swagger_client.models.small_molecule_feature module

mzTab-M reference implementation and validation API.

This is the mzTab-M reference implementation and validation API service. # noqa: E501

OpenAPI spec version: 2.0.0 Contact: nils.hoffmann@isas.de Generated by: https://github.com/swagger-api/swagger-codegen.git

class swagger_client.models.small_molecule_feature.SmallMoleculeFeature(prefix='SMF', header_prefix='SFH', smf_id=None, sme_id_refs=None, sme_id_ref_ambiguity_code=None, adduct_ion=None, isotopomer=None, exp_mass_to_charge=None, charge=None, retention_time_in_seconds=None, retention_time_in_seconds_start=None, retention_time_in_seconds_end=None, abundance_assay=None, opt=None, comment=None)

Bases: object

NOTE: This class is auto generated by the swagger code generator program.

Do not edit the class manually.

SmallMoleculeFeature - a model defined in Swagger

property abundance_assay

Gets the abundance_assay of this SmallMoleculeFeature. # noqa: E501

The feature’s abundance in every assay described in the metadata section MUST be reported. Null or zero values may be reported as appropriate. # noqa: E501

Returns

The abundance_assay of this SmallMoleculeFeature. # noqa: E501

Return type

list[float]

property adduct_ion

Gets the adduct_ion of this SmallMoleculeFeature. # noqa: E501

The assumed classification of this molecule’s adduct ion after detection, following the general style in the 2013 IUPAC recommendations on terms relating to MS e.g. [M+H]1+, [M+Na]1+, [M+NH4]1+, [M-H]1-, [M+Cl]1-, [M+H]1+. # noqa: E501

Returns

The adduct_ion of this SmallMoleculeFeature. # noqa: E501

Return type

str

attribute_map = {'abundance_assay': 'abundance_assay', 'adduct_ion': 'adduct_ion', 'charge': 'charge', 'comment': 'comment', 'exp_mass_to_charge': 'exp_mass_to_charge', 'header_prefix': 'header_prefix', 'isotopomer': 'isotopomer', 'opt': 'opt', 'prefix': 'prefix', 'retention_time_in_seconds': 'retention_time_in_seconds', 'retention_time_in_seconds_end': 'retention_time_in_seconds_end', 'retention_time_in_seconds_start': 'retention_time_in_seconds_start', 'sme_id_ref_ambiguity_code': 'sme_id_ref_ambiguity_code', 'sme_id_refs': 'sme_id_refs', 'smf_id': 'smf_id'}

property charge

Gets the charge of this SmallMoleculeFeature. # noqa: E501

The feature’s charge value using positive integers both for positive and negative polarity modes. # noqa: E501

Returns

The charge of this SmallMoleculeFeature. # noqa: E501

Return type

int

property comment

Gets the comment of this SmallMoleculeFeature. # noqa: E501

Returns

The comment of this SmallMoleculeFeature. # noqa: E501

Return type

list[Comment]

property exp_mass_to_charge

Gets the exp_mass_to_charge of this SmallMoleculeFeature. # noqa: E501

The experimental mass/charge value for the feature, by default assumed to be the mean across assays or a representative value. For approaches that report isotopomers as SMF rows, then the m/z of the isotopomer MUST be reported here. # noqa: E501

Returns

The exp_mass_to_charge of this SmallMoleculeFeature. # noqa: E501

Return type

float

property header_prefix

Gets the header_prefix of this SmallMoleculeFeature. # noqa: E501

The small molecule feature table header prefix. SFH MUST be used for the small molecule feature table header line (the column labels). # noqa: E501

Returns

The header_prefix of this SmallMoleculeFeature. # noqa: E501

Return type

str

property isotopomer

Gets the isotopomer of this SmallMoleculeFeature. # noqa: E501

If de-isotoping has not been performed, then the isotopomer quantified MUST be reported here e.g. “+1”, “+2”, “13C peak” using CV terms, otherwise (i.e. for approaches where SMF rows are de-isotoped features) this MUST be null. # noqa: E501

Returns

The isotopomer of this SmallMoleculeFeature. # noqa: E501

Return type

Parameter

property opt

Gets the opt of this SmallMoleculeFeature. # noqa: E501

Additional columns can be added to the end of the small molecule feature table. These column headers MUST start with the prefix “opt_” followed by the {identifier} of the object they reference: assay, study variable, MS run or “global” (if the value relates to all replicates). Column names MUST only contain the following characters: ‘A’-‘Z’, ‘a’-‘z’, ‘0’-‘9’, ‘’, ‘-’, ‘[’, ‘]’, and ‘:’. CV parameter accessions MAY be used for optional columns following the format: opt{identifier}_cv_{accession}_{parameter name}. Spaces within the parameter’s name MUST be replaced by ‘_’. # noqa: E501

Returns

The opt of this SmallMoleculeFeature. # noqa: E501

Return type

list[OptColumnMapping]

property prefix

Gets the prefix of this SmallMoleculeFeature. # noqa: E501

The small molecule feature table row prefix. SMF MUST be used for rows of the small molecule feature table. # noqa: E501

Returns

The prefix of this SmallMoleculeFeature. # noqa: E501

Return type

str

property retention_time_in_seconds

Gets the retention_time_in_seconds of this SmallMoleculeFeature. # noqa: E501

The apex of the feature on the retention time axis, in a Master or aggregate MS run. Retention time MUST be reported in seconds. Retention time values for individual MS runs (i.e. before alignment) MAY be reported as optional columns. Retention time SHOULD only be null in the case of direct infusion MS or other techniques where a retention time value is absent or unknown. Relative retention time or retention time index values MAY be reported as optional columns, and could be considered for inclusion in future versions of mzTab as appropriate. # noqa: E501

Returns

The retention_time_in_seconds of this SmallMoleculeFeature. # noqa: E501

Return type

float

property retention_time_in_seconds_end

Gets the retention_time_in_seconds_end of this SmallMoleculeFeature. # noqa: E501

The end time of the feature on the retention time axis, in a Master or aggregate MS run. Retention time MUST be reported in seconds. Retention time start and end SHOULD only be null in the case of direct infusion MS or other techniques where a retention time value is absent or unknown and MAY be reported in optional columns.. # noqa: E501

Returns

The retention_time_in_seconds_end of this SmallMoleculeFeature. # noqa: E501

Return type

float

property retention_time_in_seconds_start

Gets the retention_time_in_seconds_start of this SmallMoleculeFeature. # noqa: E501

The start time of the feature on the retention time axis, in a Master or aggregate MS run. Retention time MUST be reported in seconds. Retention time start and end SHOULD only be null in the case of direct infusion MS or other techniques where a retention time value is absent or unknown and MAY be reported in optional columns. # noqa: E501

Returns

The retention_time_in_seconds_start of this SmallMoleculeFeature. # noqa: E501

Return type

float

property sme_id_ref_ambiguity_code

Gets the sme_id_ref_ambiguity_code of this SmallMoleculeFeature. # noqa: E501

If multiple values are given under SME_ID_REFS, one of the following codes MUST be provided. 1=Ambiguous identification; 2=Only different evidence streams for the same molecule with no ambiguity; 3=Both ambiguous identification and multiple evidence streams. If there are no or one value under SME_ID_REFs, this MUST be reported as null. # noqa: E501

Returns

The sme_id_ref_ambiguity_code of this SmallMoleculeFeature. # noqa: E501

Return type

int

property sme_id_refs

Gets the sme_id_refs of this SmallMoleculeFeature. # noqa: E501

References to the identification evidence (SME elements) via referencing SME_ID values. Multiple values MAY be provided as a “|” separated list to indicate ambiguity in the identification or to indicate that different types of data supported the identifiction (see SME_ID_REF_ambiguity_code). For the case of a consensus approach where multiple adduct forms are used to infer the SML ID, different features should just reference the same SME_ID value(s). # noqa: E501

Returns

The sme_id_refs of this SmallMoleculeFeature. # noqa: E501

Return type

list[int]

property smf_id

Gets the smf_id of this SmallMoleculeFeature. # noqa: E501

A within file unique identifier for the small molecule feature. # noqa: E501

Returns

The smf_id of this SmallMoleculeFeature. # noqa: E501

Return type

int

swagger_types = {'abundance_assay': 'list[float]', 'adduct_ion': 'str', 'charge': 'int', 'comment': 'list[Comment]', 'exp_mass_to_charge': 'float', 'header_prefix': 'str', 'isotopomer': 'Parameter', 'opt': 'list[OptColumnMapping]', 'prefix': 'str', 'retention_time_in_seconds': 'float', 'retention_time_in_seconds_end': 'float', 'retention_time_in_seconds_start': 'float', 'sme_id_ref_ambiguity_code': 'int', 'sme_id_refs': 'list[int]', 'smf_id': 'int'}

to_dict()

Returns the model properties as a dict

to_str()

Returns the string representation of the model