schrodinger.protein.tasks.structure_alignment module

class schrodinger.protein.tasks.structure_alignment.StructAlignResult(ref_string, other_string, ref_sse, other_sse, psd, rmsd)

Bases: tuple

other_sse

Alias for field number 3

other_string

Alias for field number 1

psd

Alias for field number 4

ref_sse

Alias for field number 2

ref_string

Alias for field number 0

rmsd

Alias for field number 5

schrodinger.protein.tasks.structure_alignment.make_protein_sequence(seq_str: str, sse_str: str) → ProteinSequence

Create a ProteinSequence from a sequence string and an SSE string.

Parameters:

  • seq_str – Sequence string (single-letter codes, gaps as ‘-‘).

  • sse_str – SSE string (single-letter codes, gaps as ‘-‘).

Returns:

Protein sequence with secondary structure assigned.

schrodinger.protein.tasks.structure_alignment.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.

Parameters:

sequences (list[ProteinSequence]) – Protein sequences

Returns:

Generator of tuples of unique sequence names and sequences

Return type:

collections.abc.Iterable[tuple(str, ProteinSequence)]]

schrodinger.protein.tasks.structure_alignment.get_orig_seq_name(prefixed_name)

Given a name output by get_unique_seq_names, return the original sequence name

schrodinger.protein.tasks.structure_alignment.make_struct_align_result(ref_st: Structure, other_st: Structure, score: float, rmsd: float) → StructAlignResult

Build a StructAlignResult from a pair of structures and alignment metrics.

Parameters:

  • ref_st – Reference structure used for the alignment.

  • other_st – Mobile structure used for the alignment.

  • score – Alignment score.

  • rmsd – Root mean square deviation.

Returns:

StructAlignResult object

schrodinger.protein.tasks.structure_alignment.runStructureAlignment(ref, others, ref_asl=None, other_asl=None)

Runs protein pairwise structure alignment using cealign.

Parameters:

  • ref (tuple(str, Structure)) – Reference name and structure.

  • others (list[tuple(str, Structure)]) – Non-reference (mobile) names and structures.

  • ref_asl (str) – ASL for reference structure.

  • other_asl (str) – ASL for other structures.

Returns:

Alignment results keyed by non-reference structure names.

Return type:

dict(str, StructAlignResult)