search

MobleyLab / alchemical-setup

GNU Lesser General Public License v2.1
15 stars 9 forks source link

Improve exception handling / use MCSS file #3

Open davidlmobley opened 8 years ago

davidlmobley commented 8 years ago

Currently, the code seems not to make use of the (optional) MCSS .mol2 file, though there is some code present to use this but the execution path bypasses this code. I've raised this issue with @FEPanalysis to find out what's intended, so this is a placeholder to remind that this needs to be resolved.

Relatedly, the MCSS file may be able to improve exception handling - i.e. if the user provides BOTH a map.txt and MCSS.mol2, the two could be checked against one another to ensure one doesn't override the other (i.e. the MCSS ought to have the same number of atoms as implied by the map.txt).

How should this be dealt with?

FEPanalysis commented 8 years ago

the code seems not to make use of the (optional) MCSS .mol2 file This requires OEChem which is not free.

if the user provides BOTH a map.txt and MCSS.mol2, the two could be checked against one another

Sounds like unnecessary duplication.

How should this be dealt with?

The input should be either map.txt or MCSS.mol2. For the latter OEChem is needed.

davidlmobley commented 8 years ago

The documentation/help will need to be improved to deal with this - right now the usage info sounds like both are expected. (The people outside the group who have been using it have been providing both, because it isn't clear that they should do one or the other).

The other issue I raised by e-mail is that currently, it's required that the user provide map.txt, so there is no way to make use of a MCSS.mol2 file. Have you tested the code with an MCSS.mol2? If so, then presumably I should fix it so that map.txt isn't required?

davidlmobley commented 8 years ago

@FEPanalysis - should I update this, or did you plan to make this change?