Doc updates for new features in changelog (2024.11 - 2025.5)

[rwxayheee]

The PR adds some doc updates for new features in changelog (2024.11 - 2025.5):

• Fix mk_prepare_ligand.py --add_atom_types (Fix mk_prepare_ligand.py --add_atom_types #350) by @diogomart [https://github.com/Fix mk_prepare_ligand.py --add_atom_types #350] (merged 2025-04-23T21:01:11Z)
• add icode to BEGIN_RES (add icode to BEGIN_RES #349) by @diogomart [https://github.com/add icode to BEGIN_RES #349] (merged 2025-04-23T21:30:00Z)
• rigidify triple bonds (rigidify single bonds in single-triple-single) (rigidify triple bonds (rigidify single bonds in single-triple-single) #348) by @diogomart [https://github.com/rigidify triple bonds (rigidify single bonds in single-triple-single) #348] (merged 2025-04-23T22:55:34Z)
• Forgive extra interresidue bonds (Forgive extra interresidue bonds #347) by @diogomart [https://github.com/Forgive extra interresidue bonds #347] (merged 2025-04-23T17:26:39Z)
• remove unused Atom.interaction_vectors (remove unused Atom.interaction_vectors #346) by @diogomart [https://github.com/remove unused Atom.interaction_vectors #346] (merged 2025-04-23T06:32:58Z)
• espaloma torsion potentials in kcal/mol, not kJ/mol (espaloma torsion potentials in kcal/mol, not kJ/mol #342) by @diogomart [https://github.com/espaloma torsion potentials in kcal/mol, not kJ/mol #342] (merged 2025-04-22T06:28:08Z)
• Improve test coverage for chemtempgen.py (Improve test coverage for chemtempgen.py #340) by @rwxayheee [https://github.com/Improve test coverage for chemtempgen.py #340] (merged 2025-04-18T15:49:32Z)
• Remove attribute MoleculeSetup.is_sidechain (Remove attribute MoleculeSetup.is_sidechain #339) by @diogomart [https://github.com/Remove attribute MoleculeSetup.is_sidechain #339] (merged 2025-04-12T02:13:33Z)
• add NumPy-style, Sphinx-compliant docstring to chemtempgen.py (add NumPy-style, Sphinx-compliant docstring to chemtempgen.py #337) by @rwxayheee [https://github.com/add NumPy-style, Sphinx-compliant docstring to chemtempgen.py #337] (merged 2025-04-11T07:07:38Z)
• Add capping group NHE to residue_chem_templates.json (Add capping group NHE to residue_chem_templates.json #336) by @rwxayheee [https://github.com/Add capping group NHE to residue_chem_templates.json #336] (merged 2025-04-11T15:22:31Z)
• Making Ala Gly Pro flexible doesn't raise error, simply writes to rigid part (Making Ala Gly Pro flexible doesn't raise error, simply writes to rigid part #332) by @diogomart [https://github.com/Making Ala Gly Pro flexible doesn't raise error, simply writes to rigid part #332] (merged 2025-03-28T00:56:56Z)
• Use warnings or logger rather than print (Use warnings or logger rather than print #328) by @k-ujihara [https://github.com/Use warnings or logger rather than print #328] (merged 2025-04-22T23:04:28Z)
• Small Bugfixes in closed PR Improve basic support for elements (single-atom residues, metal, noble gas) that are unsupported by ad4 #259 (Small Bugfixes in closed PR #259 #325) by @rwxayheee [https://github.com/Small Bugfixes in closed PR #259 #325] (merged 2025-03-29T15:32:03Z)
• Remove all uppercase types CL and BR from GPF file (Remove all uppercase types CL and BR from GPF file #315) by @diogomart [https://github.com/Remove all uppercase types CL and BR from GPF file #315] (merged 2025-01-30T07:01:43Z)
• added function stitch from PR188, with options residues_to_add and bonds_to_use (added function stitch from PR188, with options residues_to_add and bonds_to_use #306) by @rwxayheee [https://github.com/added function stitch from PR188, with options residues_to_add and bonds_to_use #306] (merged 2025-04-01T04:06:36Z)
• Ranking passed templates by H_excess if tied with H_missing (Ranking passed templates by H_excess if tied with H_missing #301) by @rwxayheee [https://github.com/Ranking passed templates by H_excess if tied with H_missing #301] (merged 2025-03-29T15:31:43Z)
• Adjust positions of hydrogen isotopes as if they were regular Hs (Adjust positions of hydrogen isotopes as if they were regular Hs #296) by @rwxayheee [https://github.com/Adjust positions of hydrogen isotopes as if they were regular Hs #296] (merged 2025-01-10T20:05:18Z)
• Introduce a base class for classes with JSON-interchange functions (Introduce a base class for classes with JSON-interchange functions #292) by @rwxayheee [https://github.com/Introduce a base class for classes with JSON-interchange functions #292] (merged 2025-01-12T03:31:47Z)
• minor fixes and minor clean up (minor fixes and minor clean up #289) by @diogomart [https://github.com/minor fixes and minor clean up #289] (merged 2024-12-17T18:20:45Z)
• --cache_templates for mk_prepare_receptor.py (--cache_templates for mk_prepare_receptor.py #287) by @rwxayheee [https://github.com/--cache_templates for mk_prepare_receptor.py #287] (merged 2025-04-22T23:03:05Z)
• Polymer from PQR (Polymer from PQR #285) by @rwxayheee [https://github.com/Polymer from PQR #285] (merged 2025-04-15T06:04:52Z)
• Remove from class Ring the unused attributes to reduce overhead in molecule preparation (Remove from class Ring the unused attributes to reduce overhead in molecule preparation #276) by @rwxayheee [https://github.com/Remove from class Ring the unused attributes to reduce overhead in molecule preparation #276] (merged 2024-12-11T02:45:08Z)
• Remove dependencies from setup.py (Remove dependencies from setup.py #274) by @diogomart [https://github.com/Remove dependencies from setup.py #274] (merged 2024-12-10T08:28:27Z)
• Catch prepare errors without interrupting batch processing (Catch prepare errors without interrupting batch processing #272) by @rwxayheee [https://github.com/Catch prepare errors without interrupting batch processing #272] (merged 2024-12-09T23:26:32Z)
• don't max out substructure matches at 1000 (don't max out substructure matches at 1000 #270) by @diogomart [https://github.com/don't max out substructure matches at 1000 #270] (merged 2024-12-09T18:48:53Z)
• Format string in output file with plain line-ending character instead of os.linesep (Format string in output file with plain line-ending character instead of os.linesep #266) by @rwxayheee [https://github.com/Format string in output file with plain line-ending character instead of os.linesep #266] (merged 2024-12-07T01:25:57Z)
• docs: cli args override config file params (docs: cli args override config file params #265) by @diogomart [https://github.com/docs: cli args override config file params #265] (merged 2024-12-07T01:02:38Z)
• Merge release to develop (Merge release to develop #263) by @rwxayheee [https://github.com/Merge release to develop #263] (merged 2024-12-02T22:38:25Z)
• Read Partial Charges from mol2 and SDF (Read Partial Charges from mol2 and SDF #258) by @rwxayheee [https://github.com/Read Partial Charges from mol2 and SDF #258] (merged 2024-12-06T23:03:01Z)
• Use utility functions in jsonutils to fix Can't serialize MoleculeSetup dihedrals to JSON #151 (Use utility functions in jsonutils to fix #151 #257) by @rwxayheee [https://github.com/Use utility functions in jsonutils to fix #151 #257] (merged 2024-12-04T19:07:51Z)

[rwxayheee]

Summary

1. Added a new post for receptor preparation, similar to the existing Basic Usage post for ligand preparation.
   Preview: https://apidocmeeko.readthedocs.io/en/doc_update_for_changelog/rec_prep_basic.html

This is intended to cover (or briefly mention the updates in) #209, #285 and #292

2 Added an additional section for ligand preparation for reading precomputed charges in ligand preparation.
Preview: https://apidocmeeko.readthedocs.io/en/doc_update_for_changelog/lig_prep_basic.html

This is intended to cover #258