cheminee 0.0.14
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- checksums.yaml +7 -0
- data/Gemfile +9 -0
- data/Gemfile.lock +72 -0
- data/README.md +112 -0
- data/Rakefile +10 -0
- data/cheminee.gemspec +39 -0
- data/docs/BulkRequest.md +18 -0
- data/docs/BulkRequestDoc.md +20 -0
- data/docs/CreateIndexError.md +18 -0
- data/docs/DefaultApi.md +529 -0
- data/docs/GetIndexesResponseError.md +18 -0
- data/docs/IndexMeta.md +20 -0
- data/docs/IndexSchema.md +20 -0
- data/docs/ListIndexResponseErr.md +18 -0
- data/docs/PostIndexBulkResponseError.md +18 -0
- data/docs/PostIndexBulkResponseOk.md +18 -0
- data/docs/PostIndexBulkResponseOkStatus.md +20 -0
- data/docs/QueryResponseError.md +18 -0
- data/docs/QuerySearchHit.md +22 -0
- data/docs/Schema.md +20 -0
- data/docs/Smile.md +18 -0
- data/docs/Smiles.md +18 -0
- data/docs/StandardizedSmile.md +20 -0
- data/docs/StandardizedSmiles.md +20 -0
- data/docs/StructureResponseError.md +18 -0
- data/docs/StructureSearchHit.md +26 -0
- data/docs/SubstructureSearchHit.md +24 -0
- data/git_push.sh +57 -0
- data/lib/cheminee/api/default_api.rb +550 -0
- data/lib/cheminee/api_client.rb +393 -0
- data/lib/cheminee/api_error.rb +58 -0
- data/lib/cheminee/configuration.rb +291 -0
- data/lib/cheminee/models/bulk_request.rb +223 -0
- data/lib/cheminee/models/bulk_request_doc.rb +232 -0
- data/lib/cheminee/models/create_index_error.rb +221 -0
- data/lib/cheminee/models/get_indexes_response_error.rb +221 -0
- data/lib/cheminee/models/index_meta.rb +237 -0
- data/lib/cheminee/models/index_schema.rb +233 -0
- data/lib/cheminee/models/list_index_response_err.rb +221 -0
- data/lib/cheminee/models/post_index_bulk_response_error.rb +221 -0
- data/lib/cheminee/models/post_index_bulk_response_ok.rb +223 -0
- data/lib/cheminee/models/post_index_bulk_response_ok_status.rb +223 -0
- data/lib/cheminee/models/query_response_error.rb +221 -0
- data/lib/cheminee/models/query_search_hit.rb +249 -0
- data/lib/cheminee/models/schema.rb +233 -0
- data/lib/cheminee/models/smile.rb +221 -0
- data/lib/cheminee/models/smiles.rb +221 -0
- data/lib/cheminee/models/standardized_smile.rb +223 -0
- data/lib/cheminee/models/standardized_smiles.rb +223 -0
- data/lib/cheminee/models/structure_response_error.rb +221 -0
- data/lib/cheminee/models/structure_search_hit.rb +281 -0
- data/lib/cheminee/models/substructure_search_hit.rb +265 -0
- data/lib/cheminee/version.rb +15 -0
- data/lib/cheminee.rb +57 -0
- data/openapi-generator-config.json +7 -0
- data/openapi.json +77 -0
- data/pkg/cheminee-0.0.14.gem +0 -0
- data/spec/api/default_api_spec.rb +45 -0
- data/spec/api_client_spec.rb +228 -0
- data/spec/configuration_spec.rb +42 -0
- data/spec/models/bulk_request_doc_spec.rb +42 -0
- data/spec/models/bulk_request_spec.rb +36 -0
- data/spec/models/create_index_error_spec.rb +36 -0
- data/spec/models/get_indexes_response_error_spec.rb +36 -0
- data/spec/models/index_meta_spec.rb +42 -0
- data/spec/models/index_schema_spec.rb +42 -0
- data/spec/models/list_index_response_err_spec.rb +36 -0
- data/spec/models/post_index_bulk_response_error_spec.rb +36 -0
- data/spec/models/post_index_bulk_response_ok_spec.rb +36 -0
- data/spec/models/post_index_bulk_response_ok_status_spec.rb +42 -0
- data/spec/models/query_response_error_spec.rb +36 -0
- data/spec/models/query_search_hit_spec.rb +48 -0
- data/spec/models/schema_spec.rb +42 -0
- data/spec/models/smile_spec.rb +34 -0
- data/spec/models/smiles_spec.rb +36 -0
- data/spec/models/standardized_smile_spec.rb +40 -0
- data/spec/models/standardized_smiles_spec.rb +42 -0
- data/spec/models/structure_response_error_spec.rb +36 -0
- data/spec/models/structure_search_hit_spec.rb +60 -0
- data/spec/models/substructure_search_hit_spec.rb +54 -0
- data/spec/spec_helper.rb +111 -0
- metadata +187 -0
checksums.yaml
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SHA256:
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metadata.gz: 2245000aaf941c82d3815031b336ae318c70412ccc30e8f8e231353f190ad85c
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SHA512:
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metadata.gz: 189d84e99d4476b19d0ffe05215d90c27313ed017bbe715d335b4af97c77c8b00c3b69c881c1f5e536d89f16ff89b759a549de1bcbbd101c12eb6a4d59ffc9a2
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data.tar.gz: c27158dd5fe24d175d2a8229e16d67a4f68045024dafd1d6ebbe269614d491133e4938dd0dd47e1f5bd7de4a40b35e08c3a81aca880caacc955c635ea973448f
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data/Gemfile
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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 (0.0.14)
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typhoeus (~> 1.0, >= 1.0.1)
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GEM
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remote: https://rubygems.org/
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specs:
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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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diff-lcs (1.5.0)
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ethon (0.16.0)
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ffi (>= 1.15.0)
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ffi (1.16.3)
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jaro_winkler (1.5.6)
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method_source (1.0.0)
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parallel (1.24.0)
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parser (3.3.0.5)
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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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coderay (~> 1.1)
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method_source (~> 1.0)
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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 (5.1.2)
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stringio
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racc (1.7.3)
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rainbow (3.1.1)
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rake (13.0.6)
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rspec (3.12.0)
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rspec-core (~> 3.12.0)
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rspec-expectations (~> 3.12.0)
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rspec-mocks (~> 3.12.0)
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rspec-core (3.12.2)
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rspec-support (~> 3.12.0)
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rspec-expectations (3.12.3)
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diff-lcs (>= 1.2.0, < 2.0)
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rspec-support (~> 3.12.0)
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rspec-mocks (3.12.6)
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diff-lcs (>= 1.2.0, < 2.0)
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rspec-support (~> 3.12.0)
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rspec-support (3.12.1)
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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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parser (>= 2.5, != 2.5.1.1)
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psych (>= 3.1.0)
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rainbow (>= 2.2.2, < 4.0)
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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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stringio (3.1.0)
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typhoeus (1.4.1)
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ethon (>= 0.9.0)
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unicode-display_width (1.5.0)
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PLATFORMS
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x86_64-linux
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DEPENDENCIES
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cheminee!
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pry-byebug
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rake (~> 13.0.1)
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rspec (~> 3.6, >= 3.6.0)
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rubocop (~> 0.66.0)
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BUNDLED WITH
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2.4.10
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data/README.md
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# cheminee
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Cheminee - the Ruby gem for the Cheminée
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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: 0.0.14
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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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## Installation
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### Build a gem
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To build the Ruby code into a gem:
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```shell
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gem build cheminee.gemspec
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```
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Then either install the gem locally:
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```shell
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gem install ./cheminee-0.0.14.gem
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```
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(for development, run `gem install --dev ./cheminee-0.0.14.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', '~> 0.0.14'
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### Install from Git
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If the Ruby gem is hosted at a git repository: https://github.com/GIT_USER_ID/GIT_REPO_ID, then add the following in the Gemfile:
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gem 'cheminee', :git => 'https://github.com/GIT_USER_ID/GIT_REPO_ID.git'
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### Include the Ruby code directly
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Include the Ruby code directly using `-I` as follows:
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```shell
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ruby -Ilib script.rb
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```
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## Getting Started
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Please follow the [installation](#installation) procedure and then run the following code:
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```ruby
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# Load the gem
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require 'cheminee'
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api_instance = Cheminee::DefaultApi.new
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begin
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#List indexes
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result = api_instance.v1_indexes_get
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p result
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rescue Cheminee::ApiError => e
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puts "Exception when calling DefaultApi->v1_indexes_get: #{e}"
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end
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```
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## Documentation for API Endpoints
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All URIs are relative to *http://localhost:3000/api*
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Class | Method | HTTP request | Description
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------------ | ------------- | ------------- | -------------
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*Cheminee::DefaultApi* | [**v1_indexes_get**](docs/DefaultApi.md#v1_indexes_get) | **GET** /v1/indexes | List indexes
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*Cheminee::DefaultApi* | [**v1_indexes_index_bulk_index_post**](docs/DefaultApi.md#v1_indexes_index_bulk_index_post) | **POST** /v1/indexes/{index}/bulk_index | Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
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*Cheminee::DefaultApi* | [**v1_indexes_index_get**](docs/DefaultApi.md#v1_indexes_index_get) | **GET** /v1/indexes/{index} | Get extended information about an index
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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_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_schemas_get**](docs/DefaultApi.md#v1_schemas_get) | **GET** /v1/schemas | List schemas available for creating indexes
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*Cheminee::DefaultApi* | [**v1_standardize_post**](docs/DefaultApi.md#v1_standardize_post) | **POST** /v1/standardize | Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
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## Documentation for Models
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- [Cheminee::BulkRequest](docs/BulkRequest.md)
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- [Cheminee::BulkRequestDoc](docs/BulkRequestDoc.md)
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- [Cheminee::CreateIndexError](docs/CreateIndexError.md)
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- [Cheminee::GetIndexesResponseError](docs/GetIndexesResponseError.md)
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- [Cheminee::IndexMeta](docs/IndexMeta.md)
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- [Cheminee::IndexSchema](docs/IndexSchema.md)
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- [Cheminee::ListIndexResponseErr](docs/ListIndexResponseErr.md)
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- [Cheminee::PostIndexBulkResponseError](docs/PostIndexBulkResponseError.md)
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- [Cheminee::PostIndexBulkResponseOk](docs/PostIndexBulkResponseOk.md)
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- [Cheminee::PostIndexBulkResponseOkStatus](docs/PostIndexBulkResponseOkStatus.md)
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- [Cheminee::QueryResponseError](docs/QueryResponseError.md)
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- [Cheminee::QuerySearchHit](docs/QuerySearchHit.md)
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- [Cheminee::Schema](docs/Schema.md)
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- [Cheminee::Smiles](docs/Smiles.md)
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- [Cheminee::StandardizedSmiles](docs/StandardizedSmiles.md)
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- [Cheminee::StructureResponseError](docs/StructureResponseError.md)
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- [Cheminee::StructureSearchHit](docs/StructureSearchHit.md)
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## Documentation for Authorization
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Endpoints do not require authorization.
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data/Rakefile
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data/cheminee.gemspec
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# -*- encoding: utf-8 -*-
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=begin
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#Cheminée
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#Cheminée: The Chemical Structure Search Engine
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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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OpenAPI Generator version: 7.3.0-SNAPSHOT
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=end
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$:.push File.expand_path("../lib", __FILE__)
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require "cheminee/version"
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Gem::Specification.new do |s|
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s.name = "cheminee"
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s.version = Cheminee::VERSION
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s.platform = Gem::Platform::RUBY
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s.authors = ["Xavier Lange"]
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s.email = ["xrlange@gmail.com"]
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s.homepage = "https://github.com/rdkit-rs/cheminee-ruby"
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s.summary = "Cheminée Ruby Gem"
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s.description = "Cheminée: The Chemical Structure Search Engine"
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s.license = "Unlicense"
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s.required_ruby_version = ">= 3.0"
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s.metadata = {}
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s.add_runtime_dependency 'typhoeus', '~> 1.0', '>= 1.0.1'
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s.add_development_dependency 'rspec', '~> 3.6', '>= 3.6.0'
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s.files = `find *`.split("\n").uniq.sort.select { |f| !f.empty? }
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s.test_files = `find spec/*`.split("\n")
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s.executables = []
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s.require_paths = ["lib"]
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end
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data/docs/BulkRequest.md
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# Cheminee::BulkRequest
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## Properties
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| Name | Type | Description | Notes |
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| ---- | ---- | ----------- | ----- |
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| **docs** | [**Array<BulkRequestDoc>**](BulkRequestDoc.md) | | |
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## Example
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```ruby
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require 'cheminee'
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instance = Cheminee::BulkRequest.new(
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docs: null
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)
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```
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# Cheminee::BulkRequestDoc
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## Properties
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| Name | Type | Description | Notes |
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| ---- | ---- | ----------- | ----- |
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| **smiles** | **String** | | |
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| **extra_data** | **Object** | This value can store an arbitrary JSON object like '{}' | [optional] |
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## Example
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```ruby
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require 'cheminee'
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instance = Cheminee::BulkRequestDoc.new(
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smiles: null,
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extra_data: null
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)
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```
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# Cheminee::CreateIndexError
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## Properties
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| Name | Type | Description | Notes |
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| ---- | ---- | ----------- | ----- |
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| **error** | **String** | | |
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## Example
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```ruby
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require 'cheminee'
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instance = Cheminee::CreateIndexError.new(
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error: null
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)
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```
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