Adds support for converting small molecule structure formats (MOL2, SDF, PDB) to SMILES, addressing the requested feature for cheminformatics format interconversion.

Changes

• New converters

  • mol22smiles.py (MOL22SMILES) — Tripos MOL2 → SMILES
  • sdf2smiles.py (SDF2SMILES) — MDL SDF → SMILES (handles multi-molecule files)
  • pdb2smiles.py (PDB2SMILES) — PDB (small molecule/ligand) → SMILES

  Each converter exposes two methods: rdkit (default) and openbabel.

• Extensions — Added mol2, sdf, and smiles entries to core/extensions.py

• Test data — Added aspirin in MOL2, SDF, and PDB formats under test/data/

Usage

from bioconvert.mol22smiles import MOL22SMILES
from bioconvert.sdf2smiles import SDF2SMILES
from bioconvert.pdb2smiles import PDB2SMILES

MOL22SMILES("ligand.mol2", "out.smi")()
SDF2SMILES("compounds.sdf", "out.smi")()
PDB2SMILES("ligand.pdb", "out.smi")()
# or specify method explicitly:
SDF2SMILES("compounds.sdf", "out.smi")(method="openbabel")

Naming note: The MOL2 converter follows the existing BZ22GZ convention — double 2 in class/filename (MOL22SMILES) so the metaclass correctly parses MOL2 as the input format rather than splitting on the first 2.

• Fixes PDB to FASTA or small molecules (MOL2, PDB, SDF to SMILES) #304

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