Index Symbols | _ | A | B | C | D | F | G | I | L | M | N | P | Q | R | S | T Symbols --alignment-gap-extend mDeepFRI-predict-function command line option --alignment-gap-open mDeepFRI-predict-function command line option --angstrom-contact-thresh mDeepFRI-predict-function command line option --db-path mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --debug mDeepFRI command line option --generate-contacts mDeepFRI-predict-function command line option --input mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --input_dir mDeepFRI-make-cmaps command line option --max-length mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --min-length mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --mmseqs-max-evalue mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --mmseqs-min-bitscore mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --mmseqs-min-coverage mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --mmseqs-min-identity mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --mmseqs-sensitivity mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --no-debug mDeepFRI command line option --output mDeepFRI-get-models command line option mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --output_dir mDeepFRI-make-cmaps command line option --overwrite mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --processing-modes mDeepFRI-predict-function command line option --remove-intermediate mDeepFRI-predict-function command line option --save-cmaps mDeepFRI-predict-function command line option --save-structures mDeepFRI-predict-function command line option --scoring-matrix mDeepFRI-predict-function command line option --skip-matrix mDeepFRI-predict-function command line option --skip-pdb mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --threads mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --threshold mDeepFRI-make-cmaps command line option --tmpdir mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --top-k mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option --version mDeepFRI command line option mDeepFRI-generate-config command line option mDeepFRI-get-models command line option --weights mDeepFRI-predict-function command line option --weights_path mDeepFRI-generate-config command line option -a mDeepFRI-predict-function command line option -d mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option -i mDeepFRI-make-cmaps command line option mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option -o mDeepFRI-get-models command line option mDeepFRI-make-cmaps command line option mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option -p mDeepFRI-predict-function command line option -s mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option -t mDeepFRI-make-cmaps command line option mDeepFRI-predict-function command line option mDeepFRI-search-databases command line option -v mDeepFRI-generate-config command line option mDeepFRI-get-models command line option -w mDeepFRI-generate-config command line option mDeepFRI-predict-function command line option _ __init__() (mDeepFRI.mmseqs.QueryFile method) A align_mmseqs_results() (in module mDeepFRI.alignment) align_pairwise() (in module mDeepFRI.alignment) aligned_cmap (mDeepFRI.alignment.AlignmentResult attribute) alignment (mDeepFRI.alignment.AlignmentResult attribute) AlignmentResult (class in mDeepFRI.alignment) B best_hit_database() (in module mDeepFRI.alignment) build_align_contact_map() (in module mDeepFRI.bio_utils) C calculate_contact_map() (in module mDeepFRI.bio_utils) cmap (mDeepFRI.alignment.AlignmentResult attribute) D Database (class in mDeepFRI.database) db_name (mDeepFRI.alignment.AlignmentResult attribute) DEEPFRI_MODES (in module mDeepFRI) download_file() (in module mDeepFRI.utils) F filepath (mDeepFRI.mmseqs.QueryFile attribute) filter_sequences() (mDeepFRI.mmseqs.QueryFile method) foldcomp_db (mDeepFRI.database.Database attribute), [1] forward_pass() (mDeepFRI.predict.Predictor method) G gapped_sequence (mDeepFRI.alignment.AlignmentResult attribute) gapped_target (mDeepFRI.alignment.AlignmentResult attribute) I input_names (mDeepFRI.predict.Predictor attribute) insert_gaps() (in module mDeepFRI.alignment) (mDeepFRI.alignment.AlignmentResult method) L load_ids() (mDeepFRI.mmseqs.QueryFile method) load_sequences() (mDeepFRI.mmseqs.QueryFile method) M mDeepFRI module mDeepFRI command line option --debug --no-debug --version mDeepFRI-generate-config command line option --version --weights_path -v -w mDeepFRI-get-models command line option --output --version -o -v mDeepFRI-make-cmaps command line option --input_dir --output_dir --threshold -i -o -t mDeepFRI-predict-function command line option --alignment-gap-extend --alignment-gap-open --angstrom-contact-thresh --db-path --generate-contacts --input --max-length --min-length --mmseqs-max-evalue --mmseqs-min-bitscore --mmseqs-min-coverage --mmseqs-min-identity --mmseqs-sensitivity --output --overwrite --processing-modes --remove-intermediate --save-cmaps --save-structures --scoring-matrix --skip-matrix --skip-pdb --threads --tmpdir --top-k --weights -a -d -i -o -p -s -t -w mDeepFRI-search-databases command line option --db-path --input --max-length --min-length --mmseqs-max-evalue --mmseqs-min-bitscore --mmseqs-min-coverage --mmseqs-min-identity --mmseqs-sensitivity --output --overwrite --skip-pdb --threads --tmpdir --top-k -d -i -o -s -t mDeepFRI.mmseqs module mmseqs_db (mDeepFRI.database.Database attribute), [1] mmseqs_result (mDeepFRI.database.Database attribute), [1] model_path (mDeepFRI.predict.Predictor attribute) module mDeepFRI mDeepFRI.mmseqs N name (mDeepFRI.database.Database attribute) P pairwise_against_database() (in module mDeepFRI.alignment) predict_protein_function() (in module mDeepFRI.pipeline) Predictor (class in mDeepFRI.predict) Q query_coverage (mDeepFRI.alignment.AlignmentResult attribute) query_identity (mDeepFRI.alignment.AlignmentResult attribute) query_name (mDeepFRI.alignment.AlignmentResult attribute) query_sequence (mDeepFRI.alignment.AlignmentResult attribute) QueryFile (class in mDeepFRI.mmseqs) R remove_selenocysteine() (mDeepFRI.mmseqs.QueryFile method) remove_sequences() (mDeepFRI.mmseqs.QueryFile method) S search() (mDeepFRI.mmseqs.QueryFile method) sequence_db (mDeepFRI.database.Database attribute), [1] sequences (mDeepFRI.mmseqs.QueryFile attribute) session (mDeepFRI.predict.Predictor attribute) T target_coords (mDeepFRI.alignment.AlignmentResult attribute) target_coverage (mDeepFRI.alignment.AlignmentResult attribute) target_name (mDeepFRI.alignment.AlignmentResult attribute) target_sequence (mDeepFRI.alignment.AlignmentResult attribute) threads (mDeepFRI.predict.Predictor attribute)