cheminee 0.1.38 → 0.1.41
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- checksums.yaml +4 -4
- data/Gemfile.lock +17 -15
- data/README.md +6 -5
- data/cheminee.gemspec +1 -1
- data/docs/DefaultApi.md +85 -8
- data/lib/cheminee/api/default_api.rb +92 -9
- data/lib/cheminee/api_client.rb +1 -1
- data/lib/cheminee/api_error.rb +1 -1
- data/lib/cheminee/configuration.rb +1 -1
- data/lib/cheminee/models/bulk_request.rb +1 -1
- data/lib/cheminee/models/bulk_request_doc.rb +1 -1
- data/lib/cheminee/models/converted_mol_block.rb +1 -1
- data/lib/cheminee/models/converted_smiles.rb +1 -1
- data/lib/cheminee/models/create_index_error.rb +1 -1
- data/lib/cheminee/models/delete_index_bulk_response_error.rb +1 -1
- data/lib/cheminee/models/delete_index_bulk_response_ok.rb +1 -1
- data/lib/cheminee/models/delete_index_bulk_response_ok_status.rb +1 -1
- data/lib/cheminee/models/delete_index_error.rb +1 -1
- data/lib/cheminee/models/get_indexes_response_error.rb +1 -1
- data/lib/cheminee/models/index_meta.rb +1 -1
- data/lib/cheminee/models/index_schema.rb +1 -1
- data/lib/cheminee/models/list_index_response_err.rb +1 -1
- data/lib/cheminee/models/mol_block.rb +1 -1
- data/lib/cheminee/models/post_index_bulk_response_error.rb +1 -1
- data/lib/cheminee/models/post_index_bulk_response_ok.rb +1 -1
- data/lib/cheminee/models/post_index_bulk_response_ok_status.rb +1 -1
- data/lib/cheminee/models/query_response_error.rb +1 -1
- data/lib/cheminee/models/query_search_hit.rb +1 -1
- data/lib/cheminee/models/schema.rb +1 -1
- data/lib/cheminee/models/smiles.rb +1 -1
- data/lib/cheminee/models/standardized_smiles.rb +1 -1
- data/lib/cheminee/models/structure_response_error.rb +1 -1
- data/lib/cheminee/models/structure_search_hit.rb +1 -1
- data/lib/cheminee/version.rb +2 -2
- data/lib/cheminee.rb +1 -1
- data/pkg/cheminee-0.1.41.gem +0 -0
- data/spec/spec_helper.rb +1 -1
- metadata +3 -3
- data/pkg/cheminee-0.1.38.gem +0 -0
checksums.yaml
CHANGED
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---
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SHA256:
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metadata.gz:
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data.tar.gz:
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metadata.gz: e221ba9a3bf9c7f9f53a04449a1b2312dc8d85a328abc8d467a934636a3f5681
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data.tar.gz: bb775f632d8226591544f376f1609a140d9ce453d8ad078b9a7f614d7e0cc272
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 7c10f345407b78ee94f804413b5b2b3466c995210cac99a6cda6fed80c83313d5debcdf7fb6ffb3110bedf2cdaec83286b4acf1948833fb83743e364014d9144
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data.tar.gz: 634290512cde3c26bb07b7c6a465d5d8e99fb1636bd2599c8bdeed38964b53594c2e16600c363b53b9fd8a3605116be18ab522a8751c6938ac0fce63b5137826
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data/Gemfile.lock
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PATH
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remote: .
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specs:
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cheminee (0.1.
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cheminee (0.1.41)
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faraday (>= 1.0.1, < 3.0)
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faraday-multipart
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marcel
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ast (2.4.2)
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byebug (11.1.3)
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coderay (1.1.3)
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date (3.4.1)
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diff-lcs (1.5.1)
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faraday (2.12.
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faraday-net_http (>= 2.0, < 3.
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faraday (2.12.1)
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faraday-net_http (>= 2.0, < 3.5)
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json
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logger
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faraday-multipart (1.0.4)
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multipart-post (~> 2)
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faraday-net_http (3.
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net-http
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faraday-net_http (3.4.0)
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net-http (>= 0.5.0)
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jaro_winkler (1.5.6)
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json (2.
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logger (1.6.
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json (2.9.0)
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logger (1.6.2)
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marcel (1.0.4)
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method_source (1.1.0)
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multipart-post (2.4.1)
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uri
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parallel (1.26.3)
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parser (3.3.
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parser (3.3.6.0)
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ast (~> 2.4.1)
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racc
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pry (0.14.2)
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pry-byebug (3.10.1)
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byebug (~> 11.0)
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pry (>= 0.13, < 0.15)
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psych (5.1
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psych (5.2.1)
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date
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stringio
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racc (1.8.1)
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rainbow (3.1.1)
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rspec-core (~> 3.13.0)
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rspec-expectations (~> 3.13.0)
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rspec-mocks (~> 3.13.0)
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rspec-core (3.13.
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rspec-expectations (3.13.3)
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diff-lcs (>= 1.2.0, < 2.0)
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rspec-support (~> 3.13.0)
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rspec-mocks (3.13.
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rspec-mocks (3.13.2)
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rspec-support (~> 3.13.0)
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rspec-support (3.13.
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rspec-support (3.13.2)
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rubocop (0.66.0)
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jaro_winkler (~> 1.5.1)
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parallel (~> 1.10)
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ruby-progressbar (~> 1.7)
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unicode-display_width (>= 1.4.0, < 1.6)
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ruby-progressbar (1.13.0)
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PLATFORMS
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x86_64-linux
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data/README.md
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@@ -7,8 +7,8 @@ Cheminée: The Chemical Structure Search Engine
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This SDK is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
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- API version: 1.0
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- Package version: 0.1.
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- Generator version: 7.
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- Package version: 0.1.41
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- Generator version: 7.11.0-SNAPSHOT
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- Build package: org.openapitools.codegen.languages.RubyClientCodegen
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For more information, please visit [https://github.com/rdkit-rs/cheminee](https://github.com/rdkit-rs/cheminee)
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@@ -25,16 +25,16 @@ gem build cheminee.gemspec
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Then either install the gem locally:
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```shell
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gem install ./cheminee-0.1.
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gem install ./cheminee-0.1.41.gem
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```
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(for development, run `gem install --dev ./cheminee-0.1.
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(for development, run `gem install --dev ./cheminee-0.1.41.gem` to install the development dependencies)
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or publish the gem to a gem hosting service, e.g. [RubyGems](https://rubygems.org/).
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Finally add this to the Gemfile:
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gem 'cheminee', '~> 0.1.
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gem 'cheminee', '~> 0.1.41'
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### Install from Git
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@@ -89,6 +89,7 @@ Class | Method | HTTP request | Description
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*Cheminee::DefaultApi* | [**v1_indexes_index_post**](docs/DefaultApi.md#v1_indexes_index_post) | **POST** /v1/indexes/{index} | Create an index
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*Cheminee::DefaultApi* | [**v1_indexes_index_search_basic_get**](docs/DefaultApi.md#v1_indexes_index_search_basic_get) | **GET** /v1/indexes/{index}/search/basic | Perform basic query search against index
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*Cheminee::DefaultApi* | [**v1_indexes_index_search_identity_get**](docs/DefaultApi.md#v1_indexes_index_search_identity_get) | **GET** /v1/indexes/{index}/search/identity | Perform identity search (i.e. exact match) against index
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*Cheminee::DefaultApi* | [**v1_indexes_index_search_similarity_get**](docs/DefaultApi.md#v1_indexes_index_search_similarity_get) | **GET** /v1/indexes/{index}/search/similarity | Perform similarity search against index
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*Cheminee::DefaultApi* | [**v1_indexes_index_search_substructure_get**](docs/DefaultApi.md#v1_indexes_index_search_substructure_get) | **GET** /v1/indexes/{index}/search/substructure | Perform substructure search against index
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*Cheminee::DefaultApi* | [**v1_indexes_index_search_superstructure_get**](docs/DefaultApi.md#v1_indexes_index_search_superstructure_get) | **GET** /v1/indexes/{index}/search/superstructure | Perform superstructure search against index
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*Cheminee::DefaultApi* | [**v1_schemas_get**](docs/DefaultApi.md#v1_schemas_get) | **GET** /v1/schemas | List schemas available for creating indexes
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data/cheminee.gemspec
CHANGED
data/docs/DefaultApi.md
CHANGED
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@@ -15,6 +15,7 @@ All URIs are relative to *http://localhost:4001/api*
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| [**v1_indexes_index_post**](DefaultApi.md#v1_indexes_index_post) | **POST** /v1/indexes/{index} | Create an index |
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| [**v1_indexes_index_search_basic_get**](DefaultApi.md#v1_indexes_index_search_basic_get) | **GET** /v1/indexes/{index}/search/basic | Perform basic query search against index |
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| [**v1_indexes_index_search_identity_get**](DefaultApi.md#v1_indexes_index_search_identity_get) | **GET** /v1/indexes/{index}/search/identity | Perform identity search (i.e. exact match) against index |
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| [**v1_indexes_index_search_similarity_get**](DefaultApi.md#v1_indexes_index_search_similarity_get) | **GET** /v1/indexes/{index}/search/similarity | Perform similarity search against index |
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| [**v1_indexes_index_search_substructure_get**](DefaultApi.md#v1_indexes_index_search_substructure_get) | **GET** /v1/indexes/{index}/search/substructure | Perform substructure search against index |
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| [**v1_indexes_index_search_superstructure_get**](DefaultApi.md#v1_indexes_index_search_superstructure_get) | **GET** /v1/indexes/{index}/search/superstructure | Perform superstructure search against index |
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| [**v1_schemas_get**](DefaultApi.md#v1_schemas_get) | **GET** /v1/schemas | List schemas available for creating indexes |
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index = 'index_example' # String |
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smiles = 'smiles_example' # String |
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opts = {
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use_chirality:
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use_chirality: true, # Boolean |
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extra_query: 'extra_query_example', # String |
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use_scaffolds:
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use_scaffolds: true # Boolean |
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}
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begin
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| ---- | ---- | ----------- | ----- |
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| **index** | **String** | | |
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| **smiles** | **String** | | |
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-
| **use_chirality** | **
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| **use_chirality** | **Boolean** | | [optional] |
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| **extra_query** | **String** | | [optional] |
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| **use_scaffolds** | **Boolean** | | [optional] |
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### Return type
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715
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+
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[**Array<StructureSearchHit>**](StructureSearchHit.md)
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### Authorization
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No authorization required
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### HTTP request headers
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+
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- **Content-Type**: Not defined
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- **Accept**: application/json
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728
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## v1_indexes_index_search_similarity_get
|
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729
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+
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+
> <Array<StructureSearchHit>> v1_indexes_index_search_similarity_get(index, smiles, opts)
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731
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+
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732
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Perform similarity search against index
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733
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+
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734
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+
### Examples
|
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735
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+
|
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736
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+
```ruby
|
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737
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+
require 'time'
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738
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require 'cheminee'
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739
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+
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740
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+
api_instance = Cheminee::DefaultApi.new
|
|
741
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+
index = 'index_example' # String |
|
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742
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+
smiles = 'smiles_example' # String |
|
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743
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+
opts = {
|
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744
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+
result_limit: 56, # Integer |
|
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745
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+
tautomer_limit: 56, # Integer |
|
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746
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+
search_percent_limit: 3.4, # Float |
|
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747
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+
tanimoto_minimum: 3.4, # Float |
|
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748
|
+
extra_query: 'extra_query_example' # String |
|
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749
|
+
}
|
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750
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+
|
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751
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+
begin
|
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752
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+
# Perform similarity search against index
|
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753
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+
result = api_instance.v1_indexes_index_search_similarity_get(index, smiles, opts)
|
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754
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+
p result
|
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755
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+
rescue Cheminee::ApiError => e
|
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756
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+
puts "Error when calling DefaultApi->v1_indexes_index_search_similarity_get: #{e}"
|
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757
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+
end
|
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758
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+
```
|
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759
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+
|
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760
|
+
#### Using the v1_indexes_index_search_similarity_get_with_http_info variant
|
|
761
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+
|
|
762
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+
This returns an Array which contains the response data, status code and headers.
|
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763
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+
|
|
764
|
+
> <Array(<Array<StructureSearchHit>>, Integer, Hash)> v1_indexes_index_search_similarity_get_with_http_info(index, smiles, opts)
|
|
765
|
+
|
|
766
|
+
```ruby
|
|
767
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+
begin
|
|
768
|
+
# Perform similarity search against index
|
|
769
|
+
data, status_code, headers = api_instance.v1_indexes_index_search_similarity_get_with_http_info(index, smiles, opts)
|
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770
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+
p status_code # => 2xx
|
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771
|
+
p headers # => { ... }
|
|
772
|
+
p data # => <Array<StructureSearchHit>>
|
|
773
|
+
rescue Cheminee::ApiError => e
|
|
774
|
+
puts "Error when calling DefaultApi->v1_indexes_index_search_similarity_get_with_http_info: #{e}"
|
|
775
|
+
end
|
|
776
|
+
```
|
|
777
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+
|
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778
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+
### Parameters
|
|
779
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+
|
|
780
|
+
| Name | Type | Description | Notes |
|
|
781
|
+
| ---- | ---- | ----------- | ----- |
|
|
782
|
+
| **index** | **String** | | |
|
|
783
|
+
| **smiles** | **String** | | |
|
|
784
|
+
| **result_limit** | **Integer** | | [optional] |
|
|
785
|
+
| **tautomer_limit** | **Integer** | | [optional] |
|
|
786
|
+
| **search_percent_limit** | **Float** | | [optional] |
|
|
787
|
+
| **tanimoto_minimum** | **Float** | | [optional] |
|
|
710
788
|
| **extra_query** | **String** | | [optional] |
|
|
711
|
-
| **use_scaffolds** | **String** | | [optional] |
|
|
712
789
|
|
|
713
790
|
### Return type
|
|
714
791
|
|
|
@@ -816,11 +893,11 @@ api_instance = Cheminee::DefaultApi.new
|
|
|
816
893
|
index = 'index_example' # String |
|
|
817
894
|
smiles = 'smiles_example' # String |
|
|
818
895
|
opts = {
|
|
819
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| ---- | ---- | ----------- | ----- |
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| **index** | **String** | | |
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| **use_chirality** | **
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| **use_scaffolds** | **Boolean** | | [optional] |
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### Return type
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The version of the OpenAPI document: 1.0
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Generated by: https://openapi-generator.tech
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=end
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@@ -683,9 +683,9 @@ module Cheminee
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# @param index [String]
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# @param smiles [String]
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def v1_indexes_index_search_identity_get(index, smiles, opts = {})
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data, _status_code, _headers = v1_indexes_index_search_identity_get_with_http_info(index, smiles, opts)
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def v1_indexes_index_search_identity_get_with_http_info(index, smiles, opts = {})
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# Perform similarity search against index
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def v1_indexes_index_search_similarity_get(index, smiles, opts = {})
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data, _status_code, _headers = v1_indexes_index_search_similarity_get_with_http_info(index, smiles, opts)
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data
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end
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def v1_indexes_index_search_similarity_get_with_http_info(index, smiles, opts = {})
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end
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# verify the required parameter 'index' is set
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end
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# verify the required parameter 'smiles' is set
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end
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# resource path
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local_var_path = '/v1/indexes/{index}/search/similarity'.sub('{' + 'index' + '}', CGI.escape(index.to_s))
|
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query_params = opts[:query_params] || {}
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query_params[:'smiles'] = smiles
|
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|
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query_params[:'tautomer_limit'] = opts[:'tautomer_limit'] if !opts[:'tautomer_limit'].nil?
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|
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query_params[:'search_percent_limit'] = opts[:'search_percent_limit'] if !opts[:'search_percent_limit'].nil?
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|
+
query_params[:'tanimoto_minimum'] = opts[:'tanimoto_minimum'] if !opts[:'tanimoto_minimum'].nil?
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query_params[:'extra_query'] = opts[:'extra_query'] if !opts[:'extra_query'].nil?
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|
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|
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# header parameters
|
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|
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header_params = opts[:header_params] || {}
|
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|
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# HTTP header 'Accept' (if needed)
|
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|
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header_params['Accept'] = @api_client.select_header_accept(['application/json']) unless header_params['Accept']
|
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|
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|
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# form parameters
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|
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form_params = opts[:form_params] || {}
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|
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# http body (model)
|
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|
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post_body = opts[:debug_body]
|
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|
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|
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# return_type
|
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return_type = opts[:debug_return_type] || 'Array<StructureSearchHit>'
|
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|
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|
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# auth_names
|
|
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|
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auth_names = opts[:debug_auth_names] || []
|
|
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|
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|
|
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|
+
new_options = opts.merge(
|
|
826
|
+
:operation => :"DefaultApi.v1_indexes_index_search_similarity_get",
|
|
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|
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:header_params => header_params,
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|
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|
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:body => post_body,
|
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|
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:auth_names => auth_names,
|
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|
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:return_type => return_type
|
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|
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)
|
|
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|
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|
|
835
|
+
data, status_code, headers = @api_client.call_api(:GET, local_var_path, new_options)
|
|
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|
+
if @api_client.config.debugging
|
|
837
|
+
@api_client.config.logger.debug "API called: DefaultApi#v1_indexes_index_search_similarity_get\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
|
|
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|
+
end
|
|
839
|
+
return data, status_code, headers
|
|
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|
+
end
|
|
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|
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|
|
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|
# Perform substructure search against index
|
|
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|
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|
|
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|
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|
|
@@ -843,11 +926,11 @@ module Cheminee
|
|
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926
|
# @param index [String]
|
|
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|
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|
|
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|
|
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|
-
# @option opts [
|
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|
|
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|
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|
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|
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|
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|
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|
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# @option opts [
|
|
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|
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|
|
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934
|
# @return [Array<StructureSearchHit>]
|
|
852
935
|
def v1_indexes_index_search_superstructure_get(index, smiles, opts = {})
|
|
853
936
|
data, _status_code, _headers = v1_indexes_index_search_superstructure_get_with_http_info(index, smiles, opts)
|
|
@@ -858,11 +941,11 @@ module Cheminee
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|
# @param index [String]
|
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942
|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
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|
|
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949
|
# @return [Array<(Array<StructureSearchHit>, Integer, Hash)>] Array<StructureSearchHit> data, response status code and response headers
|
|
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|
def v1_indexes_index_search_superstructure_get_with_http_info(index, smiles, opts = {})
|
|
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|
data/lib/cheminee/api_client.rb
CHANGED
data/lib/cheminee/api_error.rb
CHANGED
data/lib/cheminee/version.rb
CHANGED
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CHANGED
|
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CHANGED
metadata
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|
--- !ruby/object:Gem::Specification
|
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|
name: cheminee
|
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|
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|
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|
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|
|
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|
platform: ruby
|
|
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|
authors:
|
|
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|
- Xavier Lange
|
|
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|
autorequire:
|
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|
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|
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|
-
date: 2024-
|
|
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|
+
date: 2024-12-03 00:00:00.000000000 Z
|
|
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|
dependencies:
|
|
13
13
|
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|
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14
14
|
name: faraday
|
|
@@ -154,7 +154,7 @@ files:
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|
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|
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|
data/pkg/cheminee-0.1.38.gem
DELETED
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|