biotite 0.39.0__cp311-cp311-macosx_11_0_arm64.whl → 0.41.0__cp311-cp311-macosx_11_0_arm64.whl

biotite/structure/sequence.py

@@ -0,0 +1,112 @@
+# This source code is part of the Biotite package and is distributed
+# under the 3-Clause BSD License. Please see 'LICENSE.rst' for further
+# information.
+
+"""
+Function for converting a structure into a sequence.
+"""
+
+__name__ = "biotite.structure"
+__author__ = "Patrick Kunzmann"
+__all__ = ["to_sequence"]
+
+import numpy as np
+from .info.misc import one_letter_code
+from .info.groups import amino_acid_names, nucleotide_names
+from .residues import get_residues
+from .chains import get_chain_starts
+from .error import BadStructureError
+from ..sequence.seqtypes import ProteinSequence, NucleotideSequence
+
+
+HETERO_PLACEHOLDER = "."
+
+
+def to_sequence(atoms, allow_hetero=False):
+    """
+    Convert each chain in a structure into a sequence.
+
+    Parameters
+    ----------
+    atoms : AtomArray or AtomArrayStack
+        The structure.
+        May contain multiple chains.
+        Each chain must be either a peptide or a nucleic acid.
+    allow_hetero : bool, optional
+        If true, residues inside a amino acid or nucleotide chain,
+        that have no one-letter code, are replaced by the respective
+        '*any*' symbol (`"X"` or `"N"`, respectively).
+        The same is true for amino acids in nucleotide chains and vice
+        versa.
+        By default, an exception is raised.
+
+    Returns
+    -------
+    sequences : list of Sequence, length=n
+        The sequence for each chain in the structure.
+    chain_start_indices : ndarray, shape=(n,), dtype=int
+        The atom index where each chain starts.
+
+    Notes
+    -----
+    Residues are considered amino acids or nucleotides based on their
+    appearance :func:`info.amino_acid_names()` or
+    :func:`info.nucleotide_names()`, respectively.
+
+    Examples
+    --------
+
+    >>> sequences, chain_starts = to_sequence(atom_array)
+    >>> print(sequences)
+    [ProteinSequence("NLYIQWLKDGGPSSGRPPPS")]
+
+    """
+    sequences = []
+    chain_start_indices = get_chain_starts(atoms, add_exclusive_stop=True)
+    for i in range(len(chain_start_indices)-1):
+        start = chain_start_indices[i]
+        stop = chain_start_indices[i+1]
+        chain = atoms[start:stop]
+        _, residues = get_residues(chain)
+        one_letter_symbols = np.array(
+            [one_letter_code(res) or HETERO_PLACEHOLDER for res in residues]
+        )
+        hetero_mask = one_letter_symbols == HETERO_PLACEHOLDER
+
+        aa_count  = np.count_nonzero(np.isin(residues, amino_acid_names()))
+        nuc_count = np.count_nonzero(np.isin(residues, nucleotide_names()))
+        if aa_count == 0 and nuc_count == 0:
+            raise BadStructureError(
+                f"Chain {chain.chain_id[0]} contains neither amino acids "
+                "nor nucleotides"
+            )
+        elif aa_count > nuc_count:
+            # Chain is a peptide
+            hetero_mask |= ~np.isin(residues, amino_acid_names())
+            if not allow_hetero and np.any(hetero_mask):
+                hetero_indices = np.where(hetero_mask)[0]
+                raise BadStructureError(
+                    f"Hetero residue(s) "
+                    f"{', '.join(residues[hetero_indices])} in peptide"
+                )
+            one_letter_symbols[hetero_mask] = "X"
+            # Replace selenocysteine and pyrrolysine
+            one_letter_symbols[one_letter_symbols == "U"] = "C"
+            one_letter_symbols[one_letter_symbols == "O"] = "K"
+            sequences.append(ProteinSequence("".join(one_letter_symbols)))
+        else:
+            # Chain is a nucleic acid
+            hetero_mask |= ~np.isin(residues, nucleotide_names())
+            if not allow_hetero and np.any(hetero_mask):
+                hetero_indices = np.where(hetero_mask)[0]
+                raise BadStructureError(
+                    f"Hetero residue(s) "
+                    f"{', '.join(residues[hetero_indices])} in nucleic acid"
+                )
+            one_letter_symbols[hetero_mask] = "N"
+            # Replace uracil
+            one_letter_symbols[one_letter_symbols == "U"] = "T"
+            sequences.append(NucleotideSequence("".join(one_letter_symbols)))
+
+    # Remove exclusive stop
+    return sequences, chain_start_indices[:-1]