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Commit f73da1da authored by Gerardo Tauriello's avatar Gerardo Tauriello
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Code/doc cleanup in mol.alg.Superpose

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......@@ -231,13 +231,14 @@ def _MatchResidueByAln(ent_a, ent_b, atoms, alnmethod):
def MatchResidueByLocalAln(ent_a, ent_b, atoms='all'):
"""
Match residues by local alignment. Takes **ent_a** and **ent_b**, extracts
the sequences chain-wise and aligns them in Smith/Waterman manner using the
BLOSUM62 matrix for scoring. The residues of the entities are then matched
based on this alignment. Only atoms present in both residues are included in
the views. Chains are processed in order of appearance. If **ent_a** and
**ent_b** contain a different number of chains, processing stops with
the lower count.
Match residues by local alignment. Takes **ent_a** and **ent_b**, extracts the
sequences chain-wise and aligns them in Smith/Waterman manner using the
BLOSUM62 matrix for scoring. Only residues which are marked as "protein" (see
:attr:`~ost.mol.ResidueHandle.is_protein`) are considered for alignment. The
residues of the entities are then matched based on this alignment. Only atoms
present in both residues are included in the views. Chains are processed in
order of appearance. If **ent_a** and **ent_b** contain a different number of
chains, processing stops with the lower count.
:param ent_a: The first entity
:type ent_a: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
......@@ -252,13 +253,9 @@ def MatchResidueByLocalAln(ent_a, ent_b, atoms='all'):
def MatchResidueByGlobalAln(ent_a, ent_b, atoms='all'):
"""
Match residues by global alignment. Takes **ent_a** and **ent_b**, extracts
the sequences chain-wise and aligns them in Needleman/Wunsch manner using the
BLOSUM62 matrix for scoring. The residues of the entities are then matched
based on this alignment. Only atoms present in both residues are included in
the views. Chains are processed in order of appearance. If **ent_a** and
**ent_b** contain a different number of chains, processing stops with
the lower count.
Match residues by global alignment.
Same as :func:`MatchResidueByLocalAln` but performs a global Needleman/Wunsch
alignment of the sequences using the BLOSUM62 matrix for scoring.
:param ent_a: The first entity
:type ent_a: :class:`~ost.mol.EntityView` or :class:`~ost.mol.EntityHandle`
......@@ -272,7 +269,8 @@ def MatchResidueByGlobalAln(ent_a, ent_b, atoms='all'):
return _MatchResidueByAln(ent_a, ent_b, atoms, ost.seq.alg.GlobalAlign)
def Superpose(ent_a, ent_b, match='number', atoms='all', iterative=False, max_iterations=5, distance_threshold=3.0):
def Superpose(ent_a, ent_b, match='number', atoms='all', iterative=False,
max_iterations=5, distance_threshold=3.0):
"""
Superposes the model entity onto the reference. To do so, two views are
created, returned with the result. *atoms* describes what goes into these
......@@ -327,11 +325,9 @@ def Superpose(ent_a, ent_b, match='number', atoms='all', iterative=False, max_it
elif match.upper() == 'INDEX':
view_a, view_b = MatchResidueByIdx(ent_a, ent_b, atoms)
elif match.upper() == 'LOCAL-ALN':
view_a, view_b = _MatchResidueByAln(ent_a, ent_b, atoms,
ost.seq.alg.LocalAlign)
view_a, view_b = MatchResidueByLocalAln(ent_a, ent_b, atoms)
elif match.upper() == 'GLOBAL-ALN':
view_a, view_b = _MatchResidueByAln(ent_a, ent_b, atoms,
ost.seq.alg.GlobalAlign)
view_a, view_b = MatchResidueByGlobalAln(ent_a, ent_b, atoms)
else:
raise ValueError(not_supported)
## action
......
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