RNA Structure & Ligand Analysis Toolkit

This toolkit provides a collection of automated Python scripts for RNA structure processing, sequence/ligand feature extraction, and batch analysis.

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Requirements

Install the core dependencies with:

pip install -r requirements.txt

Note:

For 3D visualization and file conversion, you may also need to install PyMOL and OpenBabel as system tools (conda install -c conda-forge openbabel pymol-open-source).

For parallel processing, joblib is used. RDKit is best installed via conda if possible.

📁 Tool Overview

File Name	Brief Description
remove_h_pymol.py	Remove hydrogen atoms from PDB files using PyMOL.
merge_rna_ligand.py	Merge separate RNA and ligand PDB files into a single structure.
generate_contact_map.py	Calculate RNA–ligand contact maps based on atomic distances.
split_rna.py	Split PDB/CIF structures into RNA, ligand, and protein components.
convert_cif2pdb.py	Convert mmCIF to PDB format, keeping chain info.
separate_rna_and_small_molecules_no_water_ions_residues_6Angs_CSVfile.py	Extract RNA and small molecules (exclude water/ions) within 6Å. Batch processing via CSV.
AddH_pymol_save_pdbqt_obabel_parallel_HPC.py	Add hydrogens & convert to PDBQT using PyMOL + OpenBabel, parallel HPC support.
get_sequences.py	Extract RNA sequences (FASTA) or ligand SMILES from structures.
AddH_pymol.py	Add hydrogens to PDB structure via PyMOL.
get_ligands_smiles_fingerprint.py	Extract ligand SMILES & generate RDKit fingerprints.

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Pipeline Overview

These tools can be combined for a full RNA-ligand structural workflow:

1. Split complex structures: split_rna.py
2. Standardize structures: remove_h_pymol.py → AddH_pymol.py
3. Merge components: merge_rna_ligand.py
4. Generate features: generate_contact_map.py, get_sequences.py, get_ligands_smiles_fingerprint.py
5. Batch/high-throughput: Use parallel scripts for scaling (AddH_pymol_save_pdbqt_obabel_parallel_HPC.py, CSV-driven tools).