Do pseudocode of how loader constructs site tags short names

[phraenquex]

@kaliif Document here the rules by which the short tag name of the various site tags are constructed by the loader.

Use the style of #1466 (could copy-paste from the original spec in #1277)

@mwinokan use that to update the XCA readme.

[phraenquex]

@kaliif first needs to know if the tags are now fixed (#1466). That requires Ryan to uploade - @max will coordinate.

[mwinokan]

A71EV2A is not a great example of the CrystalformSites, and CHIKV_Mac will be better. As CHIKV_Mac is blocked by #1477, @kaliif please go ahead with what you currently have

[kaliif]

Tags generated by target loader:

• Canon sites:
  Site data:

  A71EV2A-x0379+A+147+1:
    centroid_res: A71EV2A-x0379/A/38/A
    conformer_site_ids: [A71EV2A-x0379+A+147+1]
    global_reference_dtag: A71EV2A-x0528
    reference_conformer_site_id: A71EV2A-x0379+A+147+1
    residues: [A/81/LEU, A/38/ARG, A/90/TYR, A/39/ASP, A/34/GLU, A/95/GLN, A/93/ARG,
      A/96/SER, A/41/LEU, A/37/SER, A/28/TRP, A/33/TRP, A/94/TYR, A/36/SER, A/31/LEU,
      A/35/ASP, A/97/HIS, A/40/LEU, A/20/ARG]
  

  Sites are enumerated (in no particular order): ID = 1,2...
  Tag scheme: f'{ID} - {centroid_res}'
  Ex: 2 - A71EV2A-x0379/A/38/A
• Conformer sites:
  Site data:

  A71EV2A-x0202+A+201+1:
    members: [A71EV2A-x0202/A/201/1]
    reference_ligand_id: A71EV2A-x0202/A/201/1
    residues: [A/64/TYR, A/65/CYS, A/68/ARG, A/71/HIS, A/67/SER, A/72/TYR, A/70/LYS,
      A/66/SER, A/69/ARG]
  

  Sites are grouped by canon site and enumerated (in no particular order): ID = a,b...
  short name: A71EV2A-x0202+A+201+1 -> A71EV2A-x0202
  Tag scheme: f'{canon site ID}{ID} - {short name}'
  Ex: 8a - A71EV2A-x0202
• Quat assemblies:
  Assembly data:

  monomer:
      reference: A71_2A_x0090_ref_7_monomer
      biomol: A
      chains: A
  

  Sites are enumerated (in no particular order): ID = 1,2...
  Tag scheme: f'A{ID} - {assembly name}
  Ex: A1 - monomer
• Crystalforms:
  Site data:

  A71_2A_open:
    xtalform_ref: A71_2A_x0090_ref_7_monomer
    xtalform_space_group: C 1 2 1
    xtalform_cell: {a: 86.98, b: 56.66, c: 32.62, alpha: 90.0, beta: 95.68, gamma: 90.0}
  

  Sites are enumerated (in no particular order): ID = 1,2...
  Tag scheme: f'F{ID} - {crystalform name}'
  Ex: F1 - A71_2A_open
• Crystalform sites:
  Site data:

  A71EV2A-x0269/A/147/1:
    canonical_site_id: A71EV2A-x0395+A+148+1
    crystallographic_chain: A
    members: [A71EV2A-x0269/A/147/1, A71EV2A-x0152/A/201/1, A71EV2A-x0194/A/147/1,
      A71EV2A-x0202/A/147/1, A71EV2A-x0341/A/147/1, A71EV2A-x0375/A/147/1, A71EV2A-x0395/A/147/1,
      A71EV2A-x0395/A/148/1, A71EV2A-x0831/A/147/1, A71EV2A-x1105/A/147/1, A71EV2A-x1105/A/148/1]
    xtalform_id: A71_2A_open    
  

  chain letter: A71EV2A-x0269/A/147/1 -> A
  Sites are ordered by number of site observations and enumerated alphabetically starting from the chain letter: ID = chain letter,...
  crystalform site name sans version: A71EV2A-x0269/A/147/1 -> A71EV2A-x0269/A/147
  Tag scheme: f'F{crystalform ID}{ID} - {crystalform site name sans version}'
  Ex: F1d - A71EV2A-x0269/A/147

[mwinokan]

@phraenquex will take a closer look at the pseudocode before it goes into the xca/USER_GUIDE (maybe linked but not embedded directly)

[kaliif]

Tag generation updated (as per the comment in #1482's thread here)

Tags generated by target loader:

• Canon sites:
  Site data:

  A71EV2A-x0379+A+147+1:
    centroid_res: A71EV2A-x0379/A/38/A
    conformer_site_ids: [A71EV2A-x0379+A+147+1]
    global_reference_dtag: A71EV2A-x0528
    reference_conformer_site_id: A71EV2A-x0379+A+147+1
    residues: [A/81/LEU, A/38/ARG, A/90/TYR, A/39/ASP, A/34/GLU, A/95/GLN, A/93/ARG,
      A/96/SER, A/41/LEU, A/37/SER, A/28/TRP, A/33/TRP, A/94/TYR, A/36/SER, A/31/LEU,
      A/35/ASP, A/97/HIS, A/40/LEU, A/20/ARG]
  

  Sites are enumerated (in no particular order): ID = 1,2...
  Tag scheme: f'{ID} - {name}'
  Ex: 2 - A71EV2A-x0379+A+147+1
• Conformer sites:
  Site data:

  A71EV2A-x0202+A+201+1:
    members: [A71EV2A-x0202/A/201/1]
    reference_ligand_id: A71EV2A-x0202/A/201/1
    residues: [A/64/TYR, A/65/CYS, A/68/ARG, A/71/HIS, A/67/SER, A/72/TYR, A/70/LYS,
      A/66/SER, A/69/ARG]
  

  Sites are grouped by canon site and enumerated (in no particular order): ID = a,b...
  Tag scheme: f'{canon site ID}{ID} - {name}'
  Ex: 8a - A71EV2A-x0202+A+201+1
• Quat assemblies:
  Assembly data:

  monomer:
      reference: A71_2A_x0090_ref_7_monomer
      biomol: A
      chains: A
  

  Sites are enumerated (in no particular order): ID = 1,2...
  Tag scheme: f'A{ID} - {assembly name}
  Ex: A1 - monomer
• Crystalforms:
  Site data:

  A71_2A_open:
    xtalform_ref: A71_2A_x0090_ref_7_monomer
    xtalform_space_group: C 1 2 1
    xtalform_cell: {a: 86.98, b: 56.66, c: 32.62, alpha: 90.0, beta: 95.68, gamma: 90.0}
  

  Sites are enumerated (in no particular order): ID = 1,2...
  Tag scheme: f'F{ID} - {crystalform name}'
  Ex: F1 - A71_2A_open
• Crystalform sites:
  Site data:

  A71EV2A-x0269/A/147/1:
    canonical_site_id: A71EV2A-x0395+A+148+1
    crystallographic_chain: A
    members: [A71EV2A-x0269/A/147/1, A71EV2A-x0152/A/201/1, A71EV2A-x0194/A/147/1,
      A71EV2A-x0202/A/147/1, A71EV2A-x0341/A/147/1, A71EV2A-x0375/A/147/1, A71EV2A-x0395/A/147/1,
      A71EV2A-x0395/A/148/1, A71EV2A-x0831/A/147/1, A71EV2A-x1105/A/147/1, A71EV2A-x1105/A/148/1]
    xtalform_id: A71_2A_open    
  

  chain letter: A71EV2A-x0269/A/147/1 -> A
  Sites are ordered by number of site observations and enumerated alphabetically starting from the chain letter: ID = chain letter,...
  Tag scheme: f'F{crystalform ID}{ID} - {crystalform site name}'
  Ex: F1d - A71EV2A-x0269/A/147/1

[mwinokan]

@Waztom please check this against the new diagram and update documentation (w/ @phraenquex )