Bioplib
Protein Structure C Library
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Bioplib

Bioplib - a high quality programming library for protein bioinformatics

Author
Dr. Andrew C.R. Martin with additions by Dr. Craig T. Porter

Bioplib is a programming library, written in the C programming language, for handling bioinformatics data – primarily protein structures, but also sequence data.

Click the 'Related Pages' link above for information on installation and detailed listings of what the library contains

The library has equivalents for other programming languages such as Python (BioPython) and Perl (BioPerl) and another C library and tool-set (EMBOSS) is also available. However, the focus of all these other libraries is on protein and DNA sequence rather than structure. Conversely, Bioplib is a very comprehensive library for handling protein structure, with some support for protein and DNA sequences. The fact that the code is implemented in C means that it is ideal for more complex and CPU-intensive tasks since C (unlike Perl and Python) is a compiled language.

Some of the most significant work in Bioplib includes:

The Bioplib library currently consists of approximately 47,700 lines of C-code including comments, or 31,000 lines excluding comments.

Functions exist for:

Include files

Data Structures

Handling Stucture Data

Handling Sequence Data

Utility Functions

Example of usage

#include "bioplib/pdb.h"
#include "bioplib/macros.h"
WHOLEPDB *wpdb = NULL;
PDB *p = NULL;
if((fp_in = fopen("input_file.pdb","r"))!=NULL)
{
wpdb = blReadWholePDB(fp_in);
close(fp_in);
if((wpdb != NULL) && (wpdb->pdb != NULL))
{
for(p=wpdb->pdb; p != NULL; NEXT(p))
{
_do_something_here_
}
if((fp_out = fopen("output_file.pdb","w"))!=NULL)
{
blWriteWholePDB(fp_out, wpdb);
fclose(fp_out);
}
// --- else handle error ---
}
// --- else handle error ---
}
// --- else handle error ---