demianriccardi/hackamol-x-sasa

Extension for solvent accessible surface area calculations

hackamol-x-sasa's Issues

Alternative algorithms

How good is POPS?

http://mathbio.nimr.mrc.ac.uk/wiki/POPS

Implement in another role, either an interface or the algorithm

Changing numbers of atoms during SASA calculations

One unavoidable issue with SASA calculations using external programs is that the number of atoms will often change. The source of these differences is likely from residues with multiple orientations or from water molecules. There is no way around it. A direct interface between the perl call and the sasa call via the C library would ensure that you get what you ask for, but this hasn't been implemented yet.

-embracing the molecules output seems reasonable for now so that the results correspond to something more firm.
-some utility methods to identify changes would be helpful.

check for executable

throw an exception if it isn't set correctly

Use Roles to inject interfaces to different SASA calculators

Currently, working with surface racer, which is closed source and requires permission to use. It processes the pdb (stripping hydrogens, waters) before analyzing the surface, which makes things a little tricky, all the specific hacks should be contained within a Surface Racer role.