Minimal Fixes for --reactive_flexres and --box_center_off_reactive_res

This PR includes some minimal changes and updates of relevant help messages to support --reactive_flexres and --box_center_off_reactive_res and to enable writing of reactive atom types in the output _flex.pdbqt.

The changes are:

1. Fix --reactive_flexres

Before the changes, reactive_flexres (dict) and all_flexres (set) had inconsistent types and were therefore not mergeable by union.

This issue was addressed by first creating a dictionary reactive_flexres_name and then a set reactive_flexres for the interoperability with the existing functions.

The parser parse_residue_string was still used for --reactive_flexres to be able to pass the residue names and compare to the default atom name specification of reactive_atom.

2. Enable writing reactive atom types to _flex.pdbqt

Before the changes, the reactive atom types were not written to the output file _flex.pdbqt.

This issue was resolved with minimal edits, even though PDBQTReceptor.make_flexres_reactive was still used to update flexres_pdbqt for the reactive flexible residues.

3. Uncomment --reactive_name

Before the changes, processing of --reactive_name was commented even though the argument was available.

This issue was resolved with some organization of the codes, to ensure that the options are applied in the following order: (1) --reactive_name may overwrite the default name set of reactive_atom; (2) --reactive_flexres must only contain the residue names that are specified by the default name set; (3) --reactive_name_specific can be used to overwrite an existing or add a new reactive flexible residue.

4. Fix --box_center_off_reactive_res and Clean Up Argument Dependency Evaluations

The changes affected parsing of reactive flexible residues and hereby minor edits to the handling of box_center_off_reactive_res were applied. Additionally, the changes addressed the argument dependency issue that --box_center_off_reactive_res requires box_size. Some redundant argument dependency evaluations were cleaned up.

5. Update help msg

(1) For --flexres, multiple residues may be passed at once and unspecified chain ID should be skipped (no space kept). (2) For --reactive_flexres, the expected syntax after the changes is: -r "A:LYS:100" -r "A:LYS:255" Because parse_residue_string needs exactly 2 delimiters (:), the flag needs to be repeated for each reactive flexible residue. (3) For --box_center_off_reactive_res, it needs exactly one reactive flexible residue and requires box_size.

Two quick tests to validate the above changes

Input: 1d3g_input.zip

(a) Regarding usage of --reactive_flexres, --reactive_name, and --reactive_name_specific mk_prepare_receptor.py --pdb 1d3g_input/1d3g_receptor.pdb --allow_bad_res --reactive_flexres "A:LYS:100" --reactive_flexres "A:LYS:255" --flexres "A:145,356" --ligand 1d3g_input/1d3g_FMN.pdb --padding 2 --reactive_name "LYS:CG" --reactive_name_specific "A:LYS:255:NZ" --output_filename 1d3g_output_a

Output: output_a.zip

(b) Regarding the use of --box_center_off_reactive_res mk_prepare_receptor.py --pdb 1d3g_input/1d3g_receptor.pdb --allow_bad_res --reactive_flexres "A:LYS:255" --reactive_name "LYS:CG" --flexres "A:145,356" --box_center_off_reactive_res --box_size 50 50 50 -o 1d3g_output_b

Output: output_b.zip

forlilab / Meeko