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.