Biskit :: Dock :: Docker :: Docker :: Class Docker

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Class Docker

Prepare and run a hex docking for one or several models of a receptor and ligand pair. Collect docking results into a growing ComplexList.

The docking runs are started in seperate Threads. External objects can register a method with call_when_done() that is called whenever a docking has finished. The waitForLastHex() method can be called to wait until all currently running dockings are finished.

The models in the 2 given dictionaries might get different chainIds but Docker doesn't save them.

To Do: implement that as JobMaster / JobSlave instead, so that also the Hex-file parsing is distributed.

Instance Methods

__init__(self, recDic, ligDic, recPdb=None, ligPdb=None, comPdb=None, out='hex_%s', soln=512, recChainId=None, ligChainId=None, macDock=None, bin=settings.hex_bin, verbose=1)

str prepareOutFolder(self, fout)
Setup an output folder

PDBModel __setChainID(self, m, ids)
set chaiID for Hex pdb files

dict prepareHexPdbs(self, modelDic, idList, subDir)
create HEX-formatted PDB for each model

(str, str) createHexInp(self, nRec, nLig)
Create a HEX macro file for docking a rec lig pair.

runHex(self, finp, log=0, ncpu=2, nice=0, host=os.uname() [1])

countDifferentModels(self, lst)

doneHex(self, runner)
Do something after hex has finished.

failedHex(self, runner)
notify of failed hex run.

waitForLastHex(self)
Return after the last hex thread has finished.

set_call_when_done(RunThread)

set_call_when_failed(RunThread)

Method Details

init(self, recDic, ligDic, recPdb=None, ligPdb=None, comPdb=None, out='hex_%s', soln=512, recChainId=None, ligChainId=None, macDock=None, bin=settings.hex_bin, verbose=1)
(Constructor)

Parameters:

recDic (dict) - receptor dictionary
ligDic (dict) - ligand dictionary
recPdb (str) - hex-formatted PDB with rec models
ligPdb (str) - hex-formatted PDB with lig models
comPdb (str) - hex-formatted PDB with com models
soln (int) - number of solutions to keep from HEX (default 512)
recChainId ([str]) - force chain IDs only for HEX
ligChainId ([str]) - force chain IDs only for HEX
out (str) - out folder name, will be formatted against date
macDock (1|0) - force macro docking ON or OFF (default: size decides)
bin (str) - path to HEX binary
verbose (1|0) - verbosity level (default: 1)

prepareOutFolder(self, fout)

Setup an output folder

Parameters:

fout (str) - outfile name

Returns: str: out path

__setChainID(self, m, ids)

set chaiID for Hex pdb files

Parameters:

m (PDBModel) - model
ids ([str]) - chain id, len(ids) == m.lenChains

Returns: PDBModel: m is changed directly

prepareHexPdbs(self, modelDic, idList, subDir)

create HEX-formatted PDB for each model

Parameters:

modelDic (dict) - model dictionary to be prepared for HEX
idList ([str]) - force chain IDs for HEX pdb files
subDir (str) - 'rec' or 'lig'

Returns: dict: { modelNumber : file_name_created, .. }

createHexInp(self, nRec, nLig)

Create a HEX macro file for docking a rec lig pair.

Parameters:

nRec (int) - model number rec in model dictionaries
nLig (int) - model number lig in model dictionaries

Returns: (str, str): macro file name, future out file name

Raises:

DockerError - if macro dock option is different from previous call

runHex(self, finp, log=0, ncpu=2, nice=0, host=os.uname() [1])

Parameters:

finp (str) - hex macro file
log (1|0) - write log file
ncpu (int) - number of cpus to use
nice (int) - nice value for HEX job (default: 0)
host (str) - host to run jon on

countDifferentModels(self, lst)

doneHex(self, runner)

Do something after hex has finished. Notify all threads waiting on self.lockMsg

failedHex(self, runner)

notify of failed hex run.

waitForLastHex(self)

Return after the last hex thread has finished.

set_call_when_done(RunThread)

set_call_when_failed(RunThread)