Quickmodel modification and adding documentation.

[MehtapIsik]

I modified parser.py so that it is possible to skip experiments and analyze part of the plate with quickmodel. To skip an experiment (a pair of protein and buffer rows), ligand name must be recorded as skip in ligand_order section of inputs.py.

For example: 'ligand_order' : ['skip', 'skip', 'Dansylglycine', 'Dansylglycine'] will only analyze rows E, F, G and H.

This skipping option became necessary when I used two different excitation wavelengths, thus two different fluorescence measurement sections for two halves of the plate.

I also added Useful Scripts page to Assaytools documentation. I recorded this new option there. I also described how the following scripts should be used in coordination to analyze an experiment:

• inputs.py
• calculate_L_stated_array.py
• quickmodel.py

[jchodera]

Good idea! Let's be sure to get @sonyahanson's input too.

What about using None (the Python object, not the string) instead of 'skip'?

[MehtapIsik]

I realized viewing the newly added documentation page is not possible until it is merged. This is what it looks like: Useful Scripts — assaytools 0.1.0 documentation.pdf

[jchodera]

When did calculate_Lstated_array sneak in there? We should add that as an entry_point to setup.py here: https://github.com/choderalab/assaytools/blob/master/setup.py#L35-L37

[MehtapIsik]

Thanks for pointing that out. I will add it.

[MehtapIsik]

I think this branch is ready to merge.

[sonyahanson]

Looks good! Thanks for this Mehtap.

Just to clarify the format for skipping rows in your inputs.py:

'ligand_order' : [None, None, 'Dansylglycine', 'Dansylglycine']

Thanks for adding to the docs, til now I've just been updating the examples, but it's a good time to explicitly describe some of the intricacies of using quickmodel in the docs. Hopefully I can take a stab at clarifying and expanding what you've started here over the weekend.

[sonyahanson]

Merging.