Difference between revisions of "XML RPC Procedures"

From DISI
Jump to navigation Jump to search
 
 
(4 intermediate revisions by 2 users not shown)
Line 5: Line 5:
 
== DOCK Blaster ==
 
== DOCK Blaster ==
  
=== startdockblaster() ===
+
=== dockblaster() ===
 +
dockblaster(rec,xtallig,actives,inactives,cofactor,pin,voucher)
 +
where
 +
rec is receptor in PDB or mol2 format
 +
xtallig is ligand in mol2 format or binding site indicator in PDB format
 +
actives are SMILES of actives (up to 50)
 +
inactives are SMILES of inactives (up to 50)
 +
cofactor is a cofactor parameter file, empty file if not required
 +
pin is a personal identification code, or '' if not wanted
 +
voucher is a code to bypass IP-based limit throttles, or ''
 +
 
 +
returns job_id number or messasge indicating reason for failure
 +
Results generated using this procedure may be browsed online at http://blaster.docking.org/cgi-bin/jobwatch.pl?job_id=<job_id>
 +
 
 +
Purpose: to launch a docking calculation
 +
Restrictions: throttle limits in effect, as calculations can consume significant CPU
  
 
=== queryrun() ===
 
=== queryrun() ===
 +
queryrun(job_id,pin)
 +
where
 +
job_id is a valid DOCK Blaster job identification number
 +
pin is the PIN code used to start the job
 +
 +
* Purpose: this procedure reports on the current status of the job
 +
* Restrictions: PIN must match
  
 
=== analyzerun() ===
 
=== analyzerun() ===
 +
analyzerun(job_id,pin)
 +
where
 +
job_id is a valid DOCK Blaster job identification number
 +
pin is the PIN code used to start the job
  
=== myquotas() ===
+
Purpose: to analyze results of a docking calculation
 
+
Restrictions: PIN must match
  
 
== ZINC ==
 
== ZINC ==
  
 
===  getmolfromID() ===
 
===  getmolfromID() ===
 +
getmolfromID(zinc_id)
 +
where
 +
zinc_id is a valid ZINC identification number or an array of ZINC ID numbers
  
=== uploadtoZINC() ===
+
=== uploadZINC() ===
 +
uploadZINC(smiles,voucher)
 +
where
 +
smiles is an array of SMILES with optional identifiers seaparated by whitespace
 +
voucher is an optional voucher to bypass IP based throttles, or ''
  
 
=== similarto() ===
 
=== similarto() ===
 +
similarto(smiles,tanimoto,voucher)
 +
where
 +
smiles is an array of SMILES with optional identifiers separated by whitespace
 +
tanimoto is a tanimoto similarity cutoff value (0-100)
 +
voucher is an optional bypass of IP based throttles, or ''
 +
  
 
=== propertydecoys() ===
 
=== propertydecoys() ===
 
+
propertydecoys(smiles,number,voucher)
 +
where
 +
smiles is an array of SMILES with optional identifiers separated by whitespace
 +
tanimoto is a tanimoto similarity cutoff value (0-100)
 +
voucher is an optional bypass of IP based throttles, or ''
  
 
== SEA ==
 
== SEA ==
 
+
sea(smiles, method, voucher)
=== letsgosea() ===
+
where
 +
smiles is an array of SMILES with optional identifiers separated by whitespace
 +
method specifies the method, or the database to use, default ''
 +
voucher is an optional bypass of IP based throttles, or ''
  
 
== THC ==
 
== THC ==
  
 
=== listTHCtargets() ===
 
=== listTHCtargets() ===
 +
listTHCtargets()
  
=== listtopN() ===
+
Purpose: to list the targets that are currently available in THC.
 +
Restrictions: none
  
 +
=== THClisttopN() ===
 +
THClisttopN(thc_id)
 +
where
 +
thc_id is the thc entry number, which is availble in listTHCtargets() above
 +
 +
* Result:
 +
* Purpose: to list the opt
 +
* Restrictions:
  
 
== DUD ==
 
== DUD ==
  
 
=== listDUDtargets() ===
 
=== listDUDtargets() ===
 +
listDUDtargets()
 +
where
 +
xx
 +
 +
* Result:
 +
* Purpose:
 +
* Restrictions:
 +
  
 
=== getactives() ===
 
=== getactives() ===
  
 
=== getdecoys() ===
 
=== getdecoys() ===
 +
 +
== SEA ==
  
  
 
== General ==
 
== General ==
 +
 +
=== listMethods() ===
 +
listMethods()
 +
 +
Purpose:
 +
 +
=== myquotas() ===
 +
 +
myquotas()
 +
 +
Purpose: to report limits in effect on using DOCK Blaster and other services
 +
Restrictions: none
  
 
=== serverstatus() ==
 
=== serverstatus() ==
 +
 +
[[Category:jji]]

Latest revision as of 05:22, 14 February 2014

Remote Procedure calls supported by services.compbio.ucsf.edu. The procedures below may be invoked using python scripts from any client that can see services.compbio.ucsf.edu. Sample scripts and data are included. Usage throttles apply.


DOCK Blaster

dockblaster()

dockblaster(rec,xtallig,actives,inactives,cofactor,pin,voucher)

where

rec is receptor in PDB or mol2 format
xtallig is ligand in mol2 format or binding site indicator in PDB format
actives are SMILES of actives (up to 50)
inactives are SMILES of inactives (up to 50)
cofactor is a cofactor parameter file, empty file if not required
pin is a personal identification code, or  if not wanted
voucher is a code to bypass IP-based limit throttles, or 
returns job_id number or messasge indicating reason for failure

Results generated using this procedure may be browsed online at http://blaster.docking.org/cgi-bin/jobwatch.pl?job_id=<job_id>

Purpose: to launch a docking calculation Restrictions: throttle limits in effect, as calculations can consume significant CPU

queryrun()

queryrun(job_id,pin)

where

job_id is a valid DOCK Blaster job identification number
pin is the PIN code used to start the job
  • Purpose: this procedure reports on the current status of the job
  • Restrictions: PIN must match

analyzerun()

analyzerun(job_id,pin)

where

job_id is a valid DOCK Blaster job identification number
pin is the PIN code used to start the job

Purpose: to analyze results of a docking calculation Restrictions: PIN must match

ZINC

getmolfromID()

getmolfromID(zinc_id)

where

zinc_id is a valid ZINC identification number or an array of ZINC ID numbers

uploadZINC()

uploadZINC(smiles,voucher)

where

smiles is an array of SMILES with optional identifiers seaparated by whitespace
voucher is an optional voucher to bypass IP based throttles, or 

similarto()

similarto(smiles,tanimoto,voucher)

where

smiles is an array of SMILES with optional identifiers separated by whitespace
tanimoto is a tanimoto similarity cutoff value (0-100)
voucher is an optional bypass of IP based throttles, or 


propertydecoys()

propertydecoys(smiles,number,voucher)

where

smiles is an array of SMILES with optional identifiers separated by whitespace
tanimoto is a tanimoto similarity cutoff value (0-100)
voucher is an optional bypass of IP based throttles, or 

SEA

sea(smiles, method, voucher)

where

smiles is an array of SMILES with optional identifiers separated by whitespace
method specifies the method, or the database to use, default 
voucher is an optional bypass of IP based throttles, or 

THC

listTHCtargets()

listTHCtargets()

Purpose: to list the targets that are currently available in THC. Restrictions: none

THClisttopN()

THClisttopN(thc_id)

where

thc_id is the thc entry number, which is availble in listTHCtargets() above
  • Result:
  • Purpose: to list the opt
  • Restrictions:

DUD

listDUDtargets()

listDUDtargets()

where

xx
  • Result:
  • Purpose:
  • Restrictions:


getactives()

getdecoys()

SEA

General

listMethods()

listMethods()

Purpose:

myquotas()

myquotas()

Purpose: to report limits in effect on using DOCK Blaster and other services Restrictions: none

= serverstatus()