LICENSE.txt
README.md
pyproject.toml
setup.py
bin/paras
bin/paras-residues
bin/paras-test
paras/__init__.py
paras/features.py
paras/run.py
paras.egg-info/PKG-INFO
paras.egg-info/SOURCES.txt
paras.egg-info/dependency_links.txt
paras.egg-info/requires.txt
paras.egg-info/top_level.txt
paras/common/__init__.py
paras/common/clear_temp.py
paras/common/fasta.py
paras/common/get_model_structures.py
paras/common/parsers.py
paras/common/rename_fastas.py
paras/common/writers.py
paras/data/__init__.py
paras/data/active_site_34.fasta
paras/data/classifier_version.txt
paras/data/paras.classifier
paras/data/reference_sequence.fasta
paras/data/sequences.fasta
paras/data/smiles.txt
paras/data/specificities.txt
paras/data/stach.fasta
paras/data/aa_properties/15_aa_properties.txt
paras/data/aa_properties/15_aa_properties_normalised.txt
paras/data/aa_properties/__init__.py
paras/data/hmm/AMP-binding_full.hmm
paras/data/hmm/AMP-binding_full.hmm.h3f
paras/data/hmm/AMP-binding_full.hmm.h3i
paras/data/hmm/AMP-binding_full.hmm.h3m
paras/data/hmm/AMP-binding_full.hmm.h3p
paras/data/hmm/__init__.py
paras/data/positions/Apositions.txt
paras/data/positions/Apositions_34.txt
paras/data/positions/Apositions_34_hmm.txt
paras/data/positions/Apositions_hmm.txt
paras/data/positions/Apositions_start_end.txt
paras/data/positions/__init__.py
paras/data/temp/__init__.py
paras/data/temp/temp_in_alignment.fasta
paras/data/temp/temp_out_alignment.fasta
paras/data/train_and_test_data/__init__.py
paras/data/train_and_test_data/sequences/__init__.py
paras/data/train_and_test_data/sequences/test_sequences.fasta
paras/data/train_and_test_data/sequences/train_sequences.fasta
paras/data/train_and_test_data/structure_alignments/__init__.py
paras/data/train_and_test_data/structure_alignments/training_alignment.fasta
paras/data/train_and_test_data/structure_alignments/training_alignment_validation_01.fasta
paras/data/train_and_test_data/structure_alignments/training_alignment_validation_02.fasta
paras/data/train_and_test_data/structure_alignments/training_alignment_validation_03.fasta
paras/data/train_and_test_data/structure_alignments/training_alignment_validation_04.fasta
paras/data/train_and_test_data/structure_alignments/training_alignment_validation_05.fasta
paras/data/train_and_test_data/structure_alignments/training_alignment_validation_06.fasta
paras/data/train_and_test_data/structure_alignments/training_alignment_validation_07.fasta
paras/data/train_and_test_data/structure_alignments/training_alignment_validation_08.fasta
paras/data/train_and_test_data/structure_alignments/training_alignment_validation_09.fasta
paras/data/train_and_test_data/structure_alignments/training_alignment_validation_10.fasta
paras/data_preparation/__init__.py
paras/data_preparation/assign_smiles.py
paras/data_preparation/compare_alignment_methods.py
paras/data_preparation/get_sequences.py
paras/data_preparation/move_structures_to_folders.py
paras/data_preparation/substrate_names.py
paras/domain_extraction/__init__.py
paras/domain_extraction/align.py
paras/domain_extraction/extract_active_sites_hmm.py
paras/domain_extraction/extract_adomains.py
paras/domain_extraction/extract_residues.py
paras/domain_extraction/read_positions.py
paras/feature_extraction/__init__.py
paras/feature_extraction/get_sequence_features.py
paras/feature_extraction/get_substrate_features.py
paras/feature_extraction/normalise_amino_acid_properties.py
paras/training/__init__.py
paras/training/check_classifier.py
paras/training/get_test_set.py
paras/training/train_paras.py