Index

_

__enter__() (psims.mzid.writer.MzIdentMLWriter method) (psims.mzml.writer.IndexedMzMLWriter method) __exit__() (psims.mzid.writer.MzIdentMLWriter method) (psims.mzml.writer.IndexedMzMLWriter method)

__getattr__() (psims.mzid.writer.MzIdentMLWriter method) (psims.mzml.writer.IndexedMzMLWriter method) _element() (in module psims.xml)

A

accession (psims.xml.CVParam attribute) Activation (class in psims.mzml.components) AmbiguousResidue (class in psims.mzid.components) AnalysisData (class in psims.mzid.components) AnalysisProtocolCollection (class in psims.mzid.components)

AnalysisSampleCollection (class in psims.mzid.components) AnalysisSoftware (class in psims.mzid.components) AnalysisSoftwareList (class in psims.mzid.components) Analyzer (class in psims.mzml.components) attrs (psims.xml.TagBase attribute) AuditCollection (class in psims.mzid.components)

B

begin() (psims.mzid.writer.MzIdentMLWriter method) (psims.mzml.writer.IndexedMzMLWriter method) (psims.xml.XMLDocumentWriter method) BibliographicReference (class in psims.mzid.components)

Binary (class in psims.mzml.components) BinaryDataArray (class in psims.mzml.components) BinaryDataArrayList (class in psims.mzml.components) buffer_blocks (psims.mzmlb.writer.MzMLbWriter attribute) build() (psims.mzml.components.ComponentList class method)

C

cache_exists (psims.controlled_vocabulary.controlled_vocabulary.OBOCache attribute) cache_path (psims.controlled_vocabulary.controlled_vocabulary.OBOCache attribute) checksum() (psims.mzml.components.SourceFile method) children (psims.controlled_vocabulary.entity.Entity attribute) Chromatogram (class in psims.mzml.components) chromatogram_count (psims.mzml.writer.IndexedMzMLWriter attribute) ComponentBase (class in psims.mzid.components) ComponentDispatcher (class in psims.mzid.components) ComponentList (class in psims.mzml.components) compression_map (in module psims.mzml.writer) Contact (class in psims.mzml.components)

context (psims.mzid.writer.MzIdentMLWriter attribute) controlled_vocabularies() (psims.mzid.writer.MzIdentMLWriter method) (psims.mzml.writer.IndexedMzMLWriter method) (psims.xml.XMLDocumentWriter method) ControlledVocabulary (class in psims.controlled_vocabulary.controlled_vocabulary) converter (psims.xml.ProvidedCV attribute) create_array() (psims.mzmlb.writer.MzMLbWriter method) create_buffer() (psims.mzmlb.writer.MzMLbWriter method) CV (class in psims.xml) CVList (class in psims.mzid.components) (class in psims.mzml.components) CVParam (class in psims.xml)

D

data (psims.controlled_vocabulary.entity.Entity attribute) data_processing_list() (psims.mzml.writer.IndexedMzMLWriter method) DatabaseTranslation (class in psims.mzid.components) DataCollection (class in psims.mzid.components)

DataProcessing (class in psims.mzml.components) DataProcessingList (class in psims.mzml.components) DBSequence (class in psims.mzid.components) definition (psims.controlled_vocabulary.entity.Entity attribute) Detector (class in psims.mzml.components)

E

element() (in module psims.xml) (psims.mzid.writer.MzIdentMLWriter method) (psims.mzml.writer.IndexedMzMLWriter method) (psims.xml.XMLDocumentWriter method) (psims.xml.XMLWriterMixin method) enabled (psims.controlled_vocabulary.controlled_vocabulary.OBOCache attribute)

end() (psims.mzid.writer.MzIdentMLWriter method) (psims.mzml.writer.IndexedMzMLWriter method) (psims.xml.XMLDocumentWriter method) Entity (class in psims.controlled_vocabulary.entity) Enzyme (class in psims.mzid.components) Enzymes (class in psims.mzid.components)

F

fallback() (psims.controlled_vocabulary.controlled_vocabulary.OBOCache method) file_description() (psims.mzml.writer.IndexedMzMLWriter method) FileContent (class in psims.mzml.components) FileDescription (class in psims.mzml.components) Filter (class in psims.mzid.components) format() (psims.mzid.writer.MzIdentMLWriter method) (psims.mzml.writer.IndexedMzMLWriter method) (psims.xml.XMLDocumentWriter method)

FragmentationTable (class in psims.mzid.components) FragmentTolerance (class in psims.mzid.components) from_obo() (psims.controlled_vocabulary.controlled_vocabulary.ControlledVocabulary class method) full_name (psims.xml.CV attribute)

G

GenericCollection (class in psims.mzid.components)

get() (psims.controlled_vocabulary.entity.Entity method)

H

h5_blocksize (psims.mzmlb.writer.MzMLbWriter attribute) h5_compression (psims.mzmlb.writer.MzMLbWriter attribute)

h5_compressor_options (psims.mzmlb.writer.MzMLbWriter attribute) has_custom_resolver() (psims.controlled_vocabulary.controlled_vocabulary.OBOCache method)

I

id (psims.controlled_vocabulary.controlled_vocabulary.ControlledVocabulary attribute), [1] (psims.controlled_vocabulary.entity.Entity attribute) (psims.xml.CV attribute) (psims.xml.TagBase attribute) IDGenericCollection (class in psims.mzid.components) index_builder (psims.mzml.writer.IndexedMzMLWriter attribute) IndexedMzML (class in psims.mzml.components) IndexedMzMLWriter (class in psims.mzml.writer) input_stream (psims.transform.mzml.MzMLTransformer attribute)

Inputs (class in psims.mzid.components) instrument_configuration_list() (psims.mzml.writer.IndexedMzMLWriter method) InstrumentConfiguration (class in psims.mzml.components) InstrumentConfigurationList (class in psims.mzml.components) IonType (class in psims.mzid.components) is_of_type() (psims.controlled_vocabulary.entity.Entity method) is_open (psims.xml.TagBase attribute) IsolationWindow (class in psims.mzml.components) items() (psims.controlled_vocabulary.controlled_vocabulary.ControlledVocabulary method) (psims.controlled_vocabulary.entity.Entity method)

K

keys() (psims.controlled_vocabulary.controlled_vocabulary.ControlledVocabulary method) (psims.controlled_vocabulary.entity.Entity method)

M

MassTable (class in psims.mzid.components) Measure (class in psims.mzid.components) metadata (psims.controlled_vocabulary.controlled_vocabulary.ControlledVocabulary attribute) Modification (class in psims.mzid.components) module psims.controlled_vocabulary.controlled_vocabulary psims.mzid.components psims.mzid.writer psims.mzml.components psims.mzml.writer psims.mzmlb.writer psims.transform.mzml psims.xml

MzIdentML (class in psims.mzid.components) MzIdentMLWriter (class in psims.mzid.writer) MzML (class in psims.mzml.components) MzMLbWriter (class in psims.mzmlb.writer) MzMLToMzMLb (class in psims.transform.mzml) MzMLTransformer (class in psims.transform.mzml)

N

name (psims.controlled_vocabulary.controlled_vocabulary.ControlledVocabulary attribute) (psims.xml.CVParam attribute)

names() (psims.controlled_vocabulary.controlled_vocabulary.ControlledVocabulary method) native_id_format (psims.mzml.writer.IndexedMzMLWriter property)

O

OBOCache (class in psims.controlled_vocabulary.controlled_vocabulary) options (psims.xml.CV attribute) Organization (class in psims.mzid.components) (class in psims.mzml.components)

outfile (psims.mzid.writer.MzIdentMLWriter attribute) (psims.xml.XMLDocumentWriter attribute) output_stream (psims.transform.mzml.MzMLTransformer attribute)

P

ParamGroupReference (class in psims.xml) parent() (psims.controlled_vocabulary.entity.Entity method) ParentTolerance (class in psims.mzid.components) path_for() (psims.controlled_vocabulary.controlled_vocabulary.OBOCache method) Peptide (class in psims.mzid.components) PeptideEvidence (class in psims.mzid.components) PeptideHypothesis (class in psims.mzid.components) Person (class in psims.mzid.components) (class in psims.mzml.components) Precursor (class in psims.mzml.components) precursor_builder() (psims.mzml.writer.IndexedMzMLWriter method) PrecursorList (class in psims.mzml.components) prepare_precursor_information() (psims.mzml.writer.IndexedMzMLWriter method) ProcessingMethod (class in psims.mzml.components) Product (class in psims.mzml.components) ProductList (class in psims.mzml.components) ProteinAmbiguityGroup (class in psims.mzid.components) ProteinDetection (class in psims.mzid.components) ProteinDetectionHypothesis (class in psims.mzid.components) ProteinDetectionList (class in psims.mzid.components)

ProteinDetectionProtocol (class in psims.mzid.components) provenance() (psims.mzid.writer.MzIdentMLWriter method) ProvidedCV (class in psims.xml) Provider (class in psims.mzid.components) psims.controlled_vocabulary.controlled_vocabulary module psims.mzid.components module psims.mzid.writer module psims.mzml.components module psims.mzml.writer module psims.mzmlb.writer module psims.transform.mzml module psims.xml module

Q

query() (psims.controlled_vocabulary.controlled_vocabulary.ControlledVocabulary method)

R

reference_param_group_list() (psims.mzml.writer.IndexedMzMLWriter method) ReferenceableParamGroup (class in psims.mzml.components) ReferenceableParamGroupList (class in psims.mzml.components) register() (psims.mzid.writer.MzIdentMLWriter method) (psims.mzml.writer.IndexedMzMLWriter method)

Residue (class in psims.mzid.components) resolve() (psims.controlled_vocabulary.controlled_vocabulary.OBOCache method) resolver (psims.xml.CV attribute) resolvers (psims.controlled_vocabulary.controlled_vocabulary.OBOCache attribute) Run (class in psims.mzml.components) run() (psims.mzml.writer.IndexedMzMLWriter method)

S

Sample (class in psims.mzid.components) (class in psims.mzml.components) sample_list() (psims.mzml.writer.IndexedMzMLWriter method) SampleList (class in psims.mzml.components) Scan (class in psims.mzml.components) ScanList (class in psims.mzml.components) ScanSettings (class in psims.mzml.components) ScanSettingsList (class in psims.mzml.components) ScanWindow (class in psims.mzml.components) ScanWindowList (class in psims.mzml.components) search() (psims.controlled_vocabulary.controlled_vocabulary.ControlledVocabulary method) SearchDatabase (class in psims.mzid.components) SearchModification (class in psims.mzid.components) SelectedIon (class in psims.mzml.components) SelectedIonList (class in psims.mzml.components) SequenceCollection (class in psims.mzid.components) set_resolver() (psims.controlled_vocabulary.controlled_vocabulary.OBOCache method) Software (class in psims.mzml.components) software_list() (psims.mzml.writer.IndexedMzMLWriter method)

SoftwareList (class in psims.mzml.components) sort_by_scan_time (psims.transform.mzml.MzMLTransformer attribute) Source (class in psims.mzml.components) SourceFile (class in psims.mzid.components) (class in psims.mzml.components) SourceFileList (class in psims.mzml.components) SourceFileRef (class in psims.mzml.components) SpecificityRules (class in psims.mzid.components) SpectraData (class in psims.mzid.components) Spectrum (class in psims.mzml.components) spectrum() (psims.mzml.writer.IndexedMzMLWriter method) spectrum_count (psims.mzml.writer.IndexedMzMLWriter attribute) SpectrumIdentification (class in psims.mzid.components) SpectrumIdentificationItem (class in psims.mzid.components) SpectrumIdentificationList (class in psims.mzid.components) SpectrumIdentificationProtocol (class in psims.mzid.components) SpectrumIdentificationResult (class in psims.mzid.components) SpectrumList (class in psims.mzml.components) SubstitutionModification (class in psims.mzid.components)

T

tag_name (psims.xml.TagBase attribute) TagBase (class in psims.xml) Target (class in psims.mzml.components) TargetList (class in psims.mzml.components) terms (psims.controlled_vocabulary.controlled_vocabulary.ControlledVocabulary attribute) text (psims.xml.TagBase attribute) Threshold (class in psims.mzid.components)

toplevel (psims.mzid.writer.MzIdentMLWriter attribute) (psims.xml.XMLDocumentWriter attribute) toplevel_tag() (psims.xml.XMLDocumentWriter static method) transform (psims.transform.mzml.MzMLTransformer attribute) transform_description (psims.transform.mzml.MzMLTransformer attribute) TranslationTable (class in psims.mzid.components) type_attrs (psims.xml.TagBase attribute)

U

uri (psims.xml.CV attribute) use_remote (psims.controlled_vocabulary.controlled_vocabulary.OBOCache attribute)

user_agent_emulation (psims.controlled_vocabulary.controlled_vocabulary.OBOCache attribute) UserParam (class in psims.xml)

V

validate() (psims.mzid.writer.MzIdentMLWriter method) (psims.mzml.writer.IndexedMzMLWriter method) (psims.xml.XMLDocumentWriter method) value (psims.xml.CVParam attribute) values() (psims.controlled_vocabulary.entity.Entity method)

verbose (psims.xml.XMLWriterMixin attribute) version (psims.controlled_vocabulary.controlled_vocabulary.ControlledVocabulary attribute) (psims.xml.CV attribute) vocabulary (psims.controlled_vocabulary.entity.Entity attribute) (psims.xml.CV attribute)

W

write() (psims.mzid.writer.MzIdentMLWriter method) (psims.mzml.writer.IndexedMzMLWriter method) (psims.transform.mzml.MzMLTransformer method) (psims.xml.XMLDocumentWriter method) (psims.xml.XMLWriterMixin method)

write_spectrum() (psims.mzml.writer.IndexedMzMLWriter method) writer (psims.mzid.writer.MzIdentMLWriter attribute) (psims.xml.XMLDocumentWriter attribute) (psims.xml.XMLWriterMixin attribute)

X

XMLDocumentWriter (class in psims.xml) xmlfile (psims.mzid.writer.MzIdentMLWriter attribute) (psims.xml.XMLDocumentWriter attribute)

XMLWriterMixin (class in psims.xml)