biobb_haddock

Introduction

biobb_haddock is the Biobb module collection to compute information-driven flexible protein-protein docking. Biobb (BioExcel building blocks) packages are Python building blocks that create new layer of compatibility and interoperability over popular bioinformatics tools. The latest documentation of this package can be found in our readthedocs site: latest API documentation.

Version

v4.1.0 2024.1

Install CNS

1 Download the source code of CNS

In this case: cns_solve_1.3_all.tar.gz

From the CNS site create a new folder in the Haddock folder and uncompress it.

# Replace /__PATH__/__to__/ by your path to the haddock3 directory.
cd /__PATH__/__to__/haddock3
mkdir haddock3/CNS
cp cns_solve_1.3_all.tar.gz haddock3/CNS/
cd haddock3/CNS/
tar xvzf cns_solve_1.3_all.tar.gz

2 Download the Intel Fortran and C++ offline compilers

In this case: m_fortran-compiler-classic_p_2022.0.0.63_offline.dmg and m_cpp-compiler-classic_p_2022.0.0.62_offline.dmg

From the Intel developers site and double click to install them.

3 Configure the CNS environment

3.1 cns_solve_env:

# Replace /__PATH__/__to__/ by your path to the haddock3 directory.
cd /__PATH__/__to__/haddock3/CNS
vim cns_solve_1.3/cns_solve_env

Modify the CNS_SOLVE env var:

# CHANGE THE NEXT LINE TO POINT TO THE LOCATION OF THE CNSsolve DIRECTORY

            setenv CNS_SOLVE '_CNSsolve_location_'

#
# ==========================================================================

In this case:

# Replace /__PATH__/__to__/ by your path to the haddock3 directory.

            setenv CNS_SOLVE '/__PATH__/__to__/haddock3/CNS/cns_solve_1.3/'

3.2 rtf.inc:

# Replace /__PATH__/__to__/ by your path to the haddock3 directory.
cd /__PATH__/__to__/haddock3/CNS
vim cns_solve_1.3/source/rtf.inc

Modify all the MX (maximum) variables adding one extra zero to all of them:

PARAMETER (MXRTRS=200,NICM=50) --> PARAMETER (MXRTRS=2000,NICM=50)
PARAMETER (MXRTA=2000)         --> PARAMETER (MXRTA=20000)
PARAMETER (MXRTX=2000)         --> PARAMETER (MXRTX=20000)
PARAMETER (MXRTB=2000)         --> PARAMETER (MXRTB=20000)
PARAMETER (MXRTT=3000)         --> PARAMETER (MXRTT=30000)
PARAMETER (MXRTP=2000)         --> PARAMETER (MXRTP=20000)
PARAMETER (MXRTI=2000)         --> PARAMETER (MXRTI=20000)

4 Compile and link CNS

# Replace /__PATH__/__to__/ by your path to the haddock3 directory.
cd /__PATH__/__to__/haddock3/CNS/cns_solve_1.3
make install

If everything ended well, one of the last output lines will be:

created executable file cns_solve-xxxxxxxxx.exe

The xxxxxxxxx will be a different number on each build.

Finally link the CNS binary:

# Replace /__PATH__/__to__/ by your path to the haddock3 directory.
cd /__PATH__/__to__/haddock3
mkdir -p bin/
#Replace the  `xxxxxxxxx` and the __PATH__TO_BIN__ by your binary file
ln -s CNS/__PATH__TO_BIN__/cns_solve-xxxxxxxxx.exe bin/cns

Installation

Using PIP:

Important: PIP only installs the package. All the dependencies must be installed separately. To perform a complete installation, please use ANACONDA, DOCKER or SINGULARITY.

• Installation:

    pip install "biobb_haddock>=4.1.0"
  

• Usage: Python API documentation

Using ANACONDA:

• Installation:

    conda install -c bioconda "biobb_haddock>=4.1.0"
  

• Usage: With conda installation BioBBs can be used with the Python API documentation and the Command Line documentation

Using DOCKER:

• Installation:

    docker pull quay.io/biocontainers/biobb_haddock:4.1.0--pyhdfd78af_0
  

• Usage:

    docker run quay.io/biocontainers/biobb_haddock:4.1.0--pyhdfd78af_0 <command>
  

Using SINGULARITY:

MacOS users: it’s strongly recommended to avoid Singularity and use Docker as containerization system.

• Installation:

    singularity pull --name biobb_haddock.sif https://depot.galaxyproject.org/singularity/biobb_haddock:4.1.0--pyhdfd78af_0
  

• Usage:

    singularity exec biobb_haddock.sif <command>
  

The command list and specification can be found at the Command Line documentation.

Copyright & Licensing

This software has been developed in the MMB group at the BSC & IRB for the European BioExcel, funded by the European Commission (EU H2020 823830, EU H2020 675728), EU Horizon Europe [101093290] (https://cordis.europa.eu/project/id/101093290).

• (c) 2015-2024 Barcelona Supercomputing Center

• (c) 2015-2024 Institute for Research in Biomedicine

Licensed under the Apache License 2.0, see the file LICENSE for details.