* feat: add structure class that loads biotite array and rdkit mol

* feat: update structure class

* feat: update structure class

* fix: fix issues with different aspects of code

* fix: dump python to 3.10 and update pyproject.toml

* feat: add properties extractor classmethod to Structure

* feat: added an actual loader

* chore: fix linting

* feat: re-write loader

* feat: update src/plinder/core/structure/structure.py

* feat: deprecate src/plinder/data/common/constants.py

* feat: deprecate src/plinder/data/structure/atoms.py

* feat: deprecate src/plinder/data/structure/contacts.py

* feat: update src/plinder/core/system/system.py

* feat: update code to match data/structure -> core/structure migration

* feat: move src/plinder/data/utils/diffdock_utils.py to core

* feat: add pinder code to src

* feat: add loader example notebook

* feat: handle exception for alt_structures

* feat: update notebook

* fix: rework structure and loader

* refactor: input_smiles_dict

* ligand input SMILES to conformer to result structure matching

* feat: conformer to hololigand atom mapping

* refactor: make pinder-like structure

* chore: cleanup, linting and typing

* chore: rebase and cleanup

* chore: rebased one more time

* chore: rebase and linting

* fix: minor nit

* chore: type hinting

* fix: more type hinting

* bugfix: results2 vs results reassignment

* change maps to atom stacks

* chore: typing

* chore: even more type hinting

* chore: linting+typing

* chore: fix issues with mask and bad conformer

* chore: fix typing and linting

* style: ruff

* chore: .......

* style: ruff

* chore: linter complaints

* chore: pre-empt versioned docs

* refactor: add/rename system props and fix tests

* fix: plinder system

* fix: drop pinder

* fix: drop biotite<1

* chore: add detailed info to notebook

* chore: add more details to loader notebook

* feat: more resilient ligand confgen + ruff

* chore: type

* chore: add PlinderSystem content

* doc: fix column descriptions

* fix: smiles and linked structure handling

* refactor: dataset

* refactor

* refactor: use validator, rename fields, use PlinderSystem style

* doc: update loader notebook

* doc: update mlsb notebook

* chore: lint

* mods to ligand loading

* updated loader example docs

* chore: linting WIP

* test: add tests

* test: add tests

* add back protein full atom representation

* chore: add full atom representation tosequence

* featurizer fix + typing

* chore: fix tests

* chore: addd test av.zip

* test: add structure test

* feat: add superpose function to Structure

* feat: cleanup

* feat: superimpose

* fix: minor

* fix: guh

* test: atoms module passes

* test: there's no way this is good enough

* feat: add atom array functions

* rm pdb_engine (not used) + dedup superimpose fn + lint

* chore: more lint

* chore: lint WIP

* tests: fix cif file

* modify conformer gen + fix/add tests

* more tests for ligand order stacks

* chore: .gitignore only systems subfolders

* chore: added nonempty zips

* one more try for mount

* feat: cleanup notebook

* docs: update notebooks

* remove apo download

* lint

* make docs build

* fix lexing error

* fix link

* add packages

* remove plinder.data import

* chore: add discord link

---------

Co-authored-by: OleinikovasV <v.oleinikovas@gmail.com>
Co-authored-by: Thomas Duignan <thomas.j.duignan@gmail.com>
Co-authored-by: Ninjani <janani.durairaj@gmail.com>