ccpn.framework.lib.ccpnNef package

Subpackages

Submodules

ccpn.framework.lib.ccpnNef.CcpnNefCommon module

Module Documentation here

ccpn.framework.lib.ccpnNef.CcpnNefContent module

Module Documentation here

class ccpn.framework.lib.ccpnNef.CcpnNefContent.CcpnNefContent[source]

Bases: object

contentNef(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None)[source]

Verify import of selection from dataBlock into existing/empty Project

content_ccpn_additional_data(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
content_ccpn_assignment(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
content_ccpn_calculation_data(parent, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, value: Optional[str] = None) → Optional[ccpn.util.OrderedSet.OrderedSet][source]

Get the contents for ccpn_calculation_data loop

content_ccpn_calculation_step(parent, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, value: Optional[str] = None) → Optional[ccpn.util.OrderedSet.OrderedSet][source]

Get the contents for ccpn_calculation_step loop

content_ccpn_collections(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
content_ccpn_complex(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents of ccpn_complex saveFrame

content_ccpn_complex_chain(parent: ccpn.core.Complex.Complex, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents of ccpn_complex_chain loop

content_ccpn_dataframe(parent, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, dataSet: str, name: str, key) → Optional[ccpn.util.OrderedSet.OrderedSet][source]

Get the contents for ccpn_dataframe loop

content_ccpn_dataset(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
content_ccpn_datatable(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents of ccpn_datatable saveFrame

content_ccpn_group_spectrum(parent: ccpn.core.SpectrumGroup.SpectrumGroup, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents of ccpn_group_spectrum loop

content_ccpn_history(parent, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, date: Optional[str] = None) → Optional[ccpn.util.OrderedSet.OrderedSet][source]

Get the contents for ccpn_history loop

content_ccpn_integral(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None, itemLength=None)[source]
content_ccpn_integral_list(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None, itemLength=None)[source]
content_ccpn_logging(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
content_ccpn_multiplet(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None, itemLength=None)[source]
content_ccpn_multiplet_list(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None, itemLength=None)[source]
content_ccpn_multiplet_peaks(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents of ccpn_multiplet_peaks loop

content_ccpn_notes(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
content_ccpn_parameter(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
content_ccpn_peak_cluster(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None, itemLength=None)[source]
content_ccpn_peak_cluster_peaks(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents of ccpn_peak_cluster_peaks loop

content_ccpn_peak_list(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None, itemLength=None)[source]
content_ccpn_restraint_violation(restraintTable: ccpn.core.RestraintTable.RestraintTable, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemLength: Optional[int] = None) → Optional[ccpn.util.OrderedSet.OrderedSet][source]

Get the contents for ccpn_restraint_violation loops

content_ccpn_restraint_violation_list(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents of ccpn_distance_restraint_violation_list saveFrame

content_ccpn_sample(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
content_ccpn_sample_component(parent: ccpn.core.Sample.Sample, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, sampleName: Optional[str] = None) → Optional[ccpn.util.OrderedSet.OrderedSet][source]

Get the contents for ccpn_sample_component loop

content_ccpn_spectrum_group(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents of ccpn_spectrum_group saveFrame

content_ccpn_spectrum_reference_substances(parent: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **kwargs)[source]

Get the contents of ccpn_group_spectrum loop

content_ccpn_substance(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents of ccpn_substance saveFrame

content_ccpn_substance_reference_spectra(parent: ccpn.core.Substance.Substance, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **kwargs)[source]

Get the contents of ccpn_group_spectrum loop

content_nef_chemical_shift(parent: ccpn.core.ChemicalShiftList.ChemicalShiftList, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame) → ccpn.util.OrderedSet.OrderedSet[source]

Get the contents of nef_chemical_shift loop

content_nef_chemical_shift_list(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents of nef_chemical_shift_list saveFrame

get the contents of nef_covalent_links loop

content_nef_molecular_system(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents nef_molecular_system saveFrame

content_nef_nmr_spectrum(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
content_nef_peak(peakList: ccpn.core.PeakList.PeakList, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None, itemLength: Optional[int] = None)[source]

Get the contents of nef_peak loop

content_nef_peak_assignments(peakList: ccpn.core.PeakList.PeakList, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None, itemLength: Optional[int] = None)[source]

Get the contents of nef_peak_assignments from nef_peak loop

content_nef_peaks(peakList: ccpn.core.PeakList.PeakList, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None, itemLength: Optional[int] = None)[source]

Get the contents of nef_peak loop

content_nef_restraint(restraintTable: ccpn.core.RestraintTable.RestraintTable, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemLength: Optional[int] = None) → Optional[ccpn.util.OrderedSet.OrderedSet][source]

Get the contents for nef_distance_restraint, nef_dihedral_restraint, nef_rdc_restraint and ccpn_restraint loops

content_nef_restraint_list(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Get the contents of nef_restraint_list saveFrame

content_nef_sequence(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame) → ccpn.util.OrderedSet.OrderedSet[source]

get contents of the nef_sequence loop

contents = {'ccpn_additional_data': <function CcpnNefContent.content_ccpn_additional_data>, 'ccpn_assignment': <function CcpnNefContent.content_ccpn_assignment>, 'ccpn_calculation_data': <function CcpnNefContent.content_ccpn_calculation_data>, 'ccpn_calculation_step': <function CcpnNefContent.content_ccpn_calculation_step>, 'ccpn_collection': <function CcpnNefContent._noLoopContent>, 'ccpn_collections': <function CcpnNefContent.content_ccpn_collections>, 'ccpn_complex': <function CcpnNefContent.content_ccpn_complex>, 'ccpn_complex_chain': <function CcpnNefContent.content_ccpn_complex_chain>, 'ccpn_dataframe': <function CcpnNefContent.content_ccpn_dataframe>, 'ccpn_dataset': <function CcpnNefContent.content_ccpn_dataset>, 'ccpn_datatable': <function CcpnNefContent.content_ccpn_datatable>, 'ccpn_datatable_data': <function CcpnNefContent._noLoopContent>, 'ccpn_datatable_metadata': <function CcpnNefContent._noLoopContent>, 'ccpn_dihedral_restraint_violation': functools.partial(<function CcpnNefContent.content_ccpn_restraint_violation>, itemLength=4), 'ccpn_dihedral_restraint_violation_list': <function CcpnNefContent.content_ccpn_restraint_violation_list>, 'ccpn_distance_restraint_violation': functools.partial(<function CcpnNefContent.content_ccpn_restraint_violation>, itemLength=2), 'ccpn_distance_restraint_violation_list': <function CcpnNefContent.content_ccpn_restraint_violation_list>, 'ccpn_group_spectrum': <function CcpnNefContent.content_ccpn_group_spectrum>, 'ccpn_history': <function CcpnNefContent.content_ccpn_history>, 'ccpn_integral': <function CcpnNefContent.content_ccpn_integral>, 'ccpn_integral_list': <function CcpnNefContent.content_ccpn_integral_list>, 'ccpn_internal_data': <function CcpnNefContent._noLoopContent>, 'ccpn_logging': <function CcpnNefContent.content_ccpn_logging>, 'ccpn_multiplet': <function CcpnNefContent.content_ccpn_multiplet>, 'ccpn_multiplet_list': <function CcpnNefContent.content_ccpn_multiplet_list>, 'ccpn_multiplet_peaks': <function CcpnNefContent._noLoopContent>, 'ccpn_note': <function CcpnNefContent._noLoopContent>, 'ccpn_notes': <function CcpnNefContent.content_ccpn_notes>, 'ccpn_parameter': <function CcpnNefContent.content_ccpn_parameter>, 'ccpn_peak_cluster': <function CcpnNefContent.content_ccpn_peak_cluster>, 'ccpn_peak_cluster_list': <function CcpnNefContent._contentLoops>, 'ccpn_peak_cluster_peaks': <function CcpnNefContent.content_ccpn_peak_cluster_peaks>, 'ccpn_peak_list': <function CcpnNefContent.content_ccpn_peak_list>, 'ccpn_rdc_restraint_violation': functools.partial(<function CcpnNefContent.content_ccpn_restraint_violation>, itemLength=2), 'ccpn_rdc_restraint_violation_list': <function CcpnNefContent.content_ccpn_restraint_violation_list>, 'ccpn_restraint': functools.partial(<function CcpnNefContent.content_nef_restraint>, itemLength=2), 'ccpn_restraint_list': <function CcpnNefContent.content_nef_restraint_list>, 'ccpn_restraint_violation_list_metadata': <function CcpnNefContent._noLoopContent>, 'ccpn_sample': <function CcpnNefContent.content_ccpn_sample>, 'ccpn_sample_component': <function CcpnNefContent.content_ccpn_sample_component>, 'ccpn_spectrum_dimension': <function CcpnNefContent._noLoopContent>, 'ccpn_spectrum_group': <function CcpnNefContent.content_ccpn_spectrum_group>, 'ccpn_spectrum_reference_substances': <function CcpnNefContent.content_ccpn_spectrum_reference_substances>, 'ccpn_substance': <function CcpnNefContent.content_ccpn_substance>, 'ccpn_substance_reference_spectra': <function CcpnNefContent.content_ccpn_substance_reference_spectra>, 'ccpn_substance_synonym': <function CcpnNefContent._noLoopContent>, 'nef_chemical_shift': <function CcpnNefContent.content_nef_chemical_shift>, 'nef_chemical_shift_list': <function CcpnNefContent.content_nef_chemical_shift_list>, 'nef_covalent_links': <function CcpnNefContent.content_nef_covalent_links>, 'nef_dihedral_restraint': functools.partial(<function CcpnNefContent.content_nef_restraint>, itemLength=4), 'nef_dihedral_restraint_list': <function CcpnNefContent.content_nef_restraint_list>, 'nef_distance_restraint': functools.partial(<function CcpnNefContent.content_nef_restraint>, itemLength=2), 'nef_distance_restraint_list': <function CcpnNefContent.content_nef_restraint_list>, 'nef_molecular_system': <function CcpnNefContent.content_nef_molecular_system>, 'nef_nmr_meta_data': <function CcpnNefContent._contentLoops>, 'nef_nmr_spectrum': <function CcpnNefContent.content_nef_nmr_spectrum>, 'nef_peak': <function CcpnNefContent.content_nef_peak>, 'nef_peak_assignments': <function CcpnNefContent.content_nef_peak_assignments>, 'nef_peak_restraint_link': <function CcpnNefContent._noLoopContent>, 'nef_peak_restraint_links': <function CcpnNefContent.content_nef_peak_restraint_links>, 'nef_peaks': <function CcpnNefContent.content_nef_peaks>, 'nef_program_script': <function CcpnNefContent._noLoopContent>, 'nef_rdc_restraint': functools.partial(<function CcpnNefContent.content_nef_restraint>, itemLength=2), 'nef_rdc_restraint_list': <function CcpnNefContent.content_nef_restraint_list>, 'nef_related_entries': <function CcpnNefContent._noLoopContent>, 'nef_run_history': <function CcpnNefContent._noLoopContent>, 'nef_sequence': <function CcpnNefContent.content_nef_sequence>, 'nef_spectrum_dimension': <function CcpnNefContent._noLoopContent>, 'nef_spectrum_dimension_transfer': <function CcpnNefContent._noLoopContent>, 'nmr_atom': <function CcpnNefContent._noLoopContent>, 'nmr_chain': <function CcpnNefContent._noLoopContent>, 'nmr_residue': <function CcpnNefContent._noLoopContent>}
traverseDataBlock(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None, traverseFunc=None)[source]

Traverse the saveFrames in the correct order

ccpn.framework.lib.ccpnNef.CcpnNefHelper module

This file contains CcpnNefImporter class

ccpn.framework.lib.ccpnNef.CcpnNefImporter module

This file contains CcpnNefImporter class

class ccpn.framework.lib.ccpnNef.CcpnNefImporter.CcpnNefImporter(errorLogging='standard', validateDictPath=None, hidePrefix=True)[source]

Bases: ccpn.util.nef.NefImporter.NefImporter

A class for customization of the general NefImporter class

property collections

- None, mutable -

importIntoProject(project)[source]

Import the data of self into project, using a previously attached reader (auto-generated if None).

Parameters

project – a Project instance

loadFile(fileName=None, mode='standard')[source]

Load and parse Nef-file fileName :param fileName: path to a Nef-file :return a NmrDataBlock instance

loadText(text, mode='standard')[source]

Load and parse Nef-formatted text :param text: Nef-formatted text :return a NmrDataBlock instance

upgradeDataSetIds()[source]

Update the saveFrames Replace occurrences of DATANAME_DEPRECATED with DATANAME

ccpn.framework.lib.ccpnNef.CcpnNefIo module

Code for CCPN-specific NEF I/O

class ccpn.framework.lib.ccpnNef.CcpnNefIo.CcpnNefReader(application, specificationFile: Optional[str] = None, mode: str = 'standard', testing: bool = False)[source]

Bases: ccpn.framework.lib.ccpnNef.CcpnNefContent.CcpnNefContent

clearSaveFrames(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None, traverseFunc=None)[source]

Clear the contents and rowErrors of the nef dict

error(message: str, source, objects: Optional[tuple] = None)[source]

Update the error log with the message

fetchStructureData(sDataName: Optional[str] = None, serial: Optional[int] = None)[source]

Fetch StructureData with given serial. If input is None, use self.defaultDataSetSerial If that too is None, create a new DataSet and use its serial as the default

NB when reading, all StructureData with known serials should be instantiated BEFORE calling with input None

getNMRStarData(path: str)[source]

Get NEF data structure from file

getNefData(path: str)[source]

Get NEF data structure from file

getStructureData(serial: Optional[int] = None)[source]

Get the required DataSet with given serial. If input is None, use self.defaultDataSetSerial If that too is None, create a new DataSet and use its serial as the default

NB when reading, all StructureData with known serials should be instantiated BEFORE calling with input None

importExistingProject(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None)[source]

Import selection from dataBlock into existing/empty Project

importNewNMRStarProject(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True)[source]

Import entire project from dataBlock into empty Project

importNewProject(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True)[source]

Import entire project from dataBlock into empty Project

importers = {'ccpn_additional_data': <function CcpnNefReader.load_ccpn_additional_data>, 'ccpn_assignment': <function CcpnNefReader.load_ccpn_assignment>, 'ccpn_calculation_data': <function CcpnNefReader.load_ccpn_calculation_data>, 'ccpn_calculation_step': <function CcpnNefReader.load_ccpn_calculation_step>, 'ccpn_collections': <function CcpnNefReader.load_ccpn_collections>, 'ccpn_complex': <function CcpnNefReader.load_ccpn_complex>, 'ccpn_complex_chain': <function CcpnNefReader.load_ccpn_complex_chain>, 'ccpn_dataframe': <function CcpnNefReader.load_ccpn_dataframe>, 'ccpn_dataset': <function CcpnNefReader.load_ccpn_dataset>, 'ccpn_datatable': <function CcpnNefReader.load_ccpn_datatable>, 'ccpn_datatable_data': <function CcpnNefReader.load_ccpn_datatable_data>, 'ccpn_datatable_metadata': <function CcpnNefReader.load_ccpn_datatable_metadata>, 'ccpn_dihedral_restraint_violation': <function CcpnNefReader.load_ccpn_restraint_violation>, 'ccpn_dihedral_restraint_violation_list': <function CcpnNefReader.load_ccpn_restraint_violation_list>, 'ccpn_distance_restraint_violation': <function CcpnNefReader.load_ccpn_restraint_violation>, 'ccpn_distance_restraint_violation_list': <function CcpnNefReader.load_ccpn_restraint_violation_list>, 'ccpn_group_spectrum': <function CcpnNefReader.load_ccpn_group_spectrum>, 'ccpn_history': <function CcpnNefReader.load_ccpn_history>, 'ccpn_integral': <function CcpnNefReader.load_ccpn_integral>, 'ccpn_integral_list': <function CcpnNefReader.load_ccpn_integral_list>, 'ccpn_logging': <function CcpnNefReader.load_ccpn_logging>, 'ccpn_multiplet': <function CcpnNefReader.load_ccpn_multiplet>, 'ccpn_multiplet_list': <function CcpnNefReader.load_ccpn_multiplet_list>, 'ccpn_multiplet_peaks': <function CcpnNefReader.load_ccpn_multiplet_peaks>, 'ccpn_notes': <function CcpnNefReader.load_ccpn_notes>, 'ccpn_parameter': <function CcpnNefReader.load_ccpn_parameter>, 'ccpn_peak_cluster_list': <function CcpnNefReader.load_ccpn_peak_cluster_list>, 'ccpn_peak_list': <function CcpnNefReader.load_ccpn_peak_list>, 'ccpn_rdc_restraint_violation': <function CcpnNefReader.load_ccpn_restraint_violation>, 'ccpn_rdc_restraint_violation_list': <function CcpnNefReader.load_ccpn_restraint_violation_list>, 'ccpn_restraint': <function CcpnNefReader.load_nef_restraint>, 'ccpn_restraint_list': <function CcpnNefReader.load_nef_restraint_list>, 'ccpn_restraint_violation_list_metadata': <function CcpnNefReader.load_ccpn_restraint_violation_list_metadata>, 'ccpn_sample': <function CcpnNefReader.load_ccpn_sample>, 'ccpn_sample_component': <function CcpnNefReader.load_ccpn_sample_component>, 'ccpn_spectrum_dimension': <function CcpnNefReader.load_ccpn_spectrum_dimension>, 'ccpn_spectrum_group': <function CcpnNefReader.load_ccpn_spectrum_group>, 'ccpn_spectrum_reference_substances': <function CcpnNefReader.load_ccpn_spectrum_reference_substances>, 'ccpn_substance': <function CcpnNefReader.load_ccpn_substance>, 'ccpn_substance_reference_spectra': <function CcpnNefReader.load_ccpn_substance_reference_spectra>, 'ccpn_substance_synonym': <function CcpnNefReader.load_ccpn_substance_synonym>, 'nef_chemical_shift': <function CcpnNefReader.load_nef_chemical_shift>, 'nef_chemical_shift_list': <function CcpnNefReader.load_nef_chemical_shift_list>, 'nef_covalent_links': <function CcpnNefReader.load_nef_covalent_links>, 'nef_dihedral_restraint': <function CcpnNefReader.load_nef_restraint>, 'nef_dihedral_restraint_list': <function CcpnNefReader.load_nef_restraint_list>, 'nef_distance_restraint': <function CcpnNefReader.load_nef_restraint>, 'nef_distance_restraint_list': <function CcpnNefReader.load_nef_restraint_list>, 'nef_molecular_system': <function CcpnNefReader.load_nef_molecular_system>, 'nef_nmr_meta_data': <function CcpnNefReader.load_nef_nmr_meta_data>, 'nef_nmr_spectrum': <function CcpnNefReader.load_nef_nmr_spectrum>, 'nef_peak_restraint_link': <function CcpnNefReader.load_nef_peak_restraint_link>, 'nef_peak_restraint_links': <function CcpnNefReader.load_nef_peak_restraint_links>, 'nef_rdc_restraint': <function CcpnNefReader.load_nef_restraint>, 'nef_rdc_restraint_list': <function CcpnNefReader.load_nef_restraint_list>, 'nef_sequence': <function CcpnNefReader.load_nef_sequence>}
load_ccpn_additional_data(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
load_ccpn_assignment(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
load_ccpn_calculation_data(parent: ccpn.core.StructureData.StructureData, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name: str)[source]

load dataSet.calculation_step loop

load_ccpn_calculation_step(parent: ccpn.core.StructureData.StructureData, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name: str)[source]

load dataSet.calculation_step loop

load_ccpn_collections(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
load_ccpn_complex(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
load_ccpn_complex_chain(parent: ccpn.core.Complex.Complex, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

load ccpn_complex_chain loop

load_ccpn_dataframe(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **parameters)[source]

Serves to load ccpn_distance_restraint_violation loops

load_ccpn_dataset(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

load dataSet savefame

load_ccpn_datatable(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

load ccpn_datatable saveFrame

load_ccpn_datatable_data(data: ccpn.core.Data.Data, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, run_id: str = '', itemLength: Optional[int] = None)[source]

Serves to load ccpn_<type>_datatable_data loop

load_ccpn_datatable_metadata(data: ccpn.core.Data.Data, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, run_id: str = '', itemLength: Optional[int] = None)[source]

Serves to load ccpn_<type>_datatable_metadata loops

load_ccpn_group_spectrum(parent: ccpn.core.SpectrumGroup.SpectrumGroup, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

load ccpn_group_spectrum loop

load_ccpn_history(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name: str)[source]

Serves to load ccpn_history loops

load_ccpn_integral(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, peakListId=None) → List[ccpn.core.Integral.Integral][source]
load_ccpn_integral_list(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, peakListId=None) → List[ccpn.core.IntegralList.IntegralList][source]
load_ccpn_logging(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

load ccpn_logging saveFrame

load_ccpn_multiplet(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, peakListId=None) → List[ccpn.core.Multiplet.Multiplet][source]
load_ccpn_multiplet_list(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, peakListId=None) → List[ccpn.core.MultipletList.MultipletList][source]
load_ccpn_multiplet_peaks(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, peakListId=None) → List[ccpn.core.Multiplet.Multiplet][source]
load_ccpn_notes(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
load_ccpn_parameter(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
load_ccpn_peak_cluster_list(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
load_ccpn_peak_list(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, peakListId=None) → List[ccpn.core.PeakList.PeakList][source]
load_ccpn_restraint_violation(data: ccpn.core.Data.Data, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, run_id: str = '', itemLength: Optional[int] = None)[source]

Serves to load ccpn_<type>_restraint_violation loops

load_ccpn_restraint_violation_list(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Serves to load ccpn_restraint_violation_list

load_ccpn_restraint_violation_list_metadata(data: ccpn.core.Data.Data, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, run_id: str = '', itemLength: Optional[int] = None)[source]

Serves to load ccpn_<type>_restraint_violation loops

load_ccpn_sample(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
load_ccpn_sample_component(parent: ccpn.core.Sample.Sample, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

load ccpn_sample_component loop

load_ccpn_spectrum_dimension(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame) → dict[source]

Read ccpn_spectrum_dimension loop, set the relevant values, and return the spectrum and other parameters for further processing

load_ccpn_spectrum_group(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
load_ccpn_spectrum_reference_substances(parent: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **kwargs)[source]

load reference_substances loop

load_ccpn_substance(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
load_ccpn_substance_reference_spectra(parent: ccpn.core.Substance.Substance, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **kwargs)[source]

load reference_spectra loop

load_ccpn_substance_synonym(parent: ccpn.core.Substance.Substance, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

load ccpn_substance_synonym loop

load_nef_chemical_shift(parent: ccpn.core.ChemicalShiftList.ChemicalShiftList, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

load nef_chemical_shift loop

load_nef_chemical_shift_list(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

load nef_chemical_shift_list saveFrame

Load nef_sequence loop

load_nef_molecular_system(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

load nef_molecular_system saveFrame

load_nef_nmr_meta_data(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

load nef_nmr_meta_data saveFrame

load_nef_nmr_spectrum(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Load an nmr spectrum, peaks and all associated things from the saveframe :return a PeakList instance

load_nef_peak(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, peakListId=None) → List[ccpn.core.Peak.Peak][source]

Serves to load nef_peak loop

Load nef_peak_restraint_link loop

load nef_peak_restraint_links saveFrame

load_nef_restraint(restraintTable: ccpn.core.RestraintTable.RestraintTable, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemLength: Optional[int] = None)[source]

Serves to load nef_distance_restraint, nef_dihedral_restraint, nef_rdc_restraint and ccpn_restraint loops

load_nef_restraint_list(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Serves to load nef_distance_restraint_list, nef_dihedral_restraint_list, nef_rdc_restraint_list and ccpn_restraint_list

load_nef_sequence(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Load nef_sequence loop

load_nef_spectrum_dimension_transfer(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
preloadAssignmentData(dataBlock: ccpn.util.nef.StarIo.NmrDataBlock)[source]

Set up NmrChains and NmrResidues with reserved names to ensure the serials are OK and create NmrResidues in connected nmrChains in order

NB later we can store serials in CCPN projects, but something is needed that works anyway

NB, without CCPN-specific tags you can NOT guarantee that connected stretches are stable, and that serials are put back where they came from. This heuristic creates NmrResidues in connected stretches in the order they are found, but this will break if connected stretches appear in multiple shiftlists and some are partial.

process_nef_spectrum_dimension_transfer(spectrum: ccpn.core.Spectrum.Spectrum, dataLists: Sequence[Sequence])[source]
produceNmrAtom(nmrResidue: ccpn.core.NmrResidue.NmrResidue, name: str, isotopeCode=None)[source]

Get NmrAtom from NmrResidue and name, correcting for possible errors

produceNmrChain(chainCode: Optional[str] = None)[source]

Get NmrChain, correcting for possible errors

produceNmrResidue(chainCode: Optional[str] = None, sequenceCode: Optional[str] = None, residueType: Optional[str] = None)[source]

Get NmrResidue, correcting for possible errors

read_nef_spectrum_dimension(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop)[source]

Read nef_spectrum_dimension loop and convert data to a dictionary of ccpnTag:[per-dimension-value]

read_nef_spectrum_dimension_transfer(loop: ccpn.util.nef.StarIo.NmrLoop)[source]
rename_ccpn_assignment(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, contentDataBlocks: Tuple[ccpn.util.nef.StarIo.NmrDataBlock, ...], saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemName=None, newName=None)[source]

Rename an nmr_chain in a ccpn_assignment :param itemName: name of the item to rename - dependent on saveFrame type :param newName: new item name or None to autorename to next available name

rename_ccpn_assignment_sequence_code(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, contentDataBlocks: Tuple[ccpn.util.nef.StarIo.NmrDataBlock, ...], saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemName=None, newName=None)[source]

Rename sequenceCode/serial number for @<n> nmrResidues

rename_ccpn_collection(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, contentDataBlocks: Tuple[ccpn.util.nef.StarIo.NmrDataBlock, ...], saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemName=None, newName=None)[source]

Rename a ccpn_collection in ccpn_collections :param itemName: name of the item to rename - dependent on saveFrame type :param newName: new item name or None to autorename to next available name

rename_ccpn_list(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, contentDataBlocks: Tuple[ccpn.util.nef.StarIo.NmrDataBlock, ...], saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemName=None, newName=None, _lowerCaseName='none')[source]

Rename a ccpn_list in a ccpn_assignment :param itemName: name of the item to rename - dependent on saveFrame type :param newName: new item name or None to autorename to next available name

rename_ccpn_note(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, contentDataBlocks: Tuple[ccpn.util.nef.StarIo.NmrDataBlock, ...], saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemName=None, newName=None)[source]

Rename a ccpn_note in ccpn_notes :param itemName: name of the item to rename - dependent on saveFrame type :param newName: new item name or None to autorename to next available name

rename_ccpn_peak_cluster_list(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, contentDataBlocks: Tuple[ccpn.util.nef.StarIo.NmrDataBlock, ...], saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemName=None, newName=None)[source]

Rename a ccpn_peak_cluster in ccpn_peak_cluster_list :param itemName: name of the item to rename - dependent on saveFrame type :param newName: new item name or None to autorename to next available name

rename_ccpn_peak_list(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, contentDataBlocks: Tuple[ccpn.util.nef.StarIo.NmrDataBlock, ...], saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemName=None, newName=None, _lowerCaseName='none')[source]

Rename a ccpn_list in a ccpn_assignment :param itemName: name of the item to rename - dependent on saveFrame type :param newName: new item name or None to autorename to next available name

rename_ccpn_substance(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, contentDataBlocks: Tuple[ccpn.util.nef.StarIo.NmrDataBlock, ...], saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemName=None, newName=None)[source]

Rename a ccpn_substance :param itemName: name of the item to rename - dependent on saveFrame type :param newName: new item name or None to autorename to next available name

rename_ccpn_table(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, contentDataBlocks: Tuple[ccpn.util.nef.StarIo.NmrDataBlock, ...], saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemName=None, newName=None)[source]

Rename a saveFrame :param itemName: name of the item to rename - dependent on saveFrame type :param newName: new item name or None to autorename to next available name

requires ccpn_structuredata_name

rename_nef_molecular_system(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, contentDataBlocks: Tuple[ccpn.util.nef.StarIo.NmrDataBlock, ...], saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemName=None, newName=None)[source]

Rename a chain in a nef_sequence :param itemName: name of the item to rename - dependent on saveFrame type :param newName: new item name or None to autorename to next available name

rename_saveframe(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, contentDataBlocks: Tuple[ccpn.util.nef.StarIo.NmrDataBlock, ...], saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame, itemName=None, newName=None)[source]

Rename a saveFrame :param itemName: name of the item to rename - dependent on saveFrame type :param newName: new item name or None to autorename to next available name

renames = {'ccpn_collection': <function CcpnNefReader.rename_ccpn_collection>, 'ccpn_complex': <function CcpnNefReader.rename_saveframe>, 'ccpn_dataset': <function CcpnNefReader.rename_saveframe>, 'ccpn_datatable': <function CcpnNefReader.rename_saveframe>, 'ccpn_dihedral_restraint_violation_list': <function CcpnNefReader.rename_ccpn_table>, 'ccpn_distance_restraint_violation_list': <function CcpnNefReader.rename_ccpn_table>, 'ccpn_integral_list': functools.partial(<function CcpnNefReader.rename_ccpn_list>, _lowerCaseName='integral'), 'ccpn_logging': <function CcpnNefReader.rename_saveframe>, 'ccpn_multiplet_list': functools.partial(<function CcpnNefReader.rename_ccpn_list>, _lowerCaseName='multiplet'), 'ccpn_note': <function CcpnNefReader.rename_ccpn_note>, 'ccpn_peak_cluster_list': <function CcpnNefReader.rename_ccpn_peak_cluster_list>, 'ccpn_peak_list': functools.partial(<function CcpnNefReader.rename_ccpn_peak_list>, _lowerCaseName='peak'), 'ccpn_rdc_restraint_violation_list': <function CcpnNefReader.rename_ccpn_table>, 'ccpn_restraint_list': <function CcpnNefReader.rename_saveframe>, 'ccpn_sample': <function CcpnNefReader.rename_saveframe>, 'ccpn_spectrum_group': <function CcpnNefReader.rename_saveframe>, 'ccpn_substance': <function CcpnNefReader.rename_ccpn_substance>, 'nef_chemical_shift_list': <function CcpnNefReader.rename_saveframe>, 'nef_dihedral_restraint_list': <function CcpnNefReader.rename_ccpn_table>, 'nef_distance_restraint_list': <function CcpnNefReader.rename_ccpn_table>, 'nef_rdc_restraint_list': <function CcpnNefReader.rename_ccpn_table>, 'nef_sequence': <function CcpnNefReader.rename_nef_molecular_system>, 'nmr_chain': <function CcpnNefReader.rename_ccpn_assignment>, 'nmr_sequence_code': <function CcpnNefReader.rename_ccpn_assignment_sequence_code>}
searchReplace(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None, searchFrameCode=None, replaceFrameCode=None, replace=False, validFramesOnly=False, frameSearchList=None, attributeSearchList=None, loopSearchList=None, rowSearchList=None)[source]

Search the saveframes for references to findFrameCode If replace is True, will replace all attributes of saveFrame (if in selection, or all if selection is empty) and row items

searchReplaceDict(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None, searchFrameCode=None, replaceFrameCode=None, replace=False, validFramesOnly=False, frameSearchList=None, attributeSearchList=None, loopSearchList=None, rowSearchList=None)[source]

Search the saveframes for references to findFrameCode If replace is True, will replace all attributes of saveFrame (if in selection, or all if selection is empty) and row items

searchReplaceList(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None, searchFrameCode=None, replaceFrameCode=None, replace=False, validFramesOnly=False, frameSearchList=None, attributeSearchList=None, loopSearchList=None, rowSearchList=None)[source]

Search the saveframes for references to attribute list and row list All saveframes are traversed, attributes are processed for saveFrames in categorySearch list (if exists, or all of empty) All searchframeCodes must match for replace to occur

e.g. searchFrameCode = (‘exampleName’, ‘exampleLabel’)

replaceFrameCode = (‘newName’, ‘newLabel’)

attributes to search for are defined in attributeSearchList and rowSearchList

(‘name’, ‘labelling’)

Replace will occur if name == exampleName & labelling == exampleLabel in saveFrame attributes and in row of a loop with columns ‘name’ and ‘labelling’

searchReplaceLoopListNumbered(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None, searchFrameCode=None, replaceFrameCode=None, replace=False, validFramesOnly=False, frameSearchList=None, attributeSearchList=None, loopSearchList=None, rowSearchList=None)[source]

Search the saveframes for references to attribute list and row list All saveframes are traversed, attributes are processed for saveFrames in categorySearch list (if exists, or all of empty) All searchframeCodes must match for replace to occur

e.g. searchFrameCode = (‘exampleName’, ‘exampleLabel’)

replaceFrameCode = (‘newName’, ‘newLabel’)

attributes to search for are defined in attributeSearchList and rowSearchList

(‘name’, ‘labelling’)

Replace will occur if name == exampleName & labelling == exampleLabel in saveFrame attributes and in row of a loop with columns ‘name’ and ‘labelling’

setImportAll(value)[source]

Set/clear the importAll status - used for importing subset of nef file Must be done prior to any content/verify/import

storeContent(source, objects: Optional[dict] = None)[source]

Update the ccpnContent log with the contents of the saveFrames/loops

testErrors(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None)[source]

Print the errors in the nef dict - results generated with _contentNef

testPrint(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None, traverseFunc=None)[source]

Print the contents of the nef dict

traverseDataBlock(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None, traverseFunc=None)[source]

Traverse the saveFrames in the correct order

updateContent(source, objects: Optional[dict] = None)[source]

Update the ccpnContent log with the contents of the saveFrames/loops

updateMetaData(metaDataFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Add meta information to main data set. Must be done at end of read

verifiers = {'ccpn_additional_data': <function CcpnNefReader.verify_ccpn_additional_data>, 'ccpn_assignment': <function CcpnNefReader.verify_ccpn_assignment>, 'ccpn_calculation_data': <function CcpnNefReader.verify_ccpn_calculation_data>, 'ccpn_calculation_step': <function CcpnNefReader.verify_ccpn_calculation_step>, 'ccpn_collection': <function CcpnNefReader._noLoopVerify>, 'ccpn_collections': <function CcpnNefReader.verify_ccpn_collections>, 'ccpn_complex': <function CcpnNefReader.verify_ccpn_complex>, 'ccpn_complex_chain': <function CcpnNefReader.verify_ccpn_complex_chain>, 'ccpn_dataframe': <function CcpnNefReader._noLoopVerify>, 'ccpn_dataset': <function CcpnNefReader.verify_ccpn_dataset>, 'ccpn_datatable': <function CcpnNefReader.verify_ccpn_datatable>, 'ccpn_dihedral_restraint_violation': <function CcpnNefReader.verify_ccpn_restraint_violation>, 'ccpn_dihedral_restraint_violation_list': <function CcpnNefReader.verify_ccpn_restraint_violation_list>, 'ccpn_distance_restraint_violation': <function CcpnNefReader.verify_ccpn_restraint_violation>, 'ccpn_distance_restraint_violation_list': <function CcpnNefReader.verify_ccpn_restraint_violation_list>, 'ccpn_group_spectrum': <function CcpnNefReader.verify_ccpn_group_spectrum>, 'ccpn_history': <function CcpnNefReader._noLoopVerify>, 'ccpn_integral': <function CcpnNefReader.verify_ccpn_integral>, 'ccpn_integral_list': <function CcpnNefReader.verify_ccpn_integral_list>, 'ccpn_internal_data': <function CcpnNefReader._noLoopVerify>, 'ccpn_logging': <function CcpnNefReader.verify_ccpn_logging>, 'ccpn_multiplet': <function CcpnNefReader.verify_ccpn_multiplet>, 'ccpn_multiplet_list': <function CcpnNefReader.verify_ccpn_multiplet_list>, 'ccpn_multiplet_peaks': <function CcpnNefReader.verify_ccpn_multiplet_peaks>, 'ccpn_note': <function CcpnNefReader._noLoopVerify>, 'ccpn_notes': <function CcpnNefReader.verify_ccpn_notes>, 'ccpn_parameter': <function CcpnNefReader.verify_ccpn_parameter>, 'ccpn_peak_cluster': <function CcpnNefReader.verify_ccpn_peak_cluster>, 'ccpn_peak_cluster_list': <function CcpnNefReader.verify_ccpn_peak_cluster_list>, 'ccpn_peak_cluster_peaks': <function CcpnNefReader.verify_ccpn_peak_cluster_peaks>, 'ccpn_peak_list': <function CcpnNefReader.verify_ccpn_peak_list>, 'ccpn_rcd_restraint_violation': <function CcpnNefReader.verify_ccpn_restraint_violation>, 'ccpn_rdc_restraint_violation_list': <function CcpnNefReader.verify_ccpn_restraint_violation_list>, 'ccpn_restraint': <function CcpnNefReader.verify_nef_restraint>, 'ccpn_restraint_list': <function CcpnNefReader.verify_nef_restraint_list>, 'ccpn_sample': <function CcpnNefReader.verify_ccpn_sample>, 'ccpn_sample_component': <function CcpnNefReader.verify_ccpn_sample_component>, 'ccpn_spectrum_dimension': <function CcpnNefReader._noLoopVerify>, 'ccpn_spectrum_group': <function CcpnNefReader.verify_ccpn_spectrum_group>, 'ccpn_substance': <function CcpnNefReader.verify_ccpn_substance>, 'ccpn_substance_synonym': <function CcpnNefReader._noLoopVerify>, 'nef_chemical_shift': <function CcpnNefReader.verify_nef_chemical_shift>, 'nef_chemical_shift_list': <function CcpnNefReader.verify_nef_chemical_shift_list>, 'nef_covalent_links': <function CcpnNefReader._noLoopVerify>, 'nef_dihedral_restraint': <function CcpnNefReader.verify_nef_restraint>, 'nef_dihedral_restraint_list': <function CcpnNefReader.verify_nef_restraint_list>, 'nef_distance_restraint': <function CcpnNefReader.verify_nef_restraint>, 'nef_distance_restraint_list': <function CcpnNefReader.verify_nef_restraint_list>, 'nef_molecular_system': <function CcpnNefReader._verifyLoops>, 'nef_nmr_meta_data': <function CcpnNefReader.verify_nef_nmr_meta_data>, 'nef_nmr_spectrum': <function CcpnNefReader.verify_nef_nmr_spectrum>, 'nef_peak': <function CcpnNefReader.verify_nef_peak>, 'nef_peak_restraint_link': <function CcpnNefReader._noLoopVerify>, 'nef_peak_restraint_links': <function CcpnNefReader._verifyLoops>, 'nef_program_script': <function CcpnNefReader._noLoopVerify>, 'nef_rdc_restraint': <function CcpnNefReader.verify_nef_restraint>, 'nef_rdc_restraint_list': <function CcpnNefReader.verify_nef_restraint_list>, 'nef_related_entries': <function CcpnNefReader._noLoopVerify>, 'nef_run_history': <function CcpnNefReader._noLoopVerify>, 'nef_sequence': <function CcpnNefReader.verify_nef_sequence>, 'nef_spectrum_dimension': <function CcpnNefReader._noLoopVerify>, 'nef_spectrum_dimension_transfer': <function CcpnNefReader._noLoopVerify>, 'nmr_atom': <function CcpnNefReader._noLoopVerify>, 'nmr_chain': <function CcpnNefReader._noLoopVerify>, 'nmr_residue': <function CcpnNefReader._noLoopVerify>}
verifyProject(project: ccpn.core.Project.Project, dataBlock: ccpn.util.nef.StarIo.NmrDataBlock, projectIsEmpty: bool = True, selection: Optional[dict] = None)[source]

Verify import of selection from dataBlock into existing/empty Project

verify_ccpn_additional_data(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
verify_ccpn_assignment(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
verify_ccpn_calculation_data(parent: ccpn.core.StructureData.StructureData, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name: str)[source]

verify dataSet.calculation_step loop

verify_ccpn_calculation_step(parent: ccpn.core.StructureData.StructureData, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name: str)[source]

verify dataSet.calculation_step loop

verify_ccpn_collections(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
verify_ccpn_complex(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
verify_ccpn_complex_chain(parent: ccpn.core.Complex.Complex, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

verify ccpn_complex_chain loop

verify_ccpn_dataset(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

verify contents of dataSet saveFrame

verify_ccpn_datatable(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

verify ccpn_datatable saveFrame

verify_ccpn_group_spectrum(parent: ccpn.core.SpectrumGroup.SpectrumGroup, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

verify ccpn_group_spectrum loop

verify_ccpn_integral(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **kwds)[source]
verify_ccpn_integral_list(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **kwds)[source]

Verify the integralLists

verify_ccpn_logging(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

verify ccpn_logging saveFrame

verify_ccpn_multiplet(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **kwds)[source]
verify_ccpn_multiplet_list(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **kwds)[source]

Verify the multipletLists

verify_ccpn_multiplet_peaks(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **kwds)[source]

verify ccpn_multiplet_peaks loop

verify_ccpn_notes(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
verify_ccpn_parameter(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

verify ccpn_parameter saveFrame

verify_ccpn_peak_cluster(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **kwds)[source]

Verify the peakClusters

verify_ccpn_peak_cluster_list(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Verify the peakClusters

verify_ccpn_peak_cluster_peaks(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

verify ccpn_peak_cluster_peaks loop

verify_ccpn_peak_list(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, **kwds)[source]

Verify the peakLists

verify_ccpn_restraint_violation(restraintTable: ccpn.core.RestraintTable.RestraintTable, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None, itemLength: Optional[int] = None)[source]

Verify the contents of ccpn_<type>_restraint_violation loops

verify_ccpn_restraint_violation_list(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Serves to verify ccpn_<type>_restraint_violation_list

verify_ccpn_sample(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
verify_ccpn_sample_component(parent: ccpn.core.Sample.Sample, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, sampleName: Optional[str] = None)[source]

verify ccpn_sample_component loop

verify_ccpn_spectrum_group(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
verify_ccpn_substance(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
verify_nef_chemical_shift(parent: ccpn.core.ChemicalShiftList.ChemicalShiftList, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None)[source]

verify nef_chemical_shift loop

verify_nef_chemical_shift_list(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

verify nef_chemical_shift_list saveFrame

verify_nef_nmr_meta_data(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

verify nef_nmr_meta_data saveFrame

verify_nef_nmr_spectrum(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]
verify_nef_peak(spectrum: ccpn.core.Spectrum.Spectrum, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, dimensionCount: Optional[int] = None, spectrumListSerial=None)[source]

Serves to verify nef_peak loop

verify_nef_restraint(restraintTable: ccpn.core.RestraintTable.RestraintTable, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame, name=None, itemLength: Optional[int] = None)[source]

Verify the contents of nef_distance_restraint, nef_dihedral_restraint, nef_rdc_restraint and ccpn_restraint loops

verify_nef_restraint_list(project: ccpn.core.Project.Project, saveFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

Serves to verify nef_distance_restraint_list, nef_dihedral_restraint_list, nef_rdc_restraint_list and ccpn_restraint_list

verify_nef_sequence(project: ccpn.core.Project.Project, loop: ccpn.util.nef.StarIo.NmrLoop, parentFrame: ccpn.util.nef.StarIo.NmrSaveFrame)[source]

verify nef_sequence loop

verify_preloadAssignmentData(dataBlock: ccpn.util.nef.StarIo.NmrDataBlock)[source]

Set up NmrChains and NmrResidues with reserved names to ensure the serials are OK and create NmrResidues in connected nmrChains in order

warning(message: str, loopName=None)[source]
class ccpn.framework.lib.ccpnNef.CcpnNefIo.CcpnNefWriter(project: ccpn.core.Project.Project, specificationFile: Optional[str] = None, mode: str = 'strict', programName: Optional[str] = None, programVersion: Optional[str] = None)[source]

Bases: object

CCPN NEF reader/writer

additionalData2Nef(project: ccpn.core.Project.Project) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Make singleton saveFrame for additional data (ccpnInternalData)

assignments2Nef(project: ccpn.core.Project.Project) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert NmrChains, NmrResidues and NmrAtoms to saveframe

ccpnAssignentToNef(nmrChains: List[ccpn.core.NmrChain.NmrChain])[source]

Write CCPN assignment data, to preserve serials etc.

ccpnLogging2Nef(project: ccpn.core.Project.Project)[source]

Convert ccpn logging dataSet to CCPN NEF saveframe

chains2Nef(chains: List[ccpn.core.Chain.Chain]) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert selected Chains to CCPN NEF saveframe

chemicalShiftList2Nef(chemicalShiftList: ccpn.core.ChemicalShiftList.ChemicalShiftList, includeOrphans: bool = False) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert ChemicalShiftList to CCPN NEF saveframe

collections2Nef(project: ccpn.core.Project.Project, collections) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Make singleton saveFrame for collections

complex2Nef(complex: ccpn.core.Complex.Complex) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert Complex to CCPN NEF saveframe

dataTable2Nef(project: ccpn.core.Project.Project, dataTable: ccpn.core.DataTable.DataTable) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Make a saveFrame for a datatable

exportDataSet(dataSet: ccpn.core.StructureData.StructureData) → ccpn.util.nef.StarIo.NmrDataBlock[source]

Get dataSet and all objects linked to therein as NEF object tree for export

exportObjects(expandSelection: bool = True, includeOrphans: bool = False, chains: Sequence[ccpn.core.Chain.Chain] = (), chemicalShiftLists: Sequence[ccpn.core.ChemicalShiftList.ChemicalShiftList] = (), restraintTables: Sequence[ccpn.core.RestraintTable.RestraintTable] = (), peakLists: Sequence[ccpn.core.PeakList.PeakList] = (), integralLists: Sequence[ccpn.core.IntegralList.IntegralList] = (), multipletLists: Sequence[ccpn.core.MultipletList.MultipletList] = (), samples: Sequence[ccpn.core.Sample.Sample] = (), substances: Sequence[ccpn.core.Substance.Substance] = (), nmrChains: Sequence[ccpn.core.NmrChain.NmrChain] = (), structureData: Sequence[ccpn.core.StructureData.StructureData] = (), complexes: Sequence[ccpn.core.Complex.Complex] = (), spectrumGroups: Sequence[ccpn.core.SpectrumGroup.SpectrumGroup] = (), notes: Sequence[ccpn.core.Note.Note] = (), peakClusters: Sequence[ccpn.core.PeakCluster.PeakCluster] = (), violationTables: Sequence[ccpn.core.ViolationTable.ViolationTable] = (), dataTables: Sequence[ccpn.core.DataTable.DataTable] = (), collections: Sequence[ccpn.core.Collection.Collection] = ())[source]

Export objects passed in and objects they are linked to.

if expandSelection is True (strongly recommended): Will add PeakLists (Spectra) from SpectrumGroups (first peakList only), Samples and ChemicalShiftLists from peakLists (Spectra) Samples from SpectrumHits, Substances from Samples RestraintTables from StructureData NmrChains from ChemicalShifts and Chains from Substances, SampleComponents, NmrChains, and Complexes

exportProject(expandSelection: bool = False, includeOrphans: bool = False, pidList: Optional[list] = None) → Optional[ccpn.util.nef.StarIo.NmrDataBlock][source]

Get project and all contents as NEF object tree for export

makeNefMetaData(headObject: ccpn.core.Project.Project | ccpn.core.StructureData.StructureData, coordinateFileName: Optional[str] = None) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

make NEF metadata saveframe from Project

notes2Nef(project: ccpn.core.Project.Project, notes: List[ccpn.core.Note.Note]) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert Notes to CCPN NEF saveframe

peakClusters2Nef(peakClusters) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert PeakClusters to saveframe

peakList2Nef(spectrum: ccpn.core.Spectrum.Spectrum, peakList: ccpn.core.PeakList.PeakList, peakLists, integralLists, multipletLists, exportCompleteSpectrum: bool = True, peakListSerial=1) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert PeakList to CCPN NEF saveframe. Used for all spectrum export, as there is one frame per PeakList

peakRestraintLinks2Nef(restraintTables: Sequence[ccpn.core.RestraintTable.RestraintTable]) → ccpn.util.nef.StarIo.NmrSaveFrame[source]
restraintTable2Nef(restraintTable: ccpn.core.RestraintTable.RestraintTable, singleStructureTable: bool = False) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert RestraintTable to CCPN NEF restraint_list saveframe

sample2Nef(sample: ccpn.core.Sample.Sample) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert Sample to CCPN NEF saveframe

spectrumGroup2Nef(spectrumGroup: ccpn.core.SpectrumGroup.SpectrumGroup) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert SpectrumGroup to CCPN NEF saveframe

structureData2Nef(structureData: Sequence[ccpn.core.StructureData.StructureData]) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert StructureData to CCPN NEF saveframes

substance2Nef(substance: ccpn.core.Substance.Substance) → ccpn.util.nef.StarIo.NmrSaveFrame[source]

Convert Substance to CCPN NEF saveframe

violationTable2Nef(violationTable: ccpn.core.ViolationTable.ViolationTable, singleStructureTable: bool = False) → Optional[ccpn.util.nef.StarIo.NmrSaveFrame][source]

Make a saveFrame for a violationTable

ccpn.framework.lib.ccpnNef.CcpnNefIo.convert2NefString(project: ccpn.core.Project.Project, skipPrefixes: Sequence = (), expandSelection: bool = True, includeOrphans: bool = False, pidList: Optional[list] = None)[source]

Convert project to NEF string

ccpn.framework.lib.ccpnNef.CcpnNefIo.convertToCcpnDataBlock(project: ccpn.core.Project.Project, skipPrefixes: Sequence = (), expandSelection: bool = True, includeOrphans: bool = False, pidList: Optional[list] = None)[source]

Convert project to NEF string

ccpn.framework.lib.ccpnNef.CcpnNefIo.convertToDataBlock(project: ccpn.core.Project.Project, skipPrefixes: Sequence = (), expandSelection: bool = True, includeOrphans: bool = False, pidList: Optional[Sequence] = None)[source]

export NEF file to path

ccpn.framework.lib.ccpnNef.CcpnNefIo.exportNef(project: ccpn.core.Project.Project, path: str, overwriteExisting: bool = False, skipPrefixes: Sequence = (), expandSelection: bool = True, includeOrphans: bool = False, pidList: Optional[Sequence] = None)[source]

export NEF file to path

ccpn.framework.lib.ccpnNef.CcpnNefIo.saveNefProject(project: ccpn.core.Project.Project, path: str, overwriteExisting: bool = False, skipPrefixes: Sequence = (), expandSelection: bool = True, includeOrphans: bool = False)[source]

Save project NEF file to path

ccpn.framework.lib.ccpnNef.CcpnNefIo.writeDataBlock(dataBlock, path: str, overwriteExisting: bool = False)[source]

ccpn.framework.lib.ccpnNef.CcpnNefLogging module

Functions to read/write ccpn logging information to project data The Ccpn logging data is stored/restored as a ccpn_logging saveframe in nef files.

ccpn.framework.lib.ccpnNef.CcpnNefLogging.getCcpnNefLog(project: Project, name: str)[source]

Get the required ccpnNefLogging dataframe from the project Returns a COPY of pandas dataFrame of the ccpn nef log for use in nef import/export to ensure integrity If a dataFrame cannot be found, logs an error and returns None

Columns are:

date, username, program_name, program_version, script_name, input_uuid, saveframe, comment

Raise an error if there are any issues reading parameters

Parameters

  • project – instance of type Project

  • name – string name of the log

Returns

pandas dataFrame, value or None

ccpn.framework.lib.ccpnNef.CcpnNefLogging.getCcpnNefLogNames(project: Project)[source]

Return a tuple of CcpnNef log names

Parameters

project – instance of type Project

Returns

tuple of log names, or None if undefined

ccpn.framework.lib.ccpnNef.CcpnNefLogging.resetCcpnNefLog(project: Project, name: str, overwrite=False)[source]

reset the required ccpnNefLogging dataframe in the project for use in nef import/export

Raise an error if name is not a string Returns False if the ccpnLogging already exists and overwrite is False

Creates empty dataframe with columns:

date, username, program_name, program_version, script_name, input_uuid, saveframe, comment

Parameters

  • project – instance of type Project

  • name – string name of the log

  • overwrite – True/False

Returns

True if successful

ccpn.framework.lib.ccpnNef.CcpnNefLogging.setCcpnNefLog(project: Project, name: str, dataFrame: Optional[pandas.core.frame.DataFrame] = None, overwrite=False)[source]

Set the required ccpnNefLogging dataframe in the project for use in nef import/export Stores a COPY of the dataFrame in the log

Raise an error if name or value are of the wrong types Returns False if the ccpnLogging already exists and overwrite is False

Columns are enforced to be:

date, username, program_name, program_version, script_name, input_uuid, saveframe, comment

Other columns will be ignored If value is None, wll create an empty dataFrame

Parameters

  • project – instance of type Project

  • name – string name of the log

  • dataFrame – pandas dataFrame or None

  • overwrite – True/False

Returns

True if successful