ccpn.AnalysisStructure.lib.runManagers package

Submodules

ccpn.AnalysisStructure.lib.runManagers.CyanaRunManager module

Cyana Run Manager

class ccpn.AnalysisStructure.lib.runManagers.CyanaRunManager.CyanaRunManager(**kwargs)[source]

Bases: ccpn.AnalysisStructure.lib.runManagers.RunManagerABC.RunManagerABC

Class that maintains Cyana structure calculation functionality

processCalculation()[source]

Process the resulting Cyana-generated files;

setupCalculation() ccpn.util.Path.Path[source]

This sets up the xplor_nih structure calculation; :return The absolute path to the run directory

ccpn.AnalysisStructure.lib.runManagers.RunManagerABC module

A class vor managing Structure calculation Run’s

IN_PROGRESS

class ccpn.AnalysisStructure.lib.runManagers.RunManagerABC.RunManagerABC(**kwargs)[source]

Bases: ccpn.util.traits.CcpNmrJson.CcpNmrJson

Class that maintains structure calculation and save/restore functionality

WARNING
calculationDone
chain

A trait that defines a V3-object, json serialisable through its Pid

chemicalShiftList

A trait that defines a V3-object, json serialisable through its Pid

classVersion = 3.1
fetchDirectory() ccpn.util.Path.Path[source]

Fetch (i.e. get or create if needed) the directory defined by current settings, optionally setting the timestamp depending on self.useTimeStamp save directory as the _runPath attribute for later

:return a Path instance to the directory

nefInputPath

A trait that defines a casting Path object and is json serialisable

nefOutputPath

A trait that defines a casting Path object and is json serialisable

numberOfCores
peakLists

A trait that defines a list of V3-objects, json serialisable through their Pid’s

processDone
property project

- None, immutable - :return the Project instance

restoreState(runPath=None)[source]

Restore the settings from json-file in directory runPath (defaults to the directory defined by current settings).

Parameters

runPath – the path to the directory

runId
runName
property runPath: ccpn.util.Path.Path

- ccpn.util.Path.Path, immutable - Absolute path to the structure calculation run data Either _runPath as currently defined, or

auto constructed from runType, runName, runId and timestamp.

runType
saveAllTraitsToJson = True
saveState() ccpn.util.Path.Path[source]

Save the state of self to a json file in directory self.runPath :return the path of the json file as a Path instance

scriptPath

A trait that defines a casting Path object and is json serialisable

setupCalculation(useTimeStamp) ccpn.util.Path.Path[source]

This sets up the calculation; Needs Sub-classing :param useTimeStamp: add timestamp to the run path :return The absolute path to the run directory

setupDone
useParallel
useTimeStamp
writeNefInputFile() ccpn.util.Path.Path[source]

Generate the input in Nef format :return The absolute path to the Nef input file as a Path instance

wwPdbPath

A trait that defines a casting Path object and is json serialisable

ccpn.AnalysisStructure.lib.runManagers.XplorNihRunManager module

A class for managing xplor_nih Structure calculation Run’s

IN_PROGRESS

class ccpn.AnalysisStructure.lib.runManagers.XplorNihRunManager.XplorNihRunManager(**kwargs)[source]

Bases: ccpn.AnalysisStructure.lib.runManagers.RunManagerABC.RunManagerABC

Class that maintains xplor_nih structure calculation functionality

cleanupDone
ensembleDone
nefViolationPath

A trait that defines a casting Path object and is json serialisable

processCalculation()[source]

Process the resulting Xplor-generated files; includes cleanup, violation analysis and ensemble generation

restoreState(runPath=None)[source]

Restore the settings from json-file in directory runPath (defaults to the directory defined by current settings).

Parameters

runPath – the path to the directory

setupCalculation(useTimeStamp) ccpn.util.Path.Path[source]

This sets up the xplor_nih structure calculation; :return The absolute path to the run directory

violationDone

ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations module

Routines to parse the violations from the xplor_nih fold*.sa.viols files

ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations.analyseXplorViolations(path, nefPath)[source]

Run Garys violation analysis routines on the files (extension ‘sa.viols’) in path, as obtained from an xplor_nih calculation

ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations.collapse_name(names, depth=2)[source]
ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations.collapse_right_repeated_string(target, repeating='%')[source]
ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations.data_as_nef(overall_result)[source]
ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations.generateNefFile(resultDict, nefPath)[source]

Write the resultDict to nefPath, inserting appropriate metaData

ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations.parseViolations(fileList) dict[source]

Parse the file in fileList and return a dict with the results

ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations.viol_to_nef(file_handle, model, file_path)[source]