trunk/SHAPES/forcer.cpp

#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include "forcerCmd.h"
#include "PDBReader.hpp"
#include "RigidBody.hpp"
#include "GridBuilder.hpp"
#include "SphereHarm.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;
  SphereHarm* harmonize;
  
  double mass, rpar, eps;
  double xyz3[3];
  double moments[3][3];
  string fileName;  
  char vdwFileName[2002];
  char structureFileName[2002];
  char temp[200];
  char readLine[500];
  char xyzFile[200];
  char shapeFile[200];
  char shapeName[80];
  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);
  strcpy(shapeName, token);
  strcat(xyzFile, "Ref.xyz");
  strcat(shapeFile, ".shape");
  strcat(shapeName, "_RB_0");
  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));
  }

  //build the spherical harmonic transform object
  harmonize = new SphereHarm( bandwidth );
  rb->getI(moments);
  harmonize->printShapesFileStart(shapeFile, shapeName, rb->getMass(),
                                  moments);
  
  //do the transforms and write to the shapes file
  harmonize->doTransforms(sigmaGrid);
  harmonize->printToShapesFile(shapeFile, 0);
  harmonize->doTransforms(sGrid);
  harmonize->printToShapesFile(shapeFile, 1);
  harmonize->doTransforms(epsGrid);
  harmonize->printToShapesFile(shapeFile, 2);
  
  //clean everything up
  harmonize->~SphereHarm();  
}

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:	1292
Committed:	Wed Jun 23 23:19:43 2004 UTC (20 years, 10 months ago) by chrisfen
File size:	7984 byte(s)
Log Message:	Spherical harmonic tranformations are fully integrated and working
#	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	chrisfen	1292	#include "SphereHarm.hpp"
10	gezelter	1240
11			#define MK_STR(s) # s
12			#define STR_DEFINE(t, s) t = MK_STR(s)
13			#define CHARMM 1
14			#define AMBER 2
15			#define LJ 3
16			#define GAFF 4
17			#define OPLS 5
18
19			int count_tokens(char line, char delimiters);
20			using namespace std;
21
22			class Atype{
23			public:
24			Atype() {
25			mass = 0.0;
26			rpar = 0.0;
27			eps = 0.0;
28			}
29
30			void setMass(double m) {mass = m;}
31			void setRpar(double rp) {rpar = rp;}
32			void setEps(double e) {eps = e;}
33			void setType(char* t) {strcpy(type, t);}
34			double getMass() {return mass;}
35			double getRpar() {return rpar;}
36			double getEps() {return eps;}
37			char *getType() {return type;}
38
39			private:
40			char type[100];
41			double mass;
42			double rpar;
43			double eps;
44			};
45
46			int main(int argc, char* argv[]){
47
48			gengetopt_args_info args_info;
49
50			vector<Atype*> vdwAtypes;
51			vector<Atype*>::iterator i;
52			Atype* at;
53	gezelter	1271	RigidBody* rb;
54	gezelter	1240	vector<VDWAtom*> theAtoms;
55			vector<VDWAtom*>::iterator j;
56			VDWAtom* atom;
57	chrisfen	1279	GridBuilder* gb;
58			vector<double> sigmaGrid;
59			vector<double> epsGrid;
60			vector<double> sGrid;
61	chrisfen	1292	SphereHarm* harmonize;
62	chrisfen	1279
63	gezelter	1240	double mass, rpar, eps;
64	chrisfen	1286	double xyz3[3];
65	chrisfen	1292	double moments[3][3];
66	gezelter	1240	string fileName;
67			char vdwFileName[2002];
68			char structureFileName[2002];
69			char temp[200];
70			char readLine[500];
71	chrisfen	1286	char xyzFile[200];
72	chrisfen	1287	char shapeFile[200];
73	chrisfen	1292	char shapeName[80];
74	gezelter	1240	FILE vdwFile, structureFile;
75	gezelter	1244	char* ffPath_env = "VDW_PATH";
76	gezelter	1240	char* ffPath;
77			char* eof_test;
78			char* foo;
79			char* myType;
80			char* vType;
81	chrisfen	1286	char *token;
82			const char *file;
83			const char *period = ".";
84			int k;
85	gezelter	1240	int lineNum;
86			int nTokens;
87			int FF;
88	chrisfen	1275	int bandwidth;
89	chrisfen	1287	int gridwidth;
90	gezelter	1240	short int gotMatch;
91
92			//parse the command line options
93			if (cmdline_parser (argc, argv, &args_info) != 0)
94			exit(1) ;
95
96			if (args_info.input_given){
97			fileName = args_info.input_arg;
98			}
99			else{
100			std::cerr << "Does not have input file name" << endl;
101			exit(1);
102			}
103
104	chrisfen	1286	file = fileName.c_str();
105			strcpy(xyzFile, file);
106			token = strtok(xyzFile, period);
107			strcpy(xyzFile, token);
108	chrisfen	1287	strcpy(shapeFile, token);
109	chrisfen	1292	strcpy(shapeName, token);
110	chrisfen	1287	strcat(xyzFile, "Ref.xyz");
111			strcat(shapeFile, ".shape");
112	chrisfen	1292	strcat(shapeName, "_RB_0");
113	chrisfen	1286	ofstream xfiles(xyzFile);
114
115	chrisfen	1281	//the bandwidth has a default value (default=16), so it is always given
116	chrisfen	1275	bandwidth = args_info.bandwidth_arg;
117	chrisfen	1287	gridwidth = bandwidth*2;
118	chrisfen	1275
119	gezelter	1240	if (args_info.charmm_given) {
120			FF=CHARMM;
121			strcpy(vdwFileName, "charmm27.vdw");
122			}
123
124			if (args_info.amber_given) {
125			FF=AMBER;
126			strcpy(vdwFileName, "amber99.vdw");
127			}
128
129			if (args_info.lj_given) {
130			FF=LJ;
131			strcpy(vdwFileName, "LJ.vdw");
132			}
133
134			if (args_info.gaff_given) {
135			FF=GAFF;
136			strcpy(vdwFileName, "gaff.vdw");
137			}
138
139			if (args_info.opls_given) {
140			FF=OPLS;
141			strcpy(vdwFileName, "oplsaal.vdw");
142			}
143
144	gezelter	1274
145			printf ("opening %s\n", vdwFileName);
146	gezelter	1240	vdwFile = fopen( vdwFileName, "r" );
147
148			if( vdwFile == NULL ){
149
150			// next see if the force path enviorment variable is set
151
152			ffPath = getenv( ffPath_env );
153			if( ffPath == NULL ) {
154			STR_DEFINE(ffPath, FRC_PATH );
155			}
156
157			strcpy( temp, ffPath );
158			strcat( temp, "/" );
159			strcat( temp, vdwFileName );
160			strcpy( vdwFileName, temp );
161
162	gezelter	1274	printf ("opening %s\n", vdwFileName);
163	gezelter	1240	vdwFile = fopen( vdwFileName, "r" );
164
165			if( vdwFile == NULL ){
166
167			printf( "Error opening the vanDerWaals parameter file: %s\n"
168	gezelter	1244	"Have you tried setting the VDW_PARAM_DIR environment "
169	gezelter	1240	"variable?\n",
170			vdwFileName );
171			exit(-1);
172			}
173	gezelter	1274	}
174			printf( "VDW file %s opened sucessfully.\n", vdwFileName );
175			lineNum = 0;
176
177			eof_test = fgets( readLine, sizeof(readLine), vdwFile );
178			lineNum++;
179
180			if( eof_test == NULL ){
181			printf("Error in reading Atoms from force file at line %d.\n",
182			lineNum );
183			exit(-1);
184			}
185
186			while( eof_test != NULL ){
187			// toss comment lines
188			if( readLine[0] != '!' && readLine[0] != '#' ){
189
190			nTokens = count_tokens(readLine, " ,;\t");
191			if (nTokens < 4) {
192			printf("Not enough tokens on line %d.\n", lineNum);
193			exit(-1);
194			}
195
196			at = new Atype();
197			foo = strtok(readLine, " ,;\t");
198			at->setType(foo);
199			foo = strtok(NULL, " ,;\t");
200			mass = atof(foo);
201			at->setMass(mass);
202			foo = strtok(NULL, " ,;\t");
203			rpar = atof(foo);
204			at->setRpar(rpar);
205			foo = strtok(NULL, " ,;\t");
206			eps = atof(foo);
207			at->setEps(eps);
208			vdwAtypes.push_back(at);
209			}
210	gezelter	1240	eof_test = fgets( readLine, sizeof(readLine), vdwFile );
211			lineNum++;
212	gezelter	1274	}
213
214			fclose( vdwFile );
215
216	gezelter	1240	printf("%d Atom Types read from VDW file\n", vdwAtypes.size());
217
218			// Now, open and parse the input file!
219
220			strcpy(structureFileName, fileName.c_str() );
221
222			PDBReader* PDBread = new PDBReader();
223			PDBread->setPDBfile(structureFileName);
224			theAtoms = PDBread->getAtomList();
225			printf("Found %d atoms\n", theAtoms.size());
226
227			for( j = theAtoms.begin(); j != theAtoms.end(); ++j){
228			atom = *j;
229			myType = atom->getType();
230			gotMatch = 0;
231
232			for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){
233			at = *i;
234			vType = at->getType();
235
236			if (!strcasecmp(myType, vType)) {
237			atom->setMass(at->getMass());
238			atom->setRpar(at->getRpar());
239			atom->setEps(at->getEps());
240			gotMatch = 1;
241			}
242			}
243			if (!gotMatch) {
244			printf("No matches found for %s, ", myType);
245			myType = atom->getBase();
246			printf("trying with BaseType %s\n", myType);
247			for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){
248			at = *i;
249			vType = at->getType();
250			if (!strcasecmp(myType, vType)) {
251			atom->setMass(at->getMass());
252			atom->setRpar(at->getRpar());
253			atom->setEps(at->getEps());
254			gotMatch = 1;
255			}
256			}
257			}
258
259			if (!gotMatch) {
260			printf("No matches found with BaseType!\n");
261			}
262			}
263
264	gezelter	1271	rb = new RigidBody();
265			for( j = theAtoms.begin(); j != theAtoms.end(); ++j){
266	gezelter	1274	rb->addAtom(*j);
267	gezelter	1271	}
268	chrisfen	1281
269	chrisfen	1279	rb->calcRefCoords();
270
271	chrisfen	1286	//print a reference coordinate xyz file
272			xfiles << rb->getNumAtoms() << "\n\n";
273			for (k=0; k<rb->getNumAtoms(); k++){
274			rb->getAtomRefCoor(xyz3, k);
275	chrisfen	1287	xfiles << rb->getAtomBase(k) << "\t" <<
276	chrisfen	1286	xyz3[0] << "\t" << xyz3[1] << "\t" <<
277			xyz3[2] << "\n";
278			}
279
280	chrisfen	1287	gb = new GridBuilder(rb, gridwidth);
281	chrisfen	1275
282	chrisfen	1281	cout << "Doing GridBuilder calculations...\n";
283	chrisfen	1279	gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid);
284	chrisfen	1281
285	chrisfen	1287	gb->printGridFiles();
286
287			//load the grid element values to the main grid vectors
288			for (k=0; k<gridwidth*gridwidth; k++){
289			sigmaGrid.push_back(gb->passSig(k));
290			sGrid.push_back(gb->passS(k));
291			epsGrid.push_back(gb->passEps(k));
292			}
293
294	chrisfen	1292	//build the spherical harmonic transform object
295			harmonize = new SphereHarm( bandwidth );
296			rb->getI(moments);
297			harmonize->printShapesFileStart(shapeFile, shapeName, rb->getMass(),
298			moments);
299	chrisfen	1287
300	chrisfen	1292	//do the transforms and write to the shapes file
301			harmonize->doTransforms(sigmaGrid);
302			harmonize->printToShapesFile(shapeFile, 0);
303			harmonize->doTransforms(sGrid);
304			harmonize->printToShapesFile(shapeFile, 1);
305			harmonize->doTransforms(epsGrid);
306			harmonize->printToShapesFile(shapeFile, 2);
307	chrisfen	1287
308	chrisfen	1292	//clean everything up
309			harmonize->~SphereHarm();
310	gezelter	1240	}
311
312			int count_tokens(char line, char delimiters) {
313			/* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */
314
315			char working_line; / WORKING COPY OF LINE. */
316			int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */
317			char strtok_ptr; / POINTER FOR STRTOK. */
318
319			strtok_ptr= working_line= strdup(line);
320
321			ntokens=0;
322			while (strtok(strtok_ptr,delimiters)!=NULL)
323			{
324			ntokens++;
325			strtok_ptr=NULL;
326			}
327
328			free(working_line);
329			return(ntokens);
330			}