News
Please note that this project has been renamed and moved to the following URL: https://github.com/akihirof0005/glydevkit
getting start
Install
Java (version 11.0.9)
# https://sdkman.io/
curl -s "https://get.sdkman.io" | bash
source "$HOME/.sdkman/bin/sdkman-init.sh"
# example for Mac
sdk install java 11.0.19-tem
sdk default java 11.0.19-tem JRuby
# https://github.com/rbenv/rbenv#basic-git-checkout
git clone https://github.com/rbenv/rbenv.git ~/.rbenv
echo 'eval "$(~/.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-9.3.10.0
rbenv global jruby-9.3.10.0
# optional
gem install iruby && iruby register --forceGlycoBook
gem install glycobook --pre
#This command has an issue because it will fail the first time, so please try again.
ruby -r bookinit -e BookInit.runBuild (for develop)
gem build glycobook.gemspecsample program
require 'glycobook'
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 = GlycoBook::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
wfw = GlycoBook::WurcsFrameWork.new
puts wfw.validator(w)
ssp = GlycoBook::Subsumption.new
pp ssp.topology(w)
gtc = GlycoBook::GlyTouCan.new
pp gtc.archetype(w)
gb = GlycoBook::GlycanBuilder.new
pp gb.generatePng(w,1)
pp gb.generateSvg(w)
mw = GlycoBook::MolWURCS.new
pp mw.wurcs2mol(w,"smiles")