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#include <iostream> |
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#include <fstream> |
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#include <string> |
| 4 |
#include <vector> |
| 5 |
#include "shaperCmd.h" |
| 6 |
#include "PDBReader.hpp" |
| 7 |
#include "RigidBody.hpp" |
| 8 |
#include "GridBuilder.hpp" |
| 9 |
#include "SphereHarm.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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#define CHARMM 1 |
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#define AMBER 2 |
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#define LJ 3 |
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#define GAFF 4 |
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#define OPLS 5 |
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|
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int count_tokens(char *line, char *delimiters); |
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using namespace std; |
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|
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class Atype{ |
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public: |
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Atype() { |
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mass = 0.0; |
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rpar = 0.0; |
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eps = 0.0; |
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} |
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|
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void setMass(double m) {mass = m;} |
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void setRpar(double rp) {rpar = rp;} |
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void setEps(double e) {eps = e;} |
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void setType(char* t) {strcpy(type, t);} |
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double getMass() {return mass;} |
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double getRpar() {return rpar;} |
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double getEps() {return eps;} |
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char *getType() {return type;} |
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|
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private: |
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char type[100]; |
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double mass; |
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double rpar; |
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double eps; |
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}; |
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|
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int main(int argc, char* argv[]){ |
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|
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gengetopt_args_info args_info; |
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|
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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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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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SphereHarm* harmonize; |
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|
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double mass, rpar, eps; |
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double xyz3[3]; |
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double moments[3][3]; |
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double tolerance; |
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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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char shapeFile[200]; |
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char shapeName[80]; |
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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* eof_test; |
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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; |
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const char *period = "."; |
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int k; |
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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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int gridwidth; |
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short int gotMatch; |
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|
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//parse the command line options |
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if (cmdline_parser (argc, argv, &args_info) != 0) |
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exit(1) ; |
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|
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|
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if (args_info.inputs_num > 0) { |
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fileName = args_info.inputs[0]; |
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} else { |
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std::cerr << "Does not have input file name" << endl; |
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exit(1); |
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} |
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|
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file = fileName.c_str(); |
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strcpy(xyzFile, file); |
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token = strtok(xyzFile, period); |
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strcpy(xyzFile, token); |
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strcpy(shapeFile, token); |
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strcpy(shapeName, token); |
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strcat(xyzFile, "Ref.xyz"); |
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strcat(shapeFile, ".shape"); |
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ofstream xfiles(xyzFile); |
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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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gridwidth = bandwidth*2; |
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|
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//the tolerance has a default value (default=0.01), so it is always given |
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tolerance = args_info.tolerance_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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} |
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|
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if (args_info.amber_given) { |
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FF=AMBER; |
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strcpy(vdwFileName, "amber99.vdw"); |
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} |
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|
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if (args_info.lj_given) { |
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FF=LJ; |
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strcpy(vdwFileName, "LJ.vdw"); |
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} |
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|
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if (args_info.gaff_given) { |
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FF=GAFF; |
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strcpy(vdwFileName, "gaff.vdw"); |
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} |
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|
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if (args_info.opls_given) { |
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FF=OPLS; |
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strcpy(vdwFileName, "oplsaal.vdw"); |
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} |
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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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|
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// next see if the force path enviorment variable is set |
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|
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ffPath = getenv( ffPath_env ); |
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if( ffPath == NULL ) { |
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STR_DEFINE(ffPath, FRC_PATH ); |
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} |
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|
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strcpy( temp, ffPath ); |
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strcat( temp, "/" ); |
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strcat( temp, vdwFileName ); |
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strcpy( vdwFileName, temp ); |
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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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|
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printf( "Error opening the vanDerWaals parameter file: %s\n" |
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"Have you tried setting the VDW_PARAM_DIR environment " |
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"variable?\n", |
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vdwFileName ); |
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exit(-1); |
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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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|
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fclose( vdwFile ); |
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|
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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! |
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|
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strcpy(structureFileName, fileName.c_str() ); |
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|
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PDBReader* PDBread = new PDBReader(); |
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PDBread->setPDBfileName(structureFileName); |
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theAtoms = PDBread->getAtomList(); |
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printf("Found %d atoms\n", theAtoms.size()); |
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|
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for( j = theAtoms.begin(); j != theAtoms.end(); ++j){ |
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atom = *j; |
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myType = atom->getType(); |
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gotMatch = 0; |
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|
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for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){ |
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at = *i; |
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vType = at->getType(); |
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|
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if (!strcasecmp(myType, vType)) { |
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atom->setMass(at->getMass()); |
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atom->setRpar(at->getRpar()); |
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atom->setEps(at->getEps()); |
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gotMatch = 1; |
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} |
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} |
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if (!gotMatch) { |
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printf("No matches found for %s, ", myType); |
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myType = atom->getBase(); |
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printf("trying with BaseType %s\n", myType); |
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for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){ |
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at = *i; |
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vType = at->getType(); |
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if (!strcasecmp(myType, vType)) { |
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atom->setMass(at->getMass()); |
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atom->setRpar(at->getRpar()); |
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atom->setEps(at->getEps()); |
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gotMatch = 1; |
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} |
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} |
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} |
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|
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if (!gotMatch) { |
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printf("No matches found with BaseType!\n"); |
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} |
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} |
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|
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rb = new RigidBody(); |
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for( j = theAtoms.begin(); j != theAtoms.end(); ++j){ |
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rb->addAtom(*j); |
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} |
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|
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rb->calcRefCoords(); |
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|
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//print a reference coordinate xyz file |
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xfiles << rb->getNumAtoms() << "\n\n"; |
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for (k=0; k<rb->getNumAtoms(); k++){ |
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rb->getAtomRefCoor(xyz3, k); |
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xfiles << rb->getAtomBase(k) << "\t" << |
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xyz3[0] << "\t" << xyz3[1] << "\t" << |
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xyz3[2] << "\n"; |
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} |
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|
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gb = new GridBuilder(rb, gridwidth); |
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|
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cout << "Doing GridBuilder calculations...\n"; |
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gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid); |
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|
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gb->printGridFiles(); |
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|
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//load the grid element values to the main grid vectors |
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for (k=0; k<gridwidth*gridwidth; k++){ |
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sigmaGrid.push_back(gb->passSig(k)); |
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sGrid.push_back(gb->passS(k)); |
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epsGrid.push_back(gb->passEps(k)); |
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} |
| 296 |
|
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//build the spherical harmonic transform object |
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harmonize = new SphereHarm( bandwidth ); |
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rb->getI(moments); |
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harmonize->printShapesFileStart(shapeFile, shapeName, rb->getMass(), |
| 301 |
moments); |
| 302 |
|
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printf("Doing SHAPE calculations and outputting results...\n"); |
| 304 |
//do the transforms and write to the shapes file |
| 305 |
harmonize->doTransforms(sigmaGrid); |
| 306 |
harmonize->printToShapesFile(shapeFile, 0, tolerance); |
| 307 |
harmonize->doTransforms(sGrid); |
| 308 |
harmonize->printToShapesFile(shapeFile, 1, tolerance); |
| 309 |
harmonize->doTransforms(epsGrid); |
| 310 |
harmonize->printToShapesFile(shapeFile, 2, tolerance); |
| 311 |
|
| 312 |
//clean everything up |
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harmonize->~SphereHarm(); |
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printf("Thank you for using SHAPES. Enjoy your potential!\n"); |
| 315 |
} |
| 316 |
|
| 317 |
int count_tokens(char *line, char *delimiters) { |
| 318 |
/* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */ |
| 319 |
|
| 320 |
char *working_line; /* WORKING COPY OF LINE. */ |
| 321 |
int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */ |
| 322 |
char *strtok_ptr; /* POINTER FOR STRTOK. */ |
| 323 |
|
| 324 |
strtok_ptr= working_line= strdup(line); |
| 325 |
|
| 326 |
ntokens=0; |
| 327 |
while (strtok(strtok_ptr,delimiters)!=NULL) |
| 328 |
{ |
| 329 |
ntokens++; |
| 330 |
strtok_ptr=NULL; |
| 331 |
} |
| 332 |
|
| 333 |
free(working_line); |
| 334 |
return(ntokens); |
| 335 |
} |
