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

__contains__

Return key in self.

__init__

Initialize self. See help(type(self)) for accurate signature.

__len__

Return len(self).

count(value) → integer -- return number of occurrences of value

index(value[, start[, stop]]) → integer -- return first index of value.

Raises ValueError if the value is not present.

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.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)