ccpn.AnalysisStructure.lib.runManagers package

Submodules

ccpn.AnalysisStructure.lib.runManagers.CyanaRunManager module

Cyana Run Manager

class ccpn.AnalysisStructure.lib.runManagers.CyanaRunManager.CyanaRunManager(**kwargs)

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

Class that maintains Cyana structure calculation functionality

processCalculation()

Process the resulting Cyana-generated files;

setupCalculation() → ccpn.util.Path.Path

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)

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

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)

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

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

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

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)

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()

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

restoreState(runPath=None)

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

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)

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)

ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations.collapse_right_repeated_string(target, repeating='%')

ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations.data_as_nef(overall_result)

ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations.generateNefFile(resultDict, nefPath)

Write the resultDict to nefPath, inserting appropriate metaData

ccpn.AnalysisStructure.lib.runManagers.analyseXplorViolations.parseViolations(fileList) → dict

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)