GitHub - na-ka-na/StructuredRNA: Determine Secondary structure of RNA, i.e. compute (and classify) Hydrogen bonds.

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Determine Secondary structure of RNA, i.e. compute (and classify) Hydrogen bonds.

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Name		Name	Last commit message	Last commit date
Latest commit History 3 Commits
doc		doc
inputs		inputs
lib		lib
src		src
RAG1.txt		RAG1.txt
RAG2.txt		RAG2.txt
README.txt		README.txt
RNA_Project.pptx		RNA_Project.pptx
javadoc.html.lnk		javadoc.html.lnk

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Modelled PDB data in Clojure to search for higher level topological patterns in the secondary structure of RNA. See RNA_Project.pptx for a presentation of the results.

COMPILE WINDOWS
---------------

..\IIIT_RNA_Project>java -cp lib\clojure-1.2.0-master-20100518.110252-71.jar;lib\clojure-contrib-1.2.0-20100518.110549-109.jar;lib\commons-lang-2.3.jar;classes;src clojure.main -e "(compile 'iiit)"

..\IIIT_RNA_Project>javac -classpath lib\clojure-1.2.0-master-20100518.110252-71.jar;lib\clojure-contrib-1.2.0-20100518.110549-109.jar;lib\commons-lang-2.3.jar;classes -d classes src\iiit\ToposDemo.java

..\IIIT_RNA_Project>javac -classpath lib\clojure-1.2.0-master-20100518.110252-71.jar;lib\clojure-contrib-1.2.0-20100518.110549-109.jar;lib\commons-lang-2.3.jar;classes -d classes src\iiit\HBonds.java

RUN WINDOWS
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..\IIIT_RNA_Project>java -classpath lib\clojure-1.2.0-master-20100518.110252-71.jar;lib\clojure-contrib-1.2.0-20100518.110549-109.jar;lib\commons-lang-2.3.jar;classes iiit.ToposDemo

..\IIIT_RNA_Project>java -classpath lib\clojure-1.2.0-master-20100518.110252-71.jar;lib\clojure-contrib-1.2.0-20100518.110549-109.jar;lib\commons-lang-2.3.jar;classes iiit.HBonds


COMPILE LINUX
--------------

../IIIT_RNA_Project>java -cp lib/clojure-1.2.0-master-20100518.110252-71.jar:lib/clojure-contrib-1.2.0-20100518.110549-109.jar:lib/commons-lang-2.3.jar:classes:src clojure.main -e "(compile 'iiit)"

../IIIT_RNA_Project>javac -classpath lib/clojure-1.2.0-master-20100518.110252-71.jar:lib/clojure-contrib-1.2.0-20100518.110549-109.jar:lib/commons-lang-2.3.jar:classes -d classes src/iiit/ToposDemo.java

../IIIT_RNA_Project>javac -classpath lib/clojure-1.2.0-master-20100518.110252-71.jar:lib/clojure-contrib-1.2.0-20100518.110549-109.jar:lib/commons-lang-2.3.jar:classes -d classes src/iiit/HBonds.java

RUN LINUX
-----------

../IIIT_RNA_Project>java -classpath lib/clojure-1.2.0-master-20100518.110252-71.jar:lib/clojure-contrib-1.2.0-20100518.110549-109.jar:lib/commons-lang-2.3.jar:classes iiit.ToposDemo

../IIIT_RNA_Project>java -classpath lib/clojure-1.2.0-master-20100518.110252-71.jar:lib/clojure-contrib-1.2.0-20100518.110549-109.jar:lib/commons-lang-2.3.jar:classes iiit.HBonds