pegi3s/haddock-tools repository overview

⁠This image belongs to a larger project called Bioinformatics Docker Images Project (http://pegi3s.github.io/dockerfiles⁠)

⁠(Please note that the original software licenses still apply)

This image facilitates the usage of Haddock-tools⁠, a collection of useful programs for the preparation of HADDOCK runs.

⁠Using the Haddock-tools image in Linux

You should adapt and run the following command: docker run --rm -v /your/data/dir:/data pegi3s/haddock-tools:git_07.06.2021 bash -c "/opt/haddock-tools/<haddock-tool-and-parameters>"

In this command, you should replace:

• /your/data/dir to point to the directory that contains the input files you want to analyze.
• <haddock-tool-and-parameters> to the name of the Haddock-tool you want to use and respective parameters.

⁠Note

For some HADDOCK tools their location is different than /opt/haddock-tools/

⁠Examples

Several examples of the usage of Haddock-tools are given below (the test files can be obtained here⁠):

⁠Examples 1

docker run --rm -v /your/data/dir:/data pegi3s/haddock-tools:git_07.06.2021 bash -c "/opt/haddock-tools/molprobity.py /data/1f3g.pdb > /data/1f3g_output"

docker run --rm -v /your/data/dir:/data pegi3s/haddock-tools:git_07.06.2021 bash -c "/opt/haddock-tools/passive_from_active.py /data/1f3g.pdb 38,40,45,46,69,71,78,80,94,96,141 > /data/1f3g_passive"

docker run --rm -v /your/data/dir:/data pegi3s/haddock-tools:git_07.06.2021 bash -c "/opt/haddock-tools/active-passive-to-ambig.py /data/1f3g_active_passive /data/1hdn_m1_cport_active_passive > /data/1f3g_1hdn_m1.tbl"

⁠Note 1

In the Haddock-tools manual the name of this script is incorrectly listed as active-passive_to_ambig.py

⁠Example 2

docker run --rm -v /your/data/dir:/data pegi3s/haddock-tools:git_07.06.2021 bash -c "cd /opt/haddock-tools/haddock_tbl_validation && python validate_tbl.py /data/1f3g_1hdn_m1.tbl"

⁠Note 2

The validate_tbl.py script is in a different place than the remaining scripts.

⁠Examples 3

docker run --rm -v /your/data/dir:/data pegi3s/haddock-tools:git_07.06.2021 bash -c "cd /opt/haddock-tools && python calc-accessibility.py /data/1f3g.pdb 2> /data/output"

docker run --rm -v /your/data/dir:/data pegi3s/haddock-tools:git_07.06.2021 bash -c "/opt/haddock-tools/pdb_blank_chain /data/1f3g.pdb > /data/1f3g_blank_chain.pdb"

docker run --rm -v /your/data/dir:/data pegi3s/haddock-tools:git_07.06.2021 bash -c "/opt/haddock-tools/pdb_blank_segid /data/1f3g.pdb > /data/1f3g_blank_segid.pdb"

docker run --rm -v /your/data/dir:/data pegi3s/haddock-tools:git_07.06.2021 bash -c "/opt/haddock-tools/pdb_setchain -v CHAIN=A /data/1f3g.pdb > /data/1f3g_chain.pdb"