abpytools.features package¶
Submodules¶
abpytools.features.composition module¶
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abpytools.features.composition.aa_composition(seq)[source]¶ Number of amino acids in a given sequence.
- Args:
- seq (str): A string representing a sequence
- Returns:
- Counter with amino acid composition
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abpytools.features.composition.aa_distribution(seq, aa_count, aa_distance_to_first)[source]¶ Amino acid distribution described in An alignment-free method to find similarity among protein sequences via the general form of Chou’s pseudo amino acid composition.
- Args:
- seq (str): amino acid sequence aa_count (dict): aminod acid count of sequence aa_distance_to_first (dict): distance to first for each amino acid to first position
- Returns:
- dict
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abpytools.features.composition.aa_frequency(seq)[source]¶ Normalised amino acid composition.
- Args:
- seq (str): A string representing a sequence
- Returns:
- Dictionary with amino acid frequency
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abpytools.features.composition.chou_pseudo_aa_composition(*sequences)[source]¶ M.K. Gupta , R. Niyogi & M. Misra (2013) An alignment-free method to find similarity among protein sequences via the general form of Chou’s pseudo amino acid composition, SAR and QSAR in Environmental Research, 24:7, 597-609, DOI: 10.1080/1062936X.2013.773378
- Args:
- *sequences: amino acid sequences
- Returns:
- list of Chou’s pseudo amino acid composition for each sequence
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abpytools.features.composition.distance_to_first(seq)[source]¶ Cumulative distance of each of the twenty amino acids to the first residue,
- Args:
- seq (str): A string representing a sequence
- Returns:
- Dictionary with cumulative
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abpytools.features.composition.order_seq(seq_dict)[source]¶ Orders dictionary to a list
- Args:
- seq_dict (dict): dictionary with amino acid keys
- Returns:
- A list with ordered amino acid
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abpytools.features.composition.triad_method(*sequences)[source]¶ Triad featurisation method described in Shen J. et al. (2006). Predicting protein–protein interactions based only on sequences information. PNAS, 104(11), pp: 4337-4341.
- Args:
- *sequences (list): sequence of amino acids
- Returns:
- list of lists with results of triad method
abpytools.features.regions module¶
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class
abpytools.features.regions.ChainDomains(antibody_objects=None, path=None, verbose=True, show_progressbar=True, n_threads=10)[source]¶ Bases:
abpytools.core.chain_collection.ChainCollection-
cdr_lengths()[source]¶ method to obtain cdr_lengths :return: m by n matrix with CDR lengths, where m is the number of antibodies in ChainCollection and n is three, corresponding to the three CDRs.
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