Halogen bonds, updates to web-app UI, etc.

CHANGES.md

@@ -1,6 +1,26 @@
 Changes
 =======
 
+WIP
+---
+
+1. Can select multiple interactions at once.
+2. PNG file included in download from "Save" button. Also, log.txt file, for those not comfortable with JSON.
+3. Bonds now color coded.
+4. Certain interactions turned on by default.
+5. Clear button changed to "Reset" because resets to default value.
+6. No more coloring by molecule, interaction, etc. Too confusing.
+7. JSZip now dynamic import.
+8. zip download now includes vmd state directory.
+9. Vmd state file centers on ligand automatically.
+10. changed hydrogen_bond_dist_cutoff and hydrogen_bond_angle_cutoff parameter names to hydrogen_halogen_bond_dist_cutoff
+hydrogen_halogen_bond_angle_cutoff
+11. Removed ability to toggle on and off cylinder interactions, to simplify UI. Always on for those interaction where appropriate.
+12. Some interactions are shown as spheres, others as bonds. Keeps it simplier.
+
+Halogen bonds mention in all documentation?
+Halogen bonds counted twice? Good to check. In the chart in log file.
+
 2.0
 ---
 

COMMAND_LINE_USE.md

@@ -95,8 +95,8 @@ python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.
 Though we recommend using program defaults, the following command-line tags can
 also be specified: `-close_contacts_dist1_cutoff` `-close_contacts_dist2_cutoff`
 `-electrostatic_dist_cutoff` `-active_site_flexibility_dist_cutoff`
-`-hydrophobic_dist_cutoff` `-hydrogen_bond_dist_cutoff`
-`-hydrogen_bond_angle_cutoff` `-pi_padding_dist`
+`-hydrophobic_dist_cutoff` `-hydrogen_halogen_bond_dist_cutoff`
+`-hydrogen_halogen_bond_angle_cutoff` `-pi_padding_dist`
 `-pi_pi_interacting_dist_cutoff` `-pi_stacking_angle_tolerance`
 `-T_stacking_angle_tolerance` `-T_stacking_closest_dist_cutoff`
 `-cation_pi_dist_cutoff` `-salt_bridge_dist_cutoff`
@@ -105,7 +105,7 @@ For example, if you want to tell BINANA to detect only hydrogen bonds where the
 donor and acceptor are less than 3.0 angstroms distant, run:
 
 ```bash
-python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -hydrogen_bond_dist_cutoff 3.0
+python3 run_binana.py -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -hydrogen_halogen_bond_dist_cutoff 3.0
 ```
 
 What follows is a detailed description of the BINANA algorithm and a further
@@ -195,9 +195,9 @@ BINANA allows hydroxyl and amine groups to act as hydrogen-bond donors. Oxygen
 and nitrogen atoms can act as hydrogen-bond acceptors. Fairly liberal cutoffs
 are implemented in order to accommodate low-resolution crystal structures. A
 hydrogen bond is identified if the hydrogen-bond donor comes within
-`hydrogen_bond_dist_cutoff` angstroms of the hydrogen-bond acceptor, and the
+`hydrogen_halogen_bond_dist_cutoff` angstroms of the hydrogen-bond acceptor, and the
 angle formed between the donor, the hydrogen atom, and the acceptor is no
-greater than `hydrogen_bond_angle_cutoff` degrees. BINANA tallies the number of
+greater than `hydrogen_halogen_bond_angle_cutoff` degrees. BINANA tallies the number of
 hydrogen bonds according to the secondary structure of the receptor atom, the
 side-chain/backbone status of the receptor atom, and the location (ligand or
 receptor) of the hydrogen bond donor. Thus there are twelve possible

javascript/compile.sh

@@ -7,7 +7,7 @@ rm -rf ../python/__target__/ ./lib/
 # Compile the python file.
 cd ../python/
 # --nomin
-transcrypt --build --ecom --verbose binana.py
+transcrypt --build --nomin --ecom --verbose binana.py
 cd -
 
 # Move the javascript library to the lib directory.