schrodinger.application.msv.gui.validate_align module

Helper methods for running align commands from the GUI

schrodinger.application.msv.gui.validate_align.alignment_precheck(aln)

Returns whether we have at least one sequence with at least one residue

Return type

bool

Returns

Whether we can align

exception schrodinger.application.msv.gui.validate_align.UserCanceledException

Bases: Exception

An exception raised when the user cancels the alignment in response to a message box.

__init__(*args, **kwargs)

Initialize self. See help(type(self)) for accurate signature.

args

with_traceback()

Exception.with_traceback(tb) – set self.__traceback__ to tb and return self.

schrodinger.application.msv.gui.validate_align.partial_seq_selection(aln, *, ref_seq=None)

Return whether some but not all non-reference seqs are selected :type aln: gui_alignment.GuiProteinAlignment :type ref_seq: sequence.ProteinSequence :rtype: bool

schrodinger.application.msv.gui.validate_align.get_contiguous_columns(aln)

Get reference residues marking contiguous columns with any residue selected :type aln: gui_alignment.GuiProteinAlignment

Returns

[start, end] residues of contiguous columns with selected res

Return type

iterable(tuple(Residue, Residue))

schrodinger.application.msv.gui.validate_align.get_contiguous_multi_columns(aln)

Get reference residues marking blocks of at least 2 contiguous columns with any res selected :type aln: gui_alignment.GuiProteinAlignment

Returns

[start, end] residues of contiguous columns with selected res where end.idx_in_seq > start.idx_in_seq

Return type

iterable(tuple(Residue, Residue))

schrodinger.application.msv.gui.validate_align.all_sel_multi_cols_anchored(aln)

Return whether all blocks of multiple columns with any res selected are anchored :type aln: gui_alignment.GuiProteinAlignment :rtype: bool

schrodinger.application.msv.gui.validate_align.sel_multi_cols_left_of_anchors(aln)

Return whether any blocks of multiple selected columns are anchored or left of anchors :type aln: gui_alignment.GuiProteinAlignment :rtype: bool

schrodinger.application.msv.gui.validate_align.validate_aln_sets(aln, *, aln_sets=None, loose_seqs=None)

Returns

Whether aln sets prevent aligning and an error message

Return type

tuple(bool, str)

schrodinger.application.msv.gui.validate_align.get_aln_set_align_mode(aln, *, aln_sets=None, loose_seqs=None)

Returns

The SeqAlnMode to align the Aln Sets or whether aligning can proceed if the Aln Sets are invalid

Return type

SeqAlnMode or bool

schrodinger.application.msv.gui.validate_align.get_aln_sets_and_seqs_to_align(aln)

Find the Alignment Sets that will be aligned and any loose sequences that need to be aligned to the Alignment Sets.

Returns

A list of Alignment Sets and a list of loose sequences to align to the Alignment Sets

Return type

tuple(list, list)

schrodinger.application.msv.gui.validate_align.get_residue_map_to_superimpose(aln, seqs_to_align, selected_only=False)

Create a map of aligned residues to superimpose.

Residues are considered aligned if they are structured and in a gapless column.

Parameters

selected_only – Whether to only use aligned residues that are in columns with at least one residue selected.

Returns

Map of residues keyed by entry ID

Return type

dict(int, list[protein.residue.Residue])

schrodinger.application.msv.gui.validate_align.align_command(undo_desc, pairwise=False, structure=False, split_by_anchors=False, split_res_blocks=True, can_align_sets=False, superimpose_param=None)

Decorator for methods that align the alignment.

Within the decorated function, non-selected sequences will be removed from the alignment.

The method’s class must define getAlignment(), undo_stack, and warning().

If the decorated method raises CantAlignException, this will show a warning and roll back the undo stack.

Example usage:

@align_method(undo_desc="Pairwise alignment", pairwise=True)
def runPairwiseAlignment(self):

Parameters

• undo_desc (str) – Name for the compressed undo command

• pairwise (bool) – Whether the method is a pairwise aligner

• structure (bool) – Whether the aligner requires structures

• split_by_anchors (bool) – Whether the aligner needs to split the alignment by anchored columns and align blocks between anchors

• split_res_blocks (bool) – Whether the aligner needs to split the alignment into selected residue blocks and align only them

• can_align_sets (bool) – Whether the aligner can align Alignment Sets

• superimpose_param (parameters.Param or NoneType) – Abstract param for the setting of whether the structures should be superimposed after alignment. Must start with gui_models.AlignSettingsModel.