cheminee 0.1.17 → 0.1.19

checksums.yaml

@@ -1,7 +1,7 @@
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data/Gemfile.lock

@@ -1,7 +1,7 @@
 PATH
   remote: .
   specs:
-    cheminee (0.1.17)
+    cheminee (0.1.19)
       typhoeus (~> 1.0, >= 1.0.1)
 
 GEM
@@ -43,7 +43,7 @@ GEM
     rspec-mocks (3.13.0)
       diff-lcs (>= 1.2.0, < 2.0)
       rspec-support (~> 3.13.0)
-    rspec-support (3.13.0)
+    rspec-support (3.13.1)
     rubocop (0.66.0)
       jaro_winkler (~> 1.5.1)
       parallel (~> 1.10)

data/README.md

@@ -7,7 +7,8 @@ Cheminée: The Chemical Structure Search Engine
 This SDK is automatically generated by the [OpenAPI Generator](https://openapi-generator.tech) project:
 
 - API version: 1.0
-- Package version: 0.1.17
+- Package version: 0.1.19
+- Generator version: 7.5.0-SNAPSHOT
 - Build package: org.openapitools.codegen.languages.RubyClientCodegen
 For more information, please visit [https://github.com/rdkit-rs/cheminee](https://github.com/rdkit-rs/cheminee)
 
@@ -24,16 +25,16 @@ gem build cheminee.gemspec
 Then either install the gem locally:
 
 ```shell
-gem install ./cheminee-0.1.17.gem
+gem install ./cheminee-0.1.19.gem
 ```
 
-(for development, run `gem install --dev ./cheminee-0.1.17.gem` to install the development dependencies)
+(for development, run `gem install --dev ./cheminee-0.1.19.gem` to install the development dependencies)
 
 or publish the gem to a gem hosting service, e.g. [RubyGems](https://rubygems.org/).
 
 Finally add this to the Gemfile:
 
-    gem 'cheminee', '~> 0.1.17'
+    gem 'cheminee', '~> 0.1.19'
 
 ### Install from Git
 
@@ -58,13 +59,15 @@ Please follow the [installation](#installation) procedure and then run the follo
 require 'cheminee'
 
 api_instance = Cheminee::DefaultApi.new
+sanitize = 'sanitize_example' # String | 
+mol_block = [Cheminee::MolBlock.new({mol_block: 'mol_block_example'})] # Array<MolBlock> | 
 
 begin
-  #List indexes
-  result = api_instance.v1_indexes_get
+  #Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
+  result = api_instance.v1_convert_mol_block_to_smiles_post(sanitize, mol_block)
   p result
 rescue Cheminee::ApiError => e
-  puts "Exception when calling DefaultApi->v1_indexes_get: #{e}"
+  puts "Exception when calling DefaultApi->v1_convert_mol_block_to_smiles_post: #{e}"
 end
 
 ```
@@ -75,6 +78,7 @@ All URIs are relative to *http://localhost:4001/api*
 
 Class | Method | HTTP request | Description
 ------------ | ------------- | ------------- | -------------
+*Cheminee::DefaultApi* | [**v1_convert_mol_block_to_smiles_post**](docs/DefaultApi.md#v1_convert_mol_block_to_smiles_post) | **POST** /v1/convert/mol_block_to_smiles | Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
 *Cheminee::DefaultApi* | [**v1_indexes_get**](docs/DefaultApi.md#v1_indexes_get) | **GET** /v1/indexes | List indexes
 *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
 *Cheminee::DefaultApi* | [**v1_indexes_index_get**](docs/DefaultApi.md#v1_indexes_index_get) | **GET** /v1/indexes/{index} | Get extended information about an index
@@ -89,11 +93,13 @@ Class | Method | HTTP request | Description
 
  - [Cheminee::BulkRequest](docs/BulkRequest.md)
  - [Cheminee::BulkRequestDoc](docs/BulkRequestDoc.md)
+ - [Cheminee::ConvertedSmiles](docs/ConvertedSmiles.md)
  - [Cheminee::CreateIndexError](docs/CreateIndexError.md)
  - [Cheminee::GetIndexesResponseError](docs/GetIndexesResponseError.md)
  - [Cheminee::IndexMeta](docs/IndexMeta.md)
  - [Cheminee::IndexSchema](docs/IndexSchema.md)
  - [Cheminee::ListIndexResponseErr](docs/ListIndexResponseErr.md)
+ - [Cheminee::MolBlock](docs/MolBlock.md)
  - [Cheminee::PostIndexBulkResponseError](docs/PostIndexBulkResponseError.md)
  - [Cheminee::PostIndexBulkResponseOk](docs/PostIndexBulkResponseOk.md)
  - [Cheminee::PostIndexBulkResponseOkStatus](docs/PostIndexBulkResponseOkStatus.md)

data/cheminee.gemspec

@@ -8,7 +8,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/docs/ConvertedSmiles.md

@@ -0,0 +1,20 @@
+# Cheminee::ConvertedSmiles
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **smiles** | **String** |  | [optional] |
+| **error** | **String** |  | [optional] |
+
+## Example
+
+```ruby
+require 'cheminee'
+
+instance = Cheminee::ConvertedSmiles.new(
+  smiles: null,
+  error: null
+)
+```
+

data/docs/DefaultApi.md

@@ -4,6 +4,7 @@ All URIs are relative to *http://localhost:4001/api*
 
 | Method | HTTP request | Description |
 | ------ | ------------ | ----------- |
+| [**v1_convert_mol_block_to_smiles_post**](DefaultApi.md#v1_convert_mol_block_to_smiles_post) | **POST** /v1/convert/mol_block_to_smiles | Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines |
 | [**v1_indexes_get**](DefaultApi.md#v1_indexes_get) | **GET** /v1/indexes | List indexes |
 | [**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 |
 | [**v1_indexes_index_get**](DefaultApi.md#v1_indexes_index_get) | **GET** /v1/indexes/{index} | Get extended information about an index |
@@ -14,6 +15,70 @@ All URIs are relative to *http://localhost:4001/api*
 | [**v1_standardize_post**](DefaultApi.md#v1_standardize_post) | **POST** /v1/standardize | Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines |
 
 
+## v1_convert_mol_block_to_smiles_post
+
+> <Array<ConvertedSmiles>> v1_convert_mol_block_to_smiles_post(sanitize, mol_block)
+
+Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
+
+### Examples
+
+```ruby
+require 'time'
+require 'cheminee'
+
+api_instance = Cheminee::DefaultApi.new
+sanitize = 'sanitize_example' # String | 
+mol_block = [Cheminee::MolBlock.new({mol_block: 'mol_block_example'})] # Array<MolBlock> | 
+
+begin
+  # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
+  result = api_instance.v1_convert_mol_block_to_smiles_post(sanitize, mol_block)
+  p result
+rescue Cheminee::ApiError => e
+  puts "Error when calling DefaultApi->v1_convert_mol_block_to_smiles_post: #{e}"
+end
+```
+
+#### Using the v1_convert_mol_block_to_smiles_post_with_http_info variant
+
+This returns an Array which contains the response data, status code and headers.
+
+> <Array(<Array<ConvertedSmiles>>, Integer, Hash)> v1_convert_mol_block_to_smiles_post_with_http_info(sanitize, mol_block)
+
+```ruby
+begin
+  # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
+  data, status_code, headers = api_instance.v1_convert_mol_block_to_smiles_post_with_http_info(sanitize, mol_block)
+  p status_code # => 2xx
+  p headers # => { ... }
+  p data # => <Array<ConvertedSmiles>>
+rescue Cheminee::ApiError => e
+  puts "Error when calling DefaultApi->v1_convert_mol_block_to_smiles_post_with_http_info: #{e}"
+end
+```
+
+### Parameters
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **sanitize** | **String** |  |  |
+| **mol_block** | [**Array&lt;MolBlock&gt;**](MolBlock.md) |  |  |
+
+### Return type
+
+[**Array&lt;ConvertedSmiles&gt;**](ConvertedSmiles.md)
+
+### Authorization
+
+No authorization required
+
+### HTTP request headers
+
+- **Content-Type**: application/json; charset=utf-8
+- **Accept**: application/json; charset=utf-8
+
+
 ## v1_indexes_get
 
 > <Array<IndexMeta>> v1_indexes_get
@@ -468,7 +533,7 @@ No authorization required
 
 ## v1_standardize_post
 
-> <Array<StandardizedSmiles>> v1_standardize_post(smiles)
+> <Array<StandardizedSmiles>> v1_standardize_post(smiles, opts)
 
 Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
 
@@ -480,10 +545,13 @@ require 'cheminee'
 
 api_instance = Cheminee::DefaultApi.new
 smiles = [Cheminee::Smiles.new({smiles: 'smiles_example'})] # Array<Smiles> | 
+opts = {
+  attempt_fix: 'attempt_fix_example' # String | 
+}
 
 begin
   # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
-  result = api_instance.v1_standardize_post(smiles)
+  result = api_instance.v1_standardize_post(smiles, opts)
   p result
 rescue Cheminee::ApiError => e
   puts "Error when calling DefaultApi->v1_standardize_post: #{e}"
@@ -494,12 +562,12 @@ end
 
 This returns an Array which contains the response data, status code and headers.
 
-> <Array(<Array<StandardizedSmiles>>, Integer, Hash)> v1_standardize_post_with_http_info(smiles)
+> <Array(<Array<StandardizedSmiles>>, Integer, Hash)> v1_standardize_post_with_http_info(smiles, opts)
 
 ```ruby
 begin
   # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
-  data, status_code, headers = api_instance.v1_standardize_post_with_http_info(smiles)
+  data, status_code, headers = api_instance.v1_standardize_post_with_http_info(smiles, opts)
   p status_code # => 2xx
   p headers # => { ... }
   p data # => <Array<StandardizedSmiles>>
@@ -513,6 +581,7 @@ end
 | Name | Type | Description | Notes |
 | ---- | ---- | ----------- | ----- |
 | **smiles** | [**Array&lt;Smiles&gt;**](Smiles.md) |  |  |
+| **attempt_fix** | **String** |  | [optional] |
 
 ### Return type
 

data/docs/MolBlock.md

@@ -0,0 +1,18 @@
+# Cheminee::MolBlock
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **mol_block** | **String** |  |  |
+
+## Example
+
+```ruby
+require 'cheminee'
+
+instance = Cheminee::MolBlock.new(
+  mol_block: null
+)
+```
+

data/lib/cheminee/api/default_api.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 
@@ -19,6 +19,79 @@ module Cheminee
     def initialize(api_client = ApiClient.default)
       @api_client = api_client
     end
+    # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
+    # @param sanitize [String] 
+    # @param mol_block [Array<MolBlock>] 
+    # @param [Hash] opts the optional parameters
+    # @return [Array<ConvertedSmiles>]
+    def v1_convert_mol_block_to_smiles_post(sanitize, mol_block, opts = {})
+      data, _status_code, _headers = v1_convert_mol_block_to_smiles_post_with_http_info(sanitize, mol_block, opts)
+      data
+    end
+
+    # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
+    # @param sanitize [String] 
+    # @param mol_block [Array<MolBlock>] 
+    # @param [Hash] opts the optional parameters
+    # @return [Array<(Array<ConvertedSmiles>, Integer, Hash)>] Array<ConvertedSmiles> data, response status code and response headers
+    def v1_convert_mol_block_to_smiles_post_with_http_info(sanitize, mol_block, opts = {})
+      if @api_client.config.debugging
+        @api_client.config.logger.debug 'Calling API: DefaultApi.v1_convert_mol_block_to_smiles_post ...'
+      end
+      # verify the required parameter 'sanitize' is set
+      if @api_client.config.client_side_validation && sanitize.nil?
+        fail ArgumentError, "Missing the required parameter 'sanitize' when calling DefaultApi.v1_convert_mol_block_to_smiles_post"
+      end
+      # verify the required parameter 'mol_block' is set
+      if @api_client.config.client_side_validation && mol_block.nil?
+        fail ArgumentError, "Missing the required parameter 'mol_block' when calling DefaultApi.v1_convert_mol_block_to_smiles_post"
+      end
+      # resource path
+      local_var_path = '/v1/convert/mol_block_to_smiles'
+
+      # query parameters
+      query_params = opts[:query_params] || {}
+      query_params[:'sanitize'] = sanitize
+
+      # header parameters
+      header_params = opts[:header_params] || {}
+      # HTTP header 'Accept' (if needed)
+      header_params['Accept'] = @api_client.select_header_accept(['application/json; charset=utf-8'])
+      # HTTP header 'Content-Type'
+      content_type = @api_client.select_header_content_type(['application/json; charset=utf-8'])
+      if !content_type.nil?
+          header_params['Content-Type'] = content_type
+      end
+
+      # form parameters
+      form_params = opts[:form_params] || {}
+
+      # http body (model)
+      post_body = opts[:debug_body] || @api_client.object_to_http_body(mol_block)
+
+      # return_type
+      return_type = opts[:debug_return_type] || 'Array<ConvertedSmiles>'
+
+      # auth_names
+      auth_names = opts[:debug_auth_names] || []
+
+      new_options = opts.merge(
+        :operation => :"DefaultApi.v1_convert_mol_block_to_smiles_post",
+        :header_params => header_params,
+        :query_params => query_params,
+        :form_params => form_params,
+        :body => post_body,
+        :auth_names => auth_names,
+        :return_type => return_type
+      )
+
+      data, status_code, headers = @api_client.call_api(:POST, local_var_path, new_options)
+      if @api_client.config.debugging
+        @api_client.config.logger.debug "API called: DefaultApi#v1_convert_mol_block_to_smiles_post\nData: #{data.inspect}\nStatus code: #{status_code}\nHeaders: #{headers}"
+      end
+      return data, status_code, headers
+    end
+
     # List indexes
     # @param [Hash] opts the optional parameters
     # @return [Array<IndexMeta>]
@@ -484,6 +557,7 @@ module Cheminee
     # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
     # @param smiles [Array<Smiles>] 
     # @param [Hash] opts the optional parameters
+    # @option opts [String] :attempt_fix 
     # @return [Array<StandardizedSmiles>]
     def v1_standardize_post(smiles, opts = {})
       data, _status_code, _headers = v1_standardize_post_with_http_info(smiles, opts)
@@ -493,6 +567,7 @@ module Cheminee
     # Pass a list of SMILES through fragment_parent, uncharger, and canonicalization routines
     # @param smiles [Array<Smiles>] 
     # @param [Hash] opts the optional parameters
+    # @option opts [String] :attempt_fix 
     # @return [Array<(Array<StandardizedSmiles>, Integer, Hash)>] Array<StandardizedSmiles> data, response status code and response headers
     def v1_standardize_post_with_http_info(smiles, opts = {})
       if @api_client.config.debugging
@@ -507,6 +582,7 @@ module Cheminee
 
       # query parameters
       query_params = opts[:query_params] || {}
+      query_params[:'attempt_fix'] = opts[:'attempt_fix'] if !opts[:'attempt_fix'].nil?
 
       # header parameters
       header_params = opts[:header_params] || {}

data/lib/cheminee/api_client.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/api_error.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/configuration.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/bulk_request.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/bulk_request_doc.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/converted_smiles.rb

@@ -0,0 +1,223 @@
+=begin
+#Cheminée
+
+#Cheminée: The Chemical Structure Search Engine
+
+The version of the OpenAPI document: 1.0
+
+Generated by: https://openapi-generator.tech
+Generator version: 7.5.0-SNAPSHOT
+
+=end
+
+require 'date'
+require 'time'
+
+module Cheminee
+  class ConvertedSmiles
+    attr_accessor :smiles
+
+    attr_accessor :error
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'smiles' => :'smiles',
+        :'error' => :'error'
+      }
+    end
+
+    # Returns all the JSON keys this model knows about
+    def self.acceptable_attributes
+      attribute_map.values
+    end
+
+    # Attribute type mapping.
+    def self.openapi_types
+      {
+        :'smiles' => :'String',
+        :'error' => :'String'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+      ])
+    end
+
+    # Initializes the object
+    # @param [Hash] attributes Model attributes in the form of hash
+    def initialize(attributes = {})
+      if (!attributes.is_a?(Hash))
+        fail ArgumentError, "The input argument (attributes) must be a hash in `Cheminee::ConvertedSmiles` initialize method"
+      end
+
+      # check to see if the attribute exists and convert string to symbol for hash key
+      attributes = attributes.each_with_object({}) { |(k, v), h|
+        if (!self.class.attribute_map.key?(k.to_sym))
+          fail ArgumentError, "`#{k}` is not a valid attribute in `Cheminee::ConvertedSmiles`. Please check the name to make sure it's valid. List of attributes: " + self.class.attribute_map.keys.inspect
+        end
+        h[k.to_sym] = v
+      }
+
+      if attributes.key?(:'smiles')
+        self.smiles = attributes[:'smiles']
+      end
+
+      if attributes.key?(:'error')
+        self.error = attributes[:'error']
+      end
+    end
+
+    # Show invalid properties with the reasons. Usually used together with valid?
+    # @return Array for valid properties with the reasons
+    def list_invalid_properties
+      warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
+      invalid_properties = Array.new
+      invalid_properties
+    end
+
+    # Check to see if the all the properties in the model are valid
+    # @return true if the model is valid
+    def valid?
+      warn '[DEPRECATED] the `valid?` method is obsolete'
+      true
+    end
+
+    # Checks equality by comparing each attribute.
+    # @param [Object] Object to be compared
+    def ==(o)
+      return true if self.equal?(o)
+      self.class == o.class &&
+          smiles == o.smiles &&
+          error == o.error
+    end
+
+    # @see the `==` method
+    # @param [Object] Object to be compared
+    def eql?(o)
+      self == o
+    end
+
+    # Calculates hash code according to all attributes.
+    # @return [Integer] Hash code
+    def hash
+      [smiles, error].hash
+    end
+
+    # Builds the object from hash
+    # @param [Hash] attributes Model attributes in the form of hash
+    # @return [Object] Returns the model itself
+    def self.build_from_hash(attributes)
+      return nil unless attributes.is_a?(Hash)
+      attributes = attributes.transform_keys(&:to_sym)
+      transformed_hash = {}
+      openapi_types.each_pair do |key, type|
+        if attributes.key?(attribute_map[key]) && attributes[attribute_map[key]].nil?
+          transformed_hash["#{key}"] = nil
+        elsif type =~ /\AArray<(.*)>/i
+          # check to ensure the input is an array given that the attribute
+          # is documented as an array but the input is not
+          if attributes[attribute_map[key]].is_a?(Array)
+            transformed_hash["#{key}"] = attributes[attribute_map[key]].map { |v| _deserialize($1, v) }
+          end
+        elsif !attributes[attribute_map[key]].nil?
+          transformed_hash["#{key}"] = _deserialize(type, attributes[attribute_map[key]])
+        end
+      end
+      new(transformed_hash)
+    end
+
+    # Deserializes the data based on type
+    # @param string type Data type
+    # @param string value Value to be deserialized
+    # @return [Object] Deserialized data
+    def self._deserialize(type, value)
+      case type.to_sym
+      when :Time
+        Time.parse(value)
+      when :Date
+        Date.parse(value)
+      when :String
+        value.to_s
+      when :Integer
+        value.to_i
+      when :Float
+        value.to_f
+      when :Boolean
+        if value.to_s =~ /\A(true|t|yes|y|1)\z/i
+          true
+        else
+          false
+        end
+      when :Object
+        # generic object (usually a Hash), return directly
+        value
+      when /\AArray<(?<inner_type>.+)>\z/
+        inner_type = Regexp.last_match[:inner_type]
+        value.map { |v| _deserialize(inner_type, v) }
+      when /\AHash<(?<k_type>.+?), (?<v_type>.+)>\z/
+        k_type = Regexp.last_match[:k_type]
+        v_type = Regexp.last_match[:v_type]
+        {}.tap do |hash|
+          value.each do |k, v|
+            hash[_deserialize(k_type, k)] = _deserialize(v_type, v)
+          end
+        end
+      else # model
+        # models (e.g. Pet) or oneOf
+        klass = Cheminee.const_get(type)
+        klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
+      end
+    end
+
+    # Returns the string representation of the object
+    # @return [String] String presentation of the object
+    def to_s
+      to_hash.to_s
+    end
+
+    # to_body is an alias to to_hash (backward compatibility)
+    # @return [Hash] Returns the object in the form of hash
+    def to_body
+      to_hash
+    end
+
+    # Returns the object in the form of hash
+    # @return [Hash] Returns the object in the form of hash
+    def to_hash
+      hash = {}
+      self.class.attribute_map.each_pair do |attr, param|
+        value = self.send(attr)
+        if value.nil?
+          is_nullable = self.class.openapi_nullable.include?(attr)
+          next if !is_nullable || (is_nullable && !instance_variable_defined?(:"@#{attr}"))
+        end
+
+        hash[param] = _to_hash(value)
+      end
+      hash
+    end
+
+    # Outputs non-array value in the form of hash
+    # For object, use to_hash. Otherwise, just return the value
+    # @param [Object] value Any valid value
+    # @return [Hash] Returns the value in the form of hash
+    def _to_hash(value)
+      if value.is_a?(Array)
+        value.compact.map { |v| _to_hash(v) }
+      elsif value.is_a?(Hash)
+        {}.tap do |hash|
+          value.each { |k, v| hash[k] = _to_hash(v) }
+        end
+      elsif value.respond_to? :to_hash
+        value.to_hash
+      else
+        value
+      end
+    end
+
+  end
+
+end

data/lib/cheminee/models/create_index_error.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/get_indexes_response_error.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/index_meta.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/index_schema.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/list_index_response_err.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/mol_block.rb

@@ -0,0 +1,221 @@
+=begin
+#Cheminée
+
+#Cheminée: The Chemical Structure Search Engine
+
+The version of the OpenAPI document: 1.0
+
+Generated by: https://openapi-generator.tech
+Generator version: 7.5.0-SNAPSHOT
+
+=end
+
+require 'date'
+require 'time'
+
+module Cheminee
+  class MolBlock
+    attr_accessor :mol_block
+
+    # Attribute mapping from ruby-style variable name to JSON key.
+    def self.attribute_map
+      {
+        :'mol_block' => :'mol_block'
+      }
+    end
+
+    # Returns all the JSON keys this model knows about
+    def self.acceptable_attributes
+      attribute_map.values
+    end
+
+    # Attribute type mapping.
+    def self.openapi_types
+      {
+        :'mol_block' => :'String'
+      }
+    end
+
+    # List of attributes with nullable: true
+    def self.openapi_nullable
+      Set.new([
+      ])
+    end
+
+    # Initializes the object
+    # @param [Hash] attributes Model attributes in the form of hash
+    def initialize(attributes = {})
+      if (!attributes.is_a?(Hash))
+        fail ArgumentError, "The input argument (attributes) must be a hash in `Cheminee::MolBlock` initialize method"
+      end
+
+      # check to see if the attribute exists and convert string to symbol for hash key
+      attributes = attributes.each_with_object({}) { |(k, v), h|
+        if (!self.class.attribute_map.key?(k.to_sym))
+          fail ArgumentError, "`#{k}` is not a valid attribute in `Cheminee::MolBlock`. Please check the name to make sure it's valid. List of attributes: " + self.class.attribute_map.keys.inspect
+        end
+        h[k.to_sym] = v
+      }
+
+      if attributes.key?(:'mol_block')
+        self.mol_block = attributes[:'mol_block']
+      else
+        self.mol_block = nil
+      end
+    end
+
+    # Show invalid properties with the reasons. Usually used together with valid?
+    # @return Array for valid properties with the reasons
+    def list_invalid_properties
+      warn '[DEPRECATED] the `list_invalid_properties` method is obsolete'
+      invalid_properties = Array.new
+      if @mol_block.nil?
+        invalid_properties.push('invalid value for "mol_block", mol_block cannot be nil.')
+      end
+
+      invalid_properties
+    end
+
+    # Check to see if the all the properties in the model are valid
+    # @return true if the model is valid
+    def valid?
+      warn '[DEPRECATED] the `valid?` method is obsolete'
+      return false if @mol_block.nil?
+      true
+    end
+
+    # Checks equality by comparing each attribute.
+    # @param [Object] Object to be compared
+    def ==(o)
+      return true if self.equal?(o)
+      self.class == o.class &&
+          mol_block == o.mol_block
+    end
+
+    # @see the `==` method
+    # @param [Object] Object to be compared
+    def eql?(o)
+      self == o
+    end
+
+    # Calculates hash code according to all attributes.
+    # @return [Integer] Hash code
+    def hash
+      [mol_block].hash
+    end
+
+    # Builds the object from hash
+    # @param [Hash] attributes Model attributes in the form of hash
+    # @return [Object] Returns the model itself
+    def self.build_from_hash(attributes)
+      return nil unless attributes.is_a?(Hash)
+      attributes = attributes.transform_keys(&:to_sym)
+      transformed_hash = {}
+      openapi_types.each_pair do |key, type|
+        if attributes.key?(attribute_map[key]) && attributes[attribute_map[key]].nil?
+          transformed_hash["#{key}"] = nil
+        elsif type =~ /\AArray<(.*)>/i
+          # check to ensure the input is an array given that the attribute
+          # is documented as an array but the input is not
+          if attributes[attribute_map[key]].is_a?(Array)
+            transformed_hash["#{key}"] = attributes[attribute_map[key]].map { |v| _deserialize($1, v) }
+          end
+        elsif !attributes[attribute_map[key]].nil?
+          transformed_hash["#{key}"] = _deserialize(type, attributes[attribute_map[key]])
+        end
+      end
+      new(transformed_hash)
+    end
+
+    # Deserializes the data based on type
+    # @param string type Data type
+    # @param string value Value to be deserialized
+    # @return [Object] Deserialized data
+    def self._deserialize(type, value)
+      case type.to_sym
+      when :Time
+        Time.parse(value)
+      when :Date
+        Date.parse(value)
+      when :String
+        value.to_s
+      when :Integer
+        value.to_i
+      when :Float
+        value.to_f
+      when :Boolean
+        if value.to_s =~ /\A(true|t|yes|y|1)\z/i
+          true
+        else
+          false
+        end
+      when :Object
+        # generic object (usually a Hash), return directly
+        value
+      when /\AArray<(?<inner_type>.+)>\z/
+        inner_type = Regexp.last_match[:inner_type]
+        value.map { |v| _deserialize(inner_type, v) }
+      when /\AHash<(?<k_type>.+?), (?<v_type>.+)>\z/
+        k_type = Regexp.last_match[:k_type]
+        v_type = Regexp.last_match[:v_type]
+        {}.tap do |hash|
+          value.each do |k, v|
+            hash[_deserialize(k_type, k)] = _deserialize(v_type, v)
+          end
+        end
+      else # model
+        # models (e.g. Pet) or oneOf
+        klass = Cheminee.const_get(type)
+        klass.respond_to?(:openapi_any_of) || klass.respond_to?(:openapi_one_of) ? klass.build(value) : klass.build_from_hash(value)
+      end
+    end
+
+    # Returns the string representation of the object
+    # @return [String] String presentation of the object
+    def to_s
+      to_hash.to_s
+    end
+
+    # to_body is an alias to to_hash (backward compatibility)
+    # @return [Hash] Returns the object in the form of hash
+    def to_body
+      to_hash
+    end
+
+    # Returns the object in the form of hash
+    # @return [Hash] Returns the object in the form of hash
+    def to_hash
+      hash = {}
+      self.class.attribute_map.each_pair do |attr, param|
+        value = self.send(attr)
+        if value.nil?
+          is_nullable = self.class.openapi_nullable.include?(attr)
+          next if !is_nullable || (is_nullable && !instance_variable_defined?(:"@#{attr}"))
+        end
+
+        hash[param] = _to_hash(value)
+      end
+      hash
+    end
+
+    # Outputs non-array value in the form of hash
+    # For object, use to_hash. Otherwise, just return the value
+    # @param [Object] value Any valid value
+    # @return [Hash] Returns the value in the form of hash
+    def _to_hash(value)
+      if value.is_a?(Array)
+        value.compact.map { |v| _to_hash(v) }
+      elsif value.is_a?(Hash)
+        {}.tap do |hash|
+          value.each { |k, v| hash[k] = _to_hash(v) }
+        end
+      elsif value.respond_to? :to_hash
+        value.to_hash
+      else
+        value
+      end
+    end
+
+  end
+
+end

data/lib/cheminee/models/post_index_bulk_response_error.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/post_index_bulk_response_ok.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/post_index_bulk_response_ok_status.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/query_response_error.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/query_search_hit.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/schema.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/smiles.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/standardized_smiles.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/structure_response_error.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/models/structure_search_hit.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

data/lib/cheminee/version.rb

@@ -6,10 +6,10 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 
 module Cheminee
-  VERSION = '0.1.17'
+  VERSION = '0.1.19'
 end

data/lib/cheminee.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 
@@ -19,11 +19,13 @@ require 'cheminee/configuration'
 # Models
 require 'cheminee/models/bulk_request'
 require 'cheminee/models/bulk_request_doc'
+require 'cheminee/models/converted_smiles'
 require 'cheminee/models/create_index_error'
 require 'cheminee/models/get_indexes_response_error'
 require 'cheminee/models/index_meta'
 require 'cheminee/models/index_schema'
 require 'cheminee/models/list_index_response_err'
+require 'cheminee/models/mol_block'
 require 'cheminee/models/post_index_bulk_response_error'
 require 'cheminee/models/post_index_bulk_response_ok'
 require 'cheminee/models/post_index_bulk_response_ok_status'

data/spec/models/converted_smiles_spec.rb

@@ -0,0 +1,42 @@
+=begin
+#Cheminée
+
+#Cheminée: The Chemical Structure Search Engine
+
+The version of the OpenAPI document: 1.0
+
+Generated by: https://openapi-generator.tech
+OpenAPI Generator version: 7.4.0-SNAPSHOT
+
+=end
+
+require 'spec_helper'
+require 'json'
+require 'date'
+
+# Unit tests for Cheminee::ConvertedSmiles
+# Automatically generated by openapi-generator (https://openapi-generator.tech)
+# Please update as you see appropriate
+describe Cheminee::ConvertedSmiles do
+  let(:instance) { Cheminee::ConvertedSmiles.new }
+
+  describe 'test an instance of ConvertedSmiles' do
+    it 'should create an instance of ConvertedSmiles' do
+      # uncomment below to test the instance creation
+      #expect(instance).to be_instance_of(Cheminee::ConvertedSmiles)
+    end
+  end
+
+  describe 'test attribute "smiles"' do
+    it 'should work' do
+      # assertion here. ref: https://rspec.info/features/3-12/rspec-expectations/built-in-matchers/
+    end
+  end
+
+  describe 'test attribute "error"' do
+    it 'should work' do
+      # assertion here. ref: https://rspec.info/features/3-12/rspec-expectations/built-in-matchers/
+    end
+  end
+
+end

data/spec/models/mol_block_spec.rb

@@ -0,0 +1,36 @@
+=begin
+#Cheminée
+
+#Cheminée: The Chemical Structure Search Engine
+
+The version of the OpenAPI document: 1.0
+
+Generated by: https://openapi-generator.tech
+OpenAPI Generator version: 7.4.0-SNAPSHOT
+
+=end
+
+require 'spec_helper'
+require 'json'
+require 'date'
+
+# Unit tests for Cheminee::MolBlock
+# Automatically generated by openapi-generator (https://openapi-generator.tech)
+# Please update as you see appropriate
+describe Cheminee::MolBlock do
+  let(:instance) { Cheminee::MolBlock.new }
+
+  describe 'test an instance of MolBlock' do
+    it 'should create an instance of MolBlock' do
+      # uncomment below to test the instance creation
+      #expect(instance).to be_instance_of(Cheminee::MolBlock)
+    end
+  end
+
+  describe 'test attribute "mol_block"' do
+    it 'should work' do
+      # assertion here. ref: https://rspec.info/features/3-12/rspec-expectations/built-in-matchers/
+    end
+  end
+
+end

data/spec/spec_helper.rb

@@ -6,7 +6,7 @@
 The version of the OpenAPI document: 1.0
 
 Generated by: https://openapi-generator.tech
-OpenAPI Generator version: 7.3.0-SNAPSHOT
+Generator version: 7.5.0-SNAPSHOT
 
 =end
 

metadata

@@ -1,14 +1,14 @@
 --- !ruby/object:Gem::Specification
 name: cheminee
 version: !ruby/object:Gem::Version
-  version: 0.1.17
+  version: 0.1.19
 platform: ruby
 authors:
 - Xavier Lange
 autorequire: 
 bindir: bin
 cert_chain: []
-date: 2024-02-05 00:00:00.000000000 Z
+date: 2024-04-02 00:00:00.000000000 Z
 dependencies:
 - !ruby/object:Gem::Dependency
   name: typhoeus
@@ -64,12 +64,14 @@ files:
 - cheminee.gemspec
 - docs/BulkRequest.md
 - docs/BulkRequestDoc.md
+- docs/ConvertedSmiles.md
 - docs/CreateIndexError.md
 - docs/DefaultApi.md
 - docs/GetIndexesResponseError.md
 - docs/IndexMeta.md
 - docs/IndexSchema.md
 - docs/ListIndexResponseErr.md
+- docs/MolBlock.md
 - docs/PostIndexBulkResponseError.md
 - docs/PostIndexBulkResponseOk.md
 - docs/PostIndexBulkResponseOkStatus.md
@@ -91,11 +93,13 @@ files:
 - lib/cheminee/configuration.rb
 - lib/cheminee/models/bulk_request.rb
 - lib/cheminee/models/bulk_request_doc.rb
+- lib/cheminee/models/converted_smiles.rb
 - lib/cheminee/models/create_index_error.rb
 - lib/cheminee/models/get_indexes_response_error.rb
 - lib/cheminee/models/index_meta.rb
 - lib/cheminee/models/index_schema.rb
 - lib/cheminee/models/list_index_response_err.rb
+- lib/cheminee/models/mol_block.rb
 - lib/cheminee/models/post_index_bulk_response_error.rb
 - lib/cheminee/models/post_index_bulk_response_ok.rb
 - lib/cheminee/models/post_index_bulk_response_ok_status.rb
@@ -112,17 +116,19 @@ files:
 - lib/cheminee/version.rb
 - openapi-generator-config.json
 - openapi.json
-- pkg/cheminee-0.1.17.gem
+- pkg/cheminee-0.1.19.gem
 - spec/api/default_api_spec.rb
 - spec/api_client_spec.rb
 - spec/configuration_spec.rb
 - spec/models/bulk_request_doc_spec.rb
 - spec/models/bulk_request_spec.rb
+- spec/models/converted_smiles_spec.rb
 - spec/models/create_index_error_spec.rb
 - spec/models/get_indexes_response_error_spec.rb
 - spec/models/index_meta_spec.rb
 - spec/models/index_schema_spec.rb
 - spec/models/list_index_response_err_spec.rb
+- spec/models/mol_block_spec.rb
 - spec/models/post_index_bulk_response_error_spec.rb
 - spec/models/post_index_bulk_response_ok_spec.rb
 - spec/models/post_index_bulk_response_ok_status_spec.rb
@@ -169,12 +175,14 @@ test_files:
 - spec/models/standardized_smile_spec.rb
 - spec/models/smile_spec.rb
 - spec/models/structure_response_error_spec.rb
+- spec/models/converted_smiles_spec.rb
 - spec/models/index_schema_spec.rb
 - spec/models/get_indexes_response_error_spec.rb
 - spec/models/query_search_hit_spec.rb
 - spec/models/bulk_request_spec.rb
 - spec/models/query_response_error_spec.rb
 - spec/models/substructure_search_hit_spec.rb
+- spec/models/mol_block_spec.rb
 - spec/models/bulk_request_doc_spec.rb
 - spec/models/post_index_bulk_response_ok_status_spec.rb
 - spec/models/smiles_spec.rb