| 1 |
#include <iostream> |
| 2 |
#include <fstream> |
| 3 |
#include <string> |
| 4 |
#include <vector> |
| 5 |
#include "forcerCmd.h" |
| 6 |
#include "PDBReader.hpp" |
| 7 |
#include "RigidBody.hpp" |
| 8 |
#include "GridBuilder.hpp" |
| 9 |
|
| 10 |
#define MK_STR(s) # s |
| 11 |
#define STR_DEFINE(t, s) t = MK_STR(s) |
| 12 |
#define CHARMM 1 |
| 13 |
#define AMBER 2 |
| 14 |
#define LJ 3 |
| 15 |
#define GAFF 4 |
| 16 |
#define OPLS 5 |
| 17 |
|
| 18 |
int count_tokens(char *line, char *delimiters); |
| 19 |
using namespace std; |
| 20 |
|
| 21 |
class Atype{ |
| 22 |
public: |
| 23 |
Atype() { |
| 24 |
mass = 0.0; |
| 25 |
rpar = 0.0; |
| 26 |
eps = 0.0; |
| 27 |
} |
| 28 |
|
| 29 |
void setMass(double m) {mass = m;} |
| 30 |
void setRpar(double rp) {rpar = rp;} |
| 31 |
void setEps(double e) {eps = e;} |
| 32 |
void setType(char* t) {strcpy(type, t);} |
| 33 |
double getMass() {return mass;} |
| 34 |
double getRpar() {return rpar;} |
| 35 |
double getEps() {return eps;} |
| 36 |
char *getType() {return type;} |
| 37 |
|
| 38 |
private: |
| 39 |
char type[100]; |
| 40 |
double mass; |
| 41 |
double rpar; |
| 42 |
double eps; |
| 43 |
}; |
| 44 |
|
| 45 |
int main(int argc, char* argv[]){ |
| 46 |
|
| 47 |
gengetopt_args_info args_info; |
| 48 |
|
| 49 |
vector<Atype*> vdwAtypes; |
| 50 |
vector<Atype*>::iterator i; |
| 51 |
Atype* at; |
| 52 |
RigidBody* rb; |
| 53 |
vector<VDWAtom*> theAtoms; |
| 54 |
vector<VDWAtom*>::iterator j; |
| 55 |
VDWAtom* atom; |
| 56 |
GridBuilder* gb; |
| 57 |
vector<double> sigmaGrid; |
| 58 |
vector<double> epsGrid; |
| 59 |
vector<double> sGrid; |
| 60 |
|
| 61 |
double mass, rpar, eps; |
| 62 |
string fileName; |
| 63 |
char vdwFileName[2002]; |
| 64 |
char structureFileName[2002]; |
| 65 |
char temp[200]; |
| 66 |
char readLine[500]; |
| 67 |
FILE *vdwFile, *structureFile; |
| 68 |
char* ffPath_env = "VDW_PATH"; |
| 69 |
char* ffPath; |
| 70 |
char* eof_test; |
| 71 |
char* foo; |
| 72 |
char* myType; |
| 73 |
char* vType; |
| 74 |
int lineNum; |
| 75 |
int nTokens; |
| 76 |
int FF; |
| 77 |
int bandwidth; |
| 78 |
short int gotMatch; |
| 79 |
|
| 80 |
//parse the command line options |
| 81 |
if (cmdline_parser (argc, argv, &args_info) != 0) |
| 82 |
exit(1) ; |
| 83 |
|
| 84 |
if (args_info.input_given){ |
| 85 |
fileName = args_info.input_arg; |
| 86 |
} |
| 87 |
else{ |
| 88 |
std::cerr << "Does not have input file name" << endl; |
| 89 |
exit(1); |
| 90 |
} |
| 91 |
|
| 92 |
//the bandwidth has a default value (default=8), 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"); |
| 98 |
} |
| 99 |
|
| 100 |
if (args_info.amber_given) { |
| 101 |
FF=AMBER; |
| 102 |
strcpy(vdwFileName, "amber99.vdw"); |
| 103 |
} |
| 104 |
|
| 105 |
if (args_info.lj_given) { |
| 106 |
FF=LJ; |
| 107 |
strcpy(vdwFileName, "LJ.vdw"); |
| 108 |
} |
| 109 |
|
| 110 |
if (args_info.gaff_given) { |
| 111 |
FF=GAFF; |
| 112 |
strcpy(vdwFileName, "gaff.vdw"); |
| 113 |
} |
| 114 |
|
| 115 |
if (args_info.opls_given) { |
| 116 |
FF=OPLS; |
| 117 |
strcpy(vdwFileName, "oplsaal.vdw"); |
| 118 |
} |
| 119 |
|
| 120 |
|
| 121 |
printf ("opening %s\n", vdwFileName); |
| 122 |
vdwFile = fopen( vdwFileName, "r" ); |
| 123 |
|
| 124 |
if( vdwFile == NULL ){ |
| 125 |
|
| 126 |
// next see if the force path enviorment variable is set |
| 127 |
|
| 128 |
ffPath = getenv( ffPath_env ); |
| 129 |
if( ffPath == NULL ) { |
| 130 |
STR_DEFINE(ffPath, FRC_PATH ); |
| 131 |
} |
| 132 |
|
| 133 |
strcpy( temp, ffPath ); |
| 134 |
strcat( temp, "/" ); |
| 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 ){ |
| 142 |
|
| 143 |
printf( "Error opening the vanDerWaals parameter file: %s\n" |
| 144 |
"Have you tried setting the VDW_PARAM_DIR environment " |
| 145 |
"variable?\n", |
| 146 |
vdwFileName ); |
| 147 |
exit(-1); |
| 148 |
} |
| 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 |
|
| 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! |
| 195 |
|
| 196 |
strcpy(structureFileName, fileName.c_str() ); |
| 197 |
|
| 198 |
PDBReader* PDBread = new PDBReader(); |
| 199 |
PDBread->setPDBfile(structureFileName); |
| 200 |
theAtoms = PDBread->getAtomList(); |
| 201 |
printf("Found %d atoms\n", theAtoms.size()); |
| 202 |
|
| 203 |
for( j = theAtoms.begin(); j != theAtoms.end(); ++j){ |
| 204 |
atom = *j; |
| 205 |
myType = atom->getType(); |
| 206 |
gotMatch = 0; |
| 207 |
|
| 208 |
for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){ |
| 209 |
at = *i; |
| 210 |
vType = at->getType(); |
| 211 |
|
| 212 |
if (!strcasecmp(myType, vType)) { |
| 213 |
atom->setMass(at->getMass()); |
| 214 |
atom->setRpar(at->getRpar()); |
| 215 |
atom->setEps(at->getEps()); |
| 216 |
gotMatch = 1; |
| 217 |
} |
| 218 |
} |
| 219 |
if (!gotMatch) { |
| 220 |
printf("No matches found for %s, ", myType); |
| 221 |
myType = atom->getBase(); |
| 222 |
printf("trying with BaseType %s\n", myType); |
| 223 |
for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){ |
| 224 |
at = *i; |
| 225 |
vType = at->getType(); |
| 226 |
if (!strcasecmp(myType, vType)) { |
| 227 |
atom->setMass(at->getMass()); |
| 228 |
atom->setRpar(at->getRpar()); |
| 229 |
atom->setEps(at->getEps()); |
| 230 |
gotMatch = 1; |
| 231 |
} |
| 232 |
} |
| 233 |
} |
| 234 |
|
| 235 |
if (!gotMatch) { |
| 236 |
printf("No matches found with BaseType!\n"); |
| 237 |
} |
| 238 |
} |
| 239 |
|
| 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); |
| 248 |
|
| 249 |
gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
| 250 |
|
| 251 |
|
| 252 |
} |
| 253 |
|
| 254 |
int count_tokens(char *line, char *delimiters) { |
| 255 |
/* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */ |
| 256 |
|
| 257 |
char *working_line; /* WORKING COPY OF LINE. */ |
| 258 |
int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */ |
| 259 |
char *strtok_ptr; /* POINTER FOR STRTOK. */ |
| 260 |
|
| 261 |
strtok_ptr= working_line= strdup(line); |
| 262 |
|
| 263 |
ntokens=0; |
| 264 |
while (strtok(strtok_ptr,delimiters)!=NULL) |
| 265 |
{ |
| 266 |
ntokens++; |
| 267 |
strtok_ptr=NULL; |
| 268 |
} |
| 269 |
|
| 270 |
free(working_line); |
| 271 |
return(ntokens); |
| 272 |
} |
