| 5 |
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#include "forcerCmd.h" |
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#include "PDBReader.hpp" |
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#include "RigidBody.hpp" |
| 8 |
+ |
#include "GridBuilder.hpp" |
| 9 |
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|
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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<VDWAtom*> theAtoms; |
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vector<VDWAtom*>::iterator j; |
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VDWAtom* atom; |
| 56 |
< |
|
| 56 |
> |
GridBuilder* gb; |
| 57 |
> |
vector<double> sigmaGrid; |
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> |
vector<double> epsGrid; |
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vector<double> sGrid; |
| 60 |
> |
|
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double mass, rpar, eps; |
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double xyz3[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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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; |
| 78 |
+ |
const char *period = "."; |
| 79 |
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int k; |
| 80 |
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int lineNum; |
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int nTokens; |
| 82 |
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int FF; |
| 95 |
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exit(1); |
| 96 |
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} |
| 97 |
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|
| 98 |
< |
//the bandwidth has a default value (default=8), so it is always given |
| 98 |
> |
file = fileName.c_str(); |
| 99 |
> |
strcpy(xyzFile, file); |
| 100 |
> |
token = strtok(xyzFile, period); |
| 101 |
> |
strcpy(xyzFile, token); |
| 102 |
> |
strcat(xyzFile, "ref.xyz"); |
| 103 |
> |
ofstream xfiles(xyzFile); |
| 104 |
> |
|
| 105 |
> |
//the bandwidth has a default value (default=16), so it is always given |
| 106 |
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bandwidth = args_info.bandwidth_arg; |
| 107 |
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|
| 108 |
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if (args_info.charmm_given) { |
| 254 |
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for( j = theAtoms.begin(); j != theAtoms.end(); ++j){ |
| 255 |
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rb->addAtom(*j); |
| 256 |
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} |
| 257 |
+ |
|
| 258 |
+ |
rb->calcRefCoords(); |
| 259 |
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|
| 260 |
< |
//GridBuilder gb = new GridBuilder(rb); |
| 260 |
> |
//print a reference coordinate xyz file |
| 261 |
> |
xfiles << rb->getNumAtoms() << "\n\n"; |
| 262 |
> |
for (k=0; k<rb->getNumAtoms(); k++){ |
| 263 |
> |
rb->getAtomRefCoor(xyz3, k); |
| 264 |
> |
xfiles << rb->getAtomType(k) << "\t" << |
| 265 |
> |
xyz3[0] << "\t" << xyz3[1] << "\t" << |
| 266 |
> |
xyz3[2] << "\n"; |
| 267 |
> |
} |
| 268 |
> |
|
| 269 |
> |
gb = new GridBuilder(rb, bandwidth*2); |
| 270 |
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|
| 271 |
< |
//gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 272 |
< |
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| 273 |
< |
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| 271 |
> |
cout << "Doing GridBuilder calculations...\n"; |
| 272 |
> |
gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 273 |
> |
|
| 274 |
> |
//write out the grid files |
| 275 |
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} |
| 276 |
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|
| 277 |
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int count_tokens(char *line, char *delimiters) { |
