| 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 |
|
|
| 10 |
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#define MK_STR(s) # s |
| 11 |
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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 |
< |
|
| 56 |
> |
GridBuilder* gb; |
| 57 |
> |
vector<double> sigmaGrid; |
| 58 |
> |
vector<double> epsGrid; |
| 59 |
> |
vector<double> sGrid; |
| 60 |
> |
|
| 61 |
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double mass, rpar, eps; |
| 62 |
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string fileName; |
| 63 |
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char vdwFileName[2002]; |
| 74 |
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int lineNum; |
| 75 |
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int nTokens; |
| 76 |
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int FF; |
| 77 |
+ |
int bandwidth; |
| 78 |
|
short int gotMatch; |
| 79 |
|
|
| 80 |
|
//parse the command line options |
| 89 |
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exit(1); |
| 90 |
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} |
| 91 |
|
|
| 92 |
+ |
//the bandwidth has a default value (default=16), so it is always given |
| 93 |
+ |
bandwidth = args_info.bandwidth_arg; |
| 94 |
+ |
|
| 95 |
|
if (args_info.charmm_given) { |
| 96 |
|
FF=CHARMM; |
| 97 |
|
strcpy(vdwFileName, "charmm27.vdw"); |
| 117 |
|
strcpy(vdwFileName, "oplsaal.vdw"); |
| 118 |
|
} |
| 119 |
|
|
| 120 |
+ |
|
| 121 |
+ |
printf ("opening %s\n", vdwFileName); |
| 122 |
|
vdwFile = fopen( vdwFileName, "r" ); |
| 123 |
|
|
| 124 |
|
if( vdwFile == NULL ){ |
| 135 |
|
strcat( temp, vdwFileName ); |
| 136 |
|
strcpy( vdwFileName, temp ); |
| 137 |
|
|
| 138 |
+ |
printf ("opening %s\n", vdwFileName); |
| 139 |
|
vdwFile = fopen( vdwFileName, "r" ); |
| 140 |
|
|
| 141 |
|
if( vdwFile == NULL ){ |
| 146 |
|
vdwFileName ); |
| 147 |
|
exit(-1); |
| 148 |
|
} |
| 149 |
< |
printf( "VDW file %s opened sucessfully.\n", vdwFileName ); |
| 150 |
< |
lineNum = 0; |
| 151 |
< |
|
| 149 |
> |
} |
| 150 |
> |
printf( "VDW file %s opened sucessfully.\n", vdwFileName ); |
| 151 |
> |
lineNum = 0; |
| 152 |
> |
|
| 153 |
> |
eof_test = fgets( readLine, sizeof(readLine), vdwFile ); |
| 154 |
> |
lineNum++; |
| 155 |
> |
|
| 156 |
> |
if( eof_test == NULL ){ |
| 157 |
> |
printf("Error in reading Atoms from force file at line %d.\n", |
| 158 |
> |
lineNum ); |
| 159 |
> |
exit(-1); |
| 160 |
> |
} |
| 161 |
> |
|
| 162 |
> |
while( eof_test != NULL ){ |
| 163 |
> |
// toss comment lines |
| 164 |
> |
if( readLine[0] != '!' && readLine[0] != '#' ){ |
| 165 |
> |
|
| 166 |
> |
nTokens = count_tokens(readLine, " ,;\t"); |
| 167 |
> |
if (nTokens < 4) { |
| 168 |
> |
printf("Not enough tokens on line %d.\n", lineNum); |
| 169 |
> |
exit(-1); |
| 170 |
> |
} |
| 171 |
> |
|
| 172 |
> |
at = new Atype(); |
| 173 |
> |
foo = strtok(readLine, " ,;\t"); |
| 174 |
> |
at->setType(foo); |
| 175 |
> |
foo = strtok(NULL, " ,;\t"); |
| 176 |
> |
mass = atof(foo); |
| 177 |
> |
at->setMass(mass); |
| 178 |
> |
foo = strtok(NULL, " ,;\t"); |
| 179 |
> |
rpar = atof(foo); |
| 180 |
> |
at->setRpar(rpar); |
| 181 |
> |
foo = strtok(NULL, " ,;\t"); |
| 182 |
> |
eps = atof(foo); |
| 183 |
> |
at->setEps(eps); |
| 184 |
> |
vdwAtypes.push_back(at); |
| 185 |
> |
} |
| 186 |
|
eof_test = fgets( readLine, sizeof(readLine), vdwFile ); |
| 187 |
|
lineNum++; |
| 188 |
< |
|
| 189 |
< |
if( eof_test == NULL ){ |
| 190 |
< |
printf("Error in reading Atoms from force file at line %d.\n", |
| 191 |
< |
lineNum ); |
| 146 |
< |
exit(-1); |
| 147 |
< |
} |
| 148 |
< |
|
| 149 |
< |
while( eof_test != NULL ){ |
| 150 |
< |
// toss comment lines |
| 151 |
< |
if( readLine[0] != '!' && readLine[0] != '#' ){ |
| 152 |
< |
|
| 153 |
< |
nTokens = count_tokens(readLine, " ,;\t"); |
| 154 |
< |
if (nTokens < 4) { |
| 155 |
< |
printf("Not enough tokens on line %d.\n", lineNum); |
| 156 |
< |
exit(-1); |
| 157 |
< |
} |
| 158 |
< |
|
| 159 |
< |
at = new Atype(); |
| 160 |
< |
foo = strtok(readLine, " ,;\t"); |
| 161 |
< |
at->setType(foo); |
| 162 |
< |
foo = strtok(NULL, " ,;\t"); |
| 163 |
< |
mass = atof(foo); |
| 164 |
< |
at->setMass(mass); |
| 165 |
< |
foo = strtok(NULL, " ,;\t"); |
| 166 |
< |
rpar = atof(foo); |
| 167 |
< |
at->setRpar(rpar); |
| 168 |
< |
foo = strtok(NULL, " ,;\t"); |
| 169 |
< |
eps = atof(foo); |
| 170 |
< |
at->setEps(eps); |
| 171 |
< |
vdwAtypes.push_back(at); |
| 172 |
< |
} |
| 173 |
< |
eof_test = fgets( readLine, sizeof(readLine), vdwFile ); |
| 174 |
< |
lineNum++; |
| 175 |
< |
} |
| 176 |
< |
|
| 177 |
< |
fclose( vdwFile ); |
| 178 |
< |
} |
| 188 |
> |
} |
| 189 |
> |
|
| 190 |
> |
fclose( vdwFile ); |
| 191 |
> |
|
| 192 |
|
printf("%d Atom Types read from VDW file\n", vdwAtypes.size()); |
| 193 |
|
|
| 194 |
|
// Now, open and parse the input file! |
| 239 |
|
|
| 240 |
|
rb = new RigidBody(); |
| 241 |
|
for( j = theAtoms.begin(); j != theAtoms.end(); ++j){ |
| 242 |
< |
rb->addAtom(*j); |
| 242 |
> |
rb->addAtom(*j); |
| 243 |
|
} |
| 244 |
|
|
| 245 |
< |
//GridBuilder gb = new GridBuilder(); |
| 246 |
< |
//gb->findAxesAndOrigin(theAtoms); |
| 247 |
< |
//gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 235 |
< |
|
| 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) { |
