BiopTools

BiopTools - A set of command line tools for manipulating protein structure

Description

BiopTools is a set of command line tools written in C and making use of the BiopLib library for manipulation of protein structure and sequence.

Mostly the tools are for manipulating protein structure and many of the tools act as filters taking a PDB file as input and generating a PDB file as output. The names of all programs that take only a single PDB as input start with 'pdb'.

Many of these programs have previously been distributed separately (sometimes under different names).

Available programs range from rotating structures through renumbering, calculating torsion angles and extracting individual chains through to calculation of solvent accessibility. Since the BiopLib PDB parser allows reading of PDBML (XML) files as well as standard PDB files, this provides the first software of calculation of solvent accessibility on PDBML files.

Licence

BiopLib is licenced under the Gnu Public Licence Version 3 or later. However dual licencing is also possible - please contact me if you would like to use BiopLib or any of its components in a closed source application.

Download

BiopLib is freely available from GitHub.

Github Download

Clone from GitHub with the command:

git clone git@github.com:ACRMGroup/bioptools.git

Documentation

All BiopTools take a parameter of '-h' on the command line to give help. Code is documented using doxygen format.

bioptools

Tools making use of BiopLib

See INSTALL.md for installation instructions!

chaincontacts

Calculates contacts between chains at the atom and residue level. You

can get all contacts or contacts between specified chains.

naccess2bval

Rewrites the output from naccess solvent accessibility as a standard PDB format file with accessibility in the B-val column and radius in the

occupancy column.

pdb2ms

Converts a PDB file to input for the Connoly MS program

pdb2pdbml

Converts a PDB file to PDBML format

pdbml2pdb

Converts a PDBML file to PDB format

pdb2pir

Extracts a PIR sequence file from a PDB file.

pdb2xyz

Convert PDB format to GROMOS XYZ. N.B. Does NOT correct atom order.

pdbatomcount

Counts the number of atoms within the specified radius of each atom in

a PDB structure.

pdbatoms

Extracts only the coordinates (i.e. ATOM and HETATM records) from a

PDB file, discarding the header and footer records

pdbatomsel

Selects specfied atom types from a PDB file. Assumes C-alpha if no atoms

are specified.

pdbavbr

Calculates means and standard deviations for B-values per residue.

pdbcalcrms

Calculates an RMS between 2 PDB files. No fitting is performed.

pdbcentralres

Identifies the residue closest to the centroid of a protein.

pdbchain

Splits a PDB file into chains using distance criteria.

pdbcheckforres

Checks whether a specified residue exists in a PDB file.

pdbconect

Builds CONECT records for a PDB file. Deletes existing records.

pdbcount

Counts chains, residues & atoms in a PDB file.

pdbcter

Rename C-terminal oxygens in standard style and generate second one if required.

pdbdummystrip

Removes atoms from a PDB file which have NULL coordinates (i.e.

x = y = z = 9999.0)

pdbfindresrange

Takes a PDB file as input and given a key residue and a number of residues will return the residue identifiers for residues this number

of positions before and width after the key residue.

pdbflip

pdbflip is a rather crude and simple program for correcting the atom

naming of equivalent atoms about freely rotable bonds.

pdbgetchain

pdbgetchain reads a PDB file and write out only those chains specified

on the command line.

pdbgetresidues

Takes a list of residue specifications and extracts just those residues

from a PDB file

pdbgetzone

Extracts a specified zone from a PDB file

pdbhadd

Add hydrogens to a PDB file.

pdbheader

Prints the key header information from a PDB (title; molecule and

species for each chain, etc.)

pdbhetstrip

Removes het atoms from a PDB file.

pdbhstrip

Removes hydrogens from a PDB file.

pdblistss

Calculates and lists the disulphides in a PDB file.

pdbmakepatch

Generates a patch around a specified residue.

pdborder

Correct atom order of a PDB file.

pdborigin

Moves a set of PDB coordinates to the origin.

pdbpatchbval

Takes a patch file containing residue specifications and values one to a line and patches the B-value (or occupancy) for that

residue with the specified values.

pdbpatchnumbering

Patches the numbering of a PDB file from a patch file containing

residue numbers.

pdbrenum

Renumber a PDB file

pdbrotate

Rotates a PDB file

pdbsecstr

Calculate secondary structure for a PDB file

pdbselect

Allows the extraction of different occupancies and different models

from a PDB file

pdbsolv

Performs solvent accessibility calculations according to the method of

Lee and Richards.

pdbsphere

pdbsphere identifies residues within a specified radius of a specified

residue.

pdbsplitchains

Split a PDB file into separate files for each chain

pdbsumbval

Sums the b-values over each residue and places the summed values in the

b-value column. Can also calculate averages.

pdbsymm

Applies non-cystollographic symmetry operations specified in REMARK 350 records to a PDB file. Note that this program has certain limitations.

Run pdbsymm -h for details.

pdbtorsions

Generates a set of backbone torsions from a PDB file.

pdbtranslate

Translates a PDB file

scorecons

A program similar to (and which predates) Will Valdar's scorecons program

for scoring conservation in a sequence alignment.

setpdbnumbering

Applies a standard numbering scheme to a set of PDB files.


OMICtools