int main(int argc, char** argv) {
try {
RMF_ADD_INPUT_FILE("rmf");
RMF_ADD_OUTPUT_FILE("pdb");
RMF_ADD_FRAMES;
process_options(argc, argv);
RMF::FileConstHandle rh = RMF::open_rmf_file_read_only(input);
std::ostream* out;
std::ofstream fout;
if (!output.empty()) {
fout.open(output.c_str());
if (!fout) {
std::cerr << "Error opening file " << output << std::endl;
return 1;
}
out = &fout;
} else {
out = &std::cout;
}
RMF::decorator::IntermediateParticleFactory ipf(rh);
RMF::decorator::AtomFactory af(rh);
RMF::decorator::ChainFactory cf(rh);
RMF::decorator::ResidueFactory rf(rh);
RMF::NodeConstHandle rn = rh.get_root_node();
for (unsigned int input_frame = start_frame, output_frame = 0;
input_frame < rh.get_number_of_frames();
input_frame += step_frame, ++output_frame) {
rh.set_current_frame(RMF::FrameID(input_frame));
*out << (boost::format("MODEL%1$9d") % (output_frame + 1)) << std::endl;
write_atoms(*out, 0, rn, ipf, af, cf, rf);
*out << "ENDMDL" << output_frame + 1 << std::endl;
}
return 0;
}
catch (const std::exception& e) {
std::cerr << "Error: " << e.what() << std::endl;
}
}
int main()
{
char coordinate_input[BUFSIZ];
char ammp_output[BUFSIZ];
char dictionary[BUFSIZ];
char work[1000],keep[1000];
char atype[20],aname[20];
char *fgets();
float sigma,emin;
int ifile,i,imreading,ii,myres;
FILE *in1,*dict,*output,*fopen();
printf(" atom definition file:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
dictionary[ifile -i ] = work[ifile];
dictionary[ifile -i +1 ] = '\0';
}
/* now read in the atoms */
dict = fopen( dictionary, "r");
if( dict == NULL)
{ fprintf(stderr," sorry i can't open %s\n",dictionary); exit(0);}
inkinds = 0;
while ( fgets( work,256, dict) != NULL)
{
sscanf( work,"%s %f %f %f %f %f %f %f %f %f %f %f %f %f \n",
&kinds[inkinds].type[0],
&kinds[inkinds].r ,
&kinds[inkinds].theta ,
&sigma ,
&emin ,
&kinds[inkinds].Z ,
&kinds[inkinds].angle_inc,
&kinds[inkinds].X ,
&kinds[inkinds].jaa ,
&kinds[inkinds].mass ,
&kinds[inkinds].charge ,
&kinds[inkinds].V, &kinds[inkinds].U ,
&kinds[inkinds].hybrid
);
/* kinds[inkinds].theta *= 3.14159265/180.;
*/
sigma = sigma*sigma;
sigma = sigma*sigma*sigma;
/* kinds[inkinds].b = sqrt( 4.*emin*sigma*sigma);
kinds[inkinds].a = sqrt( 4.*emin*sigma);
*/
kinds[inkinds].b = sqrt( emin*sigma*sigma);
kinds[inkinds].a = sqrt( 2*emin*sigma);
inkinds ++;
if( inkinds > MAX_ATOM)
{ fprintf( stderr," too many kinds of atoms in dictionary\n");
exit(0); }
}
fclose( dict);
printf(" Residue dictionary directory:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
dictionary[ifile -i ] = work[ifile];
dictionary[ifile -i +1 ] = '\0';
}
ifile = ifile -i ;
if( ifile == 0 ){ dictionary[ifile++] = '.';
dictionary[ifile] = '\0'; }
if( dictionary[ifile-1] != '/')
{ ifile++; dictionary[ifile-1] = '/'; dictionary[ifile] = '\0';}
printf(" atom input coordinate file:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
coordinate_input[ifile -i ] = work[ifile];
coordinate_input[ifile -i +1 ] = '\0';
}
printf(" AMMP file:>\n");
/* strip out the file name and put it in the right place for opening */
fgets( work,80,stdin );
for(i= 0; i<80; i++)
if( work[i] != ' ') break;
for( ifile = i; ifile < 80 ; ifile++)
{
if( work[ifile] == ' ' ) break;
if( work[ifile] == '\0' ) break;
if( work[ifile] == '\n' ) break;
ammp_output[ifile -i ] = work[ifile];
ammp_output[ifile -i +1 ] = '\0';
}
in1 = fopen( coordinate_input, "r");
output = fopen( ammp_output, "w");
if (in1 == NULL) goto NO_IN1_FILE;
/* read in the first residue
* stuff is read into work when the residue number changes then
* work is copied into keep, so the first atom of any residue is
* going to be in the keep buffer. to initialize we read the
* first atom into keep
*/
keep[0] = '\0';
while( !(keep[0] == 'A' && keep[1] == 'T' && keep[2] == 'O' && keep[3] == 'M')
&& !(keep[0] == 'H'&& keep[1] == 'E'
&& keep[1] == 'T'&& keep[1] == 'A'&& keep[1] == 'T' ) )
{ if( fgets(keep,90,in1) == NULL) {
fprintf(stderr," no atoms in input file ? \n") ;
NO_IN1_FILE:
printf(" enter the dictionary name >\n");
fgets( keep, 90, stdin);
i=0; while( (keep[i] == ' ' || keep[i] == '\t') && keep[i] != '\0') i++;
for( imreading = 0; imreading < 3; imreading++)
{ aname[imreading] = toupper( keep[i + imreading] ); }
aname[3] = '\0';
goto NO_ATOMS;
}
}
imreading = 0;
while( imreading == 0)
{/* begining of imreading loop */
inres = 0;
for(i=0; i< MAX_RES; i++)
{ mykind[i] = -1;
defined[i] = -1;
name[i][0] = '\0';
x[i] = 0.;
y[i] = 0.;
z[i] = 0.;
}
sscanf( &keep[22],"%d",&myres);
sscanf(&keep[29],"%f %f %f",&x[inres],&y[inres],&z[inres]);
sscanf(&keep[11],"%s",&atype[0]);
sscanf(&keep[17],"%s",&aname[0]);
serial[inres] = 100*myres + inres;
ii = 0;
for( i=0; i< 3; i++ )
{
if( aname[i] == '\0') break;
name[inres][ii++] = (char)tolower(aname[i]);
}
name[inres][ii++] = '.';
for(i=0; i< 4; i++)
{
if( atype[i] == '\0' ) break;
name[inres][ii++] = (char)tolower(atype[i]);
}
name[inres][ii] = '\0';
a[inres] = 0.; b[inres] = 0.; q[inres] = 0.; mass[inres] = 1.;
defined[inres] = 0;
for( inres = 1; inres < MAX_RES; inres ++)
{ /* start of reading an atom loop */
if( fgets( work,90,in1) == NULL) {
imreading = 1; break; }
if( work[0] != 'A' && work[0] != 'H') {
imreading = 1; break; }
/*
printf("%s\n",work);
printf("%d\n",inres);
*/
sscanf( &work[22],"%d",&ii);
if( ii != myres )
{ii = 0; while( work[ii] != '\0'){ keep[ii] = work[ii] ; ii++;}
/* inres += 1; */
break;
}
sscanf(&work[29],"%f %f %f",&x[inres],&y[inres],&z[inres]);
sscanf(&work[11],"%s",&atype[0]);
sscanf(&work[17],"%s",&aname[0]);
serial[inres] = 100*myres + inres;
ii = 0;
for( i=0; i< 3; i++ )
{
if( aname[i] == '\0') break;
name[inres][ii++] = (char)tolower(aname[i]);
}
name[inres][ii++] = '.';
for(i=0; i< 4; i++)
{
if( atype[i] == '\0' ) break;
name[inres][ii++] = (char)tolower(atype[i]);
}
name[inres][ii] = '\0';
a[inres] = 0.; b[inres] = 0.; q[inres] = 0.; mass[inres] = 1.;
defined[inres] = 0;
}/* end of reading an atom loop */
/*
for( i=0; i< inres; i++)
printf(">%s<\n",&name[i][0]);
*/
/* if here then all of the atoms in the residue are read in */
/* now we have to open and read the dictionary file
* there could be atoms in either the residue or dictionary which
* are not there i.e. oxt for a residue or a missing H */
/* prepare the filename */
NO_ATOMS:
i = 0;
while(dictionary[i] != '\0') { work[i] = dictionary[i]; i++;}
ii = 0;
while(aname[ii] != '\0') {work[i] = aname[ii]; i++; ii++;}
work[i++] = '\0';
dict = fopen(work,"r");
if( dict == NULL ){
fprintf(stderr," dictionary %s not found \n", work);
write_atoms(output);
goto DONE;
}
/* read the number of atoms */
if(fgets( work,80,dict)==NULL)
{ fprintf(stderr,"BAD DICTIONARY %s\n",aname); exit(0);}
sscanf(work,"%d",&natoms);
read_atoms( dict,natoms );
write_atoms(output);
if(fgets( work,80,dict)==NULL)
{ fprintf(stderr,"BAD DICTIONARY %s\n",aname); exit(0);}
sscanf(work,"%d",&nbond);
do_bonds( dict,nbond,output);
inbondlist = nbond;
nangle = 0;
if(fgets( work,80,dict)!=NULL)
sscanf(work,"%d",&nangle);
do_angle(dict,nangle,output);
nhybrid = 0;
if(fgets( work,80,dict)!=NULL)
sscanf(work,"%d",&nhybrid);
do_hybrid(dict,nhybrid,output);
ntorsion = 0;
if(fgets( work,80,dict)!=NULL)
sscanf(work,"%d",&ntorsion);
do_torsion(dict,ntorsion,output);
DONE:
fclose( dict );
}/* end of imreading loop */
}/* end of module main */
