Passing a list of filtering residues to MSout_np class of module MCCE4-Tools/mcce4_tools/mcce4/Msout_np.py

[CatChenal]

RE: MSout_np class with list of residues for filtering.

This class is used by the ms_protonation and ms_top2pdbs tools.
Source: MCCE4-Tools/mcce4_tools/mcce4/Msout_np.py

Current behavior:

• The user-given list ('res_kinds') is a list of 3-letter residue codes, e.g. HIS, GLU...;
• The function that creates the lookup numpy array (get_conf_info) checks whether 'kind',
  defined as the first 3 characters of head3.lst's confids, is in the list.

Feature request:

MSout_np can accept any kind of "residues" for filtering.

Minimal implementation of feature:

If get_conf_info is given a filtering list, the length of its FIRST ITEM determines what 'kind' is.
The list can be built using at least the first 3 letters of any head3.lst confid, up to the 14 maximum.
Thus, if len_1 == 3, then filtering is over residue kinds (current behavior), while if len_1 == 14, the filtering is done at the specific conformer id.

Caveat: The selection scheme reflected in the list must be consistent (i.e. no items with differing lengths), but this can be checked in the Msout.validate_kwargs function.

Examples:

Example with same list:

  res_kinds = ["HIS", "GLU"]

  len_1 = len(res_kinds[0])
  kind = confid[:len_1]         # == confid[:3]

Outcome : Current outcome.

Examples with new outcomes:

1. Specific residues in different chains:

 res_kinds = ["HIS+1A", "GLU-1B"]             # or ["HIS01A", "HIS+1A", "GLU-1B"] to get all HIS in A

 len_1 = len(res_kinds[0])
 kind = confid[:len_1]         # == confid[:6]

Outcome : Filtering for all charged:
- HIS in chain A
- GLU in chain B

2. Specific residues in (different chains) with a sequence range:

 res_kinds = ["HIS+1A0", "GLU-1B1"]        # or ["HIS+1A0", "GLU-1A1"]

 len_1 = len(res_kinds[0])
 kind = confid[:len_1]         # == confid[:7]

Outcome : Filtering for all charged:
- HIS in chain A with seqnum <= 999
- GLU in chain B with seqnum >= 1000