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[sequence.ProteinSequence]) – Protein sequences
- Returns
Generator of tuples of unique sequence names and sequences
- Return type
collections.abc.Iterable[tuple(str, sequence.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.Structure)) – Reference name and structure
others (list[tuple(str, structure.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)