Package schrodinger :: Package pipeline :: Package stages :: Module combine :: Class GenerateCovalentComplexesStage

Class GenerateCovalentComplexesStage

    UserDict.UserDict --+        
                        |        
UserDict.IterableUserDict --+    
                            |    
                  stage.Stage --+
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                               GenerateCovalentComplexesStage


Stage for combining specified receptor with specified ligands
via covalent bond to form complexes. Receptor atom number must be
specified, and a list of SMARTS patterns that match the leaving
group in the ligand. The pattern may include part of the ligand,
but the position of the leaving group atom bonded to the ligand must
also be specified.

For example, in ligand:

R-CH2-CH2-OH

The hydroxyl leaving group may be specified as:
SMARTS: [C;H2][C;H2]OH
POSITION: 3


Input1: receptor file
Input2: ligands file
Output1: generated complexes file

The keywords specific to this stage are:
    RECEP_STAYING_ATOM  Atom number in receptor to bond the ligand to.
    RECEP_LEAVING_ATOM  Atom number in receptor of atom to replace when
                        making a bond.

    SMARTS      A list of SMARTS patterns

    POSITIONS   A list of positions of atoms for each SMARTS pattern listed

    MARK_LIGAND Set the chain:resnum of ligand in the complex to this value
                 (default X:1:)

    USE_DOUBLE  Obsolete


The stage takes up to ten input structure files sets and generates one
output structure file set.

Instance Methods

[hide private]

__init__(self, *args, **kwargs)
See class docstring.

operate(self)
This method is required by base class, and gets called when the stage starts running.

writeComplex(self, complex_st)

deleteReceptorLeavingGroup(self, st, leaving_atom_num, staying_atom_num)
Called for both receptor structure.

deleteLigandLeavingGroup(self, st, leaving_atom_num)
Called for both ligand structures.

makeComplex(self, receptor_st, staying_rec_atom_num, leaving_rec_atom_num, ligand_st, leaving_lig_atom_num)
Combine receptor_st and ligand_st into one structure, break the bond between the ligand and the leaving group, remove the leaving group, and make a bond between the ligand and the receptor.

Inherited from stage.Stage: JobDJOptions, __getitem__, __getstate__, addExpectedInput, addExpectedOutput, addOutputFile, checkFile, checkFiles, checkInputs, checkParameters, checkProducts, debug, dump, error, exit, genFileName, genOutputFileName, getAdjustedNJobs, getCleanupRequested, getHostList, getHostStr, getInput, getInputNames, getJobDJ, getLocal, getMaxRetries, getNJobs, getName, getOutput, getOutputName, getOutputNames, getRuntimePath, getStageDirectory, getVerbosity, hasCompleted, hasStarted, info, iterInputs, log, lognoret, mainProduct, outputRequested, productsInstalled, reportParameters, requiredProduct, requiredProductRuntime, run, runJobDJ, setInput, setJobDJOptions, setJobOptions, setMainProduct, setOutput, setOutputName, updateJobdj, validateValues, waitForFileStatus, waitForFiles, warning

Inherited from stage.Stage (private): _adjustNJobs, _calcStsPerJob, _getNCpus, _inputCheck, _minVersionPresent, _readMessageFromDriver

Inherited from UserDict.IterableUserDict: __iter__

Inherited from UserDict.UserDict: __cmp__, __contains__, __delitem__, __len__, __repr__, __setitem__, clear, copy, get, has_key, items, iteritems, iterkeys, itervalues, keys, pop, popitem, setdefault, update, values

Class Methods

[hide private]

Inherited from UserDict.UserDict: fromkeys

Class Variables

[hide private]

Inherited from UserDict.UserDict: __hash__

Method Details

[hide private]

init(self, *args, **kwargs)
(Constructor)

See class docstring. All arguments are passed to Stage constructor.

Overrides: UserDict.UserDict.__init__

operate(self)

This method is required by base class, and gets called when the stage starts running.

Overrides: stage.Stage.operate

deleteReceptorLeavingGroup(self, st, leaving_atom_num, staying_atom_num)

Called for both receptor structure. Finds the leaving group atoms and deletes them. Returns modified structure and the renumbered staying atom.

deleteLigandLeavingGroup(self, st, leaving_atom_num)

Called for both ligand structures. Finds the leaving group atoms and deletes them. Returns modified structure and atom number which the leaving group was bound to.

makeComplex(self, receptor_st, staying_rec_atom_num, leaving_rec_atom_num, ligand_st, leaving_lig_atom_num)

Combine receptor_st and ligand_st into one structure, break the bond between the ligand and the leaving group, remove the leaving group, and make a bond between the ligand and the receptor. The length & angles of the new bond are adjusted as well.

Class GenerateCovalentComplexesStage

__init__(self, *args, **kwargs) (Constructor)

operate(self)

deleteReceptorLeavingGroup(self, st, leaving_atom_num, staying_atom_num)

deleteLigandLeavingGroup(self, st, leaving_atom_num)

makeComplex(self, receptor_st, staying_rec_atom_num, leaving_rec_atom_num, ligand_st, leaving_lig_atom_num)

init(self, *args, **kwargs)
(Constructor)