Updates to 1.2.

.gitignore

@@ -1 +1,3 @@
 .vscode
+example_commandline/*.jdd.*
+example_commandline/example_output

CHANGELOG.md

@@ -1,6 +1,27 @@
 Changes
 =======
 
+1.2
+---
+
+* Reformatted code with [Black Formatter](https://github.com/psf/black).
+* Updated email in copyright header.
+* Updated `contact_map_distance_limit` to 4.5 in example scripts, help
+  descriptions, etc., to avoid confusion (given new default, see version 1.1
+  changes).
+* Added download and citation information to the standard output.
+* Investigated Python2/3 differences. In brief, we recently noticed that WISP
+  gives slightly different output when running under Python2 (numpy 1.16.0,
+  networkx 2.2, scipy 1.2.0) vs. Python3 (numpy 1.17.4, networkx 2.2, scipy
+  1.3.1). We believe [differences in the two numpy versions are
+  responsible](https://numpy.org/doc/stable/release/1.17.0-notes.html#float16-subnormal-rounding),
+  though it is possible that similar differences may arise when running on
+  different operating systems, etc. Regardless, the top-ranked paths are the
+  same, but lower-ranked paths sometimes aren't. After some investigation and
+  test updates to the code, we now believe subtle rounding-error differences
+  to be the cause. For consistency's sake, we recommend using the same
+  Python/OS/dependencies when comparing multiple WISP analyses.
+
 1.1
 ---
 

README.md

@@ -1,4 +1,4 @@
-WISP 1.1
+WISP 1.2
 ========
 
 WISP is a trajectory analysis tool that calculates and visualizes allosteric
@@ -272,7 +272,7 @@ Notes:
 
 Example:
      python wisp.py -pdb_trajectory_filename multi_frame_pdb.pdb
-         -node_definition CA -contact_map_distance_limit 50.0
+         -node_definition CA -contact_map_distance_limit 4.5
          -load_wisp_saved_matrix false -wisp_saved_matrix_filename
          matrix.file -desired_number_of_paths 30 -source_residues
          "X_SER_1 X_LEU_4" -sink_residues X_ARG_37 -number_processors

example_commandline/simple_example.sh

@@ -1,25 +1,26 @@
 # Run wisp
-python ../wisp.py -contact_map_distance_limit 999999.999 -desired_number_of_paths 15 -load_wisp_saved_matrix FALSE -longest_path_b 0.0 -longest_path_g 0.0 -longest_path_opacity 1.0 -longest_path_r 1.0 -longest_path_radius 0.01 -node_definition RESIDUE_COM -node_sphere_b 1.0 -node_sphere_g 1.0 -node_sphere_opacity 1.0 -node_sphere_r 1.0 -node_sphere_radius 1.0 -num_frames_to_load_before_proceesing 20 -number_processors 4 -pdb_trajectory_filename trajectory_20_frames.pdb -seconds_to_wait_before_parallelizing_path_finding 5.0 -shortest_path_b 1.0 -shortest_path_g 0.0 -shortest_path_opacity 1.0 -shortest_path_r 0.0 -shortest_path_radius 1.0 -sink_residues "C_ASP_11" -source_residues "C_LEU_10" -spline_smoothness 0.01 -vmd_resolution 6 -output_directory ./example_output/
+python ../wisp.py -contact_map_distance_limit 4.5 -desired_number_of_paths 15 -load_wisp_saved_matrix FALSE -longest_path_b 0.0 -longest_path_g 0.0 -longest_path_opacity 1.0 -longest_path_r 1.0 -longest_path_radius 0.01 -node_definition RESIDUE_COM -node_sphere_b 1.0 -node_sphere_g 1.0 -node_sphere_opacity 1.0 -node_sphere_r 1.0 -node_sphere_radius 1.0 -num_frames_to_load_before_proceesing 20 -number_processors 4 -pdb_trajectory_filename trajectory_20_frames.pdb -seconds_to_wait_before_parallelizing_path_finding 5.0 -shortest_path_b 1.0 -shortest_path_g 0.0 -shortest_path_opacity 1.0 -shortest_path_r 0.0 -shortest_path_radius 1.0 -sink_residues "C_ASP_11" -source_residues "C_LEU_10" -spline_smoothness 0.01 -vmd_resolution 6 -output_directory ./example_output/
 
 # Get expected contents of example_output/simply_formatted_paths.txt
 echo
-echo "Expected contents of example_output/simply_formatted_paths.txt (if Python 3):"
+echo "Expected contents of example_output/simply_formatted_paths.txt (Python 3, numpy 1.17.4, networkx 2.2, scipy 1.3.1):"
+
 cat <<EOF
 1.1363589537262389 9 10
-1.920042178661312 9 31 10
 2.027418997284591 9 11 10
-2.0580187961654244 9 271 10
-2.072362499435586 9 104 10
-2.1979011747323174 9 260 10
 2.205901870787125 9 49 11 10
-2.2274854140539255 9 30 31 10
-2.2709631887057427 9 104 271 10
-2.3074498505687115 9 49 10
-2.31609691842617 9 36 31 10
-2.316805404722313 9 105 104 10
-2.317004756199552 9 32 31 10
-2.344862237079425 9 107 104 10
-2.3571728828116276 9 107 329 10
+2.307449850568712 9 49 10
+2.442623103273746 9 49 51 10
+2.448087831142992 9 8 10
+2.501932824731498 9 11 51 10
+2.5026984744745864 9 48 11 10
+2.621657347053458 9 49 48 11 10
+2.6370708377784413 9 31 15 10
+2.6804156982340315 9 49 11 51 10
+2.7056328296310643 9 31 11 10
+2.8932868716011986 9 49 51 11 10
+2.977212301921493 9 48 11 51 10
+3.0311375788312436 9 31 16 10
 EOF
 echo