ContactExtractor 1.0.0

Contact Extractor from PDB/mmCIF coordinate files

Contact Extractor (ContExt), ver. 1.0 (May 2025).

Installation:

pip instal ContactExtractor

Usage:

ContExt input=pathto/coordfile [OPTIONS]

As a Python function:

see https://github.com/febos/ContExt/blob/main/demo.ipynb

Description:

ContExt outputs pairs of atoms that lie closer to each other than a specified threshold in angstroms ("range" parameter). By default, ContExt searches for atom-atom pairs at a distance < 10 angstroms in a structure file specified in the "input" parameter. If another structure file is specified under the "input2" parameter, ContExt will output only the close atom pairs found between the two structures. Subsets of atoms of interest can be defined with "atoms" and "atoms2" parameters.

Requirements:

SciPy

Output:

The found atom-atom pairs are printed into stdout in the following format:

RANGE ATOM1-DESCRIPTION ATOM2-DESCRIPTION

The atom descriptions are in the following format:

#MODEL/CHAIN:RESIDUE_RESIDUENUMBER.INSERTIONCODE@ATOM_ATOMNUMBER.ALTLOC

Example output:

5.40291412 #1/A:A_12.@C1'_120. #1/A:G_13.@P_134.

6.24810643 #1/B:C_12.A@C1'_583. #2/B:G_130.@O4'_14401.B

Options:

input= - input structure in pdb/mmcif format [REQUIRED]

Path to a coordinate file in PDB or mmCIF format.

input=example.pdb - search atom pairs in example.pdb 

input2= - input structure in pdb/mmcif format [DEFAULT: input2=input]

Path to the second coordinate file in PDB or mmCIF format.

input=example.pdb input2=example2.pdb - search 
atom pairs between example.pdb and example2.pdb 

-help - type -help / --help / -h / -H to see this message [DEFAULT: FALSE]

See the help message, ignore all other options.

range= - threshold in angstroms [DEFAULT: range=10.0]

Atom distance threshold in angstroms.

atoms= - input atoms of interest [DEFAULT: atoms=#]

Specify particular subset of atoms to be used as ATOM1.
See the format description below.

atoms2= - input 2 atoms of interest [DEFAULT: atoms2=atoms]

Specify particular subset of atoms to be used as ATOM2.
See the format description below.

ATOMS SPECIFICATION FORMAT:

[#[INT][_INT]][/[STRING]][:[STRING][_INT[_INT]]][@[STRING][_INT[_INT]]]

ATOMS SPECIFICATION EXAMPLES:

atoms=#1/B:C_-1_10@O2 - O2 atoms of the residues with id from -1 to 10 of chain B from model 1

atoms=# - equivalent to an empty condition

atoms=/ - equivalent to an empty condition

atoms=: - equivalent to an empty condition

atoms=@ - equivalent to an empty condition

atoms="@C1' @C2'" - C1’ and C2' atoms

atoms="/B /C" - chain B and chain C

atoms=#1:A - adenines in model 1

atoms=A - not a keyword, i.e. error

atoms=":C@O4'" - O4' atoms of cytidines

atoms=#2_3@_1_1000 - atoms with id from 1 to 1000 from model 2 or model 3

Usage examples:

ContExt input=examples/1ffk_0_kt7.cif range=2.0 atoms="@O3'" atoms2=@P

Find O3'-P pairs at a distance under 2.0 angstroms in the
examples/1ffk_0_kt7.cif coordinate file. The output
includes pairs of consecutive nucleotides.

ContExt input=examples/1ffk_0_kt7.cif input2=examples/3d2g_A_kj.cif range=5 atoms=@P

Find P-P pairs at a distance under 5.0 angstroms
betweeen the two input coordinate files.

ContExt input=examples/2fmt.pdb atoms=:A atoms2=:ARG

Find atom-atom pairs within 10 angstroms (default range)
between adenines and arginines in the input file.