schrodinger.protein.align module

class schrodinger.protein.align.AbstractAligner(gap_open_penalty=1, gap_extend_penalty=0.0, sub_matrix=None, direct_scores=False, constraints=None, merge_all=False, ss_constraints=False)

Bases: object

Base class of objects that can perform an alignment

run(aln)

Aligns the sequences in an alignment using the parameters supplied on init

Subclasses need to override this default implementation.

Parameters:aln (schrodinger.protein.alignment.BaseAlignment) – The alignment to align
sub_matrix

Get or set the sub_matrix.

When setting, it will be converted to a numpy array.

exception schrodinger.protein.align.AlignmentException

Bases: exceptions.Exception

class schrodinger.protein.align.BasicAligner(gap_open_penalty=1, gap_extend_penalty=0.0, sub_matrix=None, direct_scores=False, constraints=None, merge_all=False, ss_constraints=False)

Bases: schrodinger.protein.align.AbstractAligner

Aligns sequences by simply adding gaps to the ends of sequences to make them the same length

run(aln)
class schrodinger.protein.align.ClustalAligner(gap_open_penalty=1, gap_extend_penalty=0.0, sub_matrix=None, direct_scores=False, constraints=None, merge_all=False, ss_constraints=False)

Bases: schrodinger.protein.align.AbstractAligner

Aligns sequences using the Clustal alignment algorithm.

class schrodinger.protein.align.ConstrainedPairwiseAlignment(**kwargs)

Bases: schrodinger.protein.align.AbstractAligner

Implements constrained dynamic programming algorithm for pairwise sequence alignment.

  1. ability to merge new sequence with existing alignment,
  2. ability to penalize gaps in secondary structure elements,
  3. ability to use custom substitution matrix generated from a family of proteins or provided by the user.
getMappedGaps(from_gaps, to_gaps)

Utility function which calculates the offsets of gaps applied to previously-aligned sequences.

Parameters:
  • from_gaps (List of ints) – Gap indices to apply to the new sequence.
  • to_gaps (List of ints) – Gap indices of the targeted sequence
getMatrixValue(code1, code2)

Returns the appropriate similarity score as defined by a similarity matrix.

Parameters:
  • code1 (char) – short code of first sequence residue
  • code2 (char) – short code of second sequence residue
Returns:

value for a residue-residue pair based on a scoring matrix
Return type:

float
run(seq1, seq2, aln_to_merge=None)

Runs the whole alignment.

Parameters:
  • seq1 (Sequence) – first sequence to be aligned
  • seq2 (Sequence) – second sequence to be aligned
  • aln_to_merge (Alignment or NoneType) – alignment that the sequences belong to, otherwise None, indicating that a merge is not requested
class schrodinger.protein.align.RescodeAligner(gap_open_penalty=1, gap_extend_penalty=0.0, sub_matrix=None, direct_scores=False, constraints=None, merge_all=False, ss_constraints=False)

Bases: schrodinger.protein.align.AbstractAligner

Aligns sequences by rescode

run(aln)
class schrodinger.protein.align.SuperpositionAligner(gap_open_penalty=None, gap_extend_penalty=None)

Bases: schrodinger.protein.align.ConstrainedPairwiseAlignment

Align structured sequences based on their superposition.

run(ref_seq, seqs, aln_to_merge)

Align sequences based on structure superposition to the reference.

Parameters: