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#include "PDBReader.hpp" |
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#include "RigidBody.hpp" |
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#include "GridBuilder.hpp" |
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#include "SphereHarm.hpp" |
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#define MK_STR(s) # s |
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#define STR_DEFINE(t, s) t = MK_STR(s) |
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vector<double> sigmaGrid; |
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vector<double> epsGrid; |
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vector<double> sGrid; |
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SphereHarm* harmonize; |
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double mass, rpar, eps; |
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double xyz3[3]; |
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double moments[3][3]; |
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string fileName; |
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char vdwFileName[2002]; |
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char structureFileName[2002]; |
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char temp[200]; |
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char readLine[500]; |
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char xyzFile[200]; |
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char shapeFile[200]; |
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char shapeName[80]; |
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FILE *vdwFile, *structureFile; |
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char* ffPath_env = "VDW_PATH"; |
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char* ffPath; |
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char* foo; |
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char* myType; |
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char* vType; |
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char *token; |
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const char *file; |
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const char *period = "."; |
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int k; |
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int lineNum; |
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int nTokens; |
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int FF; |
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int bandwidth; |
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int gridwidth; |
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short int gotMatch; |
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//parse the command line options |
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exit(1); |
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} |
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//the bandwidth has a default value (default=8), so it is always given |
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file = fileName.c_str(); |
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strcpy(xyzFile, file); |
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token = strtok(xyzFile, period); |
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strcpy(xyzFile, token); |
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strcpy(shapeFile, token); |
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strcpy(shapeName, token); |
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strcat(xyzFile, "Ref.xyz"); |
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strcat(shapeFile, ".shape"); |
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strcat(shapeName, "_RB_0"); |
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ofstream xfiles(xyzFile); |
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|
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//the bandwidth has a default value (default=16), so it is always given |
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bandwidth = args_info.bandwidth_arg; |
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gridwidth = bandwidth*2; |
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|
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if (args_info.charmm_given) { |
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FF=CHARMM; |
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for( j = theAtoms.begin(); j != theAtoms.end(); ++j){ |
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rb->addAtom(*j); |
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} |
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< |
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> |
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rb->calcRefCoords(); |
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< |
gb = new GridBuilder(rb, bandwidth); |
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//print a reference coordinate xyz file |
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xfiles << rb->getNumAtoms() << "\n\n"; |
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for (k=0; k<rb->getNumAtoms(); k++){ |
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rb->getAtomRefCoor(xyz3, k); |
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xfiles << rb->getAtomBase(k) << "\t" << |
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xyz3[0] << "\t" << xyz3[1] << "\t" << |
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xyz3[2] << "\n"; |
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} |
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|
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gb = new GridBuilder(rb, gridwidth); |
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| 282 |
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cout << "Doing GridBuilder calculations...\n"; |
| 283 |
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gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
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|
| 285 |
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gb->printGridFiles(); |
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|
| 287 |
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//load the grid element values to the main grid vectors |
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for (k=0; k<gridwidth*gridwidth; k++){ |
| 289 |
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sigmaGrid.push_back(gb->passSig(k)); |
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sGrid.push_back(gb->passS(k)); |
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epsGrid.push_back(gb->passEps(k)); |
| 292 |
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} |
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< |
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> |
//build the spherical harmonic transform object |
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harmonize = new SphereHarm( bandwidth ); |
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> |
rb->getI(moments); |
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harmonize->printShapesFileStart(shapeFile, shapeName, rb->getMass(), |
| 298 |
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moments); |
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|
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//do the transforms and write to the shapes file |
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harmonize->doTransforms(sigmaGrid); |
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harmonize->printToShapesFile(shapeFile, 0); |
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harmonize->doTransforms(sGrid); |
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harmonize->printToShapesFile(shapeFile, 1); |
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harmonize->doTransforms(epsGrid); |
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harmonize->printToShapesFile(shapeFile, 2); |
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> |
|
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//clean everything up |
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> |
harmonize->~SphereHarm(); |
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} |
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|
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int count_tokens(char *line, char *delimiters) { |
