├── BFmonitor ├── BFmonitor.md ├── __pycache__ │ ├── generic_utils.cpython-310.pyc │ ├── generic_utils.cpython-39.pyc │ ├── hits_utils.cpython-310.pyc │ ├── hits_utils.cpython-39.pyc │ ├── plotting_utils.cpython-310.pyc │ ├── plotting_utils.cpython-39.pyc │ └── utils.cpython-39.pyc ├── assets │ └── styles.css ├── figures │ ├── Extraction.png │ ├── Live_Watcher.png │ ├── Pipeline_Tracking.png │ ├── Sidebar.png │ └── binderflow.png └── utils │ ├── __pycache__ │ ├── generic_utils.cpython-310.pyc │ ├── generic_utils.cpython-39.pyc │ ├── hits_utils.cpython-310.pyc │ ├── hits_utils.cpython-39.pyc │ ├── logs_utils.cpython-310.pyc │ ├── plotting_utils.cpython-310.pyc │ ├── plotting_utils.cpython-39.pyc │ └── utils.cpython-39.pyc │ ├── dna_extraction │ └── CT │ │ └── CodonTransformer_seq.py │ ├── generic_utils.py │ ├── hits_utils.py │ └── plotting_utils.py ├── Examples ├── Initial_binder_generation │ ├── input │ │ └── PDL1_trimmed.pdb │ └── input_initial_generation.json ├── Partial_diffusion │ ├── input │ │ └── candidate_1.pdb │ └── input_partial_diff.json └── Sequence_diversity │ ├── input │ └── candidate_1.pdb │ └── input_sequence_diversity.json ├── LICENSE ├── README.md ├── __pycache__ └── BFmonitor.cpython-310.pyc ├── bfmonitor.py ├── binderflow.sh ├── binderflow ├── BinderFlow.md ├── master_scripts │ ├── aligning_filtering.sh │ ├── ending.sh │ ├── pmpnn.sh │ ├── rfd.sh │ └── scoring.sh ├── scripts │ ├── __init__.py │ ├── __pycache__ │ │ ├── __init__.cpython-310.pyc │ │ ├── __init__.cpython-38.pyc │ │ ├── biopython_align.cpython-310.pyc │ │ ├── biopython_align.cpython-38.pyc │ │ ├── biopython_align.cpython-39.pyc │ │ ├── superimpose.cpython-310.pyc │ │ └── superimpose.cpython-39.pyc │ ├── biopython_align.py │ ├── contigs_map_getter.py │ ├── fixing_residues.py │ ├── input_json_reader.py │ ├── json_variable_generation.py │ ├── partial_diffusion_numeration.py │ ├── run_ending.py │ ├── scoring_tools.py │ ├── split_fasta.py │ └── superimpose.py └── slurm_submit │ └── 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