All URIs are relative to http://localhost:8080
| Method | HTTP request | Description |
|---|---|---|
| add_aligned_features | POST /api/projects/{projectId}/aligned-features | Import (aligned) features into the project. |
| delete_aligned_feature | DELETE /api/projects/{projectId}/aligned-features/{alignedFeatureId} | Delete feature (aligned over runs) with the given identifier from the specified project-space. |
| delete_aligned_features | PUT /api/projects/{projectId}/aligned-features/delete | Delete feature (aligned over runs) with the given identifier from the specified project-space. |
| get_aligned_feature | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId} | Get feature (aligned over runs) with the given identifier from the specified project-space. |
| get_aligned_features | GET /api/projects/{projectId}/aligned-features | Get all available features (aligned over runs) in the given project-space. |
| get_aligned_features_paged | GET /api/projects/{projectId}/aligned-features/page | Get all available features (aligned over runs) in the given project-space. |
| get_best_matching_compound_classes | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/best-compound-classes | Return Best matching compound classes for given formulaId |
| get_canopus_prediction | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/canopus-prediction | All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities, |
| get_de_novo_structure_candidates_by_formula | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures | List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. |
| get_de_novo_structure_candidates_by_formula_paged | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/denovo-structures/page | Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. |
| get_de_novo_structure_candidates_paged | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/denovo-structures/page | Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint. |
| get_fingerprint_prediction | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fingerprint | Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId) |
| get_formula_annotated_ms_ms_data | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-msmsdata | Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId |
| get_formula_annotated_spectrum | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/annotated-spectrum | Returns a fragmentation spectrum (e |
| get_formula_candidate | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId} | FormulaResultContainers for the given 'formulaId' with minimal information. |
| get_formula_candidates | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas | List of FormulaResultContainers available for this feature with minimal information. |
| get_formula_candidates_paged | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/page | Page of FormulaResultContainers available for this feature with minimal information. |
| get_frag_tree | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/fragtree | Returns fragmentation tree (SIRIUS) for the given formula result identifier |
| get_isotope_pattern_annotation | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/isotope-pattern | Returns Isotope pattern information for given formulaId |
| get_lipid_annotation | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/lipid-annotation | Returns Lipid annotation (ElGordo) for the given formulaId |
| get_ms_data | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/ms-data | Mass Spec data (input data) for the given 'alignedFeatureId' . |
| get_spectral_library_match | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/{matchId} | Spectral library match for the given 'alignedFeatureId'. |
| get_spectral_library_matches | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches | List of spectral library matches for the given 'alignedFeatureId'. |
| get_spectral_library_matches_paged | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/page | Page of spectral library matches for the given 'alignedFeatureId'. |
| get_spectral_library_matches_summary | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/spectral-library-matches/summary | Summarize matched reference spectra for the given 'alignedFeatureId'. |
| get_structure_candidates | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures | List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. |
| get_structure_candidates_by_formula | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures | List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. |
| get_structure_candidates_by_formula_paged | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/formulas/{formulaId}/db-structures/page | Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. |
| get_structure_candidates_paged | GET /api/projects/{projectId}/aligned-features/{alignedFeatureId}/db-structures/page | Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. |
List[AlignedFeature] add_aligned_features(project_id, feature_import, profile=profile, opt_fields=opt_fields)
Import (aligned) features into the project.
Import (aligned) features into the project. Features must not exist in the project. Otherwise, they will exist twice.
import PySirius
from PySirius.models.aligned_feature import AlignedFeature
from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField
from PySirius.models.feature_import import FeatureImport
from PySirius.models.instrument_profile import InstrumentProfile
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to import into.
feature_import = [PySirius.FeatureImport()] # List[FeatureImport] | the feature data to be imported
profile = PySirius.InstrumentProfile() # InstrumentProfile | profile describing the instrument used to measure the data. Used to merge spectra. (optional)
opt_fields = ["none"] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' to override defaults. (optional) (default to ["none"])
try:
# Import (aligned) features into the project.
api_response = api_instance.add_aligned_features(project_id, feature_import, profile=profile, opt_fields=opt_fields)
print("The response of FeaturesApi->add_aligned_features:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->add_aligned_features: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to import into. | |
| feature_import | List[FeatureImport] | the feature data to be imported | |
| profile | InstrumentProfile | profile describing the instrument used to measure the data. Used to merge spectra. | [optional] |
| opt_fields | List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' to override defaults. | [optional] [default to ["none"]] |
No authorization required
- Content-Type: application/json
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | the Features that have been imported with specified optional fields | - |
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delete_aligned_feature(project_id, aligned_feature_id)
Delete feature (aligned over runs) with the given identifier from the specified project-space.
Delete feature (aligned over runs) with the given identifier from the specified project-space.
import PySirius
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to delete from.
aligned_feature_id = 'aligned_feature_id_example' # str | identifier of feature (aligned over runs) to delete.
try:
# Delete feature (aligned over runs) with the given identifier from the specified project-space.
api_instance.delete_aligned_feature(project_id, aligned_feature_id)
except Exception as e:
print("Exception when calling FeaturesApi->delete_aligned_feature: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to delete from. | |
| aligned_feature_id | str | identifier of feature (aligned over runs) to delete. |
void (empty response body)
No authorization required
- Content-Type: Not defined
- Accept: Not defined
| Status code | Description | Response headers |
|---|---|---|
| 200 | OK | - |
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delete_aligned_features(project_id, request_body)
Delete feature (aligned over runs) with the given identifier from the specified project-space.
Delete feature (aligned over runs) with the given identifier from the specified project-space.
import PySirius
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to delete from.
request_body = ['request_body_example'] # List[str] |
try:
# Delete feature (aligned over runs) with the given identifier from the specified project-space.
api_instance.delete_aligned_features(project_id, request_body)
except Exception as e:
print("Exception when calling FeaturesApi->delete_aligned_features: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to delete from. | |
| request_body | List[str] |
void (empty response body)
No authorization required
- Content-Type: application/json
- Accept: Not defined
| Status code | Description | Response headers |
|---|---|---|
| 200 | OK | - |
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AlignedFeature get_aligned_feature(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
Get feature (aligned over runs) with the given identifier from the specified project-space.
Get feature (aligned over runs) with the given identifier from the specified project-space.
import PySirius
from PySirius.models.aligned_feature import AlignedFeature
from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | identifier of feature (aligned over runs) to access.
ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False)
opt_fields = ["none"] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# Get feature (aligned over runs) with the given identifier from the specified project-space.
api_response = api_instance.get_aligned_feature(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
print("The response of FeaturesApi->get_aligned_feature:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_aligned_feature: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | identifier of feature (aligned over runs) to access. | |
| ms_data_search_prepared | bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] |
| opt_fields | List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | AlignedFeature with additional annotations and MS/MS data (if specified). | - |
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List[AlignedFeature] get_aligned_features(project_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
Get all available features (aligned over runs) in the given project-space.
Get all available features (aligned over runs) in the given project-space.
import PySirius
from PySirius.models.aligned_feature import AlignedFeature
from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False)
opt_fields = ["none"] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# Get all available features (aligned over runs) in the given project-space.
api_response = api_instance.get_aligned_features(project_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
print("The response of FeaturesApi->get_aligned_features:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_aligned_features: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| ms_data_search_prepared | bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] |
| opt_fields | List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | AlignedFeatures with additional annotations and MS/MS data (if specified). | - |
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PagedModelAlignedFeature get_aligned_features_paged(project_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
Get all available features (aligned over runs) in the given project-space.
Get all available features (aligned over runs) in the given project-space.
import PySirius
from PySirius.models.aligned_feature_opt_field import AlignedFeatureOptField
from PySirius.models.paged_model_aligned_feature import PagedModelAlignedFeature
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
page = 0 # int | Zero-based page index (0..N) (optional) (default to 0)
size = 20 # int | The size of the page to be returned (optional) (default to 20)
sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional)
ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False)
opt_fields = ["none"] # List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# Get all available features (aligned over runs) in the given project-space.
api_response = api_instance.get_aligned_features_paged(project_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
print("The response of FeaturesApi->get_aligned_features_paged:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_aligned_features_paged: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| page | int | Zero-based page index (0..N) | [optional] [default to 0] |
| size | int | The size of the page to be returned | [optional] [default to 20] |
| sort | List[str] | Sorting criteria in the format: property,(asc | desc). Default sort order is ascending. Multiple sort criteria are supported. |
| ms_data_search_prepared | bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] |
| opt_fields | List[AlignedFeatureOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | AlignedFeatures with additional annotations and MS/MS data (if specified). | - |
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CompoundClasses get_best_matching_compound_classes(project_id, aligned_feature_id, formula_id)
Return Best matching compound classes for given formulaId
Return Best matching compound classes for given formulaId.
Set of the highest scoring compound classes (CANOPUS) on each hierarchy level of the ClassyFire and NPC ontology,
import PySirius
from PySirius.models.compound_classes import CompoundClasses
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
try:
# Return Best matching compound classes for given formulaId
api_response = api_instance.get_best_matching_compound_classes(project_id, aligned_feature_id, formula_id)
print("The response of FeaturesApi->get_best_matching_compound_classes:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_best_matching_compound_classes: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | Best matching Predicted compound classes | - |
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CanopusPrediction get_canopus_prediction(project_id, aligned_feature_id, formula_id)
All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,
All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,
import PySirius
from PySirius.models.canopus_prediction import CanopusPrediction
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
try:
# All predicted compound classes (CANOPUS) from ClassyFire and NPC and their probabilities,
api_response = api_instance.get_canopus_prediction(project_id, aligned_feature_id, formula_id)
print("The response of FeaturesApi->get_canopus_prediction:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_canopus_prediction: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | Predicted compound classes | - |
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List[StructureCandidateScored] get_de_novo_structure_candidates_by_formula(project_id, aligned_feature_id, formula_id, opt_fields=opt_fields)
List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
import PySirius
from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField
from PySirius.models.structure_candidate_scored import StructureCandidateScored
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# List of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
api_response = api_instance.get_de_novo_structure_candidates_by_formula(project_id, aligned_feature_id, formula_id, opt_fields=opt_fields)
print("The response of FeaturesApi->get_de_novo_structure_candidates_by_formula:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_de_novo_structure_candidates_by_formula: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result | |
| opt_fields | List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
List[StructureCandidateScored]
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | StructureCandidate of this formula candidate with specified optional fields. | - |
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PagedModelStructureCandidateScored get_de_novo_structure_candidates_by_formula_paged(project_id, aligned_feature_id, formula_id, page=page, size=size, sort=sort, opt_fields=opt_fields)
Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
import PySirius
from PySirius.models.paged_model_structure_candidate_scored import PagedModelStructureCandidateScored
from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
page = 0 # int | Zero-based page index (0..N) (optional) (default to 0)
size = 20 # int | The size of the page to be returned (optional) (default to 20)
sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional)
opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
api_response = api_instance.get_de_novo_structure_candidates_by_formula_paged(project_id, aligned_feature_id, formula_id, page=page, size=size, sort=sort, opt_fields=opt_fields)
print("The response of FeaturesApi->get_de_novo_structure_candidates_by_formula_paged:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_de_novo_structure_candidates_by_formula_paged: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result | |
| page | int | Zero-based page index (0..N) | [optional] [default to 0] |
| size | int | The size of the page to be returned | [optional] [default to 20] |
| sort | List[str] | Sorting criteria in the format: property,(asc | desc). Default sort order is ascending. Multiple sort criteria are supported. |
| opt_fields | List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
PagedModelStructureCandidateScored
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | StructureCandidate of this formula candidate with specified optional fields. | - |
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PagedModelStructureCandidateFormula get_de_novo_structure_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, opt_fields=opt_fields)
Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
import PySirius
from PySirius.models.paged_model_structure_candidate_formula import PagedModelStructureCandidateFormula
from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to.
page = 0 # int | Zero-based page index (0..N) (optional) (default to 0)
size = 20 # int | The size of the page to be returned (optional) (default to 20)
sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional)
opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# Page of de novo structure candidates (e.g. generated by MsNovelist) ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint.
api_response = api_instance.get_de_novo_structure_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, opt_fields=opt_fields)
print("The response of FeaturesApi->get_de_novo_structure_candidates_paged:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_de_novo_structure_candidates_paged: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the structure candidates belong to. | |
| page | int | Zero-based page index (0..N) | [optional] [default to 0] |
| size | int | The size of the page to be returned | [optional] [default to 20] |
| sort | List[str] | Sorting criteria in the format: property,(asc | desc). Default sort order is ascending. Multiple sort criteria are supported. |
| opt_fields | List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
PagedModelStructureCandidateFormula
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | StructureCandidate of this feature (aligned over runs) candidate with specified optional fields. | - |
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List[float] get_fingerprint_prediction(project_id, aligned_feature_id, formula_id)
Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
This fingerprint is used to perform structure database search and predict compound classes.
import PySirius
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
try:
# Returns predicted fingerprint (CSI:FingerID) for the given formula result identifier (formulaId)
api_response = api_instance.get_fingerprint_prediction(project_id, aligned_feature_id, formula_id)
print("The response of FeaturesApi->get_fingerprint_prediction:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_fingerprint_prediction: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result |
List[float]
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | probabilistic fingerprint predicted by CSI:FingerID | - |
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AnnotatedMsMsData get_formula_annotated_ms_ms_data(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared)
Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId
Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId.
Returns MS/MS Spectrum (Merged MS/MS and measured MS/MS) which is annotated with fragments and losses for the given formula result identifier These annotations are only available if a fragmentation tree and the structure candidate are available.
import PySirius
from PySirius.models.annotated_ms_ms_data import AnnotatedMsMsData
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False)
try:
# Returns MS/MS Spectrum annotated with fragments and losses for provided formulaId
api_response = api_instance.get_formula_annotated_ms_ms_data(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared)
print("The response of FeaturesApi->get_formula_annotated_ms_ms_data:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_formula_annotated_ms_ms_data: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result | |
| ms_data_search_prepared | bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | Fragmentation spectra annotated with fragment formulas and losses. | - |
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AnnotatedSpectrum get_formula_annotated_spectrum(project_id, aligned_feature_id, formula_id, spectrum_index=spectrum_index, search_prepared=search_prepared)
Returns a fragmentation spectrum (e
Returns a fragmentation spectrum (e.g. Merged MS/MS) which is annotated with fragments and losses for the given formula result identifier
These annotations are only available if a fragmentation tree is available.
import PySirius
from PySirius.models.annotated_spectrum import AnnotatedSpectrum
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
spectrum_index = -1 # int | index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) (optional) (default to -1)
search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False)
try:
# Returns a fragmentation spectrum (e
api_response = api_instance.get_formula_annotated_spectrum(project_id, aligned_feature_id, formula_id, spectrum_index=spectrum_index, search_prepared=search_prepared)
print("The response of FeaturesApi->get_formula_annotated_spectrum:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_formula_annotated_spectrum: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result | |
| spectrum_index | int | index of the spectrum to be annotated. Merged MS/MS will be used if spectrumIndex < 0 (default) | [optional] [default to -1] |
| search_prepared | bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | Fragmentation spectrum annotated with fragment formulas and losses. | - |
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FormulaCandidate get_formula_candidate(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
FormulaResultContainers for the given 'formulaId' with minimal information.
FormulaResultContainers for the given 'formulaId' with minimal information. Can be enriched with an optional results overview and formula candidate information.
import PySirius
from PySirius.models.formula_candidate import FormulaCandidate
from PySirius.models.formula_candidate_opt_field import FormulaCandidateOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False)
opt_fields = ["none"] # List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# FormulaResultContainers for the given 'formulaId' with minimal information.
api_response = api_instance.get_formula_candidate(project_id, aligned_feature_id, formula_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
print("The response of FeaturesApi->get_formula_candidate:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_formula_candidate: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result | |
| ms_data_search_prepared | bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] |
| opt_fields | List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | FormulaCandidate of this feature (aligned over runs) with. | - |
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List[FormulaCandidate] get_formula_candidates(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
List of FormulaResultContainers available for this feature with minimal information.
List of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview.
import PySirius
from PySirius.models.formula_candidate import FormulaCandidate
from PySirius.models.formula_candidate_opt_field import FormulaCandidateOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False)
opt_fields = ["none"] # List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# List of FormulaResultContainers available for this feature with minimal information.
api_response = api_instance.get_formula_candidates(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
print("The response of FeaturesApi->get_formula_candidates:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_formula_candidates: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| ms_data_search_prepared | bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] |
| opt_fields | List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | All FormulaCandidate of this feature with. | - |
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PagedModelFormulaCandidate get_formula_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
Page of FormulaResultContainers available for this feature with minimal information.
Page of FormulaResultContainers available for this feature with minimal information. Can be enriched with an optional results overview.
import PySirius
from PySirius.models.formula_candidate_opt_field import FormulaCandidateOptField
from PySirius.models.paged_model_formula_candidate import PagedModelFormulaCandidate
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
page = 0 # int | Zero-based page index (0..N) (optional) (default to 0)
size = 20 # int | The size of the page to be returned (optional) (default to 20)
sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional)
ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False)
opt_fields = ["none"] # List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# Page of FormulaResultContainers available for this feature with minimal information.
api_response = api_instance.get_formula_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, ms_data_search_prepared=ms_data_search_prepared, opt_fields=opt_fields)
print("The response of FeaturesApi->get_formula_candidates_paged:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_formula_candidates_paged: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| page | int | Zero-based page index (0..N) | [optional] [default to 0] |
| size | int | The size of the page to be returned | [optional] [default to 20] |
| sort | List[str] | Sorting criteria in the format: property,(asc | desc). Default sort order is ascending. Multiple sort criteria are supported. |
| ms_data_search_prepared | bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] |
| opt_fields | List[FormulaCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | All FormulaCandidate of this feature with. | - |
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FragmentationTree get_frag_tree(project_id, aligned_feature_id, formula_id)
Returns fragmentation tree (SIRIUS) for the given formula result identifier
Returns fragmentation tree (SIRIUS) for the given formula result identifier
This tree is used to rank formula candidates (treeScore).
import PySirius
from PySirius.models.fragmentation_tree import FragmentationTree
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
try:
# Returns fragmentation tree (SIRIUS) for the given formula result identifier
api_response = api_instance.get_frag_tree(project_id, aligned_feature_id, formula_id)
print("The response of FeaturesApi->get_frag_tree:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_frag_tree: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | Fragmentation Tree | - |
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IsotopePatternAnnotation get_isotope_pattern_annotation(project_id, aligned_feature_id, formula_id)
Returns Isotope pattern information for given formulaId
Returns Isotope pattern information for given formulaId
Returns Isotope pattern information (simulated isotope pattern, measured isotope pattern, isotope pattern highlighting) for the given formula result identifier. This simulated isotope pattern is used to rank formula candidates (treeScore).
import PySirius
from PySirius.models.isotope_pattern_annotation import IsotopePatternAnnotation
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
try:
# Returns Isotope pattern information for given formulaId
api_response = api_instance.get_isotope_pattern_annotation(project_id, aligned_feature_id, formula_id)
print("The response of FeaturesApi->get_isotope_pattern_annotation:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_isotope_pattern_annotation: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | Isotope pattern information | - |
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LipidAnnotation get_lipid_annotation(project_id, aligned_feature_id, formula_id)
Returns Lipid annotation (ElGordo) for the given formulaId
Returns Lipid annotation (ElGordo) for the given formulaId.
ElGordo lipid annotation runs as part of the SIRIUS formula identification step.
import PySirius
from PySirius.models.lipid_annotation import LipidAnnotation
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
try:
# Returns Lipid annotation (ElGordo) for the given formulaId
api_response = api_instance.get_lipid_annotation(project_id, aligned_feature_id, formula_id)
print("The response of FeaturesApi->get_lipid_annotation:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_lipid_annotation: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | LipidAnnotation | - |
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MsData get_ms_data(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared)
Mass Spec data (input data) for the given 'alignedFeatureId' .
Mass Spec data (input data) for the given 'alignedFeatureId' .
import PySirius
from PySirius.models.ms_data import MsData
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the Mass Spec data belongs to.
ms_data_search_prepared = False # bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. (optional) (default to False)
try:
# Mass Spec data (input data) for the given 'alignedFeatureId' .
api_response = api_instance.get_ms_data(project_id, aligned_feature_id, ms_data_search_prepared=ms_data_search_prepared)
print("The response of FeaturesApi->get_ms_data:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_ms_data: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the Mass Spec data belongs to. | |
| ms_data_search_prepared | bool | Returns all fragment spectra in a preprocessed form as used for fast Cosine/Modified Cosine computation. Gives you spectra compatible with SpectralLibraryMatch peak assignments and reference spectra. | [optional] [default to False] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | Mass Spec data of this feature (aligned over runs). | - |
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SpectralLibraryMatch get_spectral_library_match(project_id, aligned_feature_id, match_id, opt_fields=opt_fields)
Spectral library match for the given 'alignedFeatureId'.
Spectral library match for the given 'alignedFeatureId'.
import PySirius
from PySirius.models.spectral_library_match import SpectralLibraryMatch
from PySirius.models.spectral_library_match_opt_field import SpectralLibraryMatchOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to.
match_id = 'match_id_example' # str | id of the library match to be returned.
opt_fields = ["none"] # List[SpectralLibraryMatchOptField] | (optional) (default to ["none"])
try:
# Spectral library match for the given 'alignedFeatureId'.
api_response = api_instance.get_spectral_library_match(project_id, aligned_feature_id, match_id, opt_fields=opt_fields)
print("The response of FeaturesApi->get_spectral_library_match:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_spectral_library_match: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the structure candidates belong to. | |
| match_id | str | id of the library match to be returned. | |
| opt_fields | List[SpectralLibraryMatchOptField] | [optional] [default to ["none"]] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | Spectral library match with requested mathcId. | - |
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List[SpectralLibraryMatch] get_spectral_library_matches(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields)
List of spectral library matches for the given 'alignedFeatureId'.
List of spectral library matches for the given 'alignedFeatureId'.
import PySirius
from PySirius.models.spectral_library_match import SpectralLibraryMatch
from PySirius.models.spectral_library_match_opt_field import SpectralLibraryMatchOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to.
min_shared_peaks = 1 # int | (optional) (default to 1)
min_similarity = 0.2 # float | (optional) (default to 0.2)
inchi_key = '' # str | (optional) (default to '')
opt_fields = ["none"] # List[SpectralLibraryMatchOptField] | (optional) (default to ["none"])
try:
# List of spectral library matches for the given 'alignedFeatureId'.
api_response = api_instance.get_spectral_library_matches(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields)
print("The response of FeaturesApi->get_spectral_library_matches:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_spectral_library_matches: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the structure candidates belong to. | |
| min_shared_peaks | int | [optional] [default to 1] | |
| min_similarity | float | [optional] [default to 0.2] | |
| inchi_key | str | [optional] [default to ''] | |
| opt_fields | List[SpectralLibraryMatchOptField] | [optional] [default to ["none"]] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | Spectral library matches of this feature (aligned over runs). | - |
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PagedModelSpectralLibraryMatch get_spectral_library_matches_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields)
Page of spectral library matches for the given 'alignedFeatureId'.
Page of spectral library matches for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, returns only matches for the database compound with the given InChI key.
import PySirius
from PySirius.models.paged_model_spectral_library_match import PagedModelSpectralLibraryMatch
from PySirius.models.spectral_library_match_opt_field import SpectralLibraryMatchOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to.
page = 0 # int | Zero-based page index (0..N) (optional) (default to 0)
size = 20 # int | The size of the page to be returned (optional) (default to 20)
sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional)
min_shared_peaks = 1 # int | (optional) (default to 1)
min_similarity = 0.2 # float | (optional) (default to 0.2)
inchi_key = '' # str | (optional) (default to '')
opt_fields = ["none"] # List[SpectralLibraryMatchOptField] | (optional) (default to ["none"])
try:
# Page of spectral library matches for the given 'alignedFeatureId'.
api_response = api_instance.get_spectral_library_matches_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key, opt_fields=opt_fields)
print("The response of FeaturesApi->get_spectral_library_matches_paged:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_spectral_library_matches_paged: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the structure candidates belong to. | |
| page | int | Zero-based page index (0..N) | [optional] [default to 0] |
| size | int | The size of the page to be returned | [optional] [default to 20] |
| sort | List[str] | Sorting criteria in the format: property,(asc | desc). Default sort order is ascending. Multiple sort criteria are supported. |
| min_shared_peaks | int | [optional] [default to 1] | |
| min_similarity | float | [optional] [default to 0.2] | |
| inchi_key | str | [optional] [default to ''] | |
| opt_fields | List[SpectralLibraryMatchOptField] | [optional] [default to ["none"]] |
PagedModelSpectralLibraryMatch
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | Spectral library matches of this feature (aligned over runs). | - |
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SpectralLibraryMatchSummary get_spectral_library_matches_summary(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key)
Summarize matched reference spectra for the given 'alignedFeatureId'.
Summarize matched reference spectra for the given 'alignedFeatureId'. If a 'inchiKey' (2D) is provided, summarizes only contains matches for the database compound with the given InChI key.
import PySirius
from PySirius.models.spectral_library_match_summary import SpectralLibraryMatchSummary
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to.
min_shared_peaks = 1 # int | min threshold of shared peaks. (optional) (default to 1)
min_similarity = 0.2 # float | min spectral similarity threshold. (optional) (default to 0.2)
inchi_key = '' # str | 2D inchi key of the compound in the structure database. (optional) (default to '')
try:
# Summarize matched reference spectra for the given 'alignedFeatureId'.
api_response = api_instance.get_spectral_library_matches_summary(project_id, aligned_feature_id, min_shared_peaks=min_shared_peaks, min_similarity=min_similarity, inchi_key=inchi_key)
print("The response of FeaturesApi->get_spectral_library_matches_summary:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_spectral_library_matches_summary: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the structure candidates belong to. | |
| min_shared_peaks | int | min threshold of shared peaks. | [optional] [default to 1] |
| min_similarity | float | min spectral similarity threshold. | [optional] [default to 0.2] |
| inchi_key | str | 2D inchi key of the compound in the structure database. | [optional] [default to ''] |
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | Summary object with best match, number of spectral library matches, matched reference spectra and matched database compounds of this feature (aligned over runs). | - |
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List[StructureCandidateFormula] get_structure_candidates(project_id, aligned_feature_id, opt_fields=opt_fields)
List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.
List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links.
import PySirius
from PySirius.models.structure_candidate_formula import StructureCandidateFormula
from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to.
opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# List of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.
api_response = api_instance.get_structure_candidates(project_id, aligned_feature_id, opt_fields=opt_fields)
print("The response of FeaturesApi->get_structure_candidates:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_structure_candidates: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the structure candidates belong to. | |
| opt_fields | List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
List[StructureCandidateFormula]
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | StructureCandidate of this feature (aligned over runs) candidate with specified optional fields. | - |
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List[StructureCandidateScored] get_structure_candidates_by_formula(project_id, aligned_feature_id, formula_id, opt_fields=opt_fields)
List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.
List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links.
import PySirius
from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField
from PySirius.models.structure_candidate_scored import StructureCandidateScored
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# List of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.
api_response = api_instance.get_structure_candidates_by_formula(project_id, aligned_feature_id, formula_id, opt_fields=opt_fields)
print("The response of FeaturesApi->get_structure_candidates_by_formula:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_structure_candidates_by_formula: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result | |
| opt_fields | List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
List[StructureCandidateScored]
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | StructureCandidate of this formula candidate with specified optional fields. | - |
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PagedModelStructureCandidateScored get_structure_candidates_by_formula_paged(project_id, aligned_feature_id, formula_id, page=page, size=size, sort=sort, opt_fields=opt_fields)
Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.
Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links.
import PySirius
from PySirius.models.paged_model_structure_candidate_scored import PagedModelStructureCandidateScored
from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the formula result belongs to.
formula_id = 'formula_id_example' # str | identifier of the requested formula result
page = 0 # int | Zero-based page index (0..N) (optional) (default to 0)
size = 20 # int | The size of the page to be returned (optional) (default to 20)
sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional)
opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# Page of CSI:FingerID structure database search candidates for the given 'formulaId' with minimal information.
api_response = api_instance.get_structure_candidates_by_formula_paged(project_id, aligned_feature_id, formula_id, page=page, size=size, sort=sort, opt_fields=opt_fields)
print("The response of FeaturesApi->get_structure_candidates_by_formula_paged:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_structure_candidates_by_formula_paged: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the formula result belongs to. | |
| formula_id | str | identifier of the requested formula result | |
| page | int | Zero-based page index (0..N) | [optional] [default to 0] |
| size | int | The size of the page to be returned | [optional] [default to 20] |
| sort | List[str] | Sorting criteria in the format: property,(asc | desc). Default sort order is ascending. Multiple sort criteria are supported. |
| opt_fields | List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
PagedModelStructureCandidateScored
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | StructureCandidate of this formula candidate with specified optional fields. | - |
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PagedModelStructureCandidateFormula get_structure_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, opt_fields=opt_fields)
Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.
Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information. StructureCandidates can be enriched with molecular fingerprint, structure database links.
import PySirius
from PySirius.models.paged_model_structure_candidate_formula import PagedModelStructureCandidateFormula
from PySirius.models.structure_candidate_opt_field import StructureCandidateOptField
from PySirius.rest import ApiException
from pprint import pprint
# Defining the host is optional and defaults to http://localhost:8080
# See configuration.py for a list of all supported configuration parameters.
configuration = PySirius.Configuration(
host = "http://localhost:8080"
)
# Enter a context with an instance of the API client
with PySirius.ApiClient(configuration) as api_client:
# Create an instance of the API class
api_instance = PySirius.FeaturesApi(api_client)
project_id = 'project_id_example' # str | project-space to read from.
aligned_feature_id = 'aligned_feature_id_example' # str | feature (aligned over runs) the structure candidates belong to.
page = 0 # int | Zero-based page index (0..N) (optional) (default to 0)
size = 20 # int | The size of the page to be returned (optional) (default to 20)
sort = ['sort_example'] # List[str] | Sorting criteria in the format: property,(asc|desc). Default sort order is ascending. Multiple sort criteria are supported. (optional)
opt_fields = ["none"] # List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. (optional) (default to ["none"])
try:
# Page of structure database search candidates ranked by CSI:FingerID score for the given 'alignedFeatureId' with minimal information.
api_response = api_instance.get_structure_candidates_paged(project_id, aligned_feature_id, page=page, size=size, sort=sort, opt_fields=opt_fields)
print("The response of FeaturesApi->get_structure_candidates_paged:\n")
pprint(api_response)
except Exception as e:
print("Exception when calling FeaturesApi->get_structure_candidates_paged: %s\n" % e)| Name | Type | Description | Notes |
|---|---|---|---|
| project_id | str | project-space to read from. | |
| aligned_feature_id | str | feature (aligned over runs) the structure candidates belong to. | |
| page | int | Zero-based page index (0..N) | [optional] [default to 0] |
| size | int | The size of the page to be returned | [optional] [default to 20] |
| sort | List[str] | Sorting criteria in the format: property,(asc | desc). Default sort order is ascending. Multiple sort criteria are supported. |
| opt_fields | List[StructureCandidateOptField] | set of optional fields to be included. Use 'none' only to override defaults. | [optional] [default to ["none"]] |
PagedModelStructureCandidateFormula
No authorization required
- Content-Type: Not defined
- Accept: application/json
| Status code | Description | Response headers |
|---|---|---|
| 200 | StructureCandidate of this feature (aligned over runs) candidate with specified optional fields. | - |
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