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#include <vector> |
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#include "forcerCmd.h" |
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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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|
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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<Atype*> vdwAtypes; |
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vector<Atype*>::iterator i; |
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Atype* at; |
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RigidBody* rb; |
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vector<VDWAtom*> theAtoms; |
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vector<VDWAtom*>::iterator j; |
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VDWAtom* atom; |
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|
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GridBuilder* gb; |
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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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|
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double mass, rpar, eps; |
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string fileName; |
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char vdwFileName[2002]; |
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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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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=16), so it is always given |
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bandwidth = args_info.bandwidth_arg; |
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|
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if (args_info.charmm_given) { |
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FF=CHARMM; |
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strcpy(vdwFileName, "charmm27.vdw"); |
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strcpy(vdwFileName, "oplsaal.vdw"); |
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} |
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|
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printf ("opening %s\n", vdwFileName); |
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vdwFile = fopen( vdwFileName, "r" ); |
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|
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if( vdwFile == NULL ){ |
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strcat( temp, vdwFileName ); |
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strcpy( vdwFileName, temp ); |
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printf ("opening %s\n", vdwFileName); |
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vdwFile = fopen( vdwFileName, "r" ); |
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|
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if( vdwFile == NULL ){ |
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vdwFileName ); |
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exit(-1); |
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} |
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printf( "VDW file %s opened sucessfully.\n", vdwFileName ); |
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lineNum = 0; |
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|
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} |
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printf( "VDW file %s opened sucessfully.\n", vdwFileName ); |
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lineNum = 0; |
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|
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eof_test = fgets( readLine, sizeof(readLine), vdwFile ); |
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lineNum++; |
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|
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if( eof_test == NULL ){ |
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printf("Error in reading Atoms from force file at line %d.\n", |
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lineNum ); |
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exit(-1); |
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} |
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|
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while( eof_test != NULL ){ |
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// toss comment lines |
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if( readLine[0] != '!' && readLine[0] != '#' ){ |
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|
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nTokens = count_tokens(readLine, " ,;\t"); |
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if (nTokens < 4) { |
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printf("Not enough tokens on line %d.\n", lineNum); |
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exit(-1); |
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} |
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|
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at = new Atype(); |
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foo = strtok(readLine, " ,;\t"); |
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at->setType(foo); |
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foo = strtok(NULL, " ,;\t"); |
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mass = atof(foo); |
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at->setMass(mass); |
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foo = strtok(NULL, " ,;\t"); |
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rpar = atof(foo); |
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at->setRpar(rpar); |
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foo = strtok(NULL, " ,;\t"); |
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eps = atof(foo); |
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at->setEps(eps); |
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vdwAtypes.push_back(at); |
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} |
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eof_test = fgets( readLine, sizeof(readLine), vdwFile ); |
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lineNum++; |
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|
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if( eof_test == NULL ){ |
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printf("Error in reading Atoms from force file at line %d.\n", |
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< |
lineNum ); |
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exit(-1); |
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} |
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< |
|
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< |
while( eof_test != NULL ){ |
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< |
// toss comment lines |
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< |
if( readLine[0] != '!' && readLine[0] != '#' ){ |
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< |
|
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< |
nTokens = count_tokens(readLine, " ,;\t"); |
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< |
if (nTokens < 4) { |
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< |
printf("Not enough tokens on line %d.\n", lineNum); |
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< |
exit(-1); |
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< |
} |
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< |
|
| 157 |
< |
at = new Atype(); |
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< |
foo = strtok(readLine, " ,;\t"); |
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< |
at->setType(foo); |
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< |
foo = strtok(NULL, " ,;\t"); |
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< |
mass = atof(foo); |
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< |
at->setMass(mass); |
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< |
foo = strtok(NULL, " ,;\t"); |
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< |
rpar = atof(foo); |
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< |
at->setRpar(rpar); |
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< |
foo = strtok(NULL, " ,;\t"); |
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< |
eps = atof(foo); |
| 168 |
< |
at->setEps(eps); |
| 169 |
< |
vdwAtypes.push_back(at); |
| 170 |
< |
} |
| 171 |
< |
eof_test = fgets( readLine, sizeof(readLine), vdwFile ); |
| 172 |
< |
lineNum++; |
| 173 |
< |
} |
| 174 |
< |
|
| 175 |
< |
fclose( vdwFile ); |
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< |
} |
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> |
} |
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> |
|
| 190 |
> |
fclose( vdwFile ); |
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> |
|
| 192 |
|
printf("%d Atom Types read from VDW file\n", vdwAtypes.size()); |
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|
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// Now, open and parse the input file! |
| 237 |
|
} |
| 238 |
|
} |
| 239 |
|
|
| 240 |
< |
//GridBuilder gb = new GridBuilder(); |
| 241 |
< |
//gb->findAxesAndOrigin(theAtoms); |
| 242 |
< |
//gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 243 |
< |
|
| 240 |
> |
rb = new RigidBody(); |
| 241 |
> |
for( j = theAtoms.begin(); j != theAtoms.end(); ++j){ |
| 242 |
> |
rb->addAtom(*j); |
| 243 |
> |
} |
| 244 |
|
|
| 245 |
+ |
rb->calcRefCoords(); |
| 246 |
+ |
|
| 247 |
+ |
gb = new GridBuilder(rb, bandwidth*2); |
| 248 |
+ |
|
| 249 |
+ |
cout << "Doing GridBuilder calculations...\n"; |
| 250 |
+ |
gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 251 |
+ |
|
| 252 |
+ |
//write out the grid files |
| 253 |
+ |
gb->printGridFiles(); |
| 254 |
|
} |
| 255 |
|
|
| 256 |
|
int count_tokens(char *line, char *delimiters) { |
