biotite 1.1.0__cp313-cp313-win_amd64.whl

biotite/structure/chains.py

@@ -0,0 +1,314 @@
+# 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.
+
+"""
+This module provides utility for handling data on chain level, rather than
+atom level.
+"""
+
+__name__ = "biotite.structure"
+__author__ = "Patrick Kunzmann"
+__all__ = [
+    "get_chain_starts",
+    "apply_chain_wise",
+    "spread_chain_wise",
+    "get_chain_masks",
+    "get_chain_starts_for",
+    "get_chain_positions",
+    "chain_iter",
+    "get_chains",
+    "get_chain_count",
+    "chain_iter",
+]
+
+import numpy as np
+from biotite.structure.segments import (
+    apply_segment_wise,
+    get_segment_masks,
+    get_segment_positions,
+    get_segment_starts_for,
+    segment_iter,
+    spread_segment_wise,
+)
+
+
+def get_chain_starts(array, add_exclusive_stop=False):
+    """
+    Get the indices in an atom array, which indicates the beginning of
+    a new chain.
+
+    A new chain starts, when the chain ID changes or when the residue ID
+    decreases.
+
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        The atom array (stack) to get the chain starts from.
+    add_exclusive_stop : bool, optional
+        If true, the exclusive stop of the input atom array, i.e.
+        ``array.array_length()``, is added to the returned array of
+        start indices as last element.
+
+    Returns
+    -------
+    starts : ndarray, dtype=int
+        The start indices of new chains in `array`.
+
+    Notes
+    -----
+    This method is internally used by all other chain-related
+    functions.
+
+    See also
+    --------
+    get_residue_starts
+    """
+    diff = np.diff(array.res_id)
+    res_id_decrement = diff < 0
+    # This mask is 'true' at indices where the value changes
+    chain_id_changes = array.chain_id[1:] != array.chain_id[:-1]
+
+    # Convert mask to indices
+    # Add 1, to shift the indices from the end of a chain
+    # to the start of a new chain
+    chain_starts = np.where(res_id_decrement | chain_id_changes)[0] + 1
+
+    # The first chain is not included yet -> Insert '[0]'
+    if add_exclusive_stop:
+        return np.concatenate(([0], chain_starts, [array.array_length()]))
+    else:
+        return np.concatenate(([0], chain_starts))
+
+
+def apply_chain_wise(array, data, function, axis=None):
+    """
+    Apply a function to intervals of data, where each interval
+    corresponds to one chain.
+
+    The function takes an atom array (stack) and an data array
+    (`ndarray`) of the same length. The function iterates through the
+    chain IDs of the atom array (stack) and identifies intervals of
+    the same ID. Then the data is
+    partitioned into the same intervals, and each interval (also an
+    :class:`ndarray`) is put as parameter into `function`. Each return value is
+    stored as element in the resulting :class:`ndarray`, therefore each element
+    corresponds to one chain.
+
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        The atom array (stack) to determine the chains from.
+    data : ndarray
+        The data, whose intervals are the parameter for `function`. Must
+        have same length as `array`.
+    function : function
+        The `function` must have either the form *f(data)* or
+        *f(data, axis)* in case `axis` is given. Every `function` call
+        must return a value with the same shape and data type.
+    axis : int, optional
+        This value is given to the `axis` parameter of `function`.
+
+    Returns
+    -------
+    processed_data : ndarray
+        Chain-wise evaluation of `data` by `function`. The size of the
+        first dimension of this array is equal to the amount of
+        chains.
+
+    See also
+    --------
+    apply_residue_wise
+    """
+    starts = get_chain_starts(array, add_exclusive_stop=True)
+    return apply_segment_wise(starts, data, function, axis)
+
+
+def spread_chain_wise(array, input_data):
+    """
+    Expand chain-wise data to atom-wise data.
+
+    Each value in the chain-wise input is assigned to all atoms of
+    this chain:
+
+    ``output_data[i] = input_data[j]``,
+    *i* is incremented from atom to atom,
+    *j* is incremented every chain change.
+
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        The atom array (stack) to determine the chains from.
+    input_data : ndarray
+        The data to be spread. The length of axis=0 must be equal to
+        the amount of different chain IDs in `array`.
+
+    Returns
+    -------
+    output_data : ndarray
+        Chain-wise spread `input_data`. Length is the same as
+        `array_length()` of `array`.
+
+    See also
+    --------
+    spread_residue_wise
+    """
+    starts = get_chain_starts(array, add_exclusive_stop=True)
+    return spread_segment_wise(starts, input_data)
+
+
+def get_chain_masks(array, indices):
+    """
+    Get boolean masks indicating the chains to which the given atom
+    indices belong.
+
+    Parameters
+    ----------
+    array : AtomArray, shape=(n,) or AtomArrayStack, shape=(m,n)
+        The atom array (stack) to determine the chains from.
+    indices : ndarray, dtype=int, shape=(k,)
+        These indices indicate the atoms to get the corresponding
+        chains for.
+        Negative indices are not allowed.
+
+    Returns
+    -------
+    chains_masks : ndarray, dtype=bool, shape=(k,n)
+        Multiple boolean masks, one for each given index in `indices`.
+        Each array masks the atoms that belong to the same chain as
+        the atom at the given index.
+
+    See also
+    --------
+    get_residue_masks
+    """
+    starts = get_chain_starts(array, add_exclusive_stop=True)
+    return get_segment_masks(starts, indices)
+
+
+def get_chain_starts_for(array, indices):
+    """
+    For each given atom index, get the index that points to the
+    start of the chain that atom belongs to.
+
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        The atom array (stack) to determine the chains from.
+    indices : ndarray, dtype=int, shape=(k,)
+        These indices point to the atoms to get the corresponding
+        chain starts for.
+        Negative indices are not allowed.
+
+    Returns
+    -------
+    start_indices : ndarray, dtype=int, shape=(k,)
+        The indices that point to the chain starts for the input
+        `indices`.
+
+    See also
+    --------
+    get_residue_starts_for
+    """
+    starts = get_chain_starts(array, add_exclusive_stop=True)
+    return get_segment_starts_for(starts, indices)
+
+
+def get_chain_positions(array, indices):
+    """
+    For each given atom index, obtain the position of the chain
+    corresponding to this index in the input `array`.
+
+    For example, the position of the first chain in the atom array is
+    ``0``, the the position of the second chain is ``1``, etc.
+
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        The atom array (stack) to determine the chains from.
+    indices : ndarray, dtype=int, shape=(k,)
+        These indices point to the atoms to get the corresponding
+        chain positions for.
+        Negative indices are not allowed.
+
+    Returns
+    -------
+    start_indices : ndarray, dtype=int, shape=(k,)
+        The indices that point to the position of the chains.
+
+    See also
+    --------
+    get_residue_positions
+    """
+    starts = get_chain_starts(array, add_exclusive_stop=True)
+    return get_segment_positions(starts, indices)
+
+
+def get_chains(array):
+    """
+    Get the chain IDs of an atom array (stack).
+
+    The chains are listed in the same order they occur in the array
+    (stack).
+
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        The atom array (stack), where the chains are determined.
+
+    Returns
+    -------
+    ids : ndarray, dtype=str
+        List of chain IDs.
+
+    See also
+    --------
+    get_residues
+    """
+    return array.chain_id[get_chain_starts(array)]
+
+
+def get_chain_count(array):
+    """
+    Get the amount of chains in an atom array (stack).
+
+    The count is determined from the `chain_id` annotation.
+    Each time the chain ID changes, the count is incremented.
+
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        The atom array (stack), where the chains are counted.
+
+    Returns
+    -------
+    count : int
+        Amount of chains.
+
+    See also
+    --------
+    get_residue_count
+    """
+    return len(get_chain_starts(array))
+
+
+def chain_iter(array):
+    """
+    Iterate over all chains in an atom array (stack).
+
+    Parameters
+    ----------
+    array : AtomArray or AtomArrayStack
+        The atom array (stack) to iterate over.
+
+    Yields
+    ------
+    chain : AtomArray or AtomArrayStack
+        A single chain of the input `array`.
+
+    See also
+    --------
+    residue_iter
+    """
+    starts = get_chain_starts(array, add_exclusive_stop=True)
+    return segment_iter(array, starts)