BioPipelines Tool Index (SI)¶
Single-source-of-truth listing for every public-API tool. Generated from TOOL_NAME / TOOL_VERSION in biopipelines/*.py and grouped by the categories in tool_reference.md.
Public-API count: 75 (80 TOOL_NAME entries in the codebase, minus 4 internal helpers — BoltzGenMerge, BoltzGenImport, RFDAA_PrepareLigand, Mock — and 2 base-class scaffolding entries: base, install).
| # | Tool | Category | Version | Source file |
|---|---|---|---|---|
| 1 | BoltzGen | Structure Generation | 1.0 | biopipelines/boltzgen.py |
| 2 | PocketGen | Structure Generation | 1.0 | biopipelines/pocketgen.py |
| 3 | RFdiffusion | Structure Generation | 1.0 | biopipelines/rfdiffusion.py |
| 4 | RFdiffusion3 | Structure Generation | 1.0 | biopipelines/rfdiffusion3.py |
| 5 | RFdiffusionAllAtom | Structure Generation | 1.0 | biopipelines/rfdiffusion_allatom.py |
| 6 | DNAEncoder | Sequence Design | 1.0 | biopipelines/dna_encoder.py |
| 7 | Frame2Seq | Sequence Design | 1.0 | biopipelines/frame2seq.py |
| 8 | Fuse | Sequence Design | 1.0 | biopipelines/fuse.py |
| 9 | LigandMPNN | Sequence Design | 1.0 | biopipelines/ligand_mpnn.py |
| 10 | Mutagenesis | Sequence Design | 1.0 | biopipelines/mutagenesis.py |
| 11 | MutationComposer | Sequence Design | 1.0 | biopipelines/mutation_composer.py |
| 12 | ProteinMPNN | Sequence Design | 1.0 | biopipelines/protein_mpnn.py |
| 13 | RBSDesigner | Sequence Design | 1.0 | biopipelines/rbs_designer.py |
| 14 | StitchSequences | Sequence Design | 1.0 | biopipelines/stitch_sequences.py |
| 15 | AlphaFold | Structure Prediction & Docking | 1.0 | biopipelines/alphafold.py |
| 16 | Boltz2 | Structure Prediction & Docking | 1.0 | biopipelines/boltz2.py |
| 17 | DiffDock | Structure Prediction & Docking | 1.0 | biopipelines/diffdock.py |
| 18 | DynamicBind | Structure Prediction & Docking | 1.0 | biopipelines/dynamicbind.py |
| 19 | ESMFold | Structure Prediction & Docking | 1.0 | biopipelines/esmfold.py |
| 20 | Gnina | Structure Prediction & Docking | 1.0 | biopipelines/gnina.py |
| 21 | NeuralPLexer | Structure Prediction & Docking | 1.0 | biopipelines/neuralplexer.py |
| 22 | PLACER | Structure Prediction & Docking | 1.0 | biopipelines/placer.py |
| 23 | ADMETAI | Analysis | 1.0 | biopipelines/admet_ai.py |
| 24 | AF2BIND | Analysis | 1.0 | biopipelines/af2bind.py |
| 25 | Aggrescan3D | Analysis | 1.0 | biopipelines/aggrescan3d.py |
| 26 | Angle | Analysis | 1.0 | biopipelines/angle.py |
| 27 | APBS | Analysis | 1.0 | biopipelines/apbs.py |
| 28 | BioEmu | Analysis | 1.0 | biopipelines/bioemu.py |
| 29 | CABSflex | Analysis | 1.0 | biopipelines/cabsflex.py |
| 30 | ConformationalChange | Analysis | 1.0 | biopipelines/conformational_change.py |
| 31 | Consensus | Analysis | 1.0 | biopipelines/consensus.py |
| 32 | Contacts | Analysis | 1.0 | biopipelines/contacts.py |
| 33 | Distance | Analysis | 1.0 | biopipelines/distance.py |
| 34 | DistanceSelector | Analysis | 1.0 | biopipelines/distance_selector.py |
| 35 | DSSP | Analysis | 1.0 | biopipelines/dssp.py |
| 36 | EnsembleAnalysis | Analysis | 1.0 | biopipelines/ensemble_analysis.py |
| 37 | FPocket | Analysis | 1.0 | biopipelines/fpocket.py |
| 38 | GEMS | Analysis | 1.0 | biopipelines/gems.py |
| 39 | OpenMM | Analysis | 1.0 | biopipelines/openmm.py |
| 40 | P2Rank | Analysis | 1.0 | biopipelines/p2rank.py |
| 41 | PLIP | Analysis | 1.0 | biopipelines/plip.py |
| 42 | PLM_Sol | Analysis | 1.0 | biopipelines/plm_sol.py |
| 43 | PoseBusters | Analysis | 1.0 | biopipelines/posebusters.py |
| 44 | PoseChange | Analysis | 1.0 | biopipelines/pose_change.py |
| 45 | Prodigy | Analysis | 1.0 | biopipelines/prodigy.py |
| 46 | ProLIF | Analysis | 1.0 | biopipelines/prolif.py |
| 47 | Reduce | Analysis | 1.0 | biopipelines/reduce.py |
| 48 | RTMScore | Analysis | 1.0 | biopipelines/rtmscore.py |
| 49 | SASA | Analysis | 1.0 | biopipelines/sasa.py |
| 50 | ThermoMPNN | Analysis | 1.0 | biopipelines/thermompnn.py |
| 51 | VespaG | Analysis | 1.0 | biopipelines/vespag.py |
| 52 | XTB | Analysis | 1.0 | biopipelines/xtb.py |
| 53 | OpenBabel | Cheminformatics | 1.1 | biopipelines/openbabel.py |
| 54 | RDKit | Cheminformatics | 1.0 | biopipelines/rdkit_descriptors.py |
| 55 | BayesianAdjuster | Sequence Statistics | 1.0 | biopipelines/bayesian_adjuster.py |
| 56 | MutationProfiler | Sequence Statistics | 1.0 | biopipelines/mutation_profiler.py |
| 57 | SequenceMetricCorrelation | Sequence Statistics | 1.0 | biopipelines/sequence_metric_correlation.py |
| 58 | ExtractMetrics | Data Management | 1.0 | biopipelines/extract_metrics.py |
| 59 | Panda | Data Management | 1.0 | biopipelines/panda.py |
| 60 | Pool | Data Management | 1.0 | biopipelines/pool.py |
| 61 | ReMap | Data Management | 1.0 | biopipelines/remap.py |
| 62 | Selection | Data Management | 1.0 | biopipelines/selection.py |
| 63 | MMseqs2 | MSAs | 1.0 | biopipelines/mmseqs2.py |
| 64 | MMseqs2Server | MSAs | 1.0 | biopipelines/mmseqs2.py |
| 65 | MSA | MSAs | 1.0 | biopipelines/msa.py |
| 66 | CompoundLibrary | Inputs & I/O | 1.0 | biopipelines/compound_library.py |
| 67 | Ligand | Inputs & I/O | 1.0 | biopipelines/ligand.py |
| 68 | Load | Inputs & I/O | 1.0 | biopipelines/load.py |
| 69 | PDB | Inputs & I/O | 1.0 | biopipelines/pdb.py |
| 70 | Plot | Inputs & I/O | 1.0 | biopipelines/plot.py |
| 71 | PyMOL | Inputs & I/O | 1.0 | biopipelines/pymol.py |
| 72 | RCSB | Inputs & I/O | 1.0 | biopipelines/rcsb.py |
| 73 | Sequence | Inputs & I/O | 1.0 | biopipelines/sequence.py |
| 74 | Table | Inputs & I/O | 1.0 | biopipelines/table.py |
| 75 | UniProt | Inputs & I/O | 1.0 | biopipelines/uniprot.py |
Internal / auxiliary classes (not user-facing)¶
These appear as TOOL_NAME = ... for code-reuse but are not part of the advertised public API:
| Tool | Role | Source file |
|---|---|---|
| Mock | Test-only stub-output generator (used by the pytest suite) | biopipelines/mock.py |
| BoltzGenMerge | Internal post-processing step of BoltzGen workflow | biopipelines/boltzgen.py |
| BoltzGenImport | Internal import step of BoltzGen workflow | biopipelines/boltzgen.py |
| RFDAA_PrepareLigand | Ligand preparation helper for RFdiffusionAllAtom | biopipelines/rfdiffusion_allatom.py |
base | BaseConfig scaffolding marker | biopipelines/base_config.py |
install | Dynamic per-tool installation marker | biopipelines/base_config.py |