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Halogen bonds, updates to web-app UI, etc.
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jdurrant committed Nov 7, 2021
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20 changes: 20 additions & 0 deletions
@@ -1,6 +1,26 @@


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
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.


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10 changes: 5 additions & 5 deletions
Expand Up @@ -95,8 +95,8 @@ python3 -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`
Expand All @@ -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:

python3 -receptor /path/to/receptor.pdbqt -ligand /path/to/ligand.pdbqt -hydrogen_bond_dist_cutoff 3.0
python3 -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
Expand Down Expand Up @@ -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
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2 changes: 1 addition & 1 deletion javascript/
Expand Up @@ -7,7 +7,7 @@ rm -rf ../python/__target__/ ./lib/
# Compile the python file.
cd ../python/
# --nomin
transcrypt --build --ecom --verbose
transcrypt --build --nomin --ecom --verbose
cd -

# Move the javascript library to the lib directory.
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7 changes: 4 additions & 3 deletions javascript/lib/__future__.js

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93 changes: 84 additions & 9 deletions javascript/lib/binana._cli_params._get_params.js

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