schrodinger.application.matsci.reordergui module

This module contains classes to enable use of the reorder module in a GUI.

Copyright Schrodinger, LLC. All rights reserved.

class schrodinger.application.matsci.reordergui.ComparisonFrame(master, structure_layout, list_layout, struct=None, mytype='Comparison', atomic_constraints=None)

Bases: schrodinger.application.matsci.reordergui.StructureFrame

The StructureFrame for the Comparison structure

mapAtom(index, guess=False)

Mark an atom as mapped

Parameters:
  • index (int) – The atom index to mark
  • guess (bool) – True if this atom is marked by a guess, False if it was marked by the user. The background color used depends on this parameter.
selectAtom(index)

Select an atom in both the image and listwidget

Parameters:index (int) – The atom index to select
class schrodinger.application.matsci.reordergui.ComparisonListWidget(master, atomic_constraints=None)

Bases: schrodinger.application.matsci.reordergui.StructureListWidget

The list widget for the Comparison structure.

getAtomText(atom)

Get the text to display in a row of the ListWidget

The atom text for an item is just the atom element plus index

Parameters:atom (int or _StructureAtom) – A reference to the atom to create text for
Return type:str
Returns:The text to display for this atom
markAtomMapped(index, guess=False)

Mark the row for the given atom index as mapped

Adds to the parent method by deselecting the row

Parameters:
  • index (int) – Atom to mark
  • guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.
Return type:

QListWidgetItem
Returns:

The list widget item for the affected atom
class schrodinger.application.matsci.reordergui.ReferenceFrame(*args, **kwargs)

Bases: schrodinger.application.matsci.reordergui.StructureFrame

The StructureFrame for the Reference structure

advanceSelection(index)

Move the selection to the next unmapped atom with a higher index. If none exist, start checking again at atom 1.

Parameters:index (int) – Start search for unmapped atoms with indexes higher than this number
mapAtom(ref_index, advance=True, guess=False)

Map the given atom index in the comparison structure to the given atom index in the reference structure.

Parameters:
  • ref_index (int) – The atom index of the reference molecule
  • advance (bool) – Whether to advance the selected atom or not. The selection will automatically be advanced if ref_index is the currently selected atom regardless of this setting.
selectedIndex()

Get the index of the currently selected atom

Return type:int
Returns:The index of the selected Reference atom
setStructure(struct)

Set the structure for this frame. Updates the image and the list widget

Parameters:struct (schrodinger.structure.Structure) – The structure for this frame
class schrodinger.application.matsci.reordergui.ReferenceListWidget(master, atomic_constraints=None)

Bases: schrodinger.application.matsci.reordergui.StructureListWidget

The ListWidget for the reference structure.

getAtomText(atom)

Get the text to display in a row of the ListWidget

The atom text for an item is the atom element plus index for the Reference atom, plus the atom index of any Comparison atom mapped to this atom.

Parameters:atom (int or _StructureAtom) – A reference to the atom to create text for
Return type:str
Returns:The text to display for this atom
markAtomMapped(index, guess=False)

Mark the row for the given atom index as mapped and update the text

Adds to the parent method by changing the text of the marked item to reflect the mapping.

Parameters:
  • index (int) – Atom to mark
  • guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.
Return type:

QListWidgetItem
Returns:

The list widget item for the affected atom
markAtomUnmapped(index)

Remove the mapping for atom index

Adds to the parent method by changing the text of the marked item to reflect the unmapping.

Parameters:index (int) – The atom index to unmap
Return type:QListWidgetItem
Returns:The list widget item for the affected atom
class schrodinger.application.matsci.reordergui.ReorderAtomFrame(parent=None, by_element=True, by_smiles=True, by_smarts=True, by_superposition=True, layout=None, reference_structure=None, comparison_structure=None, reference_structure_constraints=None)

Bases: schrodinger.ui.qt.swidgets.SFrame

A frame which allows the user to reorder the atoms of a comparison structure based on the atom order of a reference structure. The widgets provide the ability to guess at atom order based on multiple algorithms and also manually specify order using 2D images of the structures.

autoMap()

Automatically map no-brainer atoms based on the current mapping. No-brainer atoms are atoms that are the only atoms remaining of a given element, or hydrogens bound to mapped atoms that can be uniquely identified.

compAtomFromRefAtom(index)

Get the atom in the Comparison structure that is mapped to the given index in the Reference structure

Parameters:index (int) – The index of the Reference atom to check
Return type:int
Returns:The index of the Comparison atom mapped to the given Reference atom
doneReordering()

Check if the reordering process is done

Return type:bool
Returns:True if all the atoms in one of the structures are mapped
finishGuess()

Finish guess mode after the user has accepted or rejected the guess.

Note - this method should be callable even if not currently in a guess.

getReorderedStructure()

Get a reordered version of the comparison structure

Return type:schrodinger.structure.Structure, list or (None, None)
Returns:The comparison structure with the atoms reordered as specified in the mapping, and the list used to reorder the structure. The first element of the list is the original index of the atom that is first in the reordered structure, the second is the original index of the atom that is second in the reordered structure, etc. (None, None) is returned if the structure is not ready for reordering.
guessAccepted()

User has accpeted the guess, make the atoms truly mapped

guessMode(guessmode)

Set the current guess mode - affects label texts and enabling/disabling widgets and user interaction signals.

Parameters:guessmode (bool) – True if a guess is currently taking place and has not yet been Accepted/Rejected, False if any other situation
guessOrder()

Make a guess at the new order of the Comparison atoms

guessRejected()

User has rejected the guess remove it

highlightCompAtom(comp_index)

Highlight an atom in the Comparision structure

Parameters:comp_index (int) – The index of the comparison atom to highlight
highlightMapPair(ref_index, comp_index)

Highlight the mapped pair of atoms

Parameters:
  • ref_index (int) – The index of the reference atom to highlight
  • comp_index (int) – The index of the comparison atom to highlight
highlightRefAtom(ref_index)

Highlight an atom in the Reference structure

Parameters:ref_index (int) – The index of the reference atom to highlight
isInGuessMode()

Is the panel currently in guess mode?

Return type:bool
Returns:True if the panel is in guess mode, False if not
mapCompAtom(comp_index, ref_index=None, auto=True, advance=True)

Map an atom in the Comparison structure to an atom in the Reference structure

Parameters:
  • comp_index (int) – The atom index of the comparison atom to map
  • ref_index (int or None) – If an int, the index of the reference atom to map to. If not given, the selected reference atom will be used
  • auto (bool) – Whether to Auto guess additional atoms based on this mapping. Default is True - but autoguessing will only occur if the user has checked the Auto guess box.
  • advance (bool) – True if the Reference atom selection should be advanced, False if not
mapPair(ref_index, comp_index, advance=True, guess=False)

Create a mapping between an atom in the Comparison structure to an atom in the Reference structure.

Parameters:
  • ref_index (int) – The atom index of the reference atom to map
  • comp_index (int) – The atom index of the comparison atom to map
  • advance (bool) – True if the Reference atom selection should be advanced, False if not
  • guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.
refAtomFromCompAtom(index)

Get the atom in the Reference structure that is mapped to the given index in the Comparison structure

Parameters:index (int) – The index of the Comparison atom to check
Return type:int
Returns:The index of the Reference atom mapped to the given Comparison atom
reset(reset_structures=True)

Reset the frame

Parameters:reset_structures (bool) – True if structures should be reset, False if they should be kept
resetMap()

Reset only the map, keeping the structures

selectRefAtom(index)

Select the current atom in the reference structure

Parameters:index (int) – The index of the atom to select
setStructures(reference, comparison)

Set the reference and comparison structures

Parameters:
unmapPair(ref_index, comp_index)

Create a mapping between an atom in the Comparison structure to an atom in the Reference structure.

Parameters:
  • ref_index (int) – The atom index of the reference atom to map
  • comp_index (int) – The atom index of the comparison atom to map
class schrodinger.application.matsci.reordergui.ReorderAtomPanel(**kwargs)

Bases: schrodinger.ui.qt.appframework2.af2.JobApp

A simple panel that takes two selected entries and allows one of them to be reordered - this is mainly for testing and example purposes.

createReorderedEntry()

Create a new, reordered version of the second selected entry. If run from maestro, this will be created as a new project entry and included in the workspace.

layOut()

Lay out the widgets for this panel

loadStructures()

Load in the two structures. The first selected entry will be the reference.

setPanelOptions()

Override the generic parent class to set panel options

class schrodinger.application.matsci.reordergui.ReorderAtomsDialog(master, struct1, struct2, modality=0, struct1_atomic_constraints=None, **kwargs)

Bases: schrodinger.ui.qt.swidgets.SDialog

A Window-Modal dialog that allows the user to reorder atoms in a comparison structure based on a reference structure.

accept()

User has clicked accept, get the reordered structure, call the accept_command with it and close the dialog.

Return type:int or None
Returns:QDialog.Accepted if a structure has been reordered, or None if the reordering was incomplete and the dialog not closed
layOut()

Lay out the custom widgets in this dialog.

reject()

User has clicked reject - do nothing but call custom reject method

Return type:int
Returns:QDialog.Reject
class schrodinger.application.matsci.reordergui.StructureFrame(master, structure_layout, list_layout, struct=None, mytype='Comparison', atomic_constraints=None)

Bases: PyQt5.QtWidgets.QFrame

A QFrame that contains a 2D image of a structure. This also creates a QListWidget that is coordinated with the 2D image. This is the base class for both the Reference and Comparison structures.

highlightAtom(index, guess=False)

Highlight the given atom

Parameters:
  • index (int) – The atom index to highlight
  • guess (bool) – True if this atom is marked by a guess, False if it was marked by the user. The background color used depends on this parameter.
isValidAtomIndex(index)

Check if this index is a valid atom index for the loaded structure

Parameters:index (int) – The atom index to check
Return type:bool
Returns:True 0 < index <= atom_total, False otherwise
reset(reset_structure=True)

Reset to a blank frame, or remove any mapping but keep the structure

Parameters:reset_structure – True if the structure should be reset, False if it should be kept
setLabel(guessing=False)

Set the label that describes what the user should do

Parameters:guessing (bool) – True if there is currently a guess in place, False if not.
setStructure(struct)

Set the structure for this frame. Updates the image and the list widget

Parameters:struct (schrodinger.structure.Structure) – The structure for this frame
unmapAtom(index)

Mark an atom as unmapped

Parameters:index (int) – The atom index to mark
class schrodinger.application.matsci.reordergui.StructureListWidget(master, atomic_constraints=None)

Bases: schrodinger.ui.qt.swidgets.SListWidget

A QListWidget that interacts with a structure picture to select atoms. Clicking on a row will send a signal that an atom has been clicked on. Atoms (rows) can be marked as Mapped or Unmapped, which will result in changing the background color of the row.

There is 1 row in in the ListWidget for each atom in the structure, in the same order as atoms are in the structure. Note that row indexes start at 0 but atom indexes start at 1, so we often have to add/subtract 1 to translate between the two.

atom_clicked
fill()

Fill the items in the ListWidget using the current structure

itemSelected(row)

React to the user selecting an item in the ListWidget

Parameters:row (int) – The row of the item selected
markAtomMapped(index, guess=False)

Mark the row for the given atom index as mapped

Parameters:
  • index (int) – Atom to mark
  • guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.
Return type:

QListWidgetItem
Returns:

The list widget item for the affected atom
markAtomUnmapped(index)

Mark the row for the given atom index as unmapped

Parameters:index (int) – Atom to mark
Return type:QListWidgetItem
Returns:The list widget item for the affected atom
parseAtomText(text)

Parse the given text into an element and atom index

Parameters:text (str) – String describing the atom such as C 13, H 1, etc. Also accepts strings for mapped atoms such as “C 13 - C 12”
Return type:(str, int)
Returns:The element and atom index specified by text
selectAtom(index)

Select the item that corresponds to the atom index

Parameters:index (int) – The index of atom whose item should be selected
setStructure(struct)

Set the structure object for this widget and fill the widget

Parameters:struct (schrodinger.structure.Structure) – The structure object containing the data for this ListWidget
class schrodinger.application.matsci.reordergui.StructurePic(scene)

Bases: schrodinger.ui.qt.structure2d.structure_item

The QGraphicsItem that holds a 2D image of a structure

highlightAtom(index, guess=False)

Highlight an atom

Parameters:
  • index (int) – The atom index to highlight
  • guess (bool) – True if this atom is marked by a guess, False if it was marked by the user. The background color used depends on this parameter.
hoverMoveEvent(event)

Track when the mouse is over an atom - emit a signal when it enters a new atom or leaves an atom. An index of 0 is emitted when the mouse is not over any atom.

markAtomMapped(index, guess=False)

Mark an atom as mapped (either by guess or manually) and regenerate the picture.

Parameters:
  • index (int) – The atom index to mark
  • guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.
markAtomUnmapped(index)

Mark an atom as unmapped and regenerate the picture.

Parameters:index (int) – The atom index to mark
reset()

Clear all the annotators and remove the picture

selectAtom(index)

Select an atom in the image and regenerate the picture

Parameters:index (int) – The atom index to select
setStructure(struct)

Set the structure - create a new image of it

Parameters:struct (schrodinger.structure.Structure) – The structure object for this picture
class schrodinger.application.matsci.reordergui.StructureView(scene)

Bases: schrodinger.ui.qt.structure2d.structure_view

View which holds a structure_item object

atom_highlighted
schrodinger.application.matsci.reordergui.main(*args)
schrodinger.application.matsci.reordergui.panel()

Top-level function for bringing up the panel.