Functions for parsing pdb files. More...

#include <GKlib.h>

Include dependency graph for pdb.c:

Functions
void	gk_freepdbf (pdbf *p)
	Frees the memory of a pdbf structure. More...

pdbf *	gk_readpdbfile (char *fname)
	Reads a pdb file into a pdbf structure. More...

void	gk_showcorruption (pdbf *p)
	Decodes the corruption bitswitch and prints any problems. More...

char	gk_threetoone (char *res)
	Converts three-letter amino acid codes to one-leter codes. More...

void	gk_writealphacarbons (pdbf p, char fname)
	Writes out all the alpha carbon atoms of a structure. More...

void	gk_writebackbone (pdbf p, char fname)
	Writes out all the backbone atoms of a structure in pdb format. More...

void	gk_writecentersofmass (pdbf p, char fname)
	Writes all centers of mass in pdb-format to file fname. More...

void	gk_writefastafrompdb (pdbf pb, char fname)
	Writes the sequence of residues from a pdb file. More...

void	gk_writefullatom (pdbf p, char fname)
	Writes all atoms in p in pdb-format to file fname. More...

Detailed Description

Functions for parsing pdb files.

Pdb reader (parser). Loads arrays of pointers for easy backbone access.

Date: Started 10/20/06

Author: Kevin

Version

Id: pdb.c 10711 2011-08-31 22:23:04Z karypis

Definition in file pdb.c.

Function Documentation

◆ gk_freepdbf()

void gk_freepdbf ( pdbf * p )

Frees the memory of a pdbf structure.

This function takes a pdbf pointer and frees all the memory below it.

Parameters

p	is the pdbf structure to be freed.

Definition at line 105 of file pdb.c.

◆ gk_readpdbfile()

pdbf* gk_readpdbfile ( char * fname )

Reads a pdb file into a pdbf structure.

This function allocates a pdbf structure and reads the file fname into that structure.

Parameters

fname is the file name to be read

Returns: A filled pdbf structure.

Definition at line 132 of file pdb.c.

◆ gk_showcorruption()

void gk_showcorruption ( pdbf * p )

Decodes the corruption bitswitch and prints any problems.

Due to the totally unreliable nature of the pdb format, reading a pdb file stores a corruption bitswitch, and this function decodes that switch and prints the result on stdout.

Parameters

p	is the pdb structure to write out.
fname	is the file name to be written.

Definition at line 435 of file pdb.c.

◆ gk_threetoone()

char gk_threetoone ( char * res )

Converts three-letter amino acid codes to one-leter codes.

This function takes a three letter * and converts it to a single

Parameters

res	is the three-letter code to be converted.

Returns: A representing the amino acid.

Definition at line 24 of file pdb.c.

◆ gk_writealphacarbons()

void gk_writealphacarbons	(	pdbf *	p,
		char *	fname
	)

Writes out all the alpha carbon atoms of a structure.

This function takes a pdbf structure p and writes only the alpha carbon atoms to a filename fname.

Parameters

p	is the pdb structure to write out.
fname	is the file name to be written.

Definition at line 413 of file pdb.c.

◆ gk_writebackbone()

void gk_writebackbone	(	pdbf *	p,
		char *	fname
	)

Writes out all the backbone atoms of a structure in pdb format.

This function takes a pdbf structure p and writes only the backbone atoms to a filename fname.

Parameters

p	is the pdb structure to write out.
fname	is the file name to be written.

Definition at line 392 of file pdb.c.

◆ gk_writecentersofmass()

void gk_writecentersofmass	(	pdbf *	p,
		char *	fname
	)

Writes all centers of mass in pdb-format to file fname.

This function takes a pdbf structure and writes out the calculated mass center information to file fname as though each one was a c-alpha.

Parameters

p	is the pdbf structure to write out
fname	is the file name to be written

Definition at line 350 of file pdb.c.

◆ gk_writefastafrompdb()

void gk_writefastafrompdb	(	pdbf *	pb,
		char *	fname
	)

Writes the sequence of residues from a pdb file.

This function takes a pdbf structure and a filename, and writes out the amino acid sequence according to the atomic coordinates. The output is in fasta format.

Parameters

p	is the pdbf structure with the sequence of interest
fname	is the file name to be written

Definition at line 326 of file pdb.c.

◆ gk_writefullatom()

void gk_writefullatom	(	pdbf *	p,
		char *	fname
	)

Writes all atoms in p in pdb-format to file fname.

This function takes a pdbf structure and writes out all the atom information to file fname.

Parameters

p	is the pdbf structure to write out
fname	is the file name to be written

Definition at line 371 of file pdb.c.