glydevkit 0.2.0.pre.beta.5-java → 0.2.0.pre.beta.6-java
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- checksums.yaml +4 -4
- data/lib/glydevkit/cdk.rb +64 -0
- metadata +2 -1
checksums.yaml
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---
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metadata.gz:
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data.tar.gz:
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metadata.gz: 024fc1cdc0aaef9809c400eb99c935b285ce3cc7c377f6082e129bedec02b7da
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data.tar.gz: 52316bec1211005dd3f8809d2e393fe8de9ac3c1daf2c72c16e60fbeffeb579f
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metadata.gz: 76998af578da7b88e9821a9cc32fa89f531b5891424b318e794354df33b067acfc494d01e1e519c353c3574561d6bba6619e6cdd8763a0ce03d6fc5d17d869e9
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data.tar.gz: 38e76b7317d36f85bac5e144ce0ebfa4c4d7aa6412df2d03e5b884e2f73d745c02b25be194b0606acbbff58e32afddcc78c88699681c659b8f51717ee553b53d
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@@ -0,0 +1,64 @@
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require "java"
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require_relative '../jar/cdk.jar'
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java_import 'org.openscience.cdk.similarity.Tanimoto'
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java_import 'org.openscience.cdk.DefaultChemObjectBuilder'
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java_import 'org.openscience.cdk.smiles.SmilesParser'
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java_import 'org.openscience.cdk.fingerprint.CircularFingerprinter'
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java_import 'org.openscience.cdk.layout.StructureDiagramGenerator'
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java_import 'org.openscience.cdk.depict.DepictionGenerator'
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module GlyDevKit
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class CDK
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def sim(seq1,seq2,format)
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if format == "wurcs"
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Tanimoto.calculate(w2bit(seq1), w2bit(seq2))
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elsif format == "smiles"
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Tanimoto.calculate(smiles2bit(seq1), smiles2bit(seq2))
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end
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end
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def mol2svg(smiles)
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begin
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sp = SmilesParser.new(DefaultChemObjectBuilder.getInstance)
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molecule = sp.parseSmiles(smiles)
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sdg = StructureDiagramGenerator.new(molecule)
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sdg.generateCoordinates
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molecule = sdg.molecule
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depiction_gen = DepictionGenerator.new
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return depiction_gen.withSize(30, 30).depict(molecule).toSvgStr
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rescue => e
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puts e.message
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end
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end
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private
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def w2bit(w)
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mw = GlyDevKit::MolWURCS.new
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smiles = mw.wurcs2mol(w,"smiles")[:smiles]
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sp = SmilesParser.new(DefaultChemObjectBuilder.getInstance())
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molecule = sp.parseSmiles(smiles)
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fingerprinter = CircularFingerprinter.new
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fingerprinter.calculate(molecule)
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return fingerprinter.getBitFingerprint(molecule).asBitSet()
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end
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def smiles2bit(s)
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sp = SmilesParser.new(DefaultChemObjectBuilder.getInstance())
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molecule = sp.parseSmiles(s)
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fingerprinter = CircularFingerprinter.new
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fingerprinter.calculate(molecule)
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return fingerprinter.getBitFingerprint(molecule).asBitSet()
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end
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end
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end
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metadata
CHANGED
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@@ -1,7 +1,7 @@
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--- !ruby/object:Gem::Specification
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name: glydevkit
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version: !ruby/object:Gem::Version
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version: 0.2.0.pre.beta.
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version: 0.2.0.pre.beta.6
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platform: java
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authors:
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- Akihiro Fujita
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@@ -62,6 +62,7 @@ files:
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- jar.yml
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- lib/glydevkit.rb
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- lib/glydevkit/Loggerinit.rb
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- lib/glydevkit/cdk.rb
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- lib/glydevkit/gly_tou_can.rb
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- lib/glydevkit/glycan_builder.rb
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- lib/glydevkit/glycan_format_converter.rb
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