glycobook 0.1.0.alpha.21-java → 0.1.0.alpha.22-java
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- checksums.yaml +4 -4
- data/lib/glycobook/mol_wurcs.rb +40 -15
- metadata +3 -3
checksums.yaml
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@@ -1,7 +1,7 @@
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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: c30b663e17567babecd2deaee54be71f43e7fc30452bff1dbbd751156a5e07fb
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data.tar.gz: 9e1c862ce6ff0b91391338d4b42953ea2e53b05265550b4bccb4b1449d8bd3d0
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SHA512:
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metadata.gz:
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data.tar.gz:
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metadata.gz: e156bf8df3954c0f29a926fe00ee122ba4ef8e3eda04fe7d9d02f624abd6b6abefd2faef729de5ad8f037ba09356a9b84fcb63c358ed3637cfd0c488cb7bd18d
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data.tar.gz: 9a873652978c7c9bca1dcd975ad7afb6fd4f87d913973f860e46eb4499bac1dd3756cca68ccd9205210359b60d72e34daac383c7fbaae5594ebdebef5553efa8
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data/lib/glycobook/mol_wurcs.rb
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@@ -9,17 +9,22 @@ java_import 'org.openscience.cdk.interfaces.IAtomContainerSet'
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java_import 'org.openscience.cdk.io.IChemObjectWriter'
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java_import 'org.openscience.cdk.io.ISimpleChemObjectReader'
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java_import 'org.openscience.cdk.silent.AtomContainerSet'
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java_import 'org.openscience.cdk.DefaultChemObjectBuilder'
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java_import 'org.openscience.cdk.io.SDFWriter'
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java_import 'org.openscience.cdk.smiles.SmilesGenerator'
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java_import 'org.openscience.cdk.silent.SilentChemObjectBuilder'
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java_import 'java.io.StringReader'
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java_import 'java.nio.file.Files'
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java_import 'java.nio.file.Paths'
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java_import 'java.io.IOException'
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java_import 'java.lang.System'
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java_import 'java.util.ArrayList'
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java_import 'java.io.StringWriter'
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module GlycoBook
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class MolWURCS
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def
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def wurcs2mol(w,format)
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begin
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reader = ChemFormatType::WURCS.createReader
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@@ -33,24 +38,44 @@ def wurcs2mdlmol(w)
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end
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return if mols.nil?
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if format == "sdf"
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# write mol
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string_writer = java.io.StringWriter.new
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begin
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writer = org.openscience.cdk.io.SDFWriter.new(string_writer)
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if writer.accepts(mols.java_class)
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writer.write(mols)
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elsif writer.accepts(mols.get_atom_container(0).java_class)
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writer.write(mols.get_atom_container(0))
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end
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writer.close
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rescue Java::OrgOpenscienceCdkException::CDKException, Java::JavaIo::IOException => e
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e.printStackTrace()
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end
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return string_writer.to_s
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elsif format == "smiles"
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# SMILESジェネレータの生成
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smiles_gen = SmilesGenerator.absolute()
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string_writer = java.io.StringWriter.new
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begin
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mols.atomContainers.each do |mol|
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# 各分子に対してSMILES表現の生成
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smiles = smiles_gen.createSMILES(mol)
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string_writer.write(smiles + "\n")
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end
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# 生成したSMILESの出力
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return string_writer.toString
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rescue Java::OrgOpenscienceCdkException::CDKException, Java::JavaIo::IOException => e
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e.printStackTrace()
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return ""
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end
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writer.close
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rescue Java::OrgOpenscienceCdkException::CDKException, Java::JavaIo::IOException => e
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e.printStackTrace()
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end
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return string_writer.to_s
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end
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-
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end
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end
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metadata
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@@ -1,14 +1,14 @@
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--- !ruby/object:Gem::Specification
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name: glycobook
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version: !ruby/object:Gem::Version
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version: 0.1.0.alpha.
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version: 0.1.0.alpha.22
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platform: java
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authors:
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- Akihiro Fujita
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autorequire:
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bindir: bin
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cert_chain: []
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date: 2023-11-
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date: 2023-11-21 00:00:00.000000000 Z
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dependencies:
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- !ruby/object:Gem::Dependency
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requirement: !ruby/object:Gem::Requirement
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@@ -64,7 +64,7 @@ required_rubygems_version: !ruby/object:Gem::Requirement
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- !ruby/object:Gem::Version
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version: 1.3.1
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requirements: []
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rubygems_version: 3.
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rubygems_version: 3.2.33
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signing_key:
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specification_version: 4
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summary: Glycobook is a JRuby library for glycaninformatics
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