writepdb.c File Reference

#include "../headers/writepdb.h"

Go to the source code of this file.

Functions
void	write_pdb_atom_line (FILE *f, const char rec_name[], int id, const char atom_name[], char alt_loc, const char res_name[], const char chain[], int res_id, const char insert, float x, float y, float z, float occ, float bfactor, const char *symbol, int charge)
void	write_pqr_atom_line (FILE *f, const char *rec_name, int id, const char *atom_name, char alt_loc, const char *res_name, const char *chain, int res_id, const char insert, float x, float y, float z, float charge, float radius)

---

Function Documentation

void write_pdb_atom_line	(	FILE *	f,
		const char	rec_name[],
		int	id,
		const char	atom_name[],
		char	alt_loc,
		const char	res_name[],
		const char	chain[],
		int	res_id,
		const char	insert,
		float	x,
		float	y,
		float	z,
		float	occ,
		float	bfactor,
		const char *	symbol,
		int	charge
	)

## FUNCTION: write_pdb_atom_line

## SPECIFICATION: Write an atom in the following pdb format 2.3.

COLUMNS DATA TYPE FIELD DEFINITION

1 - 6 Record name "ATOM " 7 - 11 Integer serial Atom serial number. 13 - 16 Atom name Atom name. 17 Character altLoc Alternate location indicator. 18 - 20 Residue name resName Residue name. 22 Character chainID Chain identifier. 23 - 26 Integer resSeq Residue sequence number. 27 AChar iCode Code for insertion of residues. 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms 55 - 60 Real(6.2) occupancy Occupancy. 61 - 66 Real(6.2) tempFactor Temperature factor. 77 - 78 LString(2) element Element symbol, right-justified. 79 - 80 LString(2) charge Charge on the atom.

## PARAMETRES:

## RETURN:

Definition at line 93 of file writepdb.c.

Referenced by write_first_bfactor_density(), write_md_pocket_atoms(), write_pdb_atoms(), write_pdb_vert(), write_pocket_pdb(), and write_pocket_pdb_DB().

{
        /* Example of pdb record: */
        /* Position:          1         2         3         4         5         6 */
        /* Position: 123456789012345678901234567890123456789012345678901234567890 */
        /* Record:   ATOM    145  N   VAL A  25      32.433  16.336  57.540  1.00 */
        
        /* Position: 6         7         8 */
        /* Position: 012345678901234567890 */
        /* Record:   0 11.92           N   */

        int status = 0 ;
        char id_buf[6] = "*****",
                 res_id_buf[5] = "****",
                 charge_buf[3] = "  ";
        
        if (id < 100000) sprintf(id_buf, "%5d", id);
        else sprintf(id_buf, "%05x", id);

        if (res_id < 10000) sprintf(res_id_buf, "%4d", res_id);
        else if (res_id < 65536) sprintf(res_id_buf, "%04x", res_id);
        else sprintf(res_id_buf, "****");

        alt_loc = (alt_loc == '\0')? ' ': alt_loc;

        if(charge == -1) sprintf(charge_buf, "  ") ;
        else sprintf(charge_buf, "%2d", charge) ;

        status = fprintf(f, "%-6s%5s %4s%c%-4s%c%4s%c   %8.3f%8.3f%8.3f%6.2f%6.2f          %2s%2s\n",
                                                 rec_name, id_buf, atom_name, alt_loc, res_name, chain[0], 
                                                 res_id_buf, insert, x, y, z, occ, bfactor, symbol, charge_buf);
        
}

void write_pqr_atom_line	(	FILE *	f,
		const char *	rec_name,
		int	id,
		const char *	atom_name,
		char	alt_loc,
		const char *	res_name,
		const char *	chain,
		int	res_id,
		const char	insert,
		float	x,
		float	y,
		float	z,
		float	charge,
		float	radius
	)

## FUNCTION: write_pqr_atom_line

## SPECIFICATION: Write an atom in pqr format.

COLUMNS DATA TYPE FIELD DEFINITION

1 - 6 Record name "ATOM " 7 - 11 Integer serial Atom serial number. 13 - 16 Atom name Atom name. 17 Character altLoc Alternate location indicator. 18 - 20 Residue name resName Residue name. 22 Character chainID Chain identifier. 23 - 26 Integer resSeq Residue sequence number. 27 AChar iCode Code for insertion of residues. 31 - 38 Real(8.3) x Orthogonal coordinates for X in Angstroms 39 - 46 Real(8.3) y Orthogonal coordinates for Y in Angstroms 47 - 54 Real(8.3) z Orthogonal coordinates for Z in Angstroms charge vdw radius

## PARAMETRES:

## RETURN:

Definition at line 162 of file writepdb.c.

Referenced by write_pqr_vert().

{
        /* Example of pdb record: */
        /* Position:          1         2         3         4         5         6 */
        /* Position: 123456789012345678901234567890123456789012345678901234567890 */
        /* Record:   ATOM    145  N   VAL A  25      32.433  16.336  57.540  1.00 */
        
        /* Position: 6         7         8 */
        /* Position: 012345678901234567890 */
        /* Record:   0 11.92           N   */
        
        int status ;
        char id_buf[7],
                 res_id_buf[6];
/*               charge_buf[3] ; */
        
        if (id < 100000) sprintf(id_buf, "%5d", id);
        else sprintf(id_buf, "%05x", id);

        if (res_id < 10000) sprintf(res_id_buf, "%4d", res_id);
        else if (res_id < 65536) sprintf(res_id_buf, "%04x", res_id);
        
        alt_loc = (alt_loc == '\0')? ' ': alt_loc;
        
/*      if(charge == -1) { 
                charge_buf[0] = charge_buf[1] = ' ' ;
                charge_buf[2] = '\0' ;
        }
        else sprintf(charge_buf, "%2d", charge) ;
*/      
        status = fprintf(f, "%-6s%5s %4s%c%-4s%c%4s%c   %8.3f%8.3f%8.3f  %6.2f   %6.2f\n",
                                                 rec_name, id_buf, atom_name, alt_loc, res_name, chain[0], 
                                                 res_id_buf, insert, x, y, z, charge,radius) ;
}