schrodinger.application.msv.structure_model module

class schrodinger.application.msv.structure_model.AbstractStructureModel

Bases: PyQt5.QtCore.QObject

Manages interactions between sequences and their associated structures. A separate AbstractStructureModel subclass should be created for each program MSV can run alongside of (i.e. Maestro, PyMol, standalone). For programs with a workspace, this class also maintains the workspace alignment, which contains sequences for all structures currently included in the workspace.

This class should not be instantiated directly. Instead StructureModel should be instantiated, which will create an object of the appropriate AbstractStructureModel subclass.

Subclasses must implement _readStructures. Subclasses for programs with a workspace should implement getWorkspaceAlignment and getIncludedEntries, and should set IMPLEMENTS_GET_INCLUDED to True. Subclasses for programs with a concept of selected entries should implement getSelectedEntries, and should set IMPLEMENTS_GET_SELECTED to True.

Variables:
IMPLEMENTS_GET_INCLUDED = False
IMPLEMENTS_GET_SELECTED = False
getIncludedEntries()

Returns a list of sequences for all entries that are currently included in the workspace. Raises NotImplementedError if the associated program has no concept of a workspace. :rtype: list

getSelectedEntries()

Returns a list of sequences for all entries that are currently selected in the project table. Raises NotImplementedError if the associated program has no concept of a selected entry. :rtype: list

getWorkspaceAlignment()

Return an alignment that contains all entries included in the workspace. The structure model will ensure that this alignment is always kept in sync with the workspace. Returns None if the associated program has no concept of a workspace (i.e. StandaloneStructureModel). :rtype: alignment.BaseAlignment or NoneType

getWorkspaceColors()

Returns a dict mapping residues to their color in the workspace. Returns an empty dict if the associated program has no concept of a workspace. :rtype: dict

importFile(filename)

Return sequences for the specified file. If the file contains structural data, then the sequences will have associated structures accessible via sequence.getStructure().

Parameters:filename (basestring) – The filename to read
Returns:All sequences
Return type:list
Raises:IOError – If there was an error importing the file.
importFiles(filenames)

Return sequences for all specified files. If any of the files contain structural data, then those sequences will have associated structures accessible via sequence.getStructure().

Parameters:filenames (iterable) – The filenames to read
Returns:All sequences
Return type:list
Raises:IOError – If there was an error importing the files.
resetRequested
setWorkspaceColors(color_map)

Sets the colors in the workspace to the colors given by color_map. This is a no-op if the associated program has no concept of a workspace. :type color_map: dict

workspaceColorsChanged
class schrodinger.application.msv.structure_model.ChainData(eid, chain, all_res, vis_res, included)

Bases: PyQt5.QtCore.QObject

Information about a single chain of a single entry from the current Maestro project.

Variables:
  • wsVisibilityChangeRequested (QtCore.pyqtSignal) –

    A signal emitted when the workspace visibility of a chain should be changed. The MaestroStructureModel instance is responsible for changing the workspace visibility in response to this signal. Emitted with:

    • the entry id of the chain (int)
    • the chain name (str)
    • whether the chain should be shown (True) or hidden (False) (bool)
    • whether the entry is currently in the workspace (bool)
  • eid (int) – The entry id of the chain.
  • chain (str) – The chain name.
  • seqs (weakref.WeakSet) – A set of all sequences representing this chain.
  • workspace_seq (schrodinger.application.msv.domain.sequence.Sequence) – The sequence representing this chain in the workspace alignment (i.e. the alignment shown in the workspace tab). Note that this sequence also appears in seqs.
addSeq(seq)

Monitor a new sequence that represents this chain.

Parameters:seq (schrodinger.application.msv.domain.sequence.Sequence) – The sequence to monitor
clearVisRes()

Clear the set of residues that are currently visible in the Maestro workspace.

entryRemoved()

Respond to the entry being removed from the project. Mark all sequences as not having an associated structure and disconnect the sequences from visibility updates.

included

Whether the entry is currently included in the Maestro workspace. :type: bool

updateAllRes(added, removed)

Update the set of residues that exist in this chain.

Parameters:
  • added (set) – The set of residues that were just added to the chain.
  • removed (set) – The set of residues that were just removed from the chain.
Note:

Each residue must be a tuple of (residue number, insertion code).
updateVisRes(added, removed)

Update the set of residues that are currently visible in the Maestro workspace.

Parameters:
  • added (set) – The set of residues that were just added to the workspace.
  • removed (set) – The set of residues that were just removed from the workspace.
Note:

Each residue must be a tuple of (residue number, insertion code).
visibility

The visibility of this chain in the Maestro workspace. May not be updated directly. Use updateVisRes or updateAllRes instead. :type: Inclusion

wsVisibilityChangeRequested
class schrodinger.application.msv.structure_model.MaestroStructureModel(parent)

Bases: schrodinger.ui.qt.appframework2.maestro_callback.MaestroCallbackModelMixin, schrodinger.application.msv.structure_model.AbstractStructureModel

IMPLEMENTS_GET_INCLUDED = True
IMPLEMENTS_GET_SELECTED = True
getIncludedEntries()
getSelectedEntries()
getSeqsForEid(eid)

Get sequences for each chain in the specified entry.

Parameters:eid (int or str) – The entry id to fetch sequences for.
Returns:A list of the requested sequences.
Return type:list
getSeqsForEids(eids)

Get sequences for each chain in all specified entries.

Parameters:eid (list) – The entry ids to fetch sequences for.
Returns:A list of the requested sequences.
Return type:list
getWorkspaceAlignment()
getWorkspaceColors()

Get the colors of each sequence residue in the workspace. For amino acid residues, the color of the alpha carbon is returned; for nucleotide residues, the color of the C1’ on the sugar is returned.

Returns:The colors of each residue in the workspace. 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 mapping (string, string, int, string) to (int, int, int)
onWorkspaceChanged(changed)

Callback that is called whenever the maestro workspace changes. See maestro_callback for details.

Parameters:changed (a WORKSPACE_CHANGED_* constant in maestro.py) – What kind of change occured in the workspace
setWorkspaceColors(color_map)

Set the colors in the workspace for all the residues in the color map. If a residue is not in the color map, its color will not be changed. All atoms in a residue will be re-colored.

Parameters:color_map (dict mapping (string, string, int, string) to (int, int, int)) – The new colors that residues should have. Each residue is represented by a 4-tuple of (entry_id, chain, resnum, inscode), and each color is represented by a tuple of (r,g,b) values.
splitChains(seqs_by_entry, aln)

Splits chains for an entry while preserving gaps and structureless residues.

Parameters:seqs_by_entry (dict mapping int entry_id to a list of Sequence) – a mapping of the entry ids to seqs
Return selected_seqs:
 Split sequences, now with unique entry ids
Rtype selected_seqs:
 List of Sequence
superimposeByAlignment(selected_seqs)

Creates and runs a Maestro command to superimpose structures by aligned residues in the Multiple Sequence Viewer.

Parameters:selected_seqs (iterable(sequence.ProteinSequence)) – Current selected sequences in MSV
class schrodinger.application.msv.structure_model.PyMolStructureModel

Bases: schrodinger.application.msv.structure_model.AbstractStructureModel

A stub for a PyMol structure model.

class schrodinger.application.msv.structure_model.StandaloneStructureModel

Bases: schrodinger.application.msv.structure_model.AbstractStructureModel

A structure model for when the MSV is run directly from the command line.

Note:When copying a sequence, this structure model currently strips all

structural information from the copy. If we need the copy to retain structural information, we should make sure that setting the structure on one copied chain updates the structure on all other copied chains without affecting the structure from the original sequences.

class schrodinger.application.msv.structure_model.StructureModel

Bases: object

When instantiated, this class will return the appropriate AbstractStructureModel subclass.

class schrodinger.application.msv.structure_model.StructureModelMeta

Bases: type