swagger_client.models.small_molecule_evidence 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_evidence.SmallMoleculeEvidence(prefix='SME', header_prefix='SEH', sme_id=None, evidence_input_id=None, database_identifier=None, chemical_formula=None, smiles=None, inchi=None, chemical_name=None, uri=None, derivatized_form=None, adduct_ion=None, exp_mass_to_charge=None, charge=None, theoretical_mass_to_charge=None, spectra_ref=None, identification_method=None, ms_level=None, id_confidence_measure=None, rank=1, opt=None, comment=None)

Bases: object

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

Do not edit the class manually.

SmallMoleculeEvidence - a model defined in Swagger

property adduct_ion

Gets the adduct_ion of this SmallMoleculeEvidence. # 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]+, [M+Na]1+, [M+NH4]1+, [M-H]1-, [M+Cl]1-. If the adduct classification is ambiguous with regards to identification evidence it MAY be null. # noqa: E501

Returns

The adduct_ion of this SmallMoleculeEvidence. # noqa: E501

Return type

str

attribute_map = {'adduct_ion': 'adduct_ion', 'charge': 'charge', 'chemical_formula': 'chemical_formula', 'chemical_name': 'chemical_name', 'comment': 'comment', 'database_identifier': 'database_identifier', 'derivatized_form': 'derivatized_form', 'evidence_input_id': 'evidence_input_id', 'exp_mass_to_charge': 'exp_mass_to_charge', 'header_prefix': 'header_prefix', 'id_confidence_measure': 'id_confidence_measure', 'identification_method': 'identification_method', 'inchi': 'inchi', 'ms_level': 'ms_level', 'opt': 'opt', 'prefix': 'prefix', 'rank': 'rank', 'sme_id': 'sme_id', 'smiles': 'smiles', 'spectra_ref': 'spectra_ref', 'theoretical_mass_to_charge': 'theoretical_mass_to_charge', 'uri': 'uri'}

property charge

Gets the charge of this SmallMoleculeEvidence. # noqa: E501

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

Returns

The charge of this SmallMoleculeEvidence. # noqa: E501

Return type

int

property chemical_formula

Gets the chemical_formula of this SmallMoleculeEvidence. # noqa: E501

The chemical formula of the identified compound e.g. in a database, assumed to match the theoretical mass to charge (in some cases this will be the derivatized form, including adducts and protons). This should be specified in Hill notation (EA Hill 1900), i.e. elements in the order C, H and then alphabetically all other elements. Counts of one may be omitted. Elements should be capitalized properly to avoid confusion (e.g., “CO” vs. “Co”). The chemical formula reported should refer to the neutral form. Charge state is reported by the charge field. Example N-acetylglucosamine would be encoded by the string “C8H15NO6” # noqa: E501

Returns

The chemical_formula of this SmallMoleculeEvidence. # noqa: E501

Return type

str

property chemical_name

Gets the chemical_name of this SmallMoleculeEvidence. # noqa: E501

The small molecule’s chemical/common name, or general description if a chemical name is unavailable. # noqa: E501

Returns

The chemical_name of this SmallMoleculeEvidence. # noqa: E501

Return type

str

property comment

Gets the comment of this SmallMoleculeEvidence. # noqa: E501

Returns

The comment of this SmallMoleculeEvidence. # noqa: E501

Return type

list[Comment]

property database_identifier

Gets the database_identifier of this SmallMoleculeEvidence. # noqa: E501

The putative identification for the small molecule sourced from an external database, using the same prefix specified in database[1-n]-prefix. This could include additionally a chemical class or an identifier to a spectral library entity, even if its actual identity is unknown. For the “no database” case, “null” must be used. The unprefixed use of “null” is prohibited for any other case. If no putative identification can be reported for a particular database, it MUST be reported as the database prefix followed by null. # noqa: E501

Returns

The database_identifier of this SmallMoleculeEvidence. # noqa: E501

Return type

str

property derivatized_form

Gets the derivatized_form of this SmallMoleculeEvidence. # noqa: E501

If a derivatized form has been analysed by MS, then the functional group attached to the molecule should be reported here using suitable userParam or CV terms as appropriate. # noqa: E501

Returns

The derivatized_form of this SmallMoleculeEvidence. # noqa: E501

Return type

Parameter

property evidence_input_id

Gets the evidence_input_id of this SmallMoleculeEvidence. # noqa: E501

A within file unique identifier for the input data used to support this identification e.g. fragment spectrum, RT and m/z pair, isotope profile that was used for the identification process, to serve as a grouping mechanism, whereby multiple rows of results from the same input data share the same ID. The identifiers may be human readable but should not be assumed to be interpretable. For example, if fragmentation spectra have been searched then the ID may be the spectrum reference, or for accurate mass search, the ms_run[2]:458.75. # noqa: E501

Returns

The evidence_input_id of this SmallMoleculeEvidence. # noqa: E501

Return type

str

property exp_mass_to_charge

Gets the exp_mass_to_charge of this SmallMoleculeEvidence. # noqa: E501

The experimental mass/charge value for the precursor ion. If multiple adduct forms have been combined into a single identification event/search, then a single value e.g. for the protonated form SHOULD be reported here. # noqa: E501

Returns

The exp_mass_to_charge of this SmallMoleculeEvidence. # noqa: E501

Return type

float

property header_prefix

Gets the header_prefix of this SmallMoleculeEvidence. # noqa: E501

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

Returns

The header_prefix of this SmallMoleculeEvidence. # noqa: E501

Return type

str

property id_confidence_measure

Gets the id_confidence_measure of this SmallMoleculeEvidence. # noqa: E501

Any statistical value or score for the identification. The metadata section reports the type of score used, as id_confidence_measure[1-n] of type Param. # noqa: E501

Returns

The id_confidence_measure of this SmallMoleculeEvidence. # noqa: E501

Return type

list[float]

property identification_method

Gets the identification_method of this SmallMoleculeEvidence. # noqa: E501

The database search, search engine or process that was used to identify this small molecule e.g. the name of software, database or manual curation etc. If manual validation has been performed quality, the following CV term SHOULD be used: ‘quality estimation by manual validation’ MS:1001058. # noqa: E501

Returns

The identification_method of this SmallMoleculeEvidence. # noqa: E501

Return type

Parameter

property inchi

Gets the inchi of this SmallMoleculeEvidence. # noqa: E501

A standard IUPAC International Chemical Identifier (InChI) for the given substance. # noqa: E501

Returns

The inchi of this SmallMoleculeEvidence. # noqa: E501

Return type

str

property ms_level

Gets the ms_level of this SmallMoleculeEvidence. # noqa: E501

The highest MS level used to inform identification e.g. MS1 (accurate mass only) = “ms level=1” or from an MS2 fragmentation spectrum = “ms level=2”. For direct fragmentation or data independent approaches where fragmentation data is used, appropriate CV terms SHOULD be used . # noqa: E501

Returns

The ms_level of this SmallMoleculeEvidence. # noqa: E501

Return type

Parameter

property opt

Gets the opt of this SmallMoleculeEvidence. # noqa: E501

Additional columns can be added to the end of the small molecule evidence 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 SmallMoleculeEvidence. # noqa: E501

Return type

list[OptColumnMapping]

property prefix

Gets the prefix of this SmallMoleculeEvidence. # noqa: E501

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

Returns

The prefix of this SmallMoleculeEvidence. # noqa: E501

Return type

str

property rank

Gets the rank of this SmallMoleculeEvidence. # noqa: E501

The rank of this identification from this approach as increasing integers from 1 (best ranked identification). Ties (equal score) are represented by using the same rank – defaults to 1 if there is no ranking system used. # noqa: E501

Returns

The rank of this SmallMoleculeEvidence. # noqa: E501

Return type

int

property sme_id

Gets the sme_id of this SmallMoleculeEvidence. # noqa: E501

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

Returns

The sme_id of this SmallMoleculeEvidence. # noqa: E501

Return type

int

property smiles

Gets the smiles of this SmallMoleculeEvidence. # noqa: E501

The potential molecule’s structure in the simplified molecular-input line-entry system (SMILES) for the small molecule. # noqa: E501

Returns

The smiles of this SmallMoleculeEvidence. # noqa: E501

Return type

str

property spectra_ref

Gets the spectra_ref of this SmallMoleculeEvidence. # noqa: E501

Reference to a spectrum in a spectrum file, for example a fragmentation spectrum has been used to support the identification. If a separate spectrum file has been used for fragmentation spectrum, this MUST be reported in the metadata section as additional ms_runs. The reference must be in the format ms_run[1-n]:{SPECTRA_REF} where SPECTRA_REF MUST follow the format defined in 5.2 (including references to chromatograms where these are used to inform identification). Multiple spectra MUST be referenced using a “|” delimited list for the (rare) cases in which search engines have combined or aggregated multiple spectra in advance of the search to make identifications. If a fragmentation spectrum has not been used, the value should indicate the ms_run to which is identification is mapped e.g. “ms_run[1]”. # noqa: E501

Returns

The spectra_ref of this SmallMoleculeEvidence. # noqa: E501

Return type

list[SpectraRef]

swagger_types = {'adduct_ion': 'str', 'charge': 'int', 'chemical_formula': 'str', 'chemical_name': 'str', 'comment': 'list[Comment]', 'database_identifier': 'str', 'derivatized_form': 'Parameter', 'evidence_input_id': 'str', 'exp_mass_to_charge': 'float', 'header_prefix': 'str', 'id_confidence_measure': 'list[float]', 'identification_method': 'Parameter', 'inchi': 'str', 'ms_level': 'Parameter', 'opt': 'list[OptColumnMapping]', 'prefix': 'str', 'rank': 'int', 'sme_id': 'int', 'smiles': 'str', 'spectra_ref': 'list[SpectraRef]', 'theoretical_mass_to_charge': 'float', 'uri': 'str'}

property theoretical_mass_to_charge

Gets the theoretical_mass_to_charge of this SmallMoleculeEvidence. # noqa: E501

The theoretical mass/charge value for the small molecule or the database mass/charge value (for a spectral library match). # noqa: E501

Returns

The theoretical_mass_to_charge of this SmallMoleculeEvidence. # noqa: E501

Return type

float

to_dict()

Returns the model properties as a dict

to_str()

Returns the string representation of the model

property uri

Gets the uri of this SmallMoleculeEvidence. # noqa: E501

A URI pointing to the small molecule’s entry in a database (e.g., the small molecule’s HMDB, Chebi or KEGG entry). # noqa: E501

Returns

The uri of this SmallMoleculeEvidence. # noqa: E501

Return type

str