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.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.runStructureAlignment(ref, others, keywords=None, ref_asl=None, other_asl=None)

Runs protein pairwise structure alignment using “ska” backend.

Parameters:

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

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

• keywords (dict) – Keywords to pass to ska

• 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)