Source code for schrodinger.protein.tasks.structure_alignment

# Runs SKA structure alignment jobs
import logging
from collections import namedtuple

import schrodinger
from schrodinger.application import ska
from schrodinger.utils import log

TMP_ORIG_ATOM_IDX_PROP = "i_msv_orig_atom_idx"

SEPARATOR = "_"

logger = log.get_output_logger(__file__)
if schrodinger.in_dev_env():
    logger.setLevel(logging.DEBUG)

StructAlignResult = namedtuple(
    "StructAlignResult",
    ["ref_string", "other_string", "ref_sse", "other_sse", "psd", "rmsd"])


def get_unique_seq_names(sequences):
    """
    Create unique names for the given sequences for use with structure alignment

    The original sequence name can be recreated using `get_orig_seq_name`.

    :param sequences: Protein sequences
    :type sequences: list[sequence.ProteinSequence]

    :return: Generator of tuples of unique sequence names and sequences
    :rtype: collections.abc.Iterable[tuple(str, sequence.ProteinSequence)]]
    """
    for index, seq in enumerate(sequences):
        name = f'{index}{SEPARATOR}{seq.name}'
        yield name, seq


def get_orig_seq_name(prefixed_name):
    """
    Given a name output by `get_unique_seq_names`, return the original sequence name
    """
    return prefixed_name.split(SEPARATOR, 1)[1]


def runStructureAlignment(
    ref,
    others,
    keywords=None,
    ref_asl=None,
    other_asl=None,
):
    """
    Runs protein pairwise structure alignment using "ska" backend.

    :param ref: Reference name and structure
    :type ref: tuple(str, structure.Structure)
    :param others: Non-reference (mobile) names and structures
    :type others: list[tuple(str, structure.Structure)]
    :param keywords: Keywords to pass to ska
    :type keywords: dict
    :param ref_asl: ASL for reference structure
    :type ref_asl: str
    :param other_asl: ASL for other structures
    :type other_asl: str

    :return: Alignment results keyed by non-reference structure names
    :rtype: dict(str, StructAlignResult)
    """
    if not others:
        return {}

    if keywords is None:
        keywords = {}

    try:
        all_results = ska.pairwise_align_ct(ref,
                                            others,
                                            keywords=keywords,
                                            log=logger,
                                            save_props=True,
                                            std_res=True,
                                            asl=ref_asl,
                                            asl_mobile=other_asl)
    except RuntimeError:
        # See log for error info
        return {}

    ref_name, _ = ref

    seq_results = dict()
    for result in all_results:
        if not result.align:
            # No results to process
            continue
        ref_string = result.align.pop(ref_name)
        if len(result.align) != 1:
            raise ValueError("Expected only one non-ref item in result align "
                             f"dict, got {len(result.align)}.")
        other_name, other_string = result.align.popitem()
        struct_aln_result = StructAlignResult(ref_string, other_string,
                                              result.sse[ref_name],
                                              result.sse[other_name],
                                              result.psd, result.rmsd)
        seq_results[other_name] = struct_aln_result

    return seq_results