Menu ▾ ▴

#7 Ligand chemical names in addition to numbers in final Analysis Table

0.9.x
closed
nobody
None
2017-09-22
2017-01-19
Julio Coll
No

Would it be possible in the final Table to Analyze Results of the Vina Wizard (and the AutoDock) to add the chemical names of the ligands in a new column?
It will speed up the analysis specially when the number of ligands is large ........

I found it very frustating to find out only a numer for the description of the ligands
Is it perhaps that I a recent user of the program and met with special sdf files that only show that kind of information ?

Thank you, julio

Related

Tickets: #7

Discussion

  • Sarkis Dallakian

    Sarkis Dallakian - 2017-01-20

    Thank you Julio. In the final Table to Analyze Results of the Vina Wizard (and the AutoDock), PyRx shows receptor_ligand under Ligands column so that we can distinguish different receptor ligand complexes. I can add option in PyRx so that when it converts sdf to pdqt, users can choose title or the formula in sdf entry as the name of the pbqt file. I know that some sdf have database id as the title in the sdf entries, that might be the reason you found it very frustrating.

    Please let me know, if I understood you correctly and this is a feature you want to see in PyRx.

     

    • Julio Coll

      Julio Coll - 2017-01-20

      Yes
      The formula or name was what I was expecting to see: the chemical names

      Although both the formula / chemical names and the id are needed, when one
      wants to know more about the compounds.
      The formula helps to decide quickly what to look for the best alternative

      Could both be included in 2 differnt columns?

      Thank you.
      it just happened to be awake earlier in the morning 5.40 am, local time
      here at Madrid (Spain) !

      cheers, julio

      2017-01-20 5:21 GMT+01:00 Sarkis Dallakian sarkiss@users.sf.net:

      Thank you Julio. In the final Table to Analyze Results of the Vina Wizard
      (and the AutoDock), PyRx shows receptor_ligand under Ligands column so that
      we can distinguish different receptor ligand complexes. I can add option in
      PyRx so that when it converts sdf to pdqt, users can choose title or the
      formula in sdf entry as the name of the pbqt file. I know that some sdf
      have database id as the title in the sdf entries, that might be the reason
      you found it very frustrating.

      Please let me know, if I understood you correctly and this is a feature
      you want to see in PyRx.

      Status: open
      Milestone: 0.9.x
      Created: Thu Jan 19, 2017 02:51 PM UTC by Julio Coll
      Last Updated: Thu Jan 19, 2017 02:51 PM UTC
      Owner: nobody

      Would it be possible in the final Table to Analyze Results of the Vina
      Wizard (and the AutoDock) to add the chemical names of the ligands in a new
      column?
      It will speed up the analysis specially when the number of ligands is
      large ........

      I found it very frustating to find out only a numer for the description of
      the ligands
      Is it perhaps that I a recent user of the program and met with special sdf
      files that only show that kind of information ?

      Thank you, julio

      Sent from sourceforge.net because you indicated interest in
      https://sourceforge.net/p/pyrx/tickets/7/

      To unsubscribe from further messages, please visit
      https://sourceforge.net/auth/subscriptions/

      --

      Dr. Julio M. CollpHD in Biology.Massachusetts Institute of Technology

      Dpt.Biotecnologia (ed.Central) SGIT INIA
      crt Coruna km7 Madrid 28040
      INIA´s NIF. ES Q2821013F
      telf: 913476850 fax: 913572293 email: juliocollm@gmail.com
      juliocoll@inia.es

      Research Projects:
      http://www.imtra-vac.unileon.es/
      http://www.aquagenomics.es/

       

      Related

      Tickets: #7

      • Sarkis Dallakian

        Sarkis Dallakian - 2017-01-29

        I've added a new option in Open Bable widget so that when converting molecules to AutoDock ligand, the name of the ligand can be set to either the title of the ligand as it was before, or it can be set to formula_title. Please replace C:\users\julio.PyRx-workspace\update\PyRx\traitedBabel.py with the attached file to try this new feature. When you start PyRx with this updated file, click on Edit > Preferences, click on + icon next to Open Babel and select AutoDock Ligand. You'll see a new option there next to "Name Converted Ligand Using". There are two options: Title or Formula_Title. If you select Formula_Title, next time when PyRx makes AutoDock ligands using Open Bable, it will name ligands accordingly. Please give it a try and let me know what do you think.

         
        traitedBabel.py

      • Julio Coll

        Julio Coll - 2017-01-30

        dear Sarkis,
        I made a short trial and saw the new option in preferences.

        I have to test it with a large set of files, as soon as I have a moment.

        Thank you!
        julio

        2017-01-20 6:05 GMT+01:00 Julio Coll juliocollm@users.sf.net:

        Yes
        The formula or name was what I was expecting to see: the chemical names

        Although both the formula / chemical names and the id are needed, when one
        wants to know more about the compounds.
        The formula helps to decide quickly what to look for the best alternative

        Could both be included in 2 differnt columns?

        Thank you.
        it just happened to be awake earlier in the morning 5.40 am, local time
        here at Madrid (Spain) !

        cheers, julio

        2017-01-20 5:21 GMT+01:00 Sarkis Dallakian sarkiss@users.sf.net:

        Thank you Julio. In the final Table to Analyze Results of the Vina Wizard
        (and the AutoDock), PyRx shows receptor_ligand under Ligands column so that
        we can distinguish different receptor ligand complexes. I can add option in
        PyRx so that when it converts sdf to pdqt, users can choose title or the
        formula in sdf entry as the name of the pbqt file. I know that some sdf
        have database id as the title in the sdf entries, that might be the reason
        you found it very frustrating.

        Please let me know, if I understood you correctly and this is a feature
        you want to see in PyRx.

        Status: open
        Milestone: 0.9.x
        Created: Thu Jan 19, 2017 02:51 PM UTC by Julio Coll
        Last Updated: Thu Jan 19, 2017 02:51 PM UTC
        Owner: nobody

        Would it be possible in the final Table to Analyze Results of the Vina
        Wizard (and the AutoDock) to add the chemical names of the ligands in a new
        column?
        It will speed up the analysis specially when the number of ligands is
        large ........

        I found it very frustating to find out only a numer for the description of
        the ligands
        Is it perhaps that I a recent user of the program and met with special sdf
        files that only show that kind of information ?
        Thank you, julio

        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/pyrx/tickets/7/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --

        Dr. Julio M. CollpHD in Biology.Massachusetts Institute of Technology

        Dpt.Biotecnologia (ed.Central) SGIT INIA
        crt Coruna km7 Madrid 28040
        INIA´s NIF. ES Q2821013F
        telf: 913476850 fax: 913572293 email:
        juliocollm@gmail.com juliocollm@gmail.com juliocoll@inia.es
        juliocoll@inia.es

        Research Projects:
        http://www.imtra-vac.unileon.es/
        http://www.aquagenomics.es/

        Status: open
        Milestone: 0.9.x
        Created: Thu Jan 19, 2017 02:51 PM UTC by Julio Coll
        Last Updated: Fri Jan 20, 2017 04:21 AM UTC
        Owner: nobody

        Would it be possible in the final Table to Analyze Results of the Vina
        Wizard (and the AutoDock) to add the chemical names of the ligands in a new
        column?
        It will speed up the analysis specially when the number of ligands is
        large ........

        I found it very frustating to find out only a numer for the description of
        the ligands
        Is it perhaps that I a recent user of the program and met with special sdf
        files that only show that kind of information ?

        Thank you, julio

        Sent from sourceforge.net because you indicated interest in
        https://sourceforge.net/p/pyrx/tickets/7/

        To unsubscribe from further messages, please visit
        https://sourceforge.net/auth/subscriptions/

        --

        Dr. Julio M. CollpHD in Biology.Massachusetts Institute of Technology

        Dpt.Biotecnologia (ed.Central) SGIT INIA
        crt Coruna km7 Madrid 28040
        INIA´s NIF. ES Q2821013F
        telf: 913476850 fax: 913572293 email: juliocollm@gmail.com
        juliocoll@inia.es

        Research Projects:
        http://www.imtra-vac.unileon.es/
        http://www.aquagenomics.es/

         

        Related

        Tickets: #7

        • Sarkis Dallakian

          Sarkis Dallakian - 2017-01-31

          Dear Julio,

          Thank you for the feedback. Hope you find this feature useful.

           

  • Sarkis Dallakian

    Sarkis Dallakian - 2017-09-22
    • status: open --> closed
     

Log in to post a comment.