schrodinger.protein.tasks.structure_alignment module¶
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class
schrodinger.protein.tasks.structure_alignment.
StructAlignResult
(ref_string, other_string, ref_sse, other_sse, psd, rmsd)¶ Bases:
tuple
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__contains__
(key, /)¶ Return key in self.
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__len__
()¶ Return len(self).
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count
(value, /)¶ Return number of occurrences of value.
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index
(value, start=0, stop=9223372036854775807, /)¶ Return first index of value.
Raises ValueError if the value is not present.
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other_sse
¶ Alias for field number 3
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other_string
¶ Alias for field number 1
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psd
¶ Alias for field number 4
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ref_sse
¶ Alias for field number 2
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ref_string
¶ Alias for field number 0
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rmsd
¶ Alias for field number 5
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schrodinger.protein.tasks.structure_alignment.
get_unique_seq_names
(sequences)[source]¶ 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)]]
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schrodinger.protein.tasks.structure_alignment.
get_orig_seq_name
(prefixed_name)[source]¶ Given a name output by
get_unique_seq_names
, return the original sequence name
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schrodinger.protein.tasks.structure_alignment.
runStructureAlignment
(ref, others, keywords=None, ref_asl=None, other_asl=None)[source]¶ 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)