Angle getAngleFromLine(string line){ Angle angle = createAngle(-1, -1, -1, false); char *tokens; char *charLine = (char *)malloc(sizeof(char) * line.size()); strcpy(charLine, line.c_str()); tokens = strtok(charLine, " "); strcpy(charLine, line.c_str()); int tokenNumber = 0; while(tokens != NULL){ switch(tokenNumber){ case 0: angle.atom1 = atoi(tokens); break; case 1: angle.atom2 = atoi(tokens); break; case 2: angle.value = atof(tokens); break; case 3: if(atoi(tokens) == 1) angle.variable = true; else angle.variable = false; } tokens = strtok(NULL, " "); tokenNumber++; } return angle; }
void testGetOppositeAtom() { cout << "Testing getOppositeAtom"<< endl; Bond testBond = createBond(1,3,5.5,true); Angle testAngle = createAngle(2,6,30,false); Dihedral testDihed = createDihedral(3,7,180,true); //test with bonds assert(getOppositeAtom(testBond,1)==3); assert(getOppositeAtom(testBond,3)==1); assert(getOppositeAtom(testBond,4)==-1); //test with bonds assert(getOppositeAtom(testAngle,2)==6); assert(getOppositeAtom(testAngle,6)==2); assert(getOppositeAtom(testAngle,5)==-1); //test with bonds assert(getOppositeAtom(testDihed,3)==7); assert(getOppositeAtom(testDihed,7)==3); assert(getOppositeAtom(testDihed,6)==-1); testBond = createBond(11,12,3.5,true); testAngle = createAngle(1,22,30,false); testDihed = createDihedral(5,9,180,true); //test with bonds assert(getOppositeAtom(testBond,11)==12); assert(getOppositeAtom(testBond,12)==11); assert(getOppositeAtom(testBond,13)==-1); //test with bonds assert(getOppositeAtom(testAngle,1)==22); assert(getOppositeAtom(testAngle,22)==1); assert(getOppositeAtom(testAngle,15)==-1); //test with bonds assert(getOppositeAtom(testDihed,5)==9); assert(getOppositeAtom(testDihed,9)==5); assert(getOppositeAtom(testDihed,62)==-1); cout << "Testing getOppositeAtom Complete\n" << endl; }
Molecule createMeshZMolecules(Opls_Scan *scanner) { //1 S 200 0 0 0.000000 0 0.000000 0 0.000000 0 Atom atom1=scanner->getAtom("200"); atom1.id=1; // 2 DUM -1 0 1 0.500000 0 0.000000 0 0.000000 0 Atom atom2=createAtom(2,-1,-1,-1,-1,-1,-1,NULL); Bond bond2=createBond(2,1,0.5,false); //3 DUM -1 0 2 0.500000 1 90.000000 0 0.000000 0 Atom atom3=createAtom(3,-1,-1,-1,-1,-1,-1,NULL); Bond bond3=createBond(3,2,0.5,false); Angle angle3=createAngle(3,1,90,false); //4 hH 204 0 1 1.336532 2 90.000000 3 180.000000 0 Atom atom4=scanner->getAtom("204"); atom4.id=4; Bond bond4=createBond(4,1,1.336532,true); Angle angle4=createAngle(4,2,90,false); Dihedral dihed4=createDihedral(4,3,180,false); //5 C 217 0 1 1.811119 4 96.401770 2 180.000000 0 Atom atom5=scanner->getAtom("217"); atom5.id=5; Bond bond5=createBond(5,1,1.811119,true); Angle angle5=createAngle(5,4,96.401770,true); Dihedral dihed5=createDihedral(5,2,180,false); //6 HC 140 0 5 1.090187 1 110.255589 4 179.999947 0 Atom atom6=scanner->getAtom("140"); atom6.id=6; Bond bond6=createBond(6,5,1.090187,true); Angle angle6=createAngle(6,1,110.255589,true); Dihedral dihed6=createDihedral(6,4,179.999947,true); //7 HC 140 0 5 1.090135 6 108.527646 1 121.053891 0 Atom atom7=scanner->getAtom("140"); atom7.id=7; Bond bond7=createBond(7,5,1.090135,true); Angle angle7=createAngle(7,6,108.527646,true); Dihedral dihed7=createDihedral(7,1,121.053891,true); //8 HC 140 0 5 1.090135 6 108.527646 1 238.946114 0 Atom atom8=scanner->getAtom("140"); atom8.id=8; Bond bond8=createBond(8,5,1.090135,true); Angle angle8=createAngle(8,6,108.527646,true); Dihedral dihed8=createDihedral(8,1,238.946114,true); /* HOPS and BONDS Diagram of Mesh.z // 1--2--3 // |\ // | \ // 4 5 // /|\ // / | \ // 6 7 8 */ //All hops that have a hop distance >= 3 Hop hop1= createHop(2,6,3); Hop hop2= createHop(2,7,3); Hop hop3= createHop(2,8,3); Hop hop4= createHop(3,4,3); Hop hop5= createHop(3,5,3); Hop hop6= createHop(3,6,4); Hop hop7= createHop(3,7,4); Hop hop8= createHop(3,8,4); Hop hop9= createHop(4,6,3); Hop hop10= createHop(4,7,3); Hop hop11= createHop(4,8,3); Atom *atomPtr = new Atom[8]; Bond *bondPtr = new Bond[7]; Angle *anglePtr = new Angle[6]; Dihedral *dihedPtr = new Dihedral[5]; Hop *hopPtr = new Hop[11]; atomPtr[0]=atom1; atomPtr[1]=atom2; atomPtr[2]=atom3; atomPtr[3]=atom4; atomPtr[4]=atom5; atomPtr[5]=atom6; atomPtr[6]=atom7; atomPtr[7]=atom8; bondPtr[0]=bond2; bondPtr[1]=bond3; bondPtr[2]=bond4; bondPtr[3]=bond5; bondPtr[4]=bond6; bondPtr[5]=bond7; bondPtr[6]=bond8; anglePtr[0]=angle3; anglePtr[1]=angle4; anglePtr[2]=angle5; anglePtr[3]=angle6; anglePtr[4]=angle7; anglePtr[5]=angle8; dihedPtr[0]=dihed4; dihedPtr[1]=dihed5; dihedPtr[2]=dihed6; dihedPtr[3]=dihed7; dihedPtr[4]=dihed8; hopPtr[0]=hop1; hopPtr[1]=hop2; hopPtr[2]=hop3; hopPtr[3]=hop4; hopPtr[4]=hop5; hopPtr[5]=hop6; hopPtr[6]=hop7; hopPtr[7]=hop8; hopPtr[8]=hop9; hopPtr[9]=hop10; hopPtr[10]=hop11; return createMolecule(1,atomPtr,anglePtr,bondPtr,dihedPtr,hopPtr,8,6,7,5,11); }
vector<Molecule> createT3pdimMolecules(Opls_Scan *scanner) { // TIP3P Water Dimer Tot. E = -6.5396 //1 O 111 111 0 .000000 0 .000000 0 .000000 0 Atom atom1 = scanner->getAtom("111"); atom1.id=1; //2 DU -1 -1 1 1.000000 0 .000000 0 .000000 0 Atom atom2=createAtom(2,-1,-1,-1,-1,-1,-1,NULL); Bond bond2=createBond(2,1,1.0,false); //3 DU -1 -1 2 1.000000 1 90.000000 0 .000000 0 Atom atom3=createAtom(3,-1,-1,-1,-1,-1,-1,NULL); Bond bond3=createBond(3,2,1.0,false); Angle angle3=createAngle(3,1,90.0,false); //4 HO 112 112 1 .957200 2 127.740000 3 90.000000 0 Atom atom4=scanner->getAtom("112"); atom4.id=4; Bond bond4=createBond(4,1,.957200,false); Angle angle4=createAngle(4,2,127.740000,false); Dihedral dihed4=createDihedral(4,3,90.00,false); //5 HO 112 112 1 .957200 4 104.520000 2 180.000000 0 Atom atom5=scanner->getAtom("112"); atom5.id=5; Bond bond5=createBond(5,1,.957200,false); Angle angle5=createAngle(5,4,104.520000,false); Dihedral dihed5=createDihedral(5,2,180.00,false); //6 X -1 -1 1 .150000 4 52.260000 5 .000000 0 Atom atom6=createAtom(6,-1,-1,-1,-1,-1,-1,NULL); Bond bond6=createBond(6,1,.150000,false); Angle angle6=createAngle(6,4,52.260000,false); Dihedral dihed6=createDihedral(6,5,.00,false); //TERZ 2nd Bonded Molecule //7 O 111 111 1 2.751259 2 131.716186 3 269.946364 0 Atom atom7=scanner->getAtom("111"); atom7.id=7; Bond bond7=createBond(7,1,2.751259,false); Angle angle7=createAngle(7,2,131.716186,false); Dihedral dihed7=createDihedral(7,3,269.946364,false); //8 DU -1 -1 7 1.000000 1 21.472391 2 179.887530 0 Atom atom8=createAtom(8,-1,-1,-1,-1,-1,-1,NULL); Bond bond8=createBond(8,7,1.0,false); Angle angle8=createAngle(8,1,21.472391,false); Dihedral dihed8=createDihedral(8,2,179.887530,false); //9 DU -1 -1 8 1.000000 7 90.000000 1 179.624613 0 Atom atom9=createAtom(9,-1,-1,-1,-1,-1,-1,NULL); Bond bond9=createBond(9,8,1.0,false); Angle angle9=createAngle(9,7,90.000000,false); Dihedral dihed9=createDihedral(9,1,179.624613,false); //10 HO 112 112 7 .957200 8 127.740000 9 90.000000 0 Atom atom10=scanner->getAtom("112"); atom10.id=10; Bond bond10=createBond(10,7,0.957200,false); Angle angle10=createAngle(10,8,127.74,false); Dihedral dihed10=createDihedral(10,9,90.0,false); //11 HO 112 112 7 .957200 10 104.520000 8 180.000000 0 Atom atom11=scanner->getAtom("112"); atom11.id=11; Bond bond11=createBond(11,7,0.957200,false); Angle angle11=createAngle(11,10,104.52,false); Dihedral dihed11=createDihedral(11,8,180.0,false); //12 X -1 -1 7 .150000 10 52.260000 11 .000000 0 Atom atom12=createAtom(12,-1,-1,-1,-1,-1,-1,NULL); Bond bond12=createBond(12,7,0.15,false); Angle angle12=createAngle(12,10,52.26,false); Dihedral dihed12=createDihedral(12,11,0.0,false); /* HOPS and BONDS Diagram of Mesh.z // // // 10 11 12 // \ | / // \|/ // 7--8--9 // | // | // 1--2--3 // /|\ // / | \ // 4 5 6 */ //All intermolecular hops that have a hop distance >= 3 //bottom Molecule Hop hop1=createHop(3,4,3); Hop hop2=createHop(3,5,3); Hop hop3=createHop(3,6,3); //top Molecule Hop hop4=createHop(9,10,3); Hop hop5=createHop(9,11,3); Hop hop6=createHop(9,12,3); Atom *atomPtr = new Atom[6]; Bond *bondPtr = new Bond[5]; Angle *anglePtr = new Angle[4]; Dihedral *dihedPtr = new Dihedral[3]; Hop *hopPtr = new Hop[3]; vector<Molecule> retVect; atomPtr[0]=atom1; atomPtr[1]=atom2; atomPtr[2]=atom3; atomPtr[3]=atom4; atomPtr[4]=atom5; atomPtr[5]=atom6; bondPtr[0]=bond2; bondPtr[1]=bond3; bondPtr[2]=bond4; bondPtr[3]=bond5; bondPtr[4]=bond6; anglePtr[0]=angle3; anglePtr[1]=angle4; anglePtr[2]=angle5; anglePtr[3]=angle6; dihedPtr[0]=dihed4; dihedPtr[1]=dihed5; dihedPtr[2]=dihed6; hopPtr[0]=hop1; hopPtr[1]=hop2; hopPtr[2]=hop3; retVect.push_back( createMolecule(1,atomPtr,anglePtr,bondPtr,dihedPtr,hopPtr,6,4,5,3,3) ); Atom *atomPt = new Atom[6]; Bond *bondPt = new Bond[6]; Angle *anglePt = new Angle[6]; Dihedral *dihedPt = new Dihedral[6]; Hop *hopPt = new Hop[3]; atomPt[0]=atom7; atomPt[1]=atom8; atomPt[2]=atom9; atomPt[3]=atom10; atomPt[4]=atom11; atomPt[5]=atom12; bondPt[0]=bond7; bondPt[1]=bond8; bondPt[2]=bond9; bondPt[3]=bond10; bondPt[4]=bond11; bondPt[5]=bond12; anglePt[0]=angle7; anglePt[1]=angle8; anglePt[2]=angle9; anglePt[3]=angle10; anglePt[4]=angle11; anglePt[5]=angle12; dihedPt[0]=dihed7; dihedPt[1]=dihed8; dihedPt[2]=dihed9; dihedPt[3]=dihed10; dihedPt[4]=dihed11; dihedPt[5]=dihed12; hopPt[0]=hop4; hopPt[1]=hop5; hopPt[2]=hop6; retVect.push_back( createMolecule(7,atomPt,anglePt,bondPt,dihedPt,hopPt,6,6,6,6,3) ); return retVect; }
/* load the file, parse the text, add the elements */ bool Scene::loadFile (std::string filename) { std::ifstream fs; fs.open (filename); if (!fs.is_open ()) { fs.close (); return false; } clearScene(); int vertNum = 0; int lineNum = 0; int angleNum = 0; int fanoNum = 0; Vertex * newVerts[1024]; Line * newLines[1024]; int vertIdx = 0; int lineIdx = 0; std::cout<< "Reading in file " << filename << std::endl; std::string line; while(std::getline(fs, line)){ //line that includes data if(line.length() > 0 && (line.at(0) == 'V' || line.at(0) == 'v')){ char *copyLine = (char*)line.c_str(); char *token; token = strtok(copyLine, " ,"); token = strtok(NULL, " ,"); float x, y, z; x = atof(token); token = strtok(NULL, " ,"); y = atof(token); token = strtok(NULL, " ,"); z = atof(token); if(vertIdx == 0) newVerts[vertIdx++] = addVertex3f(x, y, z, 1); else newVerts[vertIdx++] = addVertex3f(x, y, z, 0); } else if(line.length() > 0 && (line.at(0) == 'L' || line.at(0) == 'l')){ char *copyLine = (char*)line.c_str(); char *token; token = strtok(copyLine, " ,"); token = strtok(NULL, " ,"); int v1, v2; v1 = atoi(token); token = strtok(NULL, " ,"); v2 = atoi(token); newLines[lineIdx++] = createLine(newVerts[v1], newVerts[v2]); } else if(line.length() > 0 && (line.at(0) == 'A' || line.at(0) == 'a')){ char *copyLine = (char*)line.c_str(); char *token; token = strtok(copyLine, " ,"); token = strtok(NULL, " ,"); int l1, l2; l1 = atoi(token); token = strtok(NULL, " ,"); l2 = atoi(token); createAngle(newLines[l1], newLines[l2]); } else if(line.length() > 0 && (line.at(0) == 'F' || line.at(0) == 'f')){ char *copyLine = (char*)line.c_str(); char *token; token = strtok(copyLine, " ,"); token = strtok(NULL, " ,"); int a1, a2, a3; a1 = atoi(token); token = strtok(NULL, " ,"); a2 = atoi(token); token = strtok(NULL, " ,"); a3 = atoi(token); createFano(newLines[a1], newLines[a2], newLines[a3]); } else if(line.length()>0 && (line.at(0)=='C' || line.at(0)=='c')){ char *copyLine = (char*)line.c_str(); char *token; token = strtok(copyLine, " ,"); token = strtok(NULL, " ,"); int l; float r, g, b; l = atoi(token); token = strtok(NULL, " ,"); r = atof(token); token = strtok(NULL, " ,"); g = atof(token); token = strtok(NULL, " ,"); b = atof(token); Line *a = newLines[l]; a->setColor3f(r,g,b); } } //... return true; }