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asapdiscovery / choppa

Integrated mutational and structural biology data into a concerted HTML view.
MIT License
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HBA / HBD selection fragile, should use elements #8

Closed hmacdope closed 6 months ago

hmacdope commented 7 months ago 
            # we only want to show HBD/HBA
            if contacted_lig_at.type == "N" and contacted_res_at.type == "O" or \
                            contacted_lig_at.type == "O" and contacted_res_at.type == "N":
                contacts.append([contacted_lig_at, contacted_res_at])

In util is a bit fragile as it depends on atom types, instead should query atom elements, as types can be anything.

JenkeScheen commented 7 months ago

can you point me to the atom element method in MDA?

hmacdope commented 6 months ago

should just be the contacted_lig.element https://userguide.mdanalysis.org/stable/topology_system.html

JenkeScheen commented 6 months ago

fixed in https://github.com/asapdiscovery/choppa/pull/16/commits/d7eada4d6729bb86750b7a71fc327c1b539105b2