/pk-sat

Final project CS 517 @ Oregon State. SAT/SMT implementation of RNA structure prediction with pseudoknots.

Primary LanguagePython

Installing Z3

git clone https://github.com/Z3Prover/z3.git
cd pk-sat
python3 -m venv venv
source venv/bin/activate
cd ../z3
python scripts/mk_make.py --python
cd build
make
make install
# You will find Z3 and the Python bindings installed in the virtual environment
venv/bin/z3 -h

Installing LinearPartition

From the /pk-sat directory do:

cd ..
git clone https://github.com/LinearFold/LinearPartition.git
cd LinearPartition/
make

To verify installation run:

cat ../pk-sat/CRW_00774.fa | ./linearpartition --prefix ./prob_matrix

You should see output in the text file prob_matrix_1

Testing Baseline

To test the baseline model (Ganesh et al 2012), run

python pksat.py

Testing Advanced

To test the advanced model (Sato et al 2011, run:

python ipknot.py