schrodinger.application.msv.gui.viewmodel module

class schrodinger.application.msv.gui.viewmodel.AlignmentInfoProxyModel(parent=None)

Bases: schrodinger.application.msv.gui.viewmodel.BaseAdjacentAlignmentProxyModel

A proxy model that contains sequence info for an alignment.

Column

alias of AlignmentInfoColumns

ROLES_FROM_PROXY = set([0, 7, 3, 1, <CustomRole.FixedColFontRole: 279>])
ROLES_FROM_SOURCE = set([<CustomRole.RowType: 257>, <CustomRole.Seq: 261>, 6, <CustomRole.RowHeightScale: 282>, <CustomRole.ReferenceSequence: 269>, <CustomRole.Included: 270>])
flags(index)
getAlignment()

Return the underlying alignment

Returns:The alignment if the source model exists; else None
Return type:schrodinger.protein.alignment.BaseAlignment
getTitleColumnWidth()

Return the width of the longest title currently shown, including both sequence titles and annotation names

Return type:int
Returns:The length of the longest title currently shown
orderChanged
class schrodinger.application.msv.gui.viewmodel.AlignmentMetricsProxyModel(parent, options_model)

Bases: schrodinger.application.msv.gui.viewmodel.BaseAdjacentAlignmentProxyModel

A proxy model that contains the alignment metrics, such as percentage of identity, similarity, homology and score to the reference sequence. Columns can be enabled or disabled via the options model.

Note:If all columns are disabled, then this model will be completely empty (i.e. zero rows in addition to zero columns). That’s because there’s no way to generate a valid QModelIndex object without any columns, so there would be no way to create a parent index when referring to a nested row. Instead, this model will ignore all row changes until a column is enabled, at which point it will emit modelAboutToBeReset and modelReset to resync the view.
Column

alias of AlignmentMetricsColumns

columnCount(parent=None)
endInsertRows()
endRemoveRows()
getIncludeGaps()
Returns:Whether to include gaps.
Return type:bool
rowCount(parent=None)
setIncludeGaps(include_gaps)
Parameters:include_gaps (bool) – Whether to include gaps in alignment
setOptionsModel(options_model)

Set the options model for the proxy, which are used for row filtering.

Parameters:options_model (schrodinger.application.msv.gui.preferences. OptionsModel) – The widget options.
class schrodinger.application.msv.gui.viewmodel.AnnotationProxyModel(parent=None)

Bases: schrodinger.application.msv.gui.viewmodel.PerRowFlagCacheProxyMixin, schrodinger.ui.qt.table_speed_up.MultipleRolesRoleProxyMixin, schrodinger.application.msv.gui.viewmodel.ProxyMixin, schrodinger.application.msv.gui.viewmodel.NestedProxy

A mixin to cache flags on a per-row basis instead of per-cell (which is what table_speed_up.FlagCacheProxyMixin does) since flags are the same across rows here.

Note:This mixin assumes that all indices in the same row have the same

internal ID. This is true for any NestedProxy subclasses, but is not generally true for Qt tree models.

ROLE_MAPPINGS = {0: (0, <RoleBase.SeqAnnotation: 10256>, <RoleBase.GlobalAnnotation: 11256>), 8: (8, <RoleBase.SeqBackground: 14256>, <RoleBase.GlobalBackground: 15256>), <CustomRole.DataRange: 258>: (None, <RoleBase.SeqAnnotationRange: 12256>, <RoleBase.GlobalAnnotationRange: 13256>), 3: (3, <RoleBase.SeqToolTip: 18256>, <RoleBase.GlobalToolTip: 19256>), 9: (9, <RoleBase.SeqForeground: 16256>, <RoleBase.GlobalForeground: 17256>)}
ROW_HEIGHT_SCALE_ROLES = [<ANNOTATION_TYPES.ligand_contacts: 17>, <ANNOTATION_TYPES.disulfide_bonds: 3>, <ANNOTATION_TYPES.antibody_cdr: 18>]
columnCount(parent=None)
data(proxy_index, role=0, multiple_roles=None)
endInsertColumns()
endRemoveColumns()
flags(index)
getGroupBy()

Are the rows currently grouped by sequence or by annotation type?

Returns:The current setting
Return type:GroupBy
getShownRowTypes()

Return a set of allowed annotation types

Returns:A set of annotation types. Note that the returned value is a copy of the attribute variable, so modifying it will not have any effect on this proxy.
Return type:set
groupByChanged
groupExpansionChanged
mapFromSource(source_index)
mapToSource(proxy_index)
reorderRow(proxy_from_row, proxy_to_row)

Pass the reorderRow request down to the next proxy after translating the row numbers. We override PostReorderingProxyMixin.reorderRow so we can handle drops on annotation rows appropriately. (Drops on an annotation row are treated as a drop after the sequence.)

See ReorderingProxyModel.reorderRow for documentation on arguments and the return value.

rowCount(parent=None)
setData(proxy_index, value, role=2)
setGroupBy(group_by)

Should the rows be grouped by sequence or by annotation type?

Parameters:group_by (GroupBy) – The setting to apply
setShownRowTypes(row_types)

Allow only the specified annotations

Parameters:row_types (iter) – An iterable containing the annotations to allow
setSourceModel(model)
setVisibilityForRowType(row_type, show=True)

Toggle visibility for the specified annotation

Parameters:
  • row_type (enum.Enum) – The annotation to adjust
  • show (bool) – Whether the annotation should be shown or hidden
setVisibilityForRowTypes(row_types, show=True)

Toggle visibility for the specified annotations

Parameters:
  • row_types (iter) – An iterable containing the annotations to adjust
  • show (bool) – Whether the annotations should be shown or hidden
tableWidthChanged(width)

Emit the tableWidthChangedSignal with the specified width. The RowWrapProxyModel should receive this signal and adjust the wrapping as necessary.

Parameters:width (int) – The current number of columns in the table
tableWidthChangedSignal
class schrodinger.application.msv.gui.viewmodel.BaseAdjacentAlignmentProxyModel(parent=None)

Bases: schrodinger.ui.qt.table_speed_up.MultipleRolesRoleProxyMixin, schrodinger.application.msv.gui.viewmodel.GroupExpansionProxyMixin, schrodinger.application.msv.gui.viewmodel.NestedProxy

A base proxy model to be subclassed by other proxy models that show data related to and synchronized with an alignment but in separate, adjacent views.

Variables:ROLES_FROM_SOURCE (set) – Set of data roles to query from the source model.
Column = None
FONT_SCALE = 1.25
ROLES_FROM_PROXY = set([0, 3, <CustomRole.FixedColFontRole: 279>, 7])
ROLES_FROM_SOURCE = set([<CustomRole.RowType: 257>, <CustomRole.RowHeightScale: 282>, <CustomRole.ReferenceSequence: 269>, 6, <CustomRole.Seq: 261>])
columnCount(parent=None)
data(proxy_index, role=0, multiple_roles=None)
isWorkspaceAln()
Returns:Whether this model represents the workspace alignment.
Return type:bool
mapFromSource(source_index)
mapToSource(proxy_index)
rowCount(parent=None)
rowHeightChanged
setSourceModel(model)
textSizeChanged
updateData(role, source_row)

Update a specified index when data changes.

Parameters:
  • role (enum.Enum) – Role of the data that changed.
  • source_row (int) – Index of the source model index to update.
class schrodinger.application.msv.gui.viewmodel.ExportProxyModel(*args, **kwargs)

Bases: schrodinger.application.msv.gui.viewmodel.PostAnnotationProxyMixin, PyQt5.QtCore.QIdentityProxyModel

A proxy for use when generating a static image of the table.

tableWidthChanged(*args, **kwargs)

Ignore changes in the table size rather than trying to update row wrapping.

class schrodinger.application.msv.gui.viewmodel.FixedColumn(title, tooltip=None, role=None, fmt=None, all_rows=False, align=132)

Bases: schrodinger.ui.qt.table_helper.Column

A table column that is fixed on the left or right of the scrollable columns. This object is intended to be used in the table_helper.TableColumns enum.

class schrodinger.application.msv.gui.viewmodel.GroupByAnnotationInfo(ann, seq_numbers)

Bases: future.types.newobject.newobject

Information about a sequence annotation. Used in AnnotationProxyModel.

class schrodinger.application.msv.gui.viewmodel.GroupExpansionProxyMixin

Bases: future.types.newobject.newobject

A mixin for tree models that transmit group expansion information to their view. Used in both the fixed and scrollable columns.

groupByChanged
groupExpansionChanged
setSourceModel(model)
class schrodinger.application.msv.gui.viewmodel.NestedProxy

Bases: PyQt5.QtCore.QAbstractProxyModel

A base class for proxy models that contain one level of nesting. The internal ID of indices will be either TOP_LEVEL or the row number of the parent row.

Variables:TOP_LEVEL (int) – The internal ID to use for indices that are at the top level of the table. (Internal ID is an unsigned 32-bit integer according to Qt’s QModelIndex documentation.)
TOP_LEVEL = 4294967295
buddy(index)
hasChildren(parent)
index(row, column, parent=None)
parent(index)
class schrodinger.application.msv.gui.viewmodel.PerRowFlagCacheProxyMixin(*args, **kwargs)

Bases: schrodinger.ui.qt.table_speed_up.AbstractFlagCacheProxyMixin

A mixin to cache flags on a per-row basis instead of per-cell (which is what table_speed_up.FlagCacheProxyMixin does) since flags are the same across rows here.

Note:This mixin assumes that all indices in the same row have the same

internal ID. This is true for any NestedProxy subclasses, but is not generally true for Qt tree models.

flags(index)
class schrodinger.application.msv.gui.viewmodel.PostAnnotationProxyMixin(*args, **kwargs)

Bases: schrodinger.application.msv.gui.viewmodel.GroupExpansionProxyMixin, schrodinger.application.msv.gui.viewmodel.ProxyMixin

A mixin for all proxies that are used after the AnnotationProxyModel.

getShownRowTypes()

See AnnotationProxyModel.getShownRowTypes for method documentation.

class schrodinger.application.msv.gui.viewmodel.ProxyMixin(*args, **kwargs)

Bases: schrodinger.ui.qt.table_speed_up.MultipleRolesRoleProxyPassthroughMixin

A mixin class that provides functionality common to all the proxies.

We also cache the sourceModel to avoid going through the C++ layer.

Note that this mixin should be listed first in the parents for the proxy classes that use it.

Variables:fixedColumnDataChanged (QtCore.pyqtSignal emitting a tuple of (enum.Enum, int)) – Signal emitted when the data in a fixed column is changed. Passes a tuple of the role and row index that are changing.
clearSelection()
fixedColumnDataChanged
getAlignment()

Return the underlying alignment

Returns:The alignment if the source model exists; else None
Return type:schrodinger.protein.alignment.BaseAlignment
getIndexForRes(res)

Get the model index for the given residue.

Parameters:res (schrodinger.protein.residue.Residue) – A residue
Returns:The model index of the residue
Return type:QModelIndex
getResidueDisplayMode()

Return the current residue display mode setting.

Returns:The current residue display mode.
Return type:enum.Enum
isWorkspaceAln()
Returns:Whether this model represents the workspace alignment.
Return type:bool
reorderRow(proxy_from_row, proxy_to_row)

Pass the reorderRow request down to the next proxy after translating the row numbers.

See ReorderingProxyModel.reorderRow for documentation on arguments and the return value.

residueFormatChanged
rowHeightChanged
setSelectionState(selection, selected)

Mark the residues specified by selection as either selected or deselected.

Parameters:
  • selection (QtCore.QItemSelection) – A selection containing the entries to update.
  • selected (bool) – Whether the entries should be selected (True) or deselected (False).
setSourceModel(model)
sourceModel()

We override this and return the cached source model so that we avoid going through the C++ layer

textSizeChanged
class schrodinger.application.msv.gui.viewmodel.RowWrapInsertingChildRows(source_parent_row, source_start, source_end)

Bases: future.types.newobject.newobject

An object to store RowWrapProxyModel bookkeeping for the insertion of child rows.

Variables:
  • source_parent_row (int) – The row number of the top-level row that the child rows are being inserted into.
  • source_start (int) – The row number of the first row being inserted.
  • source_start – The row number of the last row being inserted.
  • num_new_rows (int) – The number of rows being inserted.
  • wrap (int) – The wrap of RowWrapProxyModel that rows were just inserted into - see RowWrapProxyModel._sourceRowsAboutToBeInserted.
class schrodinger.application.msv.gui.viewmodel.RowWrapInsertingRows(old_source_row_count, new_source_row_count, source_start, source_end)

Bases: future.types.newobject.newobject

An object to store RowWrapProxyModel bookkeeping for the insertion of top-level rows.

Variables:
  • old_source_row_count (int) – The number of rows in the source model before the insertion.
  • new_source_row_count (int) – The number of rows in the source model after the insertion.
  • source_start (int) – The row number of the first row being inserted.
  • source_start – The row number of the last row being inserted.
  • num_new_rows (int) – The number of rows being inserted.
  • wrap (int) – The wrap of RowWrapProxyModel that rows were just inserted into - see RowWrapProxyModel._sourceRowsAboutToBeInserted.
  • update_row_num (int) – The row number of RowWrapProxyModel that was just updated; i.e., that just had child rows inserted into it - see RowWrapProxyModel._sourceRowsInserted.
class schrodinger.application.msv.gui.viewmodel.RowWrapProxyModel(parent=None)

Bases: schrodinger.application.msv.gui.viewmodel.PerRowFlagCacheProxyMixin, schrodinger.application.msv.gui.viewmodel.PostAnnotationProxyMixin, schrodinger.application.msv.gui.viewmodel.NestedProxy

A mixin to cache flags on a per-row basis instead of per-cell (which is what table_speed_up.FlagCacheProxyMixin does) since flags are the same across rows here.

Note:This mixin assumes that all indices in the same row have the same

internal ID. This is true for any NestedProxy subclasses, but is not generally true for Qt tree models.

columnCount(parent=None)
data(index, role=0, multiple_roles=None)
headerData(section, orientation, role=0)
mapFromSource(source_index)
mapToSource(proxy_index)
rowCount(parent=None)
setSourceModel(model)
tableWidthChanged(width)

Wrap the table to the specified number of columns.

Parameters:width (int) – The number of columns to wrap to.
class schrodinger.application.msv.gui.viewmodel.RowWrapRemovingChildRows(source_parent_row, source_start, source_end)

Bases: future.types.newobject.newobject

An object to store RowWrapProxyModel bookkeeping for the removal of child rows.

Variables:
  • source_parent_row (int) – The row number of the top-level row that the child rows are being removed from.
  • source_start (int) – The row number of the first row being removed.
  • source_start – The row number of the last row being removed.
  • num_rem_rows – The number of rows being removed.
  • wrap (int) – The wrap of RowWrapProxyModel that rows were just removed from - see RowWrapProxyModel._sourceRowsAboutToBeRemoved.
class schrodinger.application.msv.gui.viewmodel.RowWrapRemovingRows(old_source_row_count, new_source_row_count, source_start, source_end)

Bases: future.types.newobject.newobject

An object to store RowWrapProxyModel bookkeeping for the removal of top-level rows.

Variables:
  • old_source_row_count (int) – The number of rows in the source model before the removal.
  • new_source_row_count (int) – The number of rows in the source model after the removal.
  • source_start (int) – The row number of the first row being removed.
  • source_start – The row number of the last row being removed.
  • num_rem_rows – The number of rows being removed.
  • wrap (int) – The wrap of RowWrapProxyModel that rows were just removed from - see RowWrapProxyModel._sourceRowsAboutToBeRemoved.
class schrodinger.application.msv.gui.viewmodel.SequenceAlignmentModel(parent=None, options_model=None, display_mode=<Format.one_letter: 1>, include_gaps=False)

Bases: schrodinger.ui.qt.table_speed_up.MultipleRolesRoleModelMixin, schrodinger.ui.qt.table_helper.RowBasedTableModel

A QTable model where each row corresponds to a sequence and each column corresponds to a residue position

Note:

If the alignment contains only zero-length sequences, then this model creates a dummy column. Otherwise, we wouldn’t be able to generate any valid QModelIndex objects, which means we couldn’t create any parent indices for row insertion signals.
Variables:
  • fixedColumnDataChanged (QtCore.pyqtSignal emitting a tuple of (enum.Enum, int)) – Signal emitted when the data in a fixed column is changed. Passes a tuple of the role and row index that are changing.
  • rowHeightChanged (QtCore.pyqtSignal) – Signal emitted when the height of a row is changed is changed.
annotationTypes()

Get the current annotation types

Returns:A tuple of: - The global annotation enum - The sequence annotation enum
Return type:tuple
clearSelection()
columnCount(parent=None)
emitLayoutAboutToBeChanged()

Emit a layoutAboutToBeChanged signal. This helper makes disconnecting from the signal easier.

emitLayoutChanged()

Emit a layoutChanged signal. This helper makes disconnecting easier.

fixedColumnDataChanged
flags(index)

See Qt documentation for method documentation

getAlignment()

Return the underlying alignment object

Returns:The alignment
Return type:schrodinger.protein.alignment.BaseAlignment
getAverageColorInColumn(col_index, scheme)

Return the average color at a specified column and updates the cache if necessary.

Note:

This feature works particularly well with the Taylor scheme.
Parameters:
  • col_index (int) – index of specified column
  • scheme (color.RowColorScheme) – Row’s color scheme
Returns:

average color in the column
Return type:

QColor
Raises:

IndexError – If the alignment has no residues and the only column present is a dummy column.
getColorScheme()
Return type:dict
Returns:The color scheme currently in use
getCustomResColors()

Return a map of custom residue brushes

Returns:Map of custom residue color brushes
Return type:dict
getIDDispMode()

Are the identities shown as residues or dots?

Returns:The current setting
Return type:IdentityDisplayMode
getIndexForRes(res)

Get the model index for the given residue.

Parameters:res (schrodinger.protein.residue.Residue) – A residue
Returns:The model index of the residue
Return type:QModelIndex
getResidueColors(structured_only=True)

Get the color of residues in the sequence rows

Parameters:structured_only (bool) – Whether to only get colors of residues in sequences that have structures
Returns:The colors of each residue in the MSV. Each residue is represented by a tuple of (entry_id, chain, resnum, inscode) and each color is represented by a tuple of (r,g,b) values.
Return type:dict(tuple(string, string, int, string), tuple((int, int, int))
getResidueDisplayMode()
Return type:ResidueFormat
Returns:The residue display mode in current use
headerData(section, orientation, role=0)
isWorkspaceAln()
Returns:Whether this model represents the workspace alignment.
Return type:bool
onSelectionChanged(selected, deselected)

Update the view appropriately when residue selection has been changed

Parameters:
resetAnnotation(ann)
residueFormatChanged
rowCount(parent=None)
rowHeightChanged
sequenceCount()
Return type:int
Returns:The number of sequences in the alignment
sequencesReordered
setAlignment(aln)

Set the alignment model to display data from

Parameters:alignment (schrodinger.protein.alignment.BaseAlignment) – The alignment model
setFontSize(size)

Set the font size to the specified size

Parameters:size (int) – The new point size for the text
setIDDispMode(id_disp_mode)

Should the identities be shown as residues or dots?

Parameters:id_disp_mode (IdentityDisplayMode) – The setting to apply
setOptionsModel(options_model)

Set the options model for the model, which is used to know what antibody cdr scheme to display

Parameters:options_model (schrodinger.application.msv.gui.preferences. OptionsModel) – The widget options.
setResidueDisplayMode(mode)
Parameters:mode (ResidueFormat) – The display mode for residue text
setSelectionState(selection, selected)

Mark the residues specified by selection as either selected or deselected.

Parameters:
  • selection (QtCore.QItemSelection) – A selection containing the entries to update.
  • selected (bool) – Whether the entries should be selected (True) or deselected (False).
strucTitles()

Get all structure titles

Returns:A list containing all structure titles
Return type:list
textSizeChanged
updateColorScheme(row_type, scheme)

Used to set the color scheme of a specific row type.

updateCustomResColors(color_map)

Update the map of custom residue colors.

Parameters:color_map (dict) – Map of custom residue colors to apply
updateResidueColors(key_to_color_map)

Update the colors of residues in the sequence rows.

Parameters:key_to_color_map (dict(tuple(string, string, int, string), tuple((int, int, int))) – A map from residues to colors. Each residue is represented by a tuple of (entry_id, chain, resnum, inscode) and each color is represented by a tuple of (r,g,b) values.
class schrodinger.application.msv.gui.viewmodel.SequenceInfo(has_struc=None, anns=None)

Bases: future.types.newobject.newobject

Information about a single sequence. Used in AnnotationProxyModel.

class schrodinger.application.msv.gui.viewmodel.SequenceNums(all, structured_only)

Bases: tuple

all

Alias for field number 0

structured_only

Alias for field number 1

class schrodinger.application.msv.gui.viewmodel.ViewModel(parent, options_model)

Bases: PyQt5.QtCore.QObject

An abstraction layer for the various table models in this module

Variables:
  • orderChanged (QtCore.pyqtSignal) – A signal emitted when the sorting or row reodering (due to drag-and-drop) has changed. Emitted with the new seq indices.
  • topModelChanged (QtCore.pyqtSignal) – A signal emitted when row wrapping is toggled. The view must change models whenever this signal is emitted. Emitted with the new model that the view should use.
orderChanged
rowWrap()

Return the current row wrapping setting.

Returns:True if the rows are wrapped. False otherwise.
Return type:bool
setIncludeGaps(include_gaps)

Enable or disable gap including. Gap inclusion only affects whether gaps are used when calculating metrics.

Parameters:include_gaps (bool) – True if gaps should be included, false otherwise.
setRowWrap(enabled)

Enable or disabled row wrapping.

Parameters:enabled (bool) – True if rows should be wrapped. False otherwise.
topModelChanged