CITATION.cff
LICENSE
MANIFEST.in
NOTICE
README.md
pyproject.toml
setup.py
bin/install-nplinker-deps
src/nplinker/__init__.py
src/nplinker/arranger.py
src/nplinker/config.py
src/nplinker/defaults.py
src/nplinker/loader.py
src/nplinker/logger.py
src/nplinker/nplinker.py
src/nplinker/spec_clustering.py
src/nplinker/utils.py
src/nplinker.egg-info/PKG-INFO
src/nplinker.egg-info/SOURCES.txt
src/nplinker.egg-info/dependency_links.txt
src/nplinker.egg-info/requires.txt
src/nplinker.egg-info/top_level.txt
src/nplinker/class_info/__init__.py
src/nplinker/class_info/chem_classes.py
src/nplinker/class_info/class_matches.py
src/nplinker/class_info/runcanopus.py
src/nplinker/data/MIBiG2.0_compounds_with_AS_BGC_CF_NPC_classes.txt
src/nplinker/data/matched_mibig_gnps_update.csv
src/nplinker/data/matched_mibig_gnps_update.mgf
src/nplinker/data/nplinker.toml
src/nplinker/genomics/__init__.py
src/nplinker/genomics/aa_pred.py
src/nplinker/genomics/abc.py
src/nplinker/genomics/bgc.py
src/nplinker/genomics/gcf.py
src/nplinker/genomics/utils.py
src/nplinker/genomics/antismash/__init__.py
src/nplinker/genomics/antismash/antismash_downloader.py
src/nplinker/genomics/antismash/antismash_loader.py
src/nplinker/genomics/antismash/podp_antismash_downloader.py
src/nplinker/genomics/bigscape/__init__.py
src/nplinker/genomics/bigscape/bigscape_loader.py
src/nplinker/genomics/bigscape/runbigscape.py
src/nplinker/genomics/mibig/__init__.py
src/nplinker/genomics/mibig/mibig_downloader.py
src/nplinker/genomics/mibig/mibig_loader.py
src/nplinker/genomics/mibig/mibig_metadata.py
src/nplinker/metabolomics/__init__.py
src/nplinker/metabolomics/abc.py
src/nplinker/metabolomics/molecular_family.py
src/nplinker/metabolomics/spectrum.py
src/nplinker/metabolomics/utils.py
src/nplinker/metabolomics/gnps/__init__.py
src/nplinker/metabolomics/gnps/gnps_annotation_loader.py
src/nplinker/metabolomics/gnps/gnps_downloader.py
src/nplinker/metabolomics/gnps/gnps_extractor.py
src/nplinker/metabolomics/gnps/gnps_file_mapping_loader.py
src/nplinker/metabolomics/gnps/gnps_format.py
src/nplinker/metabolomics/gnps/gnps_molecular_family_loader.py
src/nplinker/metabolomics/gnps/gnps_spectrum_loader.py
src/nplinker/parsers/__init__.py
src/nplinker/parsers/kcb.py
src/nplinker/schemas/__init__.py
src/nplinker/schemas/genome_bgc_mappings_schema.json
src/nplinker/schemas/genome_status_schema.json
src/nplinker/schemas/podp_adapted_schema.json
src/nplinker/schemas/strain_mappings_schema.json
src/nplinker/schemas/user_strains.json
src/nplinker/scoring/__init__.py
src/nplinker/scoring/abc.py
src/nplinker/scoring/link_graph.py
src/nplinker/scoring/metcalf_scoring.py
src/nplinker/scoring/np_class_scoring.py
src/nplinker/scoring/rosetta_scoring.py
src/nplinker/scoring/score.py
src/nplinker/scoring/scoring_method.py
src/nplinker/scoring/utils.py
src/nplinker/scoring/iokr/IOKR_deprecated.py
src/nplinker/scoring/iokr/__init__.py
src/nplinker/scoring/iokr/build_input_matrix.py
src/nplinker/scoring/iokr/build_test_matrix.py
src/nplinker/scoring/iokr/formula.py
src/nplinker/scoring/iokr/iokr.py
src/nplinker/scoring/iokr/iokr_opt.py
src/nplinker/scoring/iokr/iokrdata.py
src/nplinker/scoring/iokr/mk_fprints.py
src/nplinker/scoring/iokr/nplinker_iokr.py
src/nplinker/scoring/iokr/run_iokr.py
src/nplinker/scoring/iokr/run_iokr_novel.py
src/nplinker/scoring/iokr/spectrum.py
src/nplinker/scoring/iokr/spectrum_filters.py
src/nplinker/scoring/rosetta/__init__.py
src/nplinker/scoring/rosetta/rosetta.py
src/nplinker/scoring/rosetta/rosetta_functions.py
src/nplinker/scoring/rosetta/rosetta_hit.py
src/nplinker/scoring/rosetta/spec_lib.py
src/nplinker/strain/__init__.py
src/nplinker/strain/strain.py
src/nplinker/strain/strain_collection.py
src/nplinker/strain/utils.py