trunk/SHAPES/forcer.cpp

#include <iostream>
#include <fstream>
#include <string>
#include <vector>
#include "forcerCmd.h"
#include "PDBReader.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;
  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;
  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);
  }

  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");
  }

  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 );
    
    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");
    }
  }

  //GridBuilder gb = new GridBuilder();
  //gb->findAxesAndOrigin(theAtoms);
  //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:	1244
Committed:	Fri Jun 4 16:21:23 2004 UTC (20 years, 3 months ago) by gezelter
File size:	5854 byte(s)
Log Message:	Migrated vdw files from OOPSE
#	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
8			#define MK_STR(s) # s
9			#define STR_DEFINE(t, s) t = MK_STR(s)
10			#define CHARMM 1
11			#define AMBER 2
12			#define LJ 3
13			#define GAFF 4
14			#define OPLS 5
15
16			int count_tokens(char line, char delimiters);
17			using namespace std;
18
19			class Atype{
20			public:
21			Atype() {
22			mass = 0.0;
23			rpar = 0.0;
24			eps = 0.0;
25			}
26
27			void setMass(double m) {mass = m;}
28			void setRpar(double rp) {rpar = rp;}
29			void setEps(double e) {eps = e;}
30			void setType(char* t) {strcpy(type, t);}
31			double getMass() {return mass;}
32			double getRpar() {return rpar;}
33			double getEps() {return eps;}
34			char *getType() {return type;}
35
36			private:
37			char type[100];
38			double mass;
39			double rpar;
40			double eps;
41			};
42
43			int main(int argc, char* argv[]){
44
45			gengetopt_args_info args_info;
46
47			vector<Atype*> vdwAtypes;
48			vector<Atype*>::iterator i;
49			Atype* at;
50			vector<VDWAtom*> theAtoms;
51			vector<VDWAtom*>::iterator j;
52			VDWAtom* atom;
53
54			double mass, rpar, eps;
55			string fileName;
56			char vdwFileName[2002];
57			char structureFileName[2002];
58			char temp[200];
59			char readLine[500];
60			FILE vdwFile, structureFile;
61	gezelter	1244	char* ffPath_env = "VDW_PATH";
62	gezelter	1240	char* ffPath;
63			char* eof_test;
64			char* foo;
65			char* myType;
66			char* vType;
67			int lineNum;
68			int nTokens;
69			int FF;
70			short int gotMatch;
71
72			//parse the command line options
73			if (cmdline_parser (argc, argv, &args_info) != 0)
74			exit(1) ;
75
76			if (args_info.input_given){
77			fileName = args_info.input_arg;
78			}
79			else{
80			std::cerr << "Does not have input file name" << endl;
81			exit(1);
82			}
83
84			if (args_info.charmm_given) {
85			FF=CHARMM;
86			strcpy(vdwFileName, "charmm27.vdw");
87			}
88
89			if (args_info.amber_given) {
90			FF=AMBER;
91			strcpy(vdwFileName, "amber99.vdw");
92			}
93
94			if (args_info.lj_given) {
95			FF=LJ;
96			strcpy(vdwFileName, "LJ.vdw");
97			}
98
99			if (args_info.gaff_given) {
100			FF=GAFF;
101			strcpy(vdwFileName, "gaff.vdw");
102			}
103
104			if (args_info.opls_given) {
105			FF=OPLS;
106			strcpy(vdwFileName, "oplsaal.vdw");
107			}
108
109			vdwFile = fopen( vdwFileName, "r" );
110
111			if( vdwFile == NULL ){
112
113			// next see if the force path enviorment variable is set
114
115			ffPath = getenv( ffPath_env );
116			if( ffPath == NULL ) {
117			STR_DEFINE(ffPath, FRC_PATH );
118			}
119
120			strcpy( temp, ffPath );
121			strcat( temp, "/" );
122			strcat( temp, vdwFileName );
123			strcpy( vdwFileName, temp );
124
125			vdwFile = fopen( vdwFileName, "r" );
126
127			if( vdwFile == NULL ){
128
129			printf( "Error opening the vanDerWaals parameter file: %s\n"
130	gezelter	1244	"Have you tried setting the VDW_PARAM_DIR environment "
131	gezelter	1240	"variable?\n",
132			vdwFileName );
133			exit(-1);
134			}
135			printf( "VDW file %s opened sucessfully.\n", vdwFileName );
136			lineNum = 0;
137
138			eof_test = fgets( readLine, sizeof(readLine), vdwFile );
139			lineNum++;
140
141			if( eof_test == NULL ){
142			printf("Error in reading Atoms from force file at line %d.\n",
143			lineNum );
144			exit(-1);
145			}
146
147			while( eof_test != NULL ){
148			// toss comment lines
149			if( readLine[0] != '!' && readLine[0] != '#' ){
150
151			nTokens = count_tokens(readLine, " ,;\t");
152			if (nTokens < 4) {
153			printf("Not enough tokens on line %d.\n", lineNum);
154			exit(-1);
155			}
156
157			at = new Atype();
158			foo = strtok(readLine, " ,;\t");
159			at->setType(foo);
160			foo = strtok(NULL, " ,;\t");
161			mass = atof(foo);
162			at->setMass(mass);
163			foo = strtok(NULL, " ,;\t");
164			rpar = atof(foo);
165			at->setRpar(rpar);
166			foo = strtok(NULL, " ,;\t");
167			eps = atof(foo);
168			at->setEps(eps);
169			vdwAtypes.push_back(at);
170			}
171			eof_test = fgets( readLine, sizeof(readLine), vdwFile );
172			lineNum++;
173			}
174
175			fclose( vdwFile );
176			}
177			printf("%d Atom Types read from VDW file\n", vdwAtypes.size());
178
179			// Now, open and parse the input file!
180
181			strcpy(structureFileName, fileName.c_str() );
182
183			PDBReader* PDBread = new PDBReader();
184			PDBread->setPDBfile(structureFileName);
185			theAtoms = PDBread->getAtomList();
186			printf("Found %d atoms\n", theAtoms.size());
187
188			for( j = theAtoms.begin(); j != theAtoms.end(); ++j){
189			atom = *j;
190			myType = atom->getType();
191			gotMatch = 0;
192
193			for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){
194			at = *i;
195			vType = at->getType();
196
197			if (!strcasecmp(myType, vType)) {
198			atom->setMass(at->getMass());
199			atom->setRpar(at->getRpar());
200			atom->setEps(at->getEps());
201			gotMatch = 1;
202			}
203			}
204			if (!gotMatch) {
205			printf("No matches found for %s, ", myType);
206			myType = atom->getBase();
207			printf("trying with BaseType %s\n", myType);
208			for( i = vdwAtypes.begin(); i != vdwAtypes.end(); ++i){
209			at = *i;
210			vType = at->getType();
211			if (!strcasecmp(myType, vType)) {
212			atom->setMass(at->getMass());
213			atom->setRpar(at->getRpar());
214			atom->setEps(at->getEps());
215			gotMatch = 1;
216			}
217			}
218			}
219
220			if (!gotMatch) {
221			printf("No matches found with BaseType!\n");
222			}
223			}
224
225			//GridBuilder gb = new GridBuilder();
226			//gb->findAxesAndOrigin(theAtoms);
227			//gb->launchProbe(FF, sigmaGrid, sGrid, epsGrid);
228
229
230			}
231
232			int count_tokens(char line, char delimiters) {
233			/* PURPOSE: RETURN A COUNT OF THE NUMBER OF TOKENS ON THE LINE. */
234
235			char working_line; / WORKING COPY OF LINE. */
236			int ntokens; /* NUMBER OF TOKENS FOUND IN LINE. */
237			char strtok_ptr; / POINTER FOR STRTOK. */
238
239			strtok_ptr= working_line= strdup(line);
240
241			ntokens=0;
242			while (strtok(strtok_ptr,delimiters)!=NULL)
243			{
244			ntokens++;
245			strtok_ptr=NULL;
246			}
247
248			free(working_line);
249			return(ntokens);
250			}