Tools making use of BiopLib
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README.md

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.

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.