x007D00 */ ; + E2C["AC"]= vcg::Color4b(112,171,250,255) /* 0x70ABFA */ ; + E2C["TH"]= vcg::Color4b( 0,186,255,255) /* 0x00BAFF */ ; + E2C["PA"]= vcg::Color4b( 0,161,255,255) /* 0x00A1FF */ ; + E2C["U"] = vcg::Color4b( 0,143,255,255) /* 0x008FFF */ ; + E2C["NP"]= vcg::Color4b( 0,128,255,255) /* 0x0080FF */ ; + E2C["PU"]= vcg::Color4b( 0,107,255,255) /* 0x006BFF */ ; + E2C["AM"]= vcg::Color4b( 84, 92,242,255) /* 0x545CF2 */ ; + E2C["CM"]= vcg::Color4b(120, 92,227,255) /* 0x785CE3 */ ; + E2C["BK"]= vcg::Color4b(138, 79,227,255) /* 0x8A4FE3 */ ; + E2C["CF"]= vcg::Color4b(161, 54,212,255) /* 0xA136D4 */ ; + E2C["ES"]= vcg::Color4b(179, 31,212,255) /* 0xB31FD4 */ ; + E2C["FM"]= vcg::Color4b(179, 31,186,255) /* 0xB31FBA */ ; + E2C["MD"]= vcg::Color4b(179, 13,166,255) /* 0xB30DA6 */ ; + E2C["NO"]= vcg::Color4b(189, 13,135,255) /* 0xBD0D87 */ ; + E2C["LR"]= vcg::Color4b(199, 0,102,255) /* 0xC70066 */ ; + E2C["RF"]= vcg::Color4b(204, 0, 89,255) /* 0xCC0059 */ ; + E2C["DB"]= vcg::Color4b(209, 0, 79,255) /* 0xD1004F */ ; + E2C["SG"]= vcg::Color4b(217, 0, 69,255) /* 0xD90045 */ ; + E2C["BH"]= vcg::Color4b(224, 0, 56,255) /* 0xE00038 */ ; + E2C["HS"]= vcg::Color4b(230, 0, 46,255) /* 0xE6002E */ ; + E2C["MT"]= vcg::Color4b(235, 0, 38,255) /* 0xEB0026 */ ; + } + + std::string ss0,ss1,ss2; + size_t last=std::min(atomicElement.length(),atomicElement.find_first_of(' ')); + ss0=atomicElement.substr(0,1); + vcg::Color4b color=vcg::Color4b::Black; + color=E2C[ss0]; + if((color.Red==0) && (color.Green==0) && (color.Blue==0)) + { + ss1=atomicElement.substr(0,2); + color = E2C[ss1]; + } + + return color; +} \ No newline at end of file diff --git a/src/meshlabplugins/io_pdb/io_pdb.h b/src/meshlabplugins/io_pdb/io_pdb.h new file mode 100644 index 000000000..fc91191b5 --- /dev/null +++ b/src/meshlabplugins/io_pdb/io_pdb.h @@ -0,0 +1,68 @@ +/**************************************************************************** +* MeshLab o o * +* A versatile mesh processing toolbox o o * +* _ O _ * +* Copyright(C) 2005 \/)\/ * +* Visual Computing Lab /\/| * +* ISTI - Italian National Research Council | * +* \ * +* All rights reserved. * +* * +* This program is free software; you can redistribute it and/or modify * +* it under the terms of the GNU General Public License as published by * +* the Free Software Foundation; either version 2 of the License, or * +* (at your option) any later version. * +* * +* This program is distributed in the hope that it will be useful, * +* but WITHOUT ANY WARRANTY; without even the implied warranty of * +* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the * +* GNU General Public License (http://www.gnu.org/licenses/gpl.txt) * +* for more details. * +* * +****************************************************************************/ + +#ifndef PDBIOPLUGIN_H +#define PDBIOPLUGIN_H + +#include + +#include "../../meshlab/meshmodel.h" +#include "../../meshlab/interfaces.h" + +class PDBIOPlugin : public QObject, public MeshIOInterface +{ + Q_OBJECT + Q_INTERFACES(MeshIOInterface) + + +public: + QList importFormats() const; + QList exportFormats() const; + + void GetExportMaskCapability(QString &format, int &capability, int &defaultBits) const; + + bool open(const QString &formatName, const QString &fileName, MeshModel &m, int& mask,const FilterParameterSet & par, vcg::CallBackPos *cb=0, QWidget *parent=0); + bool save(const QString &formatName, const QString &fileName, MeshModel &m, const int mask, const FilterParameterSet & par, vcg::CallBackPos *cb=0, QWidget *parent= 0); + virtual void initOpenParameter(const QString &format, MeshModel &/*m*/, FilterParameterSet & par); + virtual void applyOpenParameter(const QString &format, MeshModel &m, const FilterParameterSet &par); + void initPreOpenParameter(const QString &formatName, const QString &filename, FilterParameterSet &parlst); + + virtual void initSaveParameter(const QString &format, MeshModel &/*m*/, FilterParameterSet & par); + + //---------- PDB READER -----------// + bool PDBIOPlugin::parsePDB(const std::string &filename, CMeshO &m, const FilterParameterSet &parlst, vcg::CallBackPos *cb=0); + void PDBIOPlugin::mysscanf(const char* st, const char* format, float *f); + float PDBIOPlugin::getAtomRadius(const char* atomicElementCharP); + vcg::Color4b PDBIOPlugin::getAtomColor(const char* atomicElementCharP); + +private: + + std::vector atomDetails; + std::vector atomPos; + std::vector atomCol; + std::vector atomRad; + + +}; + +#endif diff --git a/src/meshlabplugins/io_pdb/io_pdb.pro b/src/meshlabplugins/io_pdb/io_pdb.pro new file mode 100644 index 000000000..e7da2b964 --- /dev/null +++ b/src/meshlabplugins/io_pdb/io_pdb.pro @@ -0,0 +1,10 @@ +include (../../shared.pri) + +HEADERS = io_pdb.h \ + $$VCGDIR/wrap/ply/plylib.h + +SOURCES = io_pdb.cpp \ + $$VCGDIR//wrap/ply/plylib.cpp\ + ../../meshlab/filterparameter.cpp + +TARGET = io_pdb \ No newline at end of file