How yuanhang2024/rdpepper works
RDpepper reconstructs evidence-graded cyclic-peptide chemistry from protein-bound PDB/mmCIF structures or sequence/HELM/MAP/BILN notation, then offers conversion, validation, export, prediction, and docking services. The documented principal structure workflow proceeds through reconstruction routes and chemical graph construction; the shared application layer serves CLI and GUI users. The README documents several capabilities whose implementation details were not sampled, so those modules are shown as distinct service branches without asserting internal call sequences beyond documented responsibilities.
Main entry points: application.py Application services · paths Routes A–H · pipeline.py Pipeline · main.py CLI
Components 22
User interfaces
- CLI
cli/main.py - Desktop GUI
gui/main_window.py - Application services
application.py - Service results
application.py
Reconstruction
- Reconstruction entry
reconstruction.py - Pipeline
pipeline.py - Routes A–H
paths - Structure parsing
core/structure_io.py - Monomer resolution
core/monomer_resolution.py - Peptide graph
core/cyclic_peptide_graph.py - Evidence grading
core/rigor.py
Chemistry services
- Notation conversion
sequence.py - MOL2 validation
core/mol2_format.py - Conformer export
export/conformer_ensemble.py
Ligand preparation
- PDBQT preparation
docking/workflow.py
Analysis and docking
- Structure comparison
compare - ADMET prediction
admet/predictor.py - Vina docking
docking/vina_wrapper.py
Other components
- Researcher
- PDB/mmCIF
- Sequence / notation
- AutoDock Vina
Connections 22
- Researcher → CLI: invokes
- Researcher → Desktop GUI: opens
- PDB/mmCIF → Application services: provides structure
- Sequence / notation → Application services: provides notation
- CLI → Application services: calls services
- Desktop GUI → Application services: calls services
- Application services → Reconstruction entry: requests reconstruction
- Application services → Pipeline: runs workflows
- Reconstruction entry → Routes A–H: selects route
- Routes A–H → Structure parsing: parses structure
- Routes A–H → Monomer resolution: resolves residues
- Routes A–H → Peptide graph: assembles graph
- Peptide graph → Evidence grading: grades evidence
- Application services → Notation conversion: converts notation
- Application services → MOL2 validation: reads and validates
- Application services → Conformer export: exports conformers
- Pipeline → Structure comparison: compares structures
- Pipeline → ADMET prediction: requests predictions
- Application services → PDBQT preparation: prepares ligand
- Application services → Vina docking: requests docking
- Vina docking → AutoDock Vina: runs docking
- Application services → Service results: returns results