Tags: rdk/p2rank

Bump version to 2.6-alpha

Bump version to 2.6-alpha

Lazy-init EnergyCalculator and LJEnergyCalculator in energy features

Fix ligand detection for BioJava GroupType misclassifications

BioJava assigns GroupType based on its Chemical Component Dictionary,
not structural role. Ligands in non-polymer chains can get any GroupType:
- GDP, GTP, ATP -> GroupType.NUCLEOTIDE
- SHR and similar -> GroupType.AMINOACID
- Most others -> GroupType.HETATM

Previously only HETATM groups were detected as ligands, causing errors
like "Ligand definition 'GDP' matches no ligands" for nucleotide and
amino acid derivative ligands.

Fix: any non-water group in a NONPOLYMER chain is now a ligand
candidate, regardless of GroupType. Polymer chain groups (protein AA,
DNA/RNA) are only included if they have GroupType.HETATM.

Add test PDB files (1a2kC.pdb with GDP, 1e5qA.pdb with SHR) and
comprehensive tests for all three GroupType cases.

Point export improvements: Parquet, compression, refactoring

prepare release 2.5.1

update readme

remove old models

chmod check-dependencies.sh

update formatting on stdout