Functions
pdb.c File Reference

Functions for parsing pdb files. More...

#include <GKlib.h>
Include dependency graph for pdb.c:

Go to the source code of this file.

Functions

void gk_freepdbf (pdbf *p)
 Frees the memory of a pdbf structure. More...
 
pdbfgk_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
pis 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
fnameis 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
pis the pdb structure to write out.
fnameis 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
resis 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
pis the pdb structure to write out.
fnameis 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
pis the pdb structure to write out.
fnameis 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
pis the pdbf structure to write out
fnameis 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
pis the pdbf structure with the sequence of interest
fnameis 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
pis the pdbf structure to write out
fnameis the file name to be written

Definition at line 371 of file pdb.c.



gtsam
Author(s):
autogenerated on Tue Jul 4 2023 02:40:51