libs/ck-libs/metis/GKlib/pdb.c File Reference

Functions for parsing pdb files. More...

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Functions
char	gk_threetoone (char *res)
	Converts three-letter amino acid codes to one-leter codes.
void	gk_freepdbf (pdbf *p)
	Frees the memory of a pdbf structure.
pdbf *	gk_readpdbfile (char *fname)
	Reads a pdb file into a pdbf structure.
void	gk_writefastafrompdb (pdbf *pb, char *fname)
	Writes the sequence of residues from a pdb file.
void	gk_writecentersofmass (pdbf *p, char *fname)
	Writes all centers of mass in pdb-format to file fname.
void	gk_writefullatom (pdbf *p, char *fname)
	Writes all atoms in p in pdb-format to file fname.
void	gk_writebackbone (pdbf *p, char *fname)
	Writes out all the backbone atoms of a structure in pdb format.
void	gk_writealphacarbons (pdbf *p, char *fname)
	Writes out all the alpha carbon atoms of a structure.
void	gk_showcorruption (pdbf *p)
	Decodes the corruption bitswitch and prints any problems.

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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.

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Function Documentation

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.

Referenced by gk_readpdbfile().

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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.

References pdbf::atoms, pdbf::bbs, pdbf::cas, pdbf::cm, gk_free(), atom::name, pdbf::natoms, pdbf::nresidues, atom::resname, pdbf::resSeq, and pdbf::threeresSeq.

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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.

References atom::altLoc, pdbf::atoms, pdbf::bbs, pdbf::cas, atom::chainid, pdbf::cm, pdbf::corruption, atom::element, gk_fopen(), gk_malloc(), gk_strdup(), gk_threetoone(), atom::icode, atom::name, center_of_mass::name, pdbf::natoms, pdbf::nbbs, pdbf::ncas, pdbf::nresidues, atom::opcy, atom::resname, pdbf::resSeq, atom::rserial, atom::serial, pdbf::threeresSeq, atom::tmpt, atom::x, center_of_mass::x, x, atom::y, center_of_mass::y, atom::z, and center_of_mass::z.

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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.

References gk_fopen(), pdbf::nresidues, and pdbf::resSeq.

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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.

References pdbf::cm, gk_fopen(), pdbf::nresidues, pdbf::threeresSeq, center_of_mass::x, center_of_mass::y, and center_of_mass::z.

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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.

References atom::altLoc, pdbf::atoms, atom::chainid, gk_fopen(), atom::icode, atom::name, pdbf::natoms, atom::opcy, atom::resname, atom::rserial, atom::serial, atom::tmpt, atom::x, atom::y, and atom::z.

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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.

References atom::altLoc, pdbf::bbs, atom::chainid, gk_fopen(), atom::icode, atom::name, pdbf::nbbs, atom::opcy, atom::resname, atom::rserial, atom::serial, atom::tmpt, atom::x, atom::y, and atom::z.

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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.

References atom::altLoc, pdbf::cas, atom::chainid, gk_fopen(), atom::icode, atom::name, pdbf::ncas, atom::opcy, atom::resname, atom::rserial, atom::serial, atom::tmpt, atom::x, atom::y, and atom::z.

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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.

References pdbf::corruption.