trunk/SHAPES/shaper.cpp

#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include "shaperCmd.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];
  double tolerance;
  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;
 
  //the tolerance has a default value (default=0.01), so it is always given
  tolerance = args_info.tolerance_arg;

  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);
  
  printf("Doing SHAPE calculations and outputting results...\n");
  //do the transforms and write to the shapes file
  harmonize->doTransforms(sigmaGrid);
  harmonize->printToShapesFile(shapeFile, 0, tolerance);
  harmonize->doTransforms(sGrid);
  harmonize->printToShapesFile(shapeFile, 1, tolerance);
  harmonize->doTransforms(epsGrid);
  harmonize->printToShapesFile(shapeFile, 2, tolerance);
  
  //clean everything up
  harmonize->~SphereHarm();  
  printf("Thank you for using SHAPES.  Enjoy your potential!\n");
}

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:	1313
Committed:	Sat Jun 26 15:40:49 2004 UTC (21 years, 4 months ago) by chrisfen
File size:	8284 byte(s)
Log Message:	Tolerance input is accepted with the -t flag (default 0.01)
#	User	Rev	Content
1	gezelter	1295	#include <iostream>
2			#include <fstream>
3			#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"
10
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			RigidBody* rb;
54			vector<VDWAtom*> theAtoms;
55			vector<VDWAtom*>::iterator j;
56			VDWAtom* atom;
57			GridBuilder* gb;
58			vector<double> sigmaGrid;
59			vector<double> epsGrid;
60			vector<double> sGrid;
61			SphereHarm* harmonize;
62
63			double mass, rpar, eps;
64			double xyz3[3];
65			double moments[3][3];
66	chrisfen	1312	double tolerance;
67	gezelter	1295	string fileName;
68			char vdwFileName[2002];
69			char structureFileName[2002];
70			char temp[200];
71			char readLine[500];
72			char xyzFile[200];
73			char shapeFile[200];
74			char shapeName[80];
75			FILE vdwFile, structureFile;
76			char* ffPath_env = "VDW_PATH";
77			char* ffPath;
78			char* eof_test;
79			char* foo;
80			char* myType;
81			char* vType;
82			char *token;
83			const char *file;
84			const char *period = ".";
85			int k;
86			int lineNum;
87			int nTokens;
88			int FF;
89			int bandwidth;
90			int gridwidth;
91			short int gotMatch;
92
93			//parse the command line options
94			if (cmdline_parser (argc, argv, &args_info) != 0)
95			exit(1) ;
96
97			if (args_info.input_given){
98			fileName = args_info.input_arg;
99			}
100			else{
101			std::cerr << "Does not have input file name" << endl;
102			exit(1);
103			}
104
105			file = fileName.c_str();
106			strcpy(xyzFile, file);
107			token = strtok(xyzFile, period);
108			strcpy(xyzFile, token);
109			strcpy(shapeFile, token);
110			strcpy(shapeName, token);
111			strcat(xyzFile, "Ref.xyz");
112			strcat(shapeFile, ".shape");
113			strcat(shapeName, "_RB_0");
114			ofstream xfiles(xyzFile);
115
116			//the bandwidth has a default value (default=16), so it is always given
117			bandwidth = args_info.bandwidth_arg;
118			gridwidth = bandwidth*2;
119	chrisfen	1312
120			//the tolerance has a default value (default=0.01), so it is always given
121			tolerance = args_info.tolerance_arg;
122
123	gezelter	1295	if (args_info.charmm_given) {
124			FF=CHARMM;
125			strcpy(vdwFileName, "charmm27.vdw");
126			}
127
128			if (args_info.amber_given) {
129			FF=AMBER;
130			strcpy(vdwFileName, "amber99.vdw");
131			}
132
133			if (args_info.lj_given) {
134			FF=LJ;
135			strcpy(vdwFileName, "LJ.vdw");
136			}
137
138			if (args_info.gaff_given) {
139			FF=GAFF;
140			strcpy(vdwFileName, "gaff.vdw");
141			}
142
143			if (args_info.opls_given) {
144			FF=OPLS;
145			strcpy(vdwFileName, "oplsaal.vdw");
146			}
147
148
149			printf ("opening %s\n", vdwFileName);
150			vdwFile = fopen( vdwFileName, "r" );
151
152			if( vdwFile == NULL ){
153
154			// next see if the force path enviorment variable is set
155
156			ffPath = getenv( ffPath_env );
157			if( ffPath == NULL ) {
158			STR_DEFINE(ffPath, FRC_PATH );
159			}
160
161			strcpy( temp, ffPath );
162			strcat( temp, "/" );
163			strcat( temp, vdwFileName );
164			strcpy( vdwFileName, temp );
165
166			printf ("opening %s\n", vdwFileName);
167			vdwFile = fopen( vdwFileName, "r" );
168
169			if( vdwFile == NULL ){
170
171			printf( "Error opening the vanDerWaals parameter file: %s\n"
172			"Have you tried setting the VDW_PARAM_DIR environment "
173			"variable?\n",
174			vdwFileName );
175			exit(-1);
176			}
177			}
178			printf( "VDW file %s opened sucessfully.\n", vdwFileName );
179			lineNum = 0;
180
181			eof_test = fgets( readLine, sizeof(readLine), vdwFile );
182			lineNum++;
183
184			if( eof_test == NULL ){
185			printf("Error in reading Atoms from force file at line %d.\n",
186			lineNum );
187			exit(-1);
188			}
189
190			while( eof_test != NULL ){
191			// toss comment lines
192			if( readLine[0] != '!' && readLine[0] != '#' ){
193
194			nTokens = count_tokens(readLine, " ,;\t");
195			if (nTokens < 4) {
196			printf("Not enough tokens on line %d.\n", lineNum);
197			exit(-1);
198			}
199
200			at = new Atype();
201			foo = strtok(readLine, " ,;\t");
202			at->setType(foo);
203			foo = strtok(NULL, " ,;\t");
204			mass = atof(foo);
205			at->setMass(mass);
206			foo = strtok(NULL, " ,;\t");
207			rpar = atof(foo);
208			at->setRpar(rpar);
209			foo = strtok(NULL, " ,;\t");
210			eps = atof(foo);
211			at->setEps(eps);
212			vdwAtypes.push_back(at);
213			}
214			eof_test = fgets( readLine, sizeof(readLine), vdwFile );
215			lineNum++;
216			}
217
218			fclose( vdwFile );
219
220			printf("%d Atom Types read from VDW file\n", vdwAtypes.size());
221
222			// Now, open and parse the input file!
223
224			strcpy(structureFileName, fileName.c_str() );
225
226			PDBReader* PDBread = new PDBReader();
227			PDBread->setPDBfile(structureFileName);
228			theAtoms = PDBread->getAtomList();
229			printf("Found %d atoms\n", theAtoms.size());
230
231			for( j = theAtoms.begin(); j != theAtoms.end(); ++j){
232			atom = *j;
233			myType = atom->getType();
234			gotMatch = 0;
235
236			for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){
237			at = *i;
238			vType = at->getType();
239
240			if (!strcasecmp(myType, vType)) {
241			atom->setMass(at->getMass());
242			atom->setRpar(at->getRpar());
243			atom->setEps(at->getEps());
244			gotMatch = 1;
245			}
246			}
247			if (!gotMatch) {
248			printf("No matches found for %s, ", myType);
249			myType = atom->getBase();
250			printf("trying with BaseType %s\n", myType);
251			for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){
252			at = *i;
253			vType = at->getType();
254			if (!strcasecmp(myType, vType)) {
255			atom->setMass(at->getMass());
256			atom->setRpar(at->getRpar());
257			atom->setEps(at->getEps());
258			gotMatch = 1;
259			}
260			}
261			}
262
263			if (!gotMatch) {
264			printf("No matches found with BaseType!\n");
265			}
266			}
267
268			rb = new RigidBody();
269			for( j = theAtoms.begin(); j != theAtoms.end(); ++j){
270			rb->addAtom(*j);
271			}
272
273			rb->calcRefCoords();
274
275			//print a reference coordinate xyz file
276			xfiles << rb->getNumAtoms() << "\n\n";
277			for (k=0; k<rb->getNumAtoms(); k++){
278			rb->getAtomRefCoor(xyz3, k);
279			xfiles << rb->getAtomBase(k) << "\t" <<
280			xyz3[0] << "\t" << xyz3[1] << "\t" <<
281			xyz3[2] << "\n";
282			}
283
284			gb = new GridBuilder(rb, gridwidth);
285
286			cout << "Doing GridBuilder calculations...\n";
287			gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid);
288
289			gb->printGridFiles();
290
291			//load the grid element values to the main grid vectors
292			for (k=0; k<gridwidth*gridwidth; k++){
293			sigmaGrid.push_back(gb->passSig(k));
294			sGrid.push_back(gb->passS(k));
295			epsGrid.push_back(gb->passEps(k));
296			}
297
298			//build the spherical harmonic transform object
299			harmonize = new SphereHarm( bandwidth );
300			rb->getI(moments);
301			harmonize->printShapesFileStart(shapeFile, shapeName, rb->getMass(),
302			moments);
303
304			printf("Doing SHAPE calculations and outputting results...\n");
305			//do the transforms and write to the shapes file
306			harmonize->doTransforms(sigmaGrid);
307	chrisfen	1313	harmonize->printToShapesFile(shapeFile, 0, tolerance);
308	gezelter	1295	harmonize->doTransforms(sGrid);
309	chrisfen	1313	harmonize->printToShapesFile(shapeFile, 1, tolerance);
310	gezelter	1295	harmonize->doTransforms(epsGrid);
311	chrisfen	1313	harmonize->printToShapesFile(shapeFile, 2, tolerance);
312	gezelter	1295
313			//clean everything up
314			harmonize->~SphereHarm();
315			printf("Thank you for using SHAPES. Enjoy your potential!\n");
316			}
317
318			int count_tokens(char line, char delimiters) {
319			/* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */
320
321			char working_line; / WORKING COPY OF LINE. */
322			int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */
323			char strtok_ptr; / POINTER FOR STRTOK. */
324
325			strtok_ptr= working_line= strdup(line);
326
327			ntokens=0;
328			while (strtok(strtok_ptr,delimiters)!=NULL)
329			{
330			ntokens++;
331			strtok_ptr=NULL;
332			}
333
334			free(working_line);
335			return(ntokens);
336			}