/*

* University of Illinois Open Source License

* Copyright 2009, 2011, 2012 Luthey-Schulten Group,

* All rights reserved.

*

* Developed by: Luthey-Schulten Group

* University of Illinois at Urbana-Champaign

* http://www.scs.uiuc.edu/~schulten

*

* Permission is hereby granted, free of charge, to any person obtaining a copy of

* this software and associated documentation files (the Software), to deal with

* the Software without restriction, including without limitation the rights to

* use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies

* of the Software, and to permit persons to whom the Software is furnished to

* do so, subject to the following conditions:

*

* - Redistributions of source code must retain the above copyright notice,

* this list of conditions and the following disclaimers.

*

* - Redistributions in binary form must reproduce the above copyright notice,

* this list of conditions and the following disclaimers in the documentation

* and/or other materials provided with the distribution.

*

* - Neither the names of the Luthey-Schulten Group, University of Illinois at

* Urbana-Champaign, nor the names of its contributors may be used to endorse or

* promote products derived from this Software without specific prior written

* permission.

*

* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR

* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,

* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL

* THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR

* OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,

* ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR

* OTHER DEALINGS WITH THE SOFTWARE.

*

* Author(s): Anurag Sethi, John Eargle

* Modifications by: Shantao Li, Declan Clarke (lab of Mark Gerstein,

* Yale University, 2015)

*/

#include <stdio.h>

#include <stdlib.h>

#include <string.h>

#include <math.h>

#include "pdbFile.h"

int findNumberOfAtomsPdbFile(FILE *pdbInput)

{

char line[10000];

int posn;

int nAtoms = 0;

printf("-> finding number of atoms in pdb file\n");

while (fgets(line, 10000, pdbInput) != NULL)

{

posn = strncmp(line, "ATOM", 4);

if (posn == 0) {

nAtoms++;

//printf("line %s", line);

//printf("posn %d nAtoms %d\n", posn, nAtoms);

}

}

printf("<- finding number of atoms in pdb file\n");

return nAtoms;

}

void readPdbFile(pdbFile *macromolecule, FILE *pdbInput)

{

char line[10000];

int i = 0;

int posn;

char resID[5], x[8], y[8], z[8], O[5], beta[5];

printf("-> reading macromolecule pdb\n");

//Note: Reading information from lines that start with ATOM alone (macromolecule)

while (fgets(line, 10000, pdbInput) != NULL)

{

posn = strncmp(line, "ATOM", 4);

if (posn == 0) {

strncpy(macromolecule->atom[i].name, line+13, 3);

macromolecule->atom[i].name[3] = '\0';

strncpy(macromolecule->atom[i].resName, line+17, 3);

macromolecule->atom[i].resName[3] = '\0'; // was not commented out before

strncpy(resID, line+22, 4);

resID[4] = '\0';

macromolecule->atom[i].resID = atoi(resID);

resID[4] = '\0';

macromolecule->atom[i].resID = atoi(resID);

/// Newly-introduced (dc)

strncpy(macromolecule->atom[i].chain, line+21, 1);

macromolecule->atom[i].chain[1] = '\0';

strncpy(x, line+30, 8); // line was originally: strncpy(x, line+31, 7); ########################################################

x[7] = '\0';

macromolecule->atom[i].x = atof(x);

strncpy(y, line+38, 8); // line was originally: strncpy(y, line+39, 7); ########################################################

y[7] = '\0';

macromolecule->atom[i].y = atof(y);

strncpy(z, line+46, 8); // line was originally: strncpy(z, line+47, 7); #######################################################

z[7] = '\0';

macromolecule->atom[i].z = atof(z);

strncpy(O, line+56, 4);

O[4] = '\0';

macromolecule->atom[i].occupancy = atof(O);

strncpy(beta, line+62, 4);

beta[4] = '\0';

macromolecule->atom[i].beta = atof(beta);

strncpy(macromolecule->atom[i].element, line+77, 2);

macromolecule->atom[i].element[2] = '\0';

//printf("line %s%s %s %d %f %f %f %f %f %s \n chain: |%s| \n\n", line, macromolecule->atom[i].name, macromolecule->atom[i].resName, macromolecule->atom[i].resID, macromolecule->atom[i].x, macromolecule->atom[i].y, macromolecule->atom[i].z, macromolecule->atom[i].occupancy, macromolecule->atom[i].beta, macromolecule->atom[i].element, macromolecule->atom[i].chain);

i++;

}

//printf("i %d\n", i);

}

printf("<- reading macromolecule pdb\n");

return;

}