trunk/SHAPES/forcer.cpp

#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include "forcerCmd.h"
#include "PDBReader.hpp"
#include "RigidBody.hpp"
#include "GridBuilder.hpp"

#define MK_STR(s) # s
#define STR_DEFINE(t, s) t = MK_STR(s)
#define CHARMM 1
#define AMBER  2
#define LJ     3
#define GAFF   4
#define OPLS   5

int count_tokens(char *line, char *delimiters);
using namespace std;

class Atype{
public:
  Atype() {
    mass = 0.0;
    rpar = 0.0;
    eps = 0.0;
  }

  void setMass(double m) {mass = m;}
  void setRpar(double rp) {rpar = rp;}
  void setEps(double e) {eps = e;}
  void setType(char* t) {strcpy(type, t);}
  double getMass() {return mass;}
  double getRpar() {return rpar;}
  double getEps() {return eps;}
  char *getType() {return type;}
  
private:
  char type[100];
  double mass;
  double rpar;
  double eps;
};
  
int main(int argc, char* argv[]){

  gengetopt_args_info args_info;

  vector<Atype*>   vdwAtypes;
  vector<Atype*>::iterator i;
  Atype* at;
  RigidBody* rb;
  vector<VDWAtom*> theAtoms;
  vector<VDWAtom*>::iterator j;
  VDWAtom* atom;
  GridBuilder* gb;
  vector<double> sigmaGrid;
  vector<double> epsGrid;
  vector<double> sGrid;
  
  double mass, rpar, eps;
  double xyz3[3];
  string fileName;  
  char vdwFileName[2002];
  char structureFileName[2002];
  char temp[200];
  char readLine[500];
  char xyzFile[200];
  char shapeFile[200];
  FILE *vdwFile, *structureFile;
  char* ffPath_env = "VDW_PATH";
  char* ffPath;
  char* eof_test;
  char* foo;
  char* myType;
  char* vType;
  char *token;
  const char *file;
  const char *period = ".";
  int k;
  int lineNum;
  int nTokens;
  int FF;
  int bandwidth;
  int gridwidth;
  short int gotMatch;

  //parse the command line options
  if (cmdline_parser (argc, argv, &args_info) != 0)
    exit(1) ;

  if (args_info.input_given){
    fileName = args_info.input_arg;
  }
  else{
    std::cerr << "Does not have input file name" << endl;
    exit(1);
  }

  file = fileName.c_str();
  strcpy(xyzFile, file);
  token = strtok(xyzFile, period);
  strcpy(xyzFile, token);
  strcpy(shapeFile, token);
  strcat(xyzFile, "Ref.xyz");
  strcat(shapeFile, ".shape");
  ofstream xfiles(xyzFile);
  
  //the bandwidth has a default value (default=16), so it is always given
  bandwidth = args_info.bandwidth_arg;
  gridwidth = bandwidth*2;
  
  if (args_info.charmm_given) {
    FF=CHARMM;
    strcpy(vdwFileName, "charmm27.vdw");
  }

  if (args_info.amber_given) {
    FF=AMBER;
    strcpy(vdwFileName, "amber99.vdw");
  }

  if (args_info.lj_given) {
    FF=LJ;
    strcpy(vdwFileName, "LJ.vdw");
  }

  if (args_info.gaff_given) {
    FF=GAFF;
    strcpy(vdwFileName, "gaff.vdw");
  }
  
  if (args_info.opls_given) {
    FF=OPLS;
    strcpy(vdwFileName, "oplsaal.vdw");
  }


  printf ("opening %s\n", vdwFileName);
  vdwFile = fopen( vdwFileName, "r" );
  
  if( vdwFile == NULL ){
       
    // next see if the force path enviorment variable is set
    
    ffPath = getenv( ffPath_env );
    if( ffPath == NULL ) {
      STR_DEFINE(ffPath, FRC_PATH );
    }
    
    strcpy( temp, ffPath );
    strcat( temp, "/" );
    strcat( temp, vdwFileName );
    strcpy( vdwFileName, temp );
    
    printf ("opening %s\n", vdwFileName);
    vdwFile = fopen( vdwFileName, "r" );
    
    if( vdwFile == NULL ){
      
      printf(  "Error opening the vanDerWaals parameter file: %s\n"
               "Have you tried setting the VDW_PARAM_DIR environment "
               "variable?\n",
               vdwFileName );
      exit(-1);
    }
  }
  printf( "VDW file %s opened sucessfully.\n", vdwFileName );
  lineNum = 0;
  
  eof_test = fgets( readLine, sizeof(readLine), vdwFile );
  lineNum++;
  
  if( eof_test == NULL ){
    printf("Error in reading Atoms from force file at line %d.\n",
           lineNum );
    exit(-1);
  }
  
  while( eof_test != NULL ){
    // toss comment lines
    if( readLine[0] != '!' && readLine[0] != '#' ){
      
      nTokens = count_tokens(readLine, " ,;\t");
      if (nTokens < 4) {
        printf("Not enough tokens on line %d.\n", lineNum);
        exit(-1);
      } 
      
      at = new Atype();
      foo = strtok(readLine, " ,;\t");
      at->setType(foo);
      foo = strtok(NULL, " ,;\t");       
      mass = atof(foo);
      at->setMass(mass);
      foo = strtok(NULL, " ,;\t");
      rpar = atof(foo);
      at->setRpar(rpar);
      foo = strtok(NULL, " ,;\t");
      eps = atof(foo);  
      at->setEps(eps);
      vdwAtypes.push_back(at);        
    }
    eof_test = fgets( readLine, sizeof(readLine), vdwFile );
    lineNum++;
  }          
  
  fclose( vdwFile );
  
  printf("%d Atom Types read from VDW file\n", vdwAtypes.size());

  // Now, open and parse the input file!

  strcpy(structureFileName, fileName.c_str() );

  PDBReader* PDBread = new PDBReader();
  PDBread->setPDBfile(structureFileName);
  theAtoms = PDBread->getAtomList();
  printf("Found %d atoms\n", theAtoms.size());

  for( j = theAtoms.begin(); j !=  theAtoms.end(); ++j){
    atom = *j;
    myType = atom->getType();
    gotMatch = 0;

    for( i = vdwAtypes.begin(); i !=  vdwAtypes.end(); ++i){
      at = *i;
      vType = at->getType();
      
      if (!strcasecmp(myType, vType)) {
        atom->setMass(at->getMass());
        atom->setRpar(at->getRpar());
        atom->setEps(at->getEps());
        gotMatch = 1;        
      }
    }
    if (!gotMatch) {      
      printf("No matches found for %s, ", myType);
      myType = atom->getBase();
      printf("trying with BaseType %s\n", myType);
      for( i = vdwAtypes.begin(); i !=  vdwAtypes.end(); ++i){
        at = *i;
        vType = at->getType();        
        if (!strcasecmp(myType, vType)) {
          atom->setMass(at->getMass());
          atom->setRpar(at->getRpar());
          atom->setEps(at->getEps());
          gotMatch = 1;
        }
      }
    }

    if (!gotMatch) {
      printf("No matches found with BaseType!\n");
    }
  }

  rb = new RigidBody();
  for( j = theAtoms.begin(); j !=  theAtoms.end(); ++j){
    rb->addAtom(*j);
  }

  rb->calcRefCoords();
  
  //print a reference coordinate xyz file
  xfiles << rb->getNumAtoms() << "\n\n";
  for (k=0; k<rb->getNumAtoms(); k++){
    rb->getAtomRefCoor(xyz3, k);
    xfiles << rb->getAtomBase(k) << "\t" <<
              xyz3[0] << "\t" << xyz3[1] << "\t" <<
              xyz3[2] << "\n";
  }
  
  gb = new GridBuilder(rb, gridwidth);

  cout << "Doing GridBuilder calculations...\n";
  gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid);
  
  gb->printGridFiles();
  
  //load the grid element values to the main grid vectors
  for (k=0; k<gridwidth*gridwidth; k++){
    sigmaGrid.push_back(gb->passSig(k));
    sGrid.push_back(gb->passS(k));
    epsGrid.push_back(gb->passEps(k));
  }

  
}

int count_tokens(char *line, char *delimiters) {
/* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */
 
  char *working_line;   /* WORKING COPY OF LINE. */
  int ntokens;          /* NUMBER OF TOKENS FOUND IN LINE. */
  char *strtok_ptr;     /* POINTER FOR STRTOK. */
   
  strtok_ptr= working_line= strdup(line);
   
  ntokens=0;
  while (strtok(strtok_ptr,delimiters)!=NULL)
    {
      ntokens++;
      strtok_ptr=NULL;
    }
   
  free(working_line);
  return(ntokens);
}
Revision:	1287
Committed:	Wed Jun 23 20:18:48 2004 UTC (20 years, 2 months ago) by chrisfen
File size:	7249 byte(s)
Log Message:	Major progress towards inclusion of spherical harmonic transform capability - still having some build issues...
#	User	Rev	Content
1	gezelter	1240	#include <iostream>
2			#include <fstream>
3			#include <string>
4			#include <vector>
5			#include "forcerCmd.h"
6			#include "PDBReader.hpp"
7	gezelter	1271	#include "RigidBody.hpp"
8	chrisfen	1279	#include "GridBuilder.hpp"
9	gezelter	1240
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	gezelter	1271	RigidBody* rb;
53	gezelter	1240	vector<VDWAtom*> theAtoms;
54			vector<VDWAtom*>::iterator j;
55			VDWAtom* atom;
56	chrisfen	1279	GridBuilder* gb;
57			vector<double> sigmaGrid;
58			vector<double> epsGrid;
59			vector<double> sGrid;
60
61	gezelter	1240	double mass, rpar, eps;
62	chrisfen	1286	double xyz3[3];
63	gezelter	1240	string fileName;
64			char vdwFileName[2002];
65			char structureFileName[2002];
66			char temp[200];
67			char readLine[500];
68	chrisfen	1286	char xyzFile[200];
69	chrisfen	1287	char shapeFile[200];
70	gezelter	1240	FILE vdwFile, structureFile;
71	gezelter	1244	char* ffPath_env = "VDW_PATH";
72	gezelter	1240	char* ffPath;
73			char* eof_test;
74			char* foo;
75			char* myType;
76			char* vType;
77	chrisfen	1286	char *token;
78			const char *file;
79			const char *period = ".";
80			int k;
81	gezelter	1240	int lineNum;
82			int nTokens;
83			int FF;
84	chrisfen	1275	int bandwidth;
85	chrisfen	1287	int gridwidth;
86	gezelter	1240	short int gotMatch;
87
88			//parse the command line options
89			if (cmdline_parser (argc, argv, &args_info) != 0)
90			exit(1) ;
91
92			if (args_info.input_given){
93			fileName = args_info.input_arg;
94			}
95			else{
96			std::cerr << "Does not have input file name" << endl;
97			exit(1);
98			}
99
100	chrisfen	1286	file = fileName.c_str();
101			strcpy(xyzFile, file);
102			token = strtok(xyzFile, period);
103			strcpy(xyzFile, token);
104	chrisfen	1287	strcpy(shapeFile, token);
105			strcat(xyzFile, "Ref.xyz");
106			strcat(shapeFile, ".shape");
107	chrisfen	1286	ofstream xfiles(xyzFile);
108
109	chrisfen	1281	//the bandwidth has a default value (default=16), so it is always given
110	chrisfen	1275	bandwidth = args_info.bandwidth_arg;
111	chrisfen	1287	gridwidth = bandwidth*2;
112	chrisfen	1275
113	gezelter	1240	if (args_info.charmm_given) {
114			FF=CHARMM;
115			strcpy(vdwFileName, "charmm27.vdw");
116			}
117
118			if (args_info.amber_given) {
119			FF=AMBER;
120			strcpy(vdwFileName, "amber99.vdw");
121			}
122
123			if (args_info.lj_given) {
124			FF=LJ;
125			strcpy(vdwFileName, "LJ.vdw");
126			}
127
128			if (args_info.gaff_given) {
129			FF=GAFF;
130			strcpy(vdwFileName, "gaff.vdw");
131			}
132
133			if (args_info.opls_given) {
134			FF=OPLS;
135			strcpy(vdwFileName, "oplsaal.vdw");
136			}
137
138	gezelter	1274
139			printf ("opening %s\n", vdwFileName);
140	gezelter	1240	vdwFile = fopen( vdwFileName, "r" );
141
142			if( vdwFile == NULL ){
143
144			// next see if the force path enviorment variable is set
145
146			ffPath = getenv( ffPath_env );
147			if( ffPath == NULL ) {
148			STR_DEFINE(ffPath, FRC_PATH );
149			}
150
151			strcpy( temp, ffPath );
152			strcat( temp, "/" );
153			strcat( temp, vdwFileName );
154			strcpy( vdwFileName, temp );
155
156	gezelter	1274	printf ("opening %s\n", vdwFileName);
157	gezelter	1240	vdwFile = fopen( vdwFileName, "r" );
158
159			if( vdwFile == NULL ){
160
161			printf( "Error opening the vanDerWaals parameter file: %s\n"
162	gezelter	1244	"Have you tried setting the VDW_PARAM_DIR environment "
163	gezelter	1240	"variable?\n",
164			vdwFileName );
165			exit(-1);
166			}
167	gezelter	1274	}
168			printf( "VDW file %s opened sucessfully.\n", vdwFileName );
169			lineNum = 0;
170
171			eof_test = fgets( readLine, sizeof(readLine), vdwFile );
172			lineNum++;
173
174			if( eof_test == NULL ){
175			printf("Error in reading Atoms from force file at line %d.\n",
176			lineNum );
177			exit(-1);
178			}
179
180			while( eof_test != NULL ){
181			// toss comment lines
182			if( readLine[0] != '!' && readLine[0] != '#' ){
183
184			nTokens = count_tokens(readLine, " ,;\t");
185			if (nTokens < 4) {
186			printf("Not enough tokens on line %d.\n", lineNum);
187			exit(-1);
188			}
189
190			at = new Atype();
191			foo = strtok(readLine, " ,;\t");
192			at->setType(foo);
193			foo = strtok(NULL, " ,;\t");
194			mass = atof(foo);
195			at->setMass(mass);
196			foo = strtok(NULL, " ,;\t");
197			rpar = atof(foo);
198			at->setRpar(rpar);
199			foo = strtok(NULL, " ,;\t");
200			eps = atof(foo);
201			at->setEps(eps);
202			vdwAtypes.push_back(at);
203			}
204	gezelter	1240	eof_test = fgets( readLine, sizeof(readLine), vdwFile );
205			lineNum++;
206	gezelter	1274	}
207
208			fclose( vdwFile );
209
210	gezelter	1240	printf("%d Atom Types read from VDW file\n", vdwAtypes.size());
211
212			// Now, open and parse the input file!
213
214			strcpy(structureFileName, fileName.c_str() );
215
216			PDBReader* PDBread = new PDBReader();
217			PDBread->setPDBfile(structureFileName);
218			theAtoms = PDBread->getAtomList();
219			printf("Found %d atoms\n", theAtoms.size());
220
221			for( j = theAtoms.begin(); j != theAtoms.end(); ++j){
222			atom = *j;
223			myType = atom->getType();
224			gotMatch = 0;
225
226			for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){
227			at = *i;
228			vType = at->getType();
229
230			if (!strcasecmp(myType, vType)) {
231			atom->setMass(at->getMass());
232			atom->setRpar(at->getRpar());
233			atom->setEps(at->getEps());
234			gotMatch = 1;
235			}
236			}
237			if (!gotMatch) {
238			printf("No matches found for %s, ", myType);
239			myType = atom->getBase();
240			printf("trying with BaseType %s\n", myType);
241			for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){
242			at = *i;
243			vType = at->getType();
244			if (!strcasecmp(myType, vType)) {
245			atom->setMass(at->getMass());
246			atom->setRpar(at->getRpar());
247			atom->setEps(at->getEps());
248			gotMatch = 1;
249			}
250			}
251			}
252
253			if (!gotMatch) {
254			printf("No matches found with BaseType!\n");
255			}
256			}
257
258	gezelter	1271	rb = new RigidBody();
259			for( j = theAtoms.begin(); j != theAtoms.end(); ++j){
260	gezelter	1274	rb->addAtom(*j);
261	gezelter	1271	}
262	chrisfen	1281
263	chrisfen	1279	rb->calcRefCoords();
264
265	chrisfen	1286	//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	chrisfen	1287	xfiles << rb->getAtomBase(k) << "\t" <<
270	chrisfen	1286	xyz3[0] << "\t" << xyz3[1] << "\t" <<
271			xyz3[2] << "\n";
272			}
273
274	chrisfen	1287	gb = new GridBuilder(rb, gridwidth);
275	chrisfen	1275
276	chrisfen	1281	cout << "Doing GridBuilder calculations...\n";
277	chrisfen	1279	gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid);
278	chrisfen	1281
279	chrisfen	1287	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	gezelter	1240	}
291
292			int count_tokens(char line, char delimiters) {
293			/* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */
294
295			char working_line; / WORKING COPY OF LINE. */
296			int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */
297			char strtok_ptr; / POINTER FOR STRTOK. */
298
299			strtok_ptr= working_line= strdup(line);
300
301			ntokens=0;
302			while (strtok(strtok_ptr,delimiters)!=NULL)
303			{
304			ntokens++;
305			strtok_ptr=NULL;
306			}
307
308			free(working_line);
309			return(ntokens);
310			}