Readme
This document reflects the current development status. When we release the main version, we plan to publish documentation including API documentation.
Install
Java (version Latest)
# https://sdkman.io/
curl -s "https://get.sdkman.io" | bash
source "$HOME/.sdkman/bin/sdkman-init.sh"
# example for Mac
sdk install java
sdk default java JRuby
# https://github.com/rbenv/rbenv#basic-git-checkout
git clone https://github.com/rbenv/rbenv.git ~/.rbenv
echo 'eval "$(~/.rbenv/bin/rbenv init - bash)"' >> ~/.bashrc
echo 'eval "$(~/.rbenv/bin/rbenv init - zsh)"' >> ~/.zshrc
source ~/.bashrc
source ~/.zshrc
git clone https://github.com/rbenv/ruby-build.git "$(rbenv root)"/plugins/ruby-build
rbenv install jruby
rbenv global jruby
# optional
gem install iruby && iruby register --forceGlyDevKit
stable version
gem install glydevkit
ruby -r init -e Init.runlatest version
gem install glydevkit --pre
ruby -r init -e Init.runBuild (for develop)
gem build glydevkit.gemspecAPI reference
https://akihirof0005.github.io/glydevkit/index.html
Optional configuration
# change WURCSFramework version
ruby -r init -e 'Init.switch_WFW_version("1.3.0")'
# check current WFW version
ruby -r init -e Init.check_WFW_version()sample program
require 'glydevkit'
w = "WURCS=2.0/3,5,4/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1b_1-5][a1122h-1a_1-5]/1-1-2-3-3/a4-b1_b4-c1_c3-d1_c6-e1"
gfc = GlyDevKit::GlycanFormatConverter.new
iupac = gfc.wurcs2iupac(w,"condensed")
iupacex = gfc.wurcs2iupac(w,"extended")
ct = gfc.wurcs2glycoct(w)
glycam = gfc.wurcs2glycam(w)
puts iupac
puts iupacex
puts ct
puts glycam
iupac = "Man(a1-3)[Man(a1-6)]Man(b1-4)GlcNAc(b1-4)GlcNAc(b1-"
wurcs = gfc.iupac2wurcs(iupac,"condensed" )
puts wurcs
wfw = GlyDevKit::WURCSFramework.new
puts wfw.validator(w,10)
ssp = GlyDevKit::Subsumption.new
pp ssp.topology(w)
gtc = GlyDevKit::GlyTouCan.new
pp gtc.archetype(w)
gb = GlyDevKit::GlycanBuilder.new
pp gb.generatePng(w,1)
pp gb.generateSvg(w)
mw = GlyDevKit::MolWURCS.new
pp mw.wurcs2mol(w,"smiles")
handler = GlyDevKit::GlytoucanDataHandler.new
pp handler.get_gtcid_by_wurcs("WURCS=2.0/4,11,10/[a2122h-1x_1-5_2*NCC/3=O][a1122h-1x_1-5][a1221m-1x_1-5][a2112h-1x_1-5]/1-1-2-2-1-1-2-1-3-3-4/a?-b1_a?-i1_b?-c1_c?-d1_c?-g1_d?-e1_d?-f1_g?-h1_j1-a?|b?|c?|d?|e?|f?|g?|h?|i?}_k1-a?|b?|c?|d?|e?|f?|g?|h?|i?}")
pp handler.get_wurcs_by_gtcid("G65107DM")