cheminee 0.1.11 → 0.1.14
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- checksums.yaml +4 -4
- data/Gemfile.lock +7 -7
- data/README.md +10 -6
- data/cheminee.gemspec +2 -1
- data/docs/BulkRequestDoc.md +2 -2
- data/docs/DefaultApi.md +91 -20
- data/docs/IndexSchema.md +20 -0
- data/docs/QueryResponseError.md +18 -0
- data/docs/QuerySearchHit.md +22 -0
- data/docs/Smiles.md +18 -0
- data/docs/StandardizedSmiles.md +20 -0
- data/lib/cheminee/api/default_api.rb +99 -25
- data/lib/cheminee/api_client.rb +21 -20
- data/lib/cheminee/api_error.rb +1 -1
- data/lib/cheminee/configuration.rb +1 -1
- data/lib/cheminee/models/bulk_request.rb +2 -2
- data/lib/cheminee/models/bulk_request_doc.rb +13 -13
- data/lib/cheminee/models/create_index_error.rb +2 -2
- data/lib/cheminee/models/get_indexes_response_error.rb +2 -2
- data/lib/cheminee/models/index_meta.rb +2 -2
- data/lib/cheminee/models/index_schema.rb +233 -0
- data/lib/cheminee/models/list_index_response_err.rb +2 -2
- data/lib/cheminee/models/post_index_bulk_response_error.rb +2 -2
- data/lib/cheminee/models/post_index_bulk_response_ok.rb +2 -2
- data/lib/cheminee/models/post_index_bulk_response_ok_status.rb +2 -2
- 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 +2 -2
- data/lib/cheminee/models/smiles.rb +221 -0
- data/lib/cheminee/models/standardized_smiles.rb +223 -0
- data/lib/cheminee/models/structure_response_error.rb +2 -2
- data/lib/cheminee/models/structure_search_hit.rb +2 -2
- data/lib/cheminee/version.rb +2 -2
- data/lib/cheminee.rb +6 -3
- data/pkg/cheminee-0.1.14.gem +0 -0
- data/spec/models/index_schema_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/smiles_spec.rb +36 -0
- data/spec/models/standardized_smiles_spec.rb +42 -0
- data/spec/spec_helper.rb +1 -1
- metadata +23 -3
- data/pkg/cheminee-0.1.11.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: '03914600ad91bf4f02d5719ebb11390f38ae2cb25254bc87b152a18de75cf96d'
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data.tar.gz: 6a93975791492fc56177e4e5a2d0a3c1d1e320348f0b06d8a7045cce4c8bbfd7
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: 6dbdb5cbc7911c2d851ea23471a4cb59cada080d55ea677f9116beaadfa1e078a1cca004f75c8ef7bfa958bae4b2230782aa260454844218d20d87ca4e8765d2
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+
data.tar.gz: 728abd1a932492baa18db69eacbadc273bf41b59fe338768c7a78d9308f6fc0dc2914fa256f355875cf932c3645bd145f3749252cdfc123877ddae4978a26b80
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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 (0.1.14)
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typhoeus (~> 1.0, >= 1.0.1)
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GEM
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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.
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parser (3.
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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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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 (5.1.2)
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stringio
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racc (1.7.
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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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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 (3.0
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typhoeus (1.4.
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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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data/README.md
CHANGED
@@ -7,7 +7,7 @@ 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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- Package version: 0.1.14
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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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@@ -24,16 +24,16 @@ 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-0.1.14.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-0.1.14.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', '~> 0.1.
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gem 'cheminee', '~> 0.1.14'
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### Install from Git
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@@ -79,6 +79,7 @@ Class | Method | HTTP request | Description
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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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- [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::
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- [Cheminee::
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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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data/cheminee.gemspec
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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.
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OpenAPI Generator version: 7.3.0-SNAPSHOT
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=end
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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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data/docs/BulkRequestDoc.md
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| Name | Type | Description | Notes |
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| ---- | ---- | ----------- | ----- |
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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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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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data/docs/DefaultApi.md
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| [**v1_indexes_index_bulk_index_post**](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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| [**v1_indexes_index_get**](DefaultApi.md#v1_indexes_index_get) | **GET** /v1/indexes/{index} | Get extended information about an index |
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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_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_schemas_get**](DefaultApi.md#v1_schemas_get) | **GET** /v1/schemas | List schemas available for creating indexes |
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| [**v1_standardize_post**](DefaultApi.md#v1_standardize_post) | **POST** /v1/standardize | Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines |
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api_instance = Cheminee::DefaultApi.new
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index = 'index_example' # String |
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bulk_request = Cheminee::BulkRequest.new({docs: [Cheminee::BulkRequestDoc.new({
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bulk_request = Cheminee::BulkRequest.new({docs: [Cheminee::BulkRequestDoc.new({smiles: 'smiles_example'})]}) # BulkRequest |
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begin
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# Index a list of SMILES and associated, free-form JSON attributes which are indexed and searchable
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## v1_indexes_index_get
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> <
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> <IndexSchema> v1_indexes_index_get(index)
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Get extended information about an index
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This returns an Array which contains the response data, status code and headers.
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> <Array(<
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> <Array(<IndexSchema>, Integer, Hash)> v1_indexes_index_get_with_http_info(index)
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```ruby
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begin
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data, status_code, headers = api_instance.v1_indexes_index_get_with_http_info(index)
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p status_code # => 2xx
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p headers # => { ... }
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p data # => <
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p data # => <IndexSchema>
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rescue Cheminee::ApiError => e
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puts "Error when calling DefaultApi->v1_indexes_index_get_with_http_info: #{e}"
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end
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### Return type
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-
[**
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[**IndexSchema**](IndexSchema.md)
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### Authorization
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- **Accept**: application/json; charset=utf-8
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## v1_indexes_index_search_basic_get
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> <Array<QuerySearchHit>> v1_indexes_index_search_basic_get(index, query, opts)
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Perform basic query search against index
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### Examples
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```ruby
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require 'time'
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require 'cheminee'
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api_instance = Cheminee::DefaultApi.new
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index = 'index_example' # String |
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query = 'query_example' # String |
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opts = {
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limit: 56 # Integer |
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}
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begin
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# Perform basic query search against index
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result = api_instance.v1_indexes_index_search_basic_get(index, query, opts)
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p result
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rescue Cheminee::ApiError => e
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puts "Error when calling DefaultApi->v1_indexes_index_search_basic_get: #{e}"
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end
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```
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#### Using the v1_indexes_index_search_basic_get_with_http_info variant
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This returns an Array which contains the response data, status code and headers.
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> <Array(<Array<QuerySearchHit>>, Integer, Hash)> v1_indexes_index_search_basic_get_with_http_info(index, query, opts)
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```ruby
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begin
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# Perform basic query search against index
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data, status_code, headers = api_instance.v1_indexes_index_search_basic_get_with_http_info(index, query, opts)
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p status_code # => 2xx
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p headers # => { ... }
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p data # => <Array<QuerySearchHit>>
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rescue Cheminee::ApiError => e
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puts "Error when calling DefaultApi->v1_indexes_index_search_basic_get_with_http_info: #{e}"
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end
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```
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### Parameters
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| Name | Type | Description | Notes |
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| ---- | ---- | ----------- | ----- |
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| **index** | **String** | | |
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| **query** | **String** | | |
|
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| **limit** | **Integer** | | [optional] |
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+
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### Return type
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+
|
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[**Array<QuerySearchHit>**](QuerySearchHit.md)
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+
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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; charset=utf-8
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## v1_indexes_index_search_substructure_get
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> <Array<StructureSearchHit>> v1_indexes_index_search_substructure_get(index,
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> <Array<StructureSearchHit>> v1_indexes_index_search_substructure_get(index, smiles, opts)
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Perform substructure search against index
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@@ -280,15 +349,16 @@ require 'cheminee'
|
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api_instance = Cheminee::DefaultApi.new
|
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index = 'index_example' # String |
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-
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smiles = 'smiles_example' # String |
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opts = {
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result_limit: 56, # Integer |
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tautomer_limit: 56 # Integer |
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tautomer_limit: 56, # Integer |
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extra_query: 'extra_query_example' # String |
|
287
357
|
}
|
288
358
|
|
289
359
|
begin
|
290
360
|
# Perform substructure search against index
|
291
|
-
result = api_instance.v1_indexes_index_search_substructure_get(index,
|
361
|
+
result = api_instance.v1_indexes_index_search_substructure_get(index, smiles, opts)
|
292
362
|
p result
|
293
363
|
rescue Cheminee::ApiError => e
|
294
364
|
puts "Error when calling DefaultApi->v1_indexes_index_search_substructure_get: #{e}"
|
@@ -299,12 +369,12 @@ end
|
|
299
369
|
|
300
370
|
This returns an Array which contains the response data, status code and headers.
|
301
371
|
|
302
|
-
> <Array(<Array<StructureSearchHit>>, Integer, Hash)> v1_indexes_index_search_substructure_get_with_http_info(index,
|
372
|
+
> <Array(<Array<StructureSearchHit>>, Integer, Hash)> v1_indexes_index_search_substructure_get_with_http_info(index, smiles, opts)
|
303
373
|
|
304
374
|
```ruby
|
305
375
|
begin
|
306
376
|
# Perform substructure search against index
|
307
|
-
data, status_code, headers = api_instance.v1_indexes_index_search_substructure_get_with_http_info(index,
|
377
|
+
data, status_code, headers = api_instance.v1_indexes_index_search_substructure_get_with_http_info(index, smiles, opts)
|
308
378
|
p status_code # => 2xx
|
309
379
|
p headers # => { ... }
|
310
380
|
p data # => <Array<StructureSearchHit>>
|
@@ -318,9 +388,10 @@ end
|
|
318
388
|
| Name | Type | Description | Notes |
|
319
389
|
| ---- | ---- | ----------- | ----- |
|
320
390
|
| **index** | **String** | | |
|
321
|
-
| **
|
391
|
+
| **smiles** | **String** | | |
|
322
392
|
| **result_limit** | **Integer** | | [optional] |
|
323
393
|
| **tautomer_limit** | **Integer** | | [optional] |
|
394
|
+
| **extra_query** | **String** | | [optional] |
|
324
395
|
|
325
396
|
### Return type
|
326
397
|
|
@@ -397,7 +468,7 @@ No authorization required
|
|
397
468
|
|
398
469
|
## v1_standardize_post
|
399
470
|
|
400
|
-
> <Array<
|
471
|
+
> <Array<StandardizedSmiles>> v1_standardize_post(smiles)
|
401
472
|
|
402
473
|
Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
|
403
474
|
|
@@ -408,11 +479,11 @@ require 'time'
|
|
408
479
|
require 'cheminee'
|
409
480
|
|
410
481
|
api_instance = Cheminee::DefaultApi.new
|
411
|
-
|
482
|
+
smiles = [Cheminee::Smiles.new({smiles: 'smiles_example'})] # Array<Smiles> |
|
412
483
|
|
413
484
|
begin
|
414
485
|
# Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
|
415
|
-
result = api_instance.v1_standardize_post(
|
486
|
+
result = api_instance.v1_standardize_post(smiles)
|
416
487
|
p result
|
417
488
|
rescue Cheminee::ApiError => e
|
418
489
|
puts "Error when calling DefaultApi->v1_standardize_post: #{e}"
|
@@ -423,15 +494,15 @@ end
|
|
423
494
|
|
424
495
|
This returns an Array which contains the response data, status code and headers.
|
425
496
|
|
426
|
-
> <Array(<Array<
|
497
|
+
> <Array(<Array<StandardizedSmiles>>, Integer, Hash)> v1_standardize_post_with_http_info(smiles)
|
427
498
|
|
428
499
|
```ruby
|
429
500
|
begin
|
430
501
|
# Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
|
431
|
-
data, status_code, headers = api_instance.v1_standardize_post_with_http_info(
|
502
|
+
data, status_code, headers = api_instance.v1_standardize_post_with_http_info(smiles)
|
432
503
|
p status_code # => 2xx
|
433
504
|
p headers # => { ... }
|
434
|
-
p data # => <Array<
|
505
|
+
p data # => <Array<StandardizedSmiles>>
|
435
506
|
rescue Cheminee::ApiError => e
|
436
507
|
puts "Error when calling DefaultApi->v1_standardize_post_with_http_info: #{e}"
|
437
508
|
end
|
@@ -441,11 +512,11 @@ end
|
|
441
512
|
|
442
513
|
| Name | Type | Description | Notes |
|
443
514
|
| ---- | ---- | ----------- | ----- |
|
444
|
-
| **
|
515
|
+
| **smiles** | [**Array<Smiles>**](Smiles.md) | | |
|
445
516
|
|
446
517
|
### Return type
|
447
518
|
|
448
|
-
[**Array<
|
519
|
+
[**Array<StandardizedSmiles>**](StandardizedSmiles.md)
|
449
520
|
|
450
521
|
### Authorization
|
451
522
|
|
data/docs/IndexSchema.md
ADDED
@@ -0,0 +1,20 @@
|
|
1
|
+
# Cheminee::IndexSchema
|
2
|
+
|
3
|
+
## Properties
|
4
|
+
|
5
|
+
| Name | Type | Description | Notes |
|
6
|
+
| ---- | ---- | ----------- | ----- |
|
7
|
+
| **index** | **String** | | |
|
8
|
+
| **schema** | **Object** | | |
|
9
|
+
|
10
|
+
## Example
|
11
|
+
|
12
|
+
```ruby
|
13
|
+
require 'cheminee'
|
14
|
+
|
15
|
+
instance = Cheminee::IndexSchema.new(
|
16
|
+
index: null,
|
17
|
+
schema: null
|
18
|
+
)
|
19
|
+
```
|
20
|
+
|
@@ -0,0 +1,18 @@
|
|
1
|
+
# Cheminee::QueryResponseError
|
2
|
+
|
3
|
+
## Properties
|
4
|
+
|
5
|
+
| Name | Type | Description | Notes |
|
6
|
+
| ---- | ---- | ----------- | ----- |
|
7
|
+
| **error** | **String** | | |
|
8
|
+
|
9
|
+
## Example
|
10
|
+
|
11
|
+
```ruby
|
12
|
+
require 'cheminee'
|
13
|
+
|
14
|
+
instance = Cheminee::QueryResponseError.new(
|
15
|
+
error: null
|
16
|
+
)
|
17
|
+
```
|
18
|
+
|
@@ -0,0 +1,22 @@
|
|
1
|
+
# Cheminee::QuerySearchHit
|
2
|
+
|
3
|
+
## Properties
|
4
|
+
|
5
|
+
| Name | Type | Description | Notes |
|
6
|
+
| ---- | ---- | ----------- | ----- |
|
7
|
+
| **extra_data** | **Object** | | |
|
8
|
+
| **smiles** | **String** | | |
|
9
|
+
| **query** | **String** | | |
|
10
|
+
|
11
|
+
## Example
|
12
|
+
|
13
|
+
```ruby
|
14
|
+
require 'cheminee'
|
15
|
+
|
16
|
+
instance = Cheminee::QuerySearchHit.new(
|
17
|
+
extra_data: null,
|
18
|
+
smiles: null,
|
19
|
+
query: null
|
20
|
+
)
|
21
|
+
```
|
22
|
+
|
data/docs/Smiles.md
ADDED
@@ -0,0 +1,18 @@
|
|
1
|
+
# Cheminee::Smiles
|
2
|
+
|
3
|
+
## Properties
|
4
|
+
|
5
|
+
| Name | Type | Description | Notes |
|
6
|
+
| ---- | ---- | ----------- | ----- |
|
7
|
+
| **smiles** | **String** | | |
|
8
|
+
|
9
|
+
## Example
|
10
|
+
|
11
|
+
```ruby
|
12
|
+
require 'cheminee'
|
13
|
+
|
14
|
+
instance = Cheminee::Smiles.new(
|
15
|
+
smiles: null
|
16
|
+
)
|
17
|
+
```
|
18
|
+
|
@@ -0,0 +1,20 @@
|
|
1
|
+
# Cheminee::StandardizedSmiles
|
2
|
+
|
3
|
+
## Properties
|
4
|
+
|
5
|
+
| Name | Type | Description | Notes |
|
6
|
+
| ---- | ---- | ----------- | ----- |
|
7
|
+
| **smiles** | **String** | | [optional] |
|
8
|
+
| **error** | **String** | | [optional] |
|
9
|
+
|
10
|
+
## Example
|
11
|
+
|
12
|
+
```ruby
|
13
|
+
require 'cheminee'
|
14
|
+
|
15
|
+
instance = Cheminee::StandardizedSmiles.new(
|
16
|
+
smiles: null,
|
17
|
+
error: null
|
18
|
+
)
|
19
|
+
```
|
20
|
+
|