trunk/SHAPES/forcer.cpp

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

  double mass, rpar, eps;
  string fileName;  
  char vdwFileName[2002];
  char structureFileName[2002];
  char temp[200];
  char readLine[500];
  FILE *vdwFile, *structureFile;
  char* ffPath_env = "VDW_PATH";
  char* ffPath;
  char* eof_test;
  char* foo;
  char* myType;
  char* vType;
  int lineNum;
  int nTokens;
  int FF;
  int bandwidth;
  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);
  }

  //the bandwidth has a default value (default=8), so it is always given
  bandwidth = args_info.bandwidth_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);
  }
  
  //GridBuilder gb = new GridBuilder(rb);

  //gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid);

   
}

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:	1275
Committed:	Tue Jun 15 22:36:23 2004 UTC (20 years, 3 months ago) by chrisfen
File size:	6104 byte(s)
Log Message:	Added a bandwidth command-line option
#	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	gezelter	1240
9			#define MK_STR(s) # s
10			#define STR_DEFINE(t, s) t = MK_STR(s)
11			#define CHARMM 1
12			#define AMBER 2
13			#define LJ 3
14			#define GAFF 4
15			#define OPLS 5
16
17			int count_tokens(char line, char delimiters);
18			using namespace std;
19
20			class Atype{
21			public:
22			Atype() {
23			mass = 0.0;
24			rpar = 0.0;
25			eps = 0.0;
26			}
27
28			void setMass(double m) {mass = m;}
29			void setRpar(double rp) {rpar = rp;}
30			void setEps(double e) {eps = e;}
31			void setType(char* t) {strcpy(type, t);}
32			double getMass() {return mass;}
33			double getRpar() {return rpar;}
34			double getEps() {return eps;}
35			char *getType() {return type;}
36
37			private:
38			char type[100];
39			double mass;
40			double rpar;
41			double eps;
42			};
43
44			int main(int argc, char* argv[]){
45
46			gengetopt_args_info args_info;
47
48			vector<Atype*> vdwAtypes;
49			vector<Atype*>::iterator i;
50			Atype* at;
51	gezelter	1271	RigidBody* rb;
52	gezelter	1240	vector<VDWAtom*> theAtoms;
53			vector<VDWAtom*>::iterator j;
54			VDWAtom* atom;
55
56			double mass, rpar, eps;
57			string fileName;
58			char vdwFileName[2002];
59			char structureFileName[2002];
60			char temp[200];
61			char readLine[500];
62			FILE vdwFile, structureFile;
63	gezelter	1244	char* ffPath_env = "VDW_PATH";
64	gezelter	1240	char* ffPath;
65			char* eof_test;
66			char* foo;
67			char* myType;
68			char* vType;
69			int lineNum;
70			int nTokens;
71			int FF;
72	chrisfen	1275	int bandwidth;
73	gezelter	1240	short int gotMatch;
74
75			//parse the command line options
76			if (cmdline_parser (argc, argv, &args_info) != 0)
77			exit(1) ;
78
79			if (args_info.input_given){
80			fileName = args_info.input_arg;
81			}
82			else{
83			std::cerr << "Does not have input file name" << endl;
84			exit(1);
85			}
86
87	chrisfen	1275	//the bandwidth has a default value (default=8), so it is always given
88			bandwidth = args_info.bandwidth_arg;
89
90	gezelter	1240	if (args_info.charmm_given) {
91			FF=CHARMM;
92			strcpy(vdwFileName, "charmm27.vdw");
93			}
94
95			if (args_info.amber_given) {
96			FF=AMBER;
97			strcpy(vdwFileName, "amber99.vdw");
98			}
99
100			if (args_info.lj_given) {
101			FF=LJ;
102			strcpy(vdwFileName, "LJ.vdw");
103			}
104
105			if (args_info.gaff_given) {
106			FF=GAFF;
107			strcpy(vdwFileName, "gaff.vdw");
108			}
109
110			if (args_info.opls_given) {
111			FF=OPLS;
112			strcpy(vdwFileName, "oplsaal.vdw");
113			}
114
115	gezelter	1274
116			printf ("opening %s\n", vdwFileName);
117	gezelter	1240	vdwFile = fopen( vdwFileName, "r" );
118
119			if( vdwFile == NULL ){
120
121			// next see if the force path enviorment variable is set
122
123			ffPath = getenv( ffPath_env );
124			if( ffPath == NULL ) {
125			STR_DEFINE(ffPath, FRC_PATH );
126			}
127
128			strcpy( temp, ffPath );
129			strcat( temp, "/" );
130			strcat( temp, vdwFileName );
131			strcpy( vdwFileName, temp );
132
133	gezelter	1274	printf ("opening %s\n", vdwFileName);
134	gezelter	1240	vdwFile = fopen( vdwFileName, "r" );
135
136			if( vdwFile == NULL ){
137
138			printf( "Error opening the vanDerWaals parameter file: %s\n"
139	gezelter	1244	"Have you tried setting the VDW_PARAM_DIR environment "
140	gezelter	1240	"variable?\n",
141			vdwFileName );
142			exit(-1);
143			}
144	gezelter	1274	}
145			printf( "VDW file %s opened sucessfully.\n", vdwFileName );
146			lineNum = 0;
147
148			eof_test = fgets( readLine, sizeof(readLine), vdwFile );
149			lineNum++;
150
151			if( eof_test == NULL ){
152			printf("Error in reading Atoms from force file at line %d.\n",
153			lineNum );
154			exit(-1);
155			}
156
157			while( eof_test != NULL ){
158			// toss comment lines
159			if( readLine[0] != '!' && readLine[0] != '#' ){
160
161			nTokens = count_tokens(readLine, " ,;\t");
162			if (nTokens < 4) {
163			printf("Not enough tokens on line %d.\n", lineNum);
164			exit(-1);
165			}
166
167			at = new Atype();
168			foo = strtok(readLine, " ,;\t");
169			at->setType(foo);
170			foo = strtok(NULL, " ,;\t");
171			mass = atof(foo);
172			at->setMass(mass);
173			foo = strtok(NULL, " ,;\t");
174			rpar = atof(foo);
175			at->setRpar(rpar);
176			foo = strtok(NULL, " ,;\t");
177			eps = atof(foo);
178			at->setEps(eps);
179			vdwAtypes.push_back(at);
180			}
181	gezelter	1240	eof_test = fgets( readLine, sizeof(readLine), vdwFile );
182			lineNum++;
183	gezelter	1274	}
184
185			fclose( vdwFile );
186
187	gezelter	1240	printf("%d Atom Types read from VDW file\n", vdwAtypes.size());
188
189			// Now, open and parse the input file!
190
191			strcpy(structureFileName, fileName.c_str() );
192
193			PDBReader* PDBread = new PDBReader();
194			PDBread->setPDBfile(structureFileName);
195			theAtoms = PDBread->getAtomList();
196			printf("Found %d atoms\n", theAtoms.size());
197
198			for( j = theAtoms.begin(); j != theAtoms.end(); ++j){
199			atom = *j;
200			myType = atom->getType();
201			gotMatch = 0;
202
203			for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){
204			at = *i;
205			vType = at->getType();
206
207			if (!strcasecmp(myType, vType)) {
208			atom->setMass(at->getMass());
209			atom->setRpar(at->getRpar());
210			atom->setEps(at->getEps());
211			gotMatch = 1;
212			}
213			}
214			if (!gotMatch) {
215			printf("No matches found for %s, ", myType);
216			myType = atom->getBase();
217			printf("trying with BaseType %s\n", myType);
218			for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){
219			at = *i;
220			vType = at->getType();
221			if (!strcasecmp(myType, vType)) {
222			atom->setMass(at->getMass());
223			atom->setRpar(at->getRpar());
224			atom->setEps(at->getEps());
225			gotMatch = 1;
226			}
227			}
228			}
229
230			if (!gotMatch) {
231			printf("No matches found with BaseType!\n");
232			}
233			}
234
235	gezelter	1271	rb = new RigidBody();
236			for( j = theAtoms.begin(); j != theAtoms.end(); ++j){
237	gezelter	1274	rb->addAtom(*j);
238	gezelter	1271	}
239	gezelter	1274
240			//GridBuilder gb = new GridBuilder(rb);
241	chrisfen	1275
242	gezelter	1240	//gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid);
243	chrisfen	1275
244	gezelter	1274
245	gezelter	1240	}
246
247			int count_tokens(char line, char delimiters) {
248			/* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */
249
250			char working_line; / WORKING COPY OF LINE. */
251			int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */
252			char strtok_ptr; / POINTER FOR STRTOK. */
253
254			strtok_ptr= working_line= strdup(line);
255
256			ntokens=0;
257			while (strtok(strtok_ptr,delimiters)!=NULL)
258			{
259			ntokens++;
260			strtok_ptr=NULL;
261			}
262
263			free(working_line);
264			return(ntokens);
265			}