Trying to run oddt on win 10

[Daviti Kharchilava]

Hello ! I am trying to use oddt.docking package on Windows 10. I had to run "python setup.py install --user" . "--user" at the end of mentioned line to let me run the oddt_cli (to make it appear). I had to run all the commands with pip at first from Windows Command Prompt , but OpenBabel had issues with installing in Command Prompt, so I ran all the commands again in the Anacond Prompt for "Conda Users". Conda Prompt could install openbabel and all the rest requirements.

All the other requirements were installed without a problem.

Please help me to run the docking with oddt package from conda prompt. I have gethered .sdf file (ligand) , .pdb file (macromolecule) and even vina . exe files in the directory where the oddt_cli is presented (X:\Documents\oddt-master\build\scripts-3.8) , but whenever I try to run the mentioned file it throws this error:

(base) X:\Documents\oddt-master\build\scripts-3.8>python oddt_cli

usage: oddt_cli [-h] [--toolkit {ob,rdk}] [-n N_CPU] [--version]

                [-c CHUNKSIZE] [-i IN_FORMAT] [-o OUT_FORMAT] [-O OUT_FILE]

                [--filter FILTER]

                [--similarity {ifp,sifp,usr,usr_cat,electroshape}]

                [--cutoff CUTOFF] [--query QUERY] [--dock {autodock_vina}]

                [--receptor RECEPTOR] [--auto_ligand AUTO_LIGAND]

                [--center CENTER] [--size SIZE]

                [--exhaustiveness EXHAUSTIVENESS] [--seed SEED]

                [--score {autodock_vina,rfscore,nnscore,rfscore_v1,rfscore_v2,rfscore_v3,pleclinear,plecnn,plecrf,rfscore_v1_pdbbind2007,rfscore_v2_pdbbind2007,rfscore_v3_pdbbind2007,nnscore_pdbbind2007,rfscore_v1_pdbbind2012,rfscore_v2_pdbbind2012,rfscore_v3_pdbbind2012,nnscore_pdbbind2012,rfscore_v1_pdbbind2013,rfscore_v2_pdbbind2013,rfscore_v3_pdbbind2013,nnscore_pdbbind2013,rfscore_v1_pdbbind2014,rfscore_v2_pdbbind2014,rfscore_v3_pdbbind2014,nnscore_pdbbind2014,rfscore_v1_pdbbind2015,rfscore_v2_pdbbind2015,rfscore_v3_pdbbind2015,nnscore_pdbbind2015,rfscore_v1_pdbbind2016,rfscore_v2_pdbbind2016,rfscore_v3_pdbbind2016,nnscore_pdbbind2016,pleclinear_pdbbind2016,plecnn_pdbbind2016,plecrf_pdbbind2016}]

                [--score_file SCORE_FILE] [--field SAVE_FIELDS]

                in_file [in_file ...]

oddt_cli: error: the following arguments are required: in_file

When when I type python oddt_cli -h this appears :

(base) X:\Documents\oddt-master\build\scripts-3.8>python oddt_cli -h

usage: oddt_cli [-h] [--toolkit {ob,rdk}] [-n N_CPU] [--version]

                [-c CHUNKSIZE] [-i IN_FORMAT] [-o OUT_FORMAT] [-O OUT_FILE]

                [--filter FILTER]

                [--similarity {ifp,sifp,usr,usr_cat,electroshape}]

                [--cutoff CUTOFF] [--query QUERY] [--dock {autodock_vina}]

                [--receptor RECEPTOR] [--auto_ligand AUTO_LIGAND]

                [--center CENTER] [--size SIZE]

                [--exhaustiveness EXHAUSTIVENESS] [--seed SEED]

                [--score {autodock_vina,rfscore,nnscore,rfscore_v1,rfscore_v2,rfscore_v3,pleclinear,plecnn,plecrf,rfscore_v1_pdbbind2007,rfscore_v2_pdbbind2007,rfscore_v3_pdbbind2007,nnscore_pdbbind2007,rfscore_v1_pdbbind2012,rfscore_v2_pdbbind2012,rfscore_v3_pdbbind2012,nnscore_pdbbind2012,rfscore_v1_pdbbind2013,rfscore_v2_pdbbind2013,rfscore_v3_pdbbind2013,nnscore_pdbbind2013,rfscore_v1_pdbbind2014,rfscore_v2_pdbbind2014,rfscore_v3_pdbbind2014,nnscore_pdbbind2014,rfscore_v1_pdbbind2015,rfscore_v2_pdbbind2015,rfscore_v3_pdbbind2015,nnscore_pdbbind2015,rfscore_v1_pdbbind2016,rfscore_v2_pdbbind2016,rfscore_v3_pdbbind2016,nnscore_pdbbind2016,pleclinear_pdbbind2016,plecnn_pdbbind2016,plecrf_pdbbind2016}]

                [--score_file SCORE_FILE] [--field SAVE_FIELDS]

                in_file [in_file ...]

Open Drug Discovery (ODDT) command line tools

positional arguments:

  in_file               Input files of formats supported by toolkit.

optional arguments:

  -h, --help            show this help message and exit

  --toolkit {ob,rdk}    Choose which toolkit should be used for calculations,

                        either "ob" (OpenBabel) or "rdkit" (RDKit) (default:

                        ob)

  -n N_CPU, --n_cpu N_CPU

                        The number of parallel processes. -1 automatically

                        assigns maximum number of CPUs. (default=-1)

  --version             show program's version number and exit

  -c CHUNKSIZE, --chunksize CHUNKSIZE

                        The number of molecules to process in a chunk.

                        (default=100)

  -i IN_FORMAT          Input file(s) format

  -o OUT_FORMAT         Output file format

  -O OUT_FILE, --output OUT_FILE

                        Output file

  --field SAVE_FIELDS   Field to save (eg. in CSV). Each field should be

                        specified separately.

Filtering:

  --filter FILTER       Choose built-in filters to be used (eg. "ro5", "ro3",

                        "pains")

Similarity searching:

  --similarity {ifp,sifp,usr,usr_cat,electroshape}

                        Choose similarity method to use (eg. "ifp", "sifp",

                        "usr", "usr_cat", "electroshape")

  --cutoff CUTOFF       Similarity cufoff below which molecules will be

                        ignored.

  --query QUERY         Query molecule(s) for similarity searching

Protein-Ligand docking:

  --dock {autodock_vina}

                        Choose docking software to be used

  --receptor RECEPTOR   Protein file

  --auto_ligand AUTO_LIGAND

                        Docking Box is determined on that ligand

  --center CENTER       Docking Box center (x,y,z)

  --size SIZE           Docking Box dimentions (x,y,z)

  --exhaustiveness EXHAUSTIVENESS

                        Exhaustiveness of docking

  --seed SEED           Random Seed

Rescoring:

  --score {autodock_vina,rfscore,nnscore,rfscore_v1,rfscore_v2,rfscore_v3,pleclinear,plecnn,plecrf,rfscore_v1_pdbbind2007,rfscore_v2_pdbbind2007,rfscore_v3_pdbbind2007,nnscore_pdbbind2007,rfscore_v1_pdbbind2012,rfscore_v2_pdbbind2012,rfscore_v3_pdbbind2012,nnscore_pdbbind2012,rfscore_v1_pdbbind2013,rfscore_v2_pdbbind2013,rfscore_v3_pdbbind2013,nnscore_pdbbind2013,rfscore_v1_pdbbind2014,rfscore_v2_pdbbind2014,rfscore_v3_pdbbind2014,nnscore_pdbbind2014,rfscore_v1_pdbbind2015,rfscore_v2_pdbbind2015,rfscore_v3_pdbbind2015,nnscore_pdbbind2015,rfscore_v1_pdbbind2016,rfscore_v2_pdbbind2016,rfscore_v3_pdbbind2016,nnscore_pdbbind2016,pleclinear_pdbbind2016,plecnn_pdbbind2016,plecrf_pdbbind2016}

                        Choose built-in scoring function to be used

  --score_file SCORE_FILE

                        Choose ODDT scoring function saved to file (pickle)

I can guess, this part is about docking:

Protein-Ligand docking:

  --dock {autodock_vina}

                        Choose docking software to be used

  --receptor RECEPTOR   Protein file

  --auto_ligand AUTO_LIGAND

                        Docking Box is determined on that ligand

  --center CENTER       Docking Box center (x,y,z)

  --size SIZE           Docking Box dimentions (x,y,z)

  --exhaustiveness EXHAUSTIVENESS

                        Exhaustiveness of docking

  --seed SEED           Random Seed

I am unable to guess what command to use and how to make the script understand that I want to dock mentioned .sdf and .pdb files that are already placed by me in the same directory as oddt_cli file as I have mentioned before.

Please help me to use this tool for docking. Thank you in advance! 

P.S.: I am sorry for all these details , but I also hope that Windows 10 users might find it helpful to get to my point where I am stuck right now and do not waste more time for it.

[Maciek Wójcikowski]

Hi,

What's the exact command you struggle with? You should use something like:

oddt_cli --receptor protein.pdb --auto_ligand crystal_ligand.pdb --dock autodock_vina ligands.sdf 

 If you do not have a ligand that you can autocenter you have to set coordinates maunally using --center

----
Pozdrawiam,  |  Best regards,
Maciek Wójcikowski
mac...@wojcikowski.pl

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[Daviti Kharchilava]

Hello,

Thank you so much for your attention ! I could actually resolve all the issues in Linux operating system. I recommend all Windows users to download and install Virtual Box and set up virtual machine of Linux. All the commands and functionalities work just fine on Linux.

Here is the link of a tutorial video that I found helpful: https://www.youtube.com/watch?v=QbmRXJJKsvs . It is 2 years old but works quite, fine the steps are still the same.

Best Regards,

Daviti