Update to python example.

.gitignore

@@ -29,3 +29,7 @@ make_zip_files_for_releases.sh
 releases
 python/binana/_test/output
 
+cli_example_output
+ligand_receptor_output.csv
+ligand_receptor_output.json
+test.pdb

CHANGES.md

@@ -50,23 +50,6 @@ Be sure to compress javascript
 
 MAke sure not javascript is external.
 
-DOCUMENTATION:
-
-1. Halogen bonds mention in all documentation?
-2. METAL_COORDINATION_CUTOFF. Get into web app (DONE), documentation,
-   parameters, etc.
-3. Make sure all documentation/examples account for get_all_interactions
-   (updated for metal coordination, halogen bonds)
-4. Make sure output_csv parameter documented.
-
-hydrogen_halogen_bond_angle_cutoff
-halogen_bond_dist_cutoff
-metal_coordination_dist_cutoff
-output_csv
-
-(COMMAND_LINE_USE updated)
-
-
 Clean up examples directory
 
 Tests both python2 and python3

python/example/test.sh

@@ -4,7 +4,4 @@
 python3 ../run_binana.py -receptor receptor.pdbqt -ligand ligand.pdbqt -output_file test.pdb
 python3 ../run_binana.py -receptor receptor.pdbqt -ligand ligand.pdbqt -output_dir ./cli_example_output/
 python3 ../run_binana.py -receptor receptor.pdbqt -ligand ligand.pdbqt -output_json ligand_receptor_output.json
-
-python3 ../run_binana.py -receptor metal_coordination/recep_no_zn.pdb -ligand metal_coordination/Zn_lig.pdb -output_dir ./cli_example_output/
-
-python3 ../run_binana.py -receptor ~/Downloads/binana_examples/metal/2M30.pdb -ligand ~/Downloads/binana_examples/metal/lig.pdb -output_dir ./cli_example_output/
+python3 ../run_binana.py -receptor receptor.pdbqt -ligand ligand.pdbqt -output_csv ligand_receptor_output.csv