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chemspider

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ChemSpider.rb: ChemSpider wrapped up with a Ruby bow.
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 Popularity
Downloads
11,887
Stars
1
Forks
0
Watchers
2
 Releases
Current version
0.0.3
Total releases
3
First release
2012-10-15
Latest release
2012-10-23
 Development
Primary Language
Ruby
Average date of last 50 commits
2012-10-19
Reverse Dependencies
0

 Dependencies

Development

yard
>= 0.7.2

Runtime

nokogiri
>= 1.5.0
 Project Readme

ChemSpider.rb: ChemSpider wrapped up with a Ruby bow

This is a Ruby library for working with the ChemSpider API.

Features

  • 100% coverage of REST operations (support for SOAP is coming soon).
  • REST operations support both "GET" and "POST" verbs of the HTTP protocol.
  • Provides a clean, object-oriented representation of Web services, operations and their results.
  • Results are automatically translated into Ruby objects.
  • Plays nicely with proxy servers: request URIs can be modified at runtime.

Examples

require "chemspider"

Convert an InChI into an InChIKey

inchi = "InChI=1S/C25H44N4O8/c1-14(2)25(12,37-15(3)30)19(34)29-23(8,9)17(32)27-21(4,5)16(31)26-22(6,7)18(33)28-24(10,11)20(35)36-13/h14H,1-13H3,(H,26,31)(H,27,32)(H,28,33)(H,29,34)"

inchi_key = ChemSpider::InChI::InChIToInChIKey.get!(inchi)
#=> "HLVCOUOCNKNUFB-UHFFFAOYSA-N"

or

inchi_key = ChemSpider::InChI::InChIToInChIKey.get!(:inchi => inchi)
#=> "HLVCOUOCNKNUFB-UHFFFAOYSA-N"

Convert an InChI into an InChIKey (via a proxy server)

# accepts the same options as the constructor for the URI class...
uri_options = { 
  :scheme => :https, 
  :host   => "www.mychemspiderproxy.com", 
  :port   => 443,
}

inchi_key = ChemSpider::InChI::InChIToInChIKey.get!({ :inchi => inchi }, uri_options)
#=> "HLVCOUOCNKNUFB-UHFFFAOYSA-N"

Get extended compound info

csid = 4401975
token = "YOUR_SECURITY_TOKEN"

extended_compound_info = ChemSpider::MassSpecAPI::GetExtendedCompoundInfo.get!(csid, token)
#=> #<ChemSpider::ExtendedCompoundInfo:0x1019d2338 @nominal_mass=528.0, @molecular_weight=528.6389, @molecular_formula="C_{25}H_{44}N_{4}O_{8}", @inchi_key="HLVCOUOCNKNUFB-UHFFFAOYAA", @smiles="O=C(OC)C(NC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(OC(=O)C)(C)C(C)C)(C)C)(C)C)(C)C)(C)C", @common_name="Methyl N-(2-acetoxy-2,3-dimethylbutanoyl)-2-methylalanyl-2-methylalanyl-2-methylalanyl-2-methylalaninate", @a_log_p=2.18, @monoisotopic_mass=528.315979003906, @average_mass=528.639, @inchi="InChI=1/C25H44N4O8/c1-14(2)25(12,37-15(3)30)19(34)29-23(8,9)17(32)27-21(4,5)16(31)26-22(6,7)18(33)28-24(10,11)20(35)36-13/h14H,1-13H3,(H,26,31)(H,27,32)(H,28,33)(H,29,34)", @csid=4401975, @x_log_p=0.5>

or

extended_compound_info = ChemSpider::MassSpecAPI::GetExtendedCompoundInfo.get!(:CSID => csid, :token => token)
#=> #<ChemSpider::ExtendedCompoundInfo:0x1019d2338 @nominal_mass=528.0, @molecular_weight=528.6389, @molecular_formula="C_{25}H_{44}N_{4}O_{8}", @inchi_key="HLVCOUOCNKNUFB-UHFFFAOYAA", @smiles="O=C(OC)C(NC(=O)C(NC(=O)C(NC(=O)C(NC(=O)C(OC(=O)C)(C)C(C)C)(C)C)(C)C)(C)C)(C)C", @common_name="Methyl N-(2-acetoxy-2,3-dimethylbutanoyl)-2-methylalanyl-2-methylalanyl-2-methylalanyl-2-methylalaninate", @a_log_p=2.18, @monoisotopic_mass=528.315979003906, @average_mass=528.639, @inchi="InChI=1/C25H44N4O8/c1-14(2)25(12,37-15(3)30)19(34)29-23(8,9)17(32)27-21(4,5)16(31)26-22(6,7)18(33)28-24(10,11)20(35)36-13/h14H,1-13H3,(H,26,31)(H,27,32)(H,28,33)(H,29,34)", @csid=4401975, @x_log_p=0.5>

Get metadata for an operation

ChemSpider::MassSpecAPI::GetExtendedCompoundInfo.chem_spider_service_name
#=> :MassSpecAPI

ChemSpider::MassSpecAPI::GetExtendedCompoundInfo.chem_spider_operation_name
#=> :GetExtendedCompoundInfo

ChemSpider::MassSpecAPI::GetExtendedCompoundInfo.chem_spider_param_names
#=> ["CSID", "token"]

ChemSpider::MassSpecAPI::GetExtendedCompoundInfo.chem_spider_options
#=> { :selector => "ExtendedCompoundInfo", :datatype => ChemSpider::ExtendedCompoundInfo, :first_child => true }

Perform a "Simple" Search

query = "Aspirin"
token = "YOUR_SECURITY_TOKEN"

# the maximum number of attempts...
ASYNC_SEARCH_STATUS_REQUEST_COUNT = 10

# the amount of time to "sleep" between requests...
COOLING_OFF_DURATION_SECONDS = 1.0

# $stderr.puts("[Search] #{query.inspect}")

# send the request, and receive the transaction ID...
rid = ChemSpider::Search::AsyncSimpleSearch.get!(:query => query, :token => token)

result_ready = false

(0..ASYNC_SEARCH_STATUS_REQUEST_COUNT).each do |idx|
  # request the current status for the transaction ID...
  status = ChemSpider::Search::GetAsyncSearchStatus.get!(:rid => rid, :token => token)
  
  # $stderr.puts("[Status #{idx.to_i + 1} of #{ASYNC_SEARCH_STATUS_REQUEST_COUNT}] #{rid} => #{status}")
  
  case status
  when "ResultReady"
    # toggle the flag...
    result_ready = true
    
    # we're ready to go...  
    break
  when "Failed", "Suspended", "TooManyRecords"
    # the search has failed (for some reason)...
    break
  else
    # wait...
    Kernel.sleep(COOLING_OFF_DURATION_SECONDS)
  end
end

if result_ready
  # request the results...
  csids = ChemSpider::Search::GetAsyncSearchResult.get!(:rid => rid, :token => token)
  
  # $stderr.puts("[Results (#{csids.length})] #{csids.join(", ")}")
  
  # do something with the results...
  csids.each do |csid|
    extended_compound_info = ChemSpider::MassSpecAPI::GetExtendedCompoundInfo.get!(:CSID => csid, :token => token)

    $stdout.puts(extended_compound_info.inspect)
  end
end

Dependencies

Installation

The recommended installation method is via RubyGems. To install the latest official release of ChemSpider.rb, do:

% [sudo] gem install chemspider

Download

To get a local working copy of the development repository, do:

% git clone git://github.com/markborkum/chemspider.git

Alternatively, download the latest development version as a tarball as follows:

% wget http://github.com/markborkum/chemspider/tarball/master

Resources

Authors

License

This is free and unencumbered public domain software. For more information, see http://unlicense.org/ or the accompanying {file:UNLICENSE} file.