BiopTools - A set of command line tools for manipulating protein structure
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.
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.
BiopLib is freely available from GitHub.
You can now download pre-compiled executables of BiopTools 1.10 for Windows11 (thanks to Chu'nan Liu for compiling this!). You will need to use the Windows command line to run these programs!
Clone from GitHub with the command:
git clone email@example.com:ACRMGroup/bioptools.git
All BiopTools take a parameter of '-h' on the command line to give help. Code is documented using doxygen format.
Tools making use of BiopLib
See INSTALL.md for installation instructions!
Calculates contacts between chains at the atom and residue level. You
can get all contacts or contacts between specified chains.
Rewrites the output from naccess solvent accessibility as a standard PDB format file with accessibility in the B-val column and radius in the
Converts a PDB file to input for the Connoly MS program
Converts a PDB file to PDBML format
Converts a PDBML file to PDB format
Extracts a PIR sequence file from a PDB file.
Convert PDB format to GROMOS XYZ. N.B. Does NOT correct atom order.
Counts the number of atoms within the specified radius of each atom in
a PDB structure.
Extracts only the coordinates (i.e. ATOM and HETATM records) from a
PDB file, discarding the header and footer records
Selects specfied atom types from a PDB file. Assumes C-alpha if no atoms
Calculates means and standard deviations for B-values per residue.
Calculates an RMS between 2 PDB files. No fitting is performed.
Identifies the residue closest to the centroid of a protein.
Splits a PDB file into chains using distance criteria.
Checks whether a specified residue exists in a PDB file.
Builds CONECT records for a PDB file. Deletes existing records.
Counts chains, residues & atoms in a PDB file.
Rename C-terminal oxygens in standard style and generate second one if required.
Removes atoms from a PDB file which have NULL coordinates (i.e.
x = y = z = 9999.0)
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 is a rather crude and simple program for correcting the atom
naming of equivalent atoms about freely rotable bonds.
pdbgetchain reads a PDB file and write out only those chains specified
on the command line.
Takes a list of residue specifications and extracts just those residues
from a PDB file
Extracts a specified zone from a PDB file
Add hydrogens to a PDB file.
Prints the key header information from a PDB (title; molecule and
species for each chain, etc.)
Removes het atoms from a PDB file.
Removes hydrogens from a PDB file.
Calculates and lists the disulphides in a PDB file.
Generates a patch around a specified residue.
Correct atom order of a PDB file.
Moves a set of PDB coordinates to the origin.
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.
Patches the numbering of a PDB file from a patch file containing
Renumber a PDB file
Rotates a PDB file
Calculate secondary structure for a PDB file
Allows the extraction of different occupancies and different models
from a PDB file
Performs solvent accessibility calculations according to the method of
Lee and Richards.
pdbsphere identifies residues within a specified radius of a specified
Split a PDB file into separate files for each chain
Sums the b-values over each residue and places the summed values in the
b-value column. Can also calculate averages.
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.
Generates a set of backbone torsions from a PDB file.
Translates a PDB file
A program similar to (and which predates) Will Valdar's scorecons program
for scoring conservation in a sequence alignment.
Applies a standard numbering scheme to a set of PDB files.