Enable ligand SDF output from `boltz predict`

[weitse-hsu]

Hi, This PR adds support to optionally output ligand-only SDF files when running boltz predict, which is enabled by the flag --ligand_sdf. Separate SDF files will be generated if there are multiple ligands. The file names of the output SDF files follow the pattern {record_id}_model_{rank}_ligand_{chain_id}.sdf. Existing behavior should be unchanged if the flag is not used.