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| def | __init__ (self, pep_subst_mat=seq.alg.BLOSUM62, pep_gap_open=-5, pep_gap_ext=-2, nuc_subst_mat=seq.alg.NUC44, nuc_gap_open=-4, nuc_gap_ext=-4, resnum_aln=False) |
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| def | Align (self, s1, s2, chem_type=None) |
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| def | NWAlign (self, s1, s2, chem_type) |
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| def | ResNumAlign (self, s1, s2) |
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Definition at line 1637 of file chain_mapping.py.
◆ __init__()
| def __init__ |
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self, |
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pep_subst_mat = seq.alg.BLOSUM62, |
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pep_gap_open = -5, |
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pep_gap_ext = -2, |
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nuc_subst_mat = seq.alg.NUC44, |
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nuc_gap_open = -4, |
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nuc_gap_ext = -4, |
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resnum_aln = False |
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Helper class to compute alignments
Sets default values for substitution matrix, gap open and gap extension
penalties. They are only used in default mode (Needleman-Wunsch aln).
If *resnum_aln* is True, only residue numbers of views that are attached
to input sequences are considered.
Definition at line 1638 of file chain_mapping.py.
◆ Align()
| def Align |
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self, |
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s1, |
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s2, |
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chem_type = None |
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◆ NWAlign()
| def NWAlign |
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self, |
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s1, |
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s2, |
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chem_type |
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Returns pairwise alignment using Needleman-Wunsch algorithm
:param s1: First sequence to align
:type s1: :class:`ost.seq.SequenceHandle`
:param s2: Second sequence to align
:type s2: :class:`ost.seq.SequenceHandle`
:param chem_type: Must be in [:class:`ost.mol.ChemType.AMINOACIDS`,
:class:`ost.mol.ChemType.NUCLEOTIDES`], determines
substitution matrix and gap open/extension penalties
:type chem_type: :class:`ost.mol.ChemType`
:returns: Alignment with s1 as first and s2 as second sequence
Definition at line 1664 of file chain_mapping.py.
◆ ResNumAlign()
| def ResNumAlign |
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self, |
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s1, |
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s2 |
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Returns pairwise alignment using residue numbers of attached views
Assumes that there are no insertion codes (alignment only on numerical
component) and that resnums are strictly increasing (fast min/max
identification). These requirements are assured if a structure has been
processed by :class:`ChainMapper`.
:param s1: First sequence to align, must have :class:`ost.mol.EntityView`
attached
:type s1: :class:`ost.seq.SequenceHandle`
:param s2: Second sequence to align, must have :class:`ost.mol.EntityView`
attached
:type s2: :class:`ost.seq.SequenceHandle`
Definition at line 1689 of file chain_mapping.py.
◆ nuc_gap_ext
◆ nuc_gap_open
◆ nuc_subst_mat
◆ pep_gap_ext
◆ pep_gap_open
◆ pep_subst_mat
◆ resnum_aln
The documentation for this class was generated from the following file:
