Only show hydrogen bonds with energies of -1 kJ/mol or stronger. From -1 to -3 kJ/mol, show them in blue with increasing opacity. From -3 to -30 kJ/mol, show them at a uniform opacity, maybe 0.3, but changing color through teal, green, yellow, and finally to white. If any hbonds surpass -30 kJ/mol, add a magenta tinge. The H...FH hbond has an energy of -161.5, so it's important to gracefully handle values that large.
In the .dock file output, make a dedicated section for hydrogen bonds meeting the -1 kJ/mol threshold. List the HEAVY atoms involved in each bond. The viewer will read and interpret these records in order to construct the hbonds from atom center to atom center.
Can use NGL's shape class to do this:
Only show hydrogen bonds with energies of -1 kJ/mol or stronger. From -1 to -3 kJ/mol, show them in blue with increasing opacity. From -3 to -30 kJ/mol, show them at a uniform opacity, maybe 0.3, but changing color through teal, green, yellow, and finally to white. If any hbonds surpass -30 kJ/mol, add a magenta tinge. The H...FH hbond has an energy of -161.5, so it's important to gracefully handle values that large.
In the .dock file output, make a dedicated section for hydrogen bonds meeting the -1 kJ/mol threshold. List the HEAVY atoms involved in each bond. The viewer will read and interpret these records in order to construct the hbonds from atom center to atom center.