├── .flake8 ├── .gitignore ├── .pre-commit-config.yaml ├── CONTRIBUTING.md ├── LICENSE.md ├── README.md ├── extn_coeff_fasta ├── AUTHORS.md ├── README.md ├── TEST │ ├── P43220.fasta │ ├── P43220.out │ └── P43220_OUTPUT.csv ├── extn_coeff_fasta.py └── validation_set.csv ├── liabilities ├── LICENSE ├── README.md ├── liabilities.json └── liabilities.py ├── molecular_descriptors └── molecular_descriptors.py ├── pIChemiSt ├── .flake8 ├── LICENSE ├── MANIFEST.in ├── Makefile ├── README.md ├── pichemist │ ├── __init__.py │ ├── api.py │ ├── charges.py │ ├── cli.py │ ├── config.py │ ├── core.py │ ├── data │ │ ├── fasta │ │ │ ├── convert_legacy_gauci_to_original_and_standardised.py │ │ │ ├── convert_legacy_promost_into_standardised.py │ │ │ ├── convert_legacy_short_set_to_original.py │ │ │ ├── convert_original_short_set_to_standardised.py │ │ │ ├── legacy │ │ │ │ ├── aa_legend.tsv │ │ │ │ ├── gauci.py │ │ │ │ ├── promost.py │ │ │ │ └── short_pka_sets.py │ │ │ ├── legacy_conversion.py │ │ │ ├── original_enriched │ │ │ │ └── pka_set_gauci_original.json │ │ │ ├── original_short │ │ │ │ ├── pka_set_bjellqvist_original.json │ │ │ │ ├── pka_set_dawson_original.json │ │ │ │ ├── pka_set_dtaselect_original.json │ │ │ │ ├── pka_set_emboss_original.json │ │ │ │ ├── pka_set_grimsley_original.json │ │ │ │ ├── pka_set_ipc2_peptide_original.json │ │ │ │ ├── pka_set_ipc_peptide_original.json │ │ │ │ ├── pka_set_lehninger_original.json │ │ │ │ ├── pka_set_nozaki_original.json │ │ │ │ ├── pka_set_rodwell_original.json │ │ │ │ ├── pka_set_sillero_original.json │ │ │ │ ├── pka_set_solomon_original.json │ │ │ │ ├── pka_set_thurlkill_original.json │ │ │ │ └── pka_set_toseland_original.json │ │ │ └── standardised │ │ │ │ ├── pka_set_bjellqvist_standardised.json │ │ │ │ ├── pka_set_dawson_standardised.json │ │ │ │ ├── pka_set_dtaselect_standardised.json │ │ │ │ ├── pka_set_emboss_standardised.json │ │ │ │ ├── pka_set_gauci_standardised.json │ │ │ │ ├── pka_set_grimsley_standardised.json │ │ │ │ ├── pka_set_ipc2_peptide_standardised.json │ │ │ │ ├── pka_set_ipc_peptide_standardised.json │ │ │ │ ├── pka_set_lehninger_standardised.json │ │ │ │ ├── pka_set_nozaki_standardised.json │ │ │ │ ├── pka_set_promost_standardised.json │ │ │ │ ├── pka_set_rodwell_standardised.json │ │ │ │ ├── pka_set_sillero_standardised.json │ │ │ │ ├── pka_set_solomon_standardised.json │ │ │ │ ├── pka_set_thurlkill_standardised.json │ │ │ │ └── pka_set_toseland_standardised.json │ │ └── smarts │ │ │ ├── convert_legacy_aa_smarts_to_standardised.py │ │ │ ├── convert_legacy_ss_smarts_to_standardised.py │ │ │ ├── legacy │ │ │ ├── smarts_naturalAAs.py │ │ │ ├── smarts_notes.py │ │ │ ├── smarts_pKaMatcher.dat │ │ │ └── smarts_pKaMatcher.py │ │ │ └── standardised │ │ │ ├── aa_smarts_set_standardised.json │ │ │ └── ss_smarts_set_standardised.json │ ├── fasta │ │ ├── __init__.py │ │ ├── helpers.py │ │ ├── matcher.py │ │ ├── pka_sets.py │ │ ├── scrambler.py │ │ └── smarts.py │ ├── io.py │ ├── isoelectric.py │ ├── model.py │ ├── molecule.py │ ├── pka │ │ ├── __init__.py │ │ ├── acd.py │ │ ├── pkamatcher.py │ │ └── utils.py │ ├── plot.py │ ├── smarts │ │ ├── __init__.py │ │ └── pka_set.py │ ├── stats.py │ └── utils.py ├── setup.cfg ├── setup.py └── test │ ├── examples │ ├── aa_smarts_pka_set_expected.json │ ├── fasta_pka_sets_expected.json │ ├── payload.fasta │ ├── payload_1.smi │ ├── payload_1_out.csv │ ├── payload_1_out.json │ ├── payload_1_out.sdf │ ├── payload_1_out.txt │ ├── payload_1_out_images.json │ ├── payload_2.smi │ ├── payload_2_out_fasta.txt │ ├── payload_2_out_fasta_all_capped.txt │ ├── payload_2_out_fasta_capped_cterm.txt │ ├── payload_2_out_fasta_capped_nterm.txt │ ├── payload_2_out_smiles.txt │ ├── payload_3.smi │ ├── payload_3_out.sdf │ ├── payload_3_out.txt │ ├── payload_4.sdf │ ├── payload_4_out.sdf │ ├── payload_5.smi │ ├── payload_5_out.txt │ ├── payload_6.smi │ └── ss_smarts_pka_set_expected.json │ ├── helpers.py │ ├── legacy │ ├── validation_set_modified_peptides.csv │ └── validation_set_modified_peptides_OUTPUT.csv │ ├── pytest.ini │ ├── test_api.py │ ├── test_charges.py │ ├── test_cli.py │ ├── test_data.py │ ├── test_fasta.py │ └── test_pkamatcher.py ├── peptide_tools_master ├── LICENSE ├── Makefile ├── README.md ├── peptide_tools_master.py ├── peptools │ ├── __init__.py │ ├── cli.py │ ├── io │ │ ├── __init__.py │ │ ├── _io.py │ │ ├── adapters │ │ │ ├── __init__.py │ │ │ ├── ec.py │ │ │ └── pi.py │ │ ├── fasta.py │ │ ├── file.py │ │ ├── input.py │ │ ├── multi.py │ │ ├── output.py │ │ ├── params.py │ │ └── structure.py │ ├── utils.py │ └── wrapper │ │ ├── __init__.py │ │ ├── descriptors.py │ │ ├── ec.py │ │ ├── liabilities.py │ │ └── pi.py └── test │ ├── examples │ ├── payload_1.smi │ ├── payload_10_out.json.stdout │ ├── payload_1_out.csv │ ├── payload_1_out.json.stdout │ ├── payload_1_out_fragments.json.stdout │ ├── payload_2.fasta │ ├── payload_2_out.csv │ ├── payload_3_out.json.stdout │ ├── payload_4_out.csv │ ├── payload_5.sdf │ ├── 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