schrodinger.application.bioluminate.peptide_sar.encode module

class schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer

Bases: object

N_DIMS: int = None

one_hot(seq: str) → List[List[int]]

One-hot encode a sequence.

rev_one_hot(seq_matrix: List[List[int]]) → tuple[str]

Decode a one-hot encoded sequence.

classmethod encode(char: str) → List[int]

classmethod encode_char(char: str) → int

classmethod decode(vector: List[int]) → str

classmethod decode_value(value: int) → str

schrodinger.application.bioluminate.peptide_sar.encode.vectorizer_class_factory(bins: dict[str, list[str]]) → type[schrodinger.application.bioluminate.peptide_sar.encode.Vectorizer]

Uses a dictionary of single-letter codes grouped by bin name to create a custom vectorizer class.

Parameters

bins – Dictionary of single-letter codes grouped by bin name

Returns

Custom vectorizer class

schrodinger.application.bioluminate.peptide_sar.encode.ResidueVectorizer

alias of schrodinger.application.bioluminate.peptide_sar.encode.vectorizer_class_factory.<locals>.CustomVectorizer

schrodinger.application.bioluminate.peptide_sar.encode.HydrophobicVectorizer

alias of schrodinger.application.bioluminate.peptide_sar.encode.vectorizer_class_factory.<locals>.CustomVectorizer

schrodinger.application.bioluminate.peptide_sar.encode.ChargeVectorizer

alias of schrodinger.application.bioluminate.peptide_sar.encode.vectorizer_class_factory.<locals>.CustomVectorizer

schrodinger.application.bioluminate.peptide_sar.encode.PolarityVectorizer

alias of schrodinger.application.bioluminate.peptide_sar.encode.vectorizer_class_factory.<locals>.CustomVectorizer

schrodinger.application.bioluminate.peptide_sar.encode.SizeVectorizer

alias of schrodinger.application.bioluminate.peptide_sar.encode.vectorizer_class_factory.<locals>.CustomVectorizer

schrodinger.application.bioluminate.peptide_sar.encode.encode_seqs(wt_seq: schrodinger.application.bioluminate.peptide_sar.io.ScoredSeq, scored_seqs: list[schrodinger.application.bioluminate.peptide_sar.io.ScoredSeq], vector_fn_name: str) → list[List[List[int]]]

One-hot encode sequences using the wt sequence and scores.

schrodinger.application.bioluminate.peptide_sar.encode.decode_position_vector(vector_fn_name: str, vector: List[int]) → str

Decode a one-hot encoded vector.

schrodinger.application.bioluminate.peptide_sar.encode.decode_value(vector_fn_name: str, value: int) → str

Decode a single value using the specified vectorizer.

schrodinger.application.bioluminate.peptide_sar.encode.get_mutation_encoding(wt, seq) → List[List[int]]

Get the difference vector between a sequence and the wt sequence.