| 5 |
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#include "forcerCmd.h" |
| 6 |
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#include "PDBReader.hpp" |
| 7 |
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#include "RigidBody.hpp" |
| 8 |
+ |
#include "GridBuilder.hpp" |
| 9 |
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|
| 10 |
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#define MK_STR(s) # s |
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#define STR_DEFINE(t, s) t = MK_STR(s) |
| 53 |
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vector<VDWAtom*> theAtoms; |
| 54 |
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vector<VDWAtom*>::iterator j; |
| 55 |
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VDWAtom* atom; |
| 56 |
< |
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| 56 |
> |
GridBuilder* gb; |
| 57 |
> |
vector<double> sigmaGrid; |
| 58 |
> |
vector<double> epsGrid; |
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> |
vector<double> sGrid; |
| 60 |
> |
|
| 61 |
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double mass, rpar, eps; |
| 62 |
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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]; |
| 68 |
+ |
char xyzFile[200]; |
| 69 |
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char shapeFile[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; |
| 75 |
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char* myType; |
| 76 |
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char* vType; |
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char *token; |
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const char *file; |
| 79 |
+ |
const char *period = "."; |
| 80 |
+ |
int k; |
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int lineNum; |
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int nTokens; |
| 83 |
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int FF; |
| 84 |
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int bandwidth; |
| 85 |
+ |
int gridwidth; |
| 86 |
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short int gotMatch; |
| 87 |
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|
| 88 |
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//parse the command line options |
| 97 |
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exit(1); |
| 98 |
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} |
| 99 |
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|
| 100 |
< |
//the bandwidth has a default value (default=8), so it is always given |
| 100 |
> |
file = fileName.c_str(); |
| 101 |
> |
strcpy(xyzFile, file); |
| 102 |
> |
token = strtok(xyzFile, period); |
| 103 |
> |
strcpy(xyzFile, token); |
| 104 |
> |
strcpy(shapeFile, token); |
| 105 |
> |
strcat(xyzFile, "Ref.xyz"); |
| 106 |
> |
strcat(shapeFile, ".shape"); |
| 107 |
> |
ofstream xfiles(xyzFile); |
| 108 |
> |
|
| 109 |
> |
//the bandwidth has a default value (default=16), so it is always given |
| 110 |
|
bandwidth = args_info.bandwidth_arg; |
| 111 |
+ |
gridwidth = bandwidth*2; |
| 112 |
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|
| 113 |
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if (args_info.charmm_given) { |
| 114 |
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FF=CHARMM; |
| 259 |
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for( j = theAtoms.begin(); j != theAtoms.end(); ++j){ |
| 260 |
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rb->addAtom(*j); |
| 261 |
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} |
| 239 |
– |
|
| 240 |
– |
//GridBuilder gb = new GridBuilder(rb); |
| 262 |
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|
| 263 |
< |
//gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 263 |
> |
rb->calcRefCoords(); |
| 264 |
> |
|
| 265 |
> |
//print a reference coordinate xyz file |
| 266 |
> |
xfiles << rb->getNumAtoms() << "\n\n"; |
| 267 |
> |
for (k=0; k<rb->getNumAtoms(); k++){ |
| 268 |
> |
rb->getAtomRefCoor(xyz3, k); |
| 269 |
> |
xfiles << rb->getAtomBase(k) << "\t" << |
| 270 |
> |
xyz3[0] << "\t" << xyz3[1] << "\t" << |
| 271 |
> |
xyz3[2] << "\n"; |
| 272 |
> |
} |
| 273 |
> |
|
| 274 |
> |
gb = new GridBuilder(rb, gridwidth); |
| 275 |
|
|
| 276 |
< |
|
| 276 |
> |
cout << "Doing GridBuilder calculations...\n"; |
| 277 |
> |
gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 278 |
> |
|
| 279 |
> |
gb->printGridFiles(); |
| 280 |
> |
|
| 281 |
> |
//load the grid element values to the main grid vectors |
| 282 |
> |
for (k=0; k<gridwidth*gridwidth; k++){ |
| 283 |
> |
sigmaGrid.push_back(gb->passSig(k)); |
| 284 |
> |
sGrid.push_back(gb->passS(k)); |
| 285 |
> |
epsGrid.push_back(gb->passEps(k)); |
| 286 |
> |
} |
| 287 |
> |
|
| 288 |
> |
|
| 289 |
> |
|
| 290 |
|
} |
| 291 |
|
|
| 292 |
|
int count_tokens(char *line, char *delimiters) { |
