In the previous version of DockQ, there were input arguments, -native_chain{1,2} and -model_chain{1,2}, that allow grouping chains for receptor and ligand. For example, if there are one chains (e.g., A) for receptor and two other chains (e.g., H and L) for ligand and I only interested in the interface between (A) and (H+L), how can I do this with DockQ v2? With the previous version, it can be done like the following:
DockQ.py [model] [native] -native_chain1 A -native_chain2 H L -model_chain1 A -model_chain2 H L
I noticed that DockQ v2 evaluates for every interface between chains and gives some averaged values as the metrics for the whole complex. However, I could not find optional arguments for grouping chains. I do not think averaging metrics for interested chain pairs would work neither because numerators and denominators for RMSDs and fnat are different for evaluating (A and (H+L)) compared to averaging (A and H) and (A and L).
In the previous version of DockQ, there were input arguments, -native_chain{1,2} and -model_chain{1,2}, that allow grouping chains for receptor and ligand. For example, if there are one chains (e.g., A) for receptor and two other chains (e.g., H and L) for ligand and I only interested in the interface between (A) and (H+L), how can I do this with DockQ v2? With the previous version, it can be done like the following:
I noticed that DockQ v2 evaluates for every interface between chains and gives some averaged values as the metrics for the whole complex. However, I could not find optional arguments for grouping chains. I do not think averaging metrics for interested chain pairs would work neither because numerators and denominators for RMSDs and fnat are different for evaluating (A and (H+L)) compared to averaging (A and H) and (A and L).