ruspider 0.1.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 840e5463640af4659581e42e847cb539f1dbd92a
+  data.tar.gz: f45f02a9efd829fa20e6b6bcef7b8a9bfcf1b029
+SHA512:
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+  data.tar.gz: c8cca67eb2bde5d1fa4ffc210af1294af0d1ceecc60ee0ff5e860dac96cec17e8363a50768175dca1e3729a73bfae0289c71c61de8f7eea7044a1b718c5dd913

data/.gitignore

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+/.bundle/
+/.yardoc
+/Gemfile.lock
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status
+tags

data/.rspec

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+--format documentation
+--color

data/.ruby-version

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+2.3.1

data/.travis.yml

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+sudo: false
+language: ruby
+rvm:
+  - 2.3.1
+before_install: gem install bundler -v 1.14.6

data/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at qn5043@kit.edu. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

data/Gemfile

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+source 'https://rubygems.org'
+
+# Specify your gem's dependencies in ruspider.gemspec
+gemspec
+
+gem 'nokogiri'
+
+gem 'httparty'

data/LICENSE.txt

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+The MIT License (MIT)
+
+Copyright (c) 2017 An Nguyen
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in
+all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
+THE SOFTWARE.

data/README.md

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+# Ruspider
+
+Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/ruspider`. To experiment with that code, run `bin/console` for an interactive prompt.
+
+TODO: Delete this and the text above, and describe your gem
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'ruspider'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install ruspider
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/ruspider. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+
+
+## License
+
+The gem is available as open source under the terms of the [MIT License](http://opensource.org/licenses/MIT).
+

data/Rakefile

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+require 'bundler/gem_tasks'
+require 'rspec/core/rake_task'
+
+RSpec::Core::RakeTask.new(:spec)
+
+task default: :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "ruspider"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/lib/ruspider.rb

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+# frozen_string_literal: true
+
+require 'ruspider/version'
+require 'ruspider/chemspider'

data/lib/ruspider/chemspider.rb

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+# frozen_string_literal: true
+
+require 'ruspider/rest_client'
+require 'ruspider/inchi_api'
+require 'ruspider/mass_spec_api'
+require 'ruspider/spectra_api'
+require 'ruspider/compound'
+require 'ruspider/spectrum'
+
+module Ruspider
+  # ChemSpider Ruby interface
+  class ChemSpider
+    include InchIAPI
+    include MassSpecAPI
+    include SpectraAPI
+
+    def initialize(token = '', header = {})
+      @rest = RestClient.new(token, header)
+      InchIAPI.instance_method(:initialize).bind(self).call(@rest)
+      MassSpecAPI.instance_method(:initialize).bind(self).call(@rest)
+      SpectraAPI.instance_method(:initialize).bind(self).call(@rest)
+    end
+
+    def get_compound(csid)
+      Compound.new(csid, self)
+    end
+
+    def get_compounds(csids)
+      csids.map { |x| Compound.new(x, self) }
+    end
+
+    def get_spectrum(spectrum_id)
+      Spectrum.new(spectrum_id, self)
+    end
+
+    def get_spectra(spectrum_ids)
+      spectrum_ids.map { |x| Spectrum.new(x, self) }
+    end
+
+    def get_compound_spectra(csid)
+      get_spectra_info_list([csid]).map do |x|
+        Spectrum.from_info_dict(x, self)
+      end
+    end
+  end
+end

data/lib/ruspider/compound.rb

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+# frozen_string_literal: true
+
+module Ruspider
+  # ChemSpider Compound Data container and parser
+  class Compound
+    attr_reader :csid
+
+    def initialize(csid, cs)
+      @csid = csid
+      @cs = cs
+      @extended_compound_info = nil
+    end
+
+    def image_url
+      'http://www.chemspider.com/ImagesHandler.ashx?id=%s' + @csid
+    end
+
+    def extended_compound_info
+      if @extended_compound_info.nil?
+        @extended_compound_info = @cs.get_extended_compound_info(@csid)
+      end
+
+      @extended_compound_info
+    end
+
+    def molecular_formula
+      extended_compound_info[:molecular_formula]
+    end
+
+    def smiles
+      extended_compound_info[:smiles]
+    end
+
+    def inchi
+      extended_compound_info[:inchi]
+    end
+
+    def inchikey
+      extended_compound_info[:inchikey]
+    end
+
+    def average_mass
+      extended_compound_info[:average_mass]
+    end
+
+    def molecular_weight
+      extended_compound_info[:molecular_weight]
+    end
+
+    def monoisotopic_mass
+      extended_compound_info[:monoisotopic_mass]
+    end
+
+    def nominal_mass
+      extended_compound_info[:nominal_mass]
+    end
+
+    def alogp
+      extended_compound_info[:alogp]
+    end
+
+    def xlogp
+      extended_compound_info[:xlogp]
+    end
+
+    def common_name
+      extended_compound_info[:common_name]
+    end
+
+    def mol_2d
+      @cs.get_record_mol(@csid, False)
+    end
+
+    def mol_3d
+      @cs.get_record_mol(@csid, True)
+    end
+
+    def mol_raw
+      @cs.get_original_mol(@csid)
+    end
+
+    def image
+      @cs.get_compound_thumbnail(@csid)
+    end
+
+    def spectra
+      spectra_list = @cs.get_spectra_info_list(@csid)
+      spectra_list.map { |s| Spectrum.new(s) }
+      # [Spectrum.from_info_dict(self._cs, info)
+      # for info in self._cs.get_spectra_info_list([self.csid])]
+    end
+  end
+end

data/lib/ruspider/inchi_api.rb

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+# frozen_string_literal: true
+
+require 'ruspider/rest_client'
+require 'ruspider/xml_utils'
+
+module Ruspider
+  # InChI API http://www.chemspider.com/InChI.asmx
+  module InchIAPI
+    include XmlUtils
+
+    API = 'InChi.asmx'
+
+    def initialize(rest)
+      @rest = rest
+    end
+
+    def get_original_mol(csid)
+      response = @rest.post(API, 'CSIDToMol', csid)
+      response.text
+    end
+
+    def inchi_to_csid(inchi)
+      response = @rest.post(API, 'InChIToCSID', inchi: inchi)
+      get_nodes(Nokogiri::XML(response), 'string').first.content.to_i
+    end
+
+    def inchi_key_to_csid(inchi_key)
+      response = @rest.post(API, 'InChIKeyToCSID', inchi_key: inchi_key)
+      get_nodes(Nokogiri::XML(response), 'string').first.content.to_i
+    end
+  end
+end

data/lib/ruspider/mass_spec_api.rb

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+# frozen_string_literal: true
+
+require 'ruspider/rest_client'
+require 'ruspider/xml_utils'
+
+module Ruspider
+  # MassSpec API: http://www.chemspider.com/MassSpecAPI.asmx
+  module MassSpecAPI
+    include XmlUtils
+
+    API = 'MassSpecAPI.asmx'
+
+    FIELDS = {
+      CSID: 'csid',
+      MF: 'molecular_formula',
+      SMILES: 'smiles',
+      InChI: 'inchi',
+      InChIKey: 'inchikey',
+      AverageMass: 'average_mass',
+      MolecularWeight: 'molecular_weight',
+      MonoisotopicMass: 'monoisotopic_mass',
+      NominalMass: 'nominal_mass',
+      ALogP: 'alogp',
+      XLogP: 'xlogp'
+    }.freeze
+
+    def initialize(rest)
+      @rest = rest
+    end
+
+    def databases
+      response = @rest.post(API, 'GetDatabases')
+      array_from_xml(response, 'ArrayOfString', 'string')
+    end
+
+    def get_extended_compound_info(csid)
+      response = @rest.post(API, 'GetExtendedCompoundInfo', csid: csid)
+      hash_from_string(response, 'ExtendedCompoundInfo', FIELDS)
+    end
+
+    def get_extended_compound_info_list(csids)
+      response = @rest.post(API, 'GetExtendedCompoundInfoArray', csids: csids)
+      nodes = get_nodes(response)
+      nodes.map { |node| hash_from_xml(node, FIELDS) }
+    end
+  end
+end

data/lib/ruspider/rest_client.rb

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+# frozen_string_literal: true
+
+require 'httparty'
+
+module Ruspider
+  # ChemSpider REST Webservice API Client
+  class RestClient
+    include HTTParty
+
+    HOST_NAME = 'www.chemspider.com'
+
+    def initialize(token, header = {})
+      @token = token
+      @header = header
+    end
+
+    def query_string_normalizer(query)
+      query.to_hash.map do |k, v|
+        if v.class == Array
+          v.map { |x| "#{k}=#{x}" }.join('&')
+        else
+          HTTParty::HashConversions.normalize_param(k, v)
+        end
+      end.join
+    end
+
+    def post(api, op, options = {})
+      return -1 if op.empty?
+      ops = { token: @token }.merge(options)
+      res = HTTParty.post(
+        "https://#{HOST_NAME}/#{api}/#{op}",
+        header: { header: @header }, body: ops,
+        query_string_normalizer: ->(h) { query_string_normalizer(h) }
+      )
+
+      raise "#{res.response.code}: #{res.parsed_response}" unless res.success?
+      res.response.body
+    end
+  end
+end

data/lib/ruspider/spectra_api.rb

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+# frozen_string_literal: true
+
+require 'ruspider/rest_client'
+
+module Ruspider
+  # SpectraAPI
+  module SpectraAPI
+    API = 'Spectra.asmx'
+
+    FIELDS = {
+      CommonName: 'common_name',
+      MOL2d: 'mol_2d',
+      MOL3d: 'mol_3d',
+      ReferenceCount: 'reference_count',
+      DataSourceCount: 'datasource_count',
+      PubMedCount: 'pubmed_count',
+      RSCCount: 'rsc_count',
+      ExternalReferences: 'external_references',
+      ds_name: 'datasource_name',
+      ds_url: 'datasource_url',
+      ext_id: 'external_id',
+      ext_url: 'external_url',
+      Status: 'status',
+      Count: 'count',
+      Message: 'message',
+      Elapsed: 'elapsed',
+      spc_id: 'spectrum_id',
+      spc_type: 'spectrum_type',
+      file_name: 'file_name',
+      comments: 'comments',
+      original_url: 'original_url',
+      submitted_date: 'submitted_date'
+    }.freeze
+
+    def initialize(rest)
+      @rest = rest
+    end
+
+    def all_spectra_info
+      # response = post('Spectra', 'GetAllSpectraInfo')
+      # hash_from_xml(response, FIELDS)
+    end
+
+    def get_spectrum_info(spectrum_id)
+      # response = post('Spectra', 'GetSpectrumInfo', spectrum_id)
+      # hash_from_xml(response, FIELDS)
+    end
+
+    def get_compound_spectra_info(csid)
+      # response = post('Spectra', 'GetCompoundSpectraInfo', csid=csid)
+      # hash_from_xml(response, FIELDS)
+    end
+
+    def get_spectra_info_list(csids)
+      # response = post('Spectra', 'GetSpectraInfoArray', csids=csids)
+      # hash_from_xml(response, FIELDS)
+    end
+
+    def all_spectra
+      all_spectra_info.map { |x| Spectrum.from_hash(x) }
+    end
+  end
+end

data/lib/ruspider/spectrum.rb

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+# frozen_string_literal: true
+
+module Ruspider
+  # ChemSpider Spectrym Data container and parser
+  class Spectrum
+    def initialize(cs, spectrum_id)
+      @cs = cs
+      @spectrum_info[:id] = spectrum_id
+    end
+
+    def spectrum_info
+      if spectrum_info.file_name.nil?
+        @spectrum_info = @cs.get_spectrum_info(@spectrum_info.id)
+      end
+
+      @spectrum_info
+    end
+
+    def spectrum_id
+      spectrum_info[:id]
+    end
+
+    def csid
+      spectrum_info[:csid]
+    end
+
+    def spectrum_type
+      spectrum_info[:spectrum_type]
+    end
+
+    def file_name
+      spectrum_info[:file_name]
+    end
+
+    def comments
+      spectrum_info[:comments]
+    end
+
+    def url
+      'https://www.chemspider.com/FilesHandler.ashx?type=blob&disp=1&id=%s' +
+        spectrum_info[:id]
+    end
+
+    def data
+    end
+
+    def original_url
+      spectrum_info.get('original_url')
+    end
+
+    def submitted_date
+      spectrum_info[:submitted_date]
+    end
+  end
+end

data/lib/ruspider/version.rb

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+# frozen_string_literal: true
+
+module Ruspider
+  VERSION = '0.1.0'
+end

data/lib/ruspider/xml_utils.rb

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+# frozen_string_literal: true
+
+require 'nokogiri'
+
+module Ruspider
+  # XML utilities
+  module XmlUtils
+    def get_nodes(xml, node_name)
+      xml.xpath(
+        "//cs:#{node_name}",
+        'cs' => 'http://www.chemspider.com/'
+      )
+    end
+
+    def get_first_node(xml, node_name)
+      get_nodes(xml, node_name).first
+    end
+
+    def hash_from_xml(xml, field)
+      hash = {}
+      field.each do |k, v|
+        node = xml.xpath("//cs:#{k}", 'cs' => 'http://www.chemspider.com/')
+        hash[v.to_sym] = node.first.content
+      end
+
+      hash
+    end
+
+    def hash_from_string(xml_str, obj_name, field)
+      xml = get_first_node(Nokogiri::XML(xml_str), obj_name)
+      hash_from_xml(xml, field)
+    end
+
+    def array_from_xml(xml_str, obj_name, field)
+      xml = get_nodes(Nokogiri::XML(xml_str), obj_name)
+      arr = xml.xpath("//cs:#{field}", 'cs' => 'http://www.chemspider.com/')
+      arr.map(&:content)
+    end
+  end
+end

data/ruspider.gemspec

@@ -0,0 +1,28 @@
+# frozen_string_literal: true
+
+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'ruspider/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'ruspider'
+  spec.version       = Ruspider::VERSION
+  spec.authors       = ['An Nguyen']
+  spec.email         = ['an.nguyen@kit.edu']
+
+  spec.summary       = 'Ruby gem for ChemSpider'
+  spec.description   = 'A wrapper for ChemSpider API'
+  spec.homepage      = 'https://github.com/complat/ruspider'
+  spec.license       = 'MIT'
+
+  spec.files         = `git ls-files -z`.split("\x0").reject do |f|
+    f.match(%r{^(test|spec|features)/})
+  end
+  spec.bindir        = 'exe'
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ['lib']
+
+  spec.add_development_dependency 'bundler', '~> 1.14'
+  spec.add_development_dependency 'rake', '~> 10.0'
+  spec.add_development_dependency 'rspec', '~> 3.0'
+end

metadata

@@ -0,0 +1,108 @@
+--- !ruby/object:Gem::Specification
+name: ruspider
+version: !ruby/object:Gem::Version
+  version: 0.1.0
+platform: ruby
+authors:
+- An Nguyen
+autorequire: 
+bindir: exe
+cert_chain: []
+date: 2017-09-22 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.14'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '1.14'
+- !ruby/object:Gem::Dependency
+  name: rake
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '10.0'
+- !ruby/object:Gem::Dependency
+  name: rspec
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - "~>"
+      - !ruby/object:Gem::Version
+        version: '3.0'
+description: A wrapper for ChemSpider API
+email:
+- an.nguyen@kit.edu
+executables: []
+extensions: []
+extra_rdoc_files: []
+files:
+- ".gitignore"
+- ".rspec"
+- ".ruby-version"
+- ".travis.yml"
+- CODE_OF_CONDUCT.md
+- Gemfile
+- LICENSE.txt
+- README.md
+- Rakefile
+- bin/console
+- bin/setup
+- lib/ruspider.rb
+- lib/ruspider/chemspider.rb
+- lib/ruspider/compound.rb
+- lib/ruspider/inchi_api.rb
+- lib/ruspider/mass_spec_api.rb
+- lib/ruspider/rest_client.rb
+- lib/ruspider/spectra_api.rb
+- lib/ruspider/spectrum.rb
+- lib/ruspider/version.rb
+- lib/ruspider/xml_utils.rb
+- ruspider.gemspec
+homepage: https://github.com/complat/ruspider
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - ">="
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.6.12
+signing_key: 
+specification_version: 4
+summary: Ruby gem for ChemSpider
+test_files: []