schrodinger.structutils.structalign module

A module for performing protein structure alignment. This requires Prime to be installed and licensed appropriately as the SKA program distributed with Prime is what is actually used to do the alignment.

The structural alignment is performed and the results are added as properties to the input CTs. For each template the alignment is returned along with the raw output from ska.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.structutils.structalign.StructAlign

Bases: object

This is the class used to perform the structural alignment. This class will check at initialization time if Prime is installed by trying to import schrodinger.applications.ska and will fail if it’s not installed as nothing more can be done.

There are a number of properties that can be set for instances of this class which are used to control how the alignment is done:

gap_penalty - default = 2.0 deletion_penalty = default = 1.0 use_scanning_alignment - default = False window_length - default = 5 minimum_similarity - default = 1.0 minimum_length - default = 2 use_automatic_settings - default = False use_standard_residues - default = False reorder_by_connectivity - default = False


Construct an instance of a StructAlign object. This method will check that schrodinger.application.ska is available and fail with a RuntimeError if it’s not

property gap_penalty

Access to the gap penalty for the alignment

property deletion_penalty

Access to the deletion penalty for the alignment

property use_scanning_alignment

Access to the use scanning alignment flag

property window_length

Access to the window length for the aligment

property minimum_similarity

Access to the minimum similarity used in the alignment

property minimum_length

Access to the minimum length used in the alignment

align(ref_st, sts)

Perform a structural alignment on the Structure objects in the list ‘sts’ relative to the reference structure ‘ref_st’ Each structure in the list is aligned relative to the reference structure. The coordinates of the input structures are modified to give the best structural alignment.

alignStructure(ref_st, mob_st)

Perform a structural alignment on the mob_st structure relative to the ref_st structure. The coordinates of the input mob_st structure are modified to give the best structural alignment.