Makefile

blastdb:
	mkdir -p blastdb
	wget ftp://ftp.wwpdb.org/pub/pdb/derived_data/pdb_seqres.txt.gz -O blastdb/pdb_seqres.txt.gz
	cd blastdb && gunzip -f pdb_seqres.txt.gz && \
	makeblastdb -in pdb_seqres.txt -out pdbseqres -dbtype prot	
	rm -rf blastdb/pdb_seqres.txt

pdb:
	mkdir -p data/pdb_rsync
	mkdir -p data/pdb
	rsync -rlpt -v -z --delete --port=33444 \
		rsync.wwpdb.org::ftp_data/structures/divided/pdb/ data/pdb_rsync/
	cp -r data/pdb_rsync/* data/pdb/
	gunzip -r data/pdb/

pconpy:
	git clone https://github.com/kianho/pconpy
	cd pconpy &&  python setup.py install

python_packages:
	virtualenv --python=/usr/bin/python3.5 env
	bash -i -c "source env/bin/activate && pip install -r requirements.txt"

packages:
	sudo apt-get install -y liblapack-dev gcc gfortran
	sudo apt-get install -y ncbi-blast+
	sudo apt-get install -y python3.5 python3-dev python3-tk python-virtualenv

ss:
	wget http://www.rcsb.org/pdb/files/ss.txt.gz -O ss.txt.gz
	gunzip -f ss.txt.gz
	#bash -i -c "source env/bin/activate && python -m cref.utils.import_pdb_ss data/ss.txt data/ss.db"
	##rm -rf data/ss.txt

install: packages python_packages peptide torsions blastdb ss