XML RPC Services: Difference between revisions

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We offer several XML RPC services.
We offer several XML RPC (XMLRPC) services. These are based on supported [[XML RPC Procedures]]. This page is a crib sheet on how to use these services. Note that the use of docking.org services may be subject to quotas. see [http://www.xmlrpc.com/ http://www.xmlrpc.com/]


* Step 1. Download the client
* Step 1. Download the client
** Client [http://blaster.docking.org/xmlrpc/client9.py client.py]
** Client [http://blaster.docking.org/xmlrpc/xmlclient.py xmlclient.py]
* Step 2. Download the sample data
* Step 2. Download the sample data
** Client [http://blaster.docking.org/xmlrpc/testdata.tar.gz testdata.tar.gz]
** Sample data ZIP file [http://blaster.docking.org/data/dud40.zip dud40.zip]
** gunzip testdata.tar.gz
** Browse [http://blaster.docking.org/data/dud40/ sample data]
* Step 3. Protonate receptor
** unzip dud40.zip
** cd ache
* Step 3. Protonate AChE receptor PDB file
** client.py upr ache
** xmlclient.py protonate_united ache ; expects rec.pdb ; returns newrec.pdb
*** takes rec.pdb and produces newrec.pdb
*** ; this takes rec.pdb and returns newrec.pdb, with united atoms protonated
* Step 4. Run DOCK Blaster
* Step 4. Run DOCK Blaster
** client.py blaster ache
** xmlclient.py dock ache ; returns DOCK Blaster Job ID number
** connect to browser to see results http://blaster.docking.org/cgi-bin/jobwatch.pl?jobid=999
** browse results [http://blaster.docking.org/cgi-bin/jobwatch.pl?job_id=993&pin= | results]
* Step 5. Upload data and process in ZINC
* Step 5. Upload data and process ligands in ZINC
** client.py upload actives.py
** xmlclient.py upload actives.smi ; returns ZINC upload number
* Step 6.
* Step 6. Search ZINC using SMILES
** xmlclient.py match_smiles test1.smi; returns list
* Step 7. Search ZINC using SMARTS
** xmlclient.py match_smarts test2.sma; returns list
* Step 8. Find similars in ZINC
** xmlclient.py getsimilars actives.smi; returns list
* Step 9. Find decoys in ZINC
** xmlclient.py getdecoys actives.smi; returns list
* Step 10. blah
** xmlclient.py blah blah
* Step 11. blah
** xmlclient.py blah blah
* Step 12. blah
** xmlclient.py blah blah
* Step 13. blah
** xmlclient.py blah blah
 
[[Category:ZINC]]
[[Category:DOCK Blaster]]
[[Category:Software]]

Latest revision as of 00:52, 11 March 2014

We offer several XML RPC (XMLRPC) services. These are based on supported XML RPC Procedures. This page is a crib sheet on how to use these services. Note that the use of docking.org services may be subject to quotas. see http://www.xmlrpc.com/

  • Step 1. Download the client
  • Step 2. Download the sample data
  • Step 3. Protonate AChE receptor PDB file
    • xmlclient.py protonate_united ache ; expects rec.pdb ; returns newrec.pdb
      • ; this takes rec.pdb and returns newrec.pdb, with united atoms protonated
  • Step 4. Run DOCK Blaster
    • xmlclient.py dock ache ; returns DOCK Blaster Job ID number
    • browse results | results
  • Step 5. Upload data and process ligands in ZINC
    • xmlclient.py upload actives.smi ; returns ZINC upload number
  • Step 6. Search ZINC using SMILES
    • xmlclient.py match_smiles test1.smi; returns list
  • Step 7. Search ZINC using SMARTS
    • xmlclient.py match_smarts test2.sma; returns list
  • Step 8. Find similars in ZINC
    • xmlclient.py getsimilars actives.smi; returns list
  • Step 9. Find decoys in ZINC
    • xmlclient.py getdecoys actives.smi; returns list
  • Step 10. blah
    • xmlclient.py blah blah
  • Step 11. blah
    • xmlclient.py blah blah
  • Step 12. blah
    • xmlclient.py blah blah
  • Step 13. blah
    • xmlclient.py blah blah
Retrieved from "http://wiki.docking.org/index.php?title=XML_RPC_Services&oldid=6443"