GitHub - timkartar/RNAproDB: RNAProDB developement

RNAproDB backend setup

Ensure Python 3 is installed
Run: git checkout apache-server
pip install -e pydpb/
Install other Python dependencies as required
Ensure x3dna-dssr is available in PATH
Other external dependencies are available in ./external/ and can be added to the path
Run: python rna_vis.py 1ivs (you may need to adjust pdb_path and output paths in rna_vis.py and run_dssr.py as needed)

Example output can be downloaded here: https://rohslab.usc.edu/rnaprodb/1ivs

Name		Name	Last commit message	Last commit date
Latest commit History 231 Commits
_data		_data
backend		backend
d3graph		d3graph
dnaprodb_rnascape		dnaprodb_rnascape
external		external
pypdb		pypdb
.DS_Store		.DS_Store
.gitignore		.gitignore
README.md		README.md
aa_counter.py		aa_counter.py
clean_rna.py		clean_rna.py
data.py		data.py
downloadPDBThumbnails.py		downloadPDBThumbnails.py
download_ids.py		download_ids.py
edge_cases.txt		edge_cases.txt
get_algorithm.py		get_algorithm.py
get_atom_kdtree.py		get_atom_kdtree.py
get_edges.py		get_edges.py
get_interactions.py		get_interactions.py
get_lw.py		get_lw.py
get_num_nucleotides.py		get_num_nucleotides.py
get_pca.py		get_pca.py
get_residue_id.py		get_residue_id.py
get_rnascape.py		get_rnascape.py
get_ss.py		get_ss.py
get_subgraph.py		get_subgraph.py
get_surface_residues.py		get_surface_residues.py
get_viennarna.py		get_viennarna.py
get_whbonds.py		get_whbonds.py
hbond_extractor.py		hbond_extractor.py
make_db.py		make_db.py
make_ss_graph.py		make_ss_graph.py
make_table.py		make_table.py
make_tooltip.py		make_tooltip.py
modified_parents.npz		modified_parents.npz
nakb_prna_ids.txt		nakb_prna_ids.txt
process_components.py		process_components.py
process_graph.py		process_graph.py
refresh_db.py		refresh_db.py
rna_vis.py		rna_vis.py
run_dssr.py		run_dssr.py
run_dssr.sh		run_dssr.sh
run_rna_vis.sh		run_rna_vis.sh
run_update_components.sh		run_update_components.sh
search_query.tmpl		search_query.tmpl
search_query_noprotein.tmpl		search_query_noprotein.tmpl
split_entities.py		split_entities.py
structure_data.py		structure_data.py
utilities.py		utilities.py