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.StructureListWidget(master, atomic_constraints=None)

Bases: 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

A pyqtSignal emitted by instances of the class.

__init__(master, atomic_constraints=None)

Create a StructureListWidget instance

Parameters:

• master (ReorderAtomFrame) – The mapping property of the master is used by some subclasses

• atomic_constraints (list or None) – list of atomic constraints for each atom or None

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

fill()

Fill the items in the ListWidget using the current structure

selectAtom(index)

Select the item that corresponds to the atom index

Parameters:

index (int) – The index of atom whose item should be selected

itemSelected(row)

React to the user selecting an item in the ListWidget

Parameters:

row (int) – The row of the item selected

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

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

getMarkedAtoms(guess=False)

Get atom indexes of marked atoms.

Parameters:

guess (bool) – True if this mark results from a guess, False if not. The background color used depends on this parameter.

Return type:

list(int)

Returns:

Indexes of marked atoms

class schrodinger.application.matsci.reordergui.ComparisonListWidget(*args, **kwargs)

Bases: StructureListWidget

The list widget for the Comparison structure.

__init__(*args, **kwargs)

See parent method for the documentation. Here defaults are set.

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

markSuggestedAtom(index)

Mark foreground of the suggested atom item with SUGGEST_COLOR, previously suggested atom with BLACK.

Parameters:

index (int) – Atom to mark

class schrodinger.application.matsci.reordergui.ReferenceListWidget(master, atomic_constraints=None)

Bases: StructureListWidget

The ListWidget for the reference structure.

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

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

class schrodinger.application.matsci.reordergui.StructureView(scene)

Bases: structure_view

View which holds a structure_item object

atom_highlighted

A pyqtSignal emitted by instances of the class.

class schrodinger.application.matsci.reordergui.StructurePic(scene)

Bases: structure_item

The QGraphicsItem that holds a 2D image of a structure

__init__(scene)

Create a StructurePic instance

Parameters:

scene (QGraphicsScene) – The Scene this image is placed in

reset()

Clear all the annotators and remove the picture

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.

setStructure(struct)

Set the structure - create a new image of it

Parameters:

struct (schrodinger.structure.Structure) – The structure object for this picture

selectAtom(index)

Select an atom in the image and regenerate the picture

Parameters:

index (int) – The atom index to select

markAtomMapped(index, guess=False, generate=True)

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.

• generate (bool) – Whether to regenerate the 2D picture

markAtomUnmapped(index)

Mark an atom as unmapped and regenerate the picture.

Parameters:

index (int) – The atom index to mark

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.

highlightSuggestedAtom(index)

Highlight suggested atom

Parameters:

index (int) – The atom index to highlight

class schrodinger.application.matsci.reordergui.StructureFrame(master, label_layout, structure_layout, list_layout, struct=None, mytype='Comparison', atomic_constraints=None, enable_2d_structure=True)

Bases: 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.

__init__(master, label_layout, structure_layout, list_layout, struct=None, mytype='Comparison', atomic_constraints=None, enable_2d_structure=True)

Create a StructureFrame instance

Parameters:

• master (ReorderAtomFrame) – The master Frame for this widget

• label_layout (QBoxLayout) – The layout to add the label.

• structure_layout (QBoxLayout) – The layout to add this widget to.

• list_layout (QBoxLayout) – The layout to add the associated ListWidget to.

• struct (schrodinger.structure.Structure) – The structure for this frame

• mytype (str) – Either REFERENCE or COMPARISON, the type of structure this Frame applies to.

• atomic_constraints (list or None) – list of atomic constraints for each atom or None

• enable_2d_structure (bool) – If True, enable/show 2D structure. Can be slow for inorganic materials

generatePicture()

Regenerate the 2D picture to show any changes

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

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.

unmapAtom(index)

Mark an atom as unmapped

Parameters:

index (int) – The atom index to mark

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

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

selectAtom(index)

Select an atom in both the image and listwidget

Parameters:

index (int) – The atom index to select

Return type:

structure._StructureAtom

Returns:

selected atom

mapAtom(index, guess=False, generate=True)

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.

• generate (bool) – Whether to regenerate the 2D picture

class schrodinger.application.matsci.reordergui.ComparisonFrame(master, label_layout, structure_layout, list_layout, struct=None, mytype='Comparison', atomic_constraints=None, enable_2d_structure=True)

Bases: StructureFrame

The StructureFrame for the Comparison structure

suggestCloseAtom(xyz)

Highlight and return index of the closest atom from the XYZ location taking into account PBCs.

Param:

Coordinates

Return type:

int

Returns:

Closest atom index

suggestedIndex()

Get last suggested index.

Return type:

int or None

Returns:

last suggested index

class schrodinger.application.matsci.reordergui.ReferenceFrame(*args, **kwargs)

Bases: StructureFrame

The StructureFrame for the Reference structure

__init__(*args, **kwargs)

Create a ReferenceFrame object. Parameters are described in the StructureFrame class

mapAtom(ref_index, advance=True, **kwargs)

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.

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

selectedIndex()

Get the index of the currently selected atom

Return type:

int

Returns:

The index of the selected Reference atom

class schrodinger.application.matsci.reordergui.PickPairToggleIntermediate(checkbox, pick_function, pick_text='Pick 2 atoms to define a pair', allow_locked_entries=False)

Bases: PickPairToggle

Class that allows: to call pick function in the intermediate picking state (only one atom is picked out of two); to prevent calling pick function at all if desired.

setStructures(reference, comparison)

Set the reference and comparison structures

Parameters:

• reference (schrodinger.structure.Structure) – The structure to use as the reference

• comparison (schrodinger.structure.Structure) – The structure to use as the comparison

class schrodinger.application.matsci.reordergui.ReorderAtomFrame(parent=None, by_element=True, by_smiles=True, by_smarts=True, by_superposition=True, default_method='SMARTS patterns of whole molecule or unique atoms', layout=None, reference_structure=None, comparison_structure=None, reference_structure_constraints=None, enable_2d_structure=True)

Bases: 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.

MAP_COUNTER_LABEL = '{num_mapped_atoms} of {atom_total}\natoms mapped'

__init__(parent=None, by_element=True, by_smiles=True, by_smarts=True, by_superposition=True, default_method='SMARTS patterns of whole molecule or unique atoms', layout=None, reference_structure=None, comparison_structure=None, reference_structure_constraints=None, enable_2d_structure=True)

Create a ReorderAtomFrame widget

Parameters:

• parent (QWidget) – The parent widget with a .warning(str) method

• by_element (bool) – Provide widgets to allow a guess based on lone elements

• by_smiles (bool) – Provide widgets to allow a guess based on unique SMILES order

• by_smarts (bool) – Provide widgets to allow a guess based on SMARTS patterns

• by_superposition (bool) – Provide widgets to allow a guess based on 3D superposition of the structures

• default_method (str) – Default guess method

• layout (QBoxLayout) – The layout to place this frame into

• reference_structure (schrodinger.structure.Structure) – The structure to use as the reference

• comparison_structure (schrodinger.structure.Structure) – The structure to use as the comparison

• enable_2d_structure (bool) – If True, enable/show 2D structure. Can be slow for inorganic materials

updateMapCounter()

Updates the label indicating the number of atoms mapped

Return type:

None

show2DStructures(state)

Show or hide 2D structure pictures

Parameters:

state (bool) – If True, show 2D structure picture, otherwise hide

setStructures(reference, comparison)

Set the reference and comparison structures

Parameters:

• reference (schrodinger.structure.Structure) – The structure to use as the reference

• comparison (schrodinger.structure.Structure) – The structure to use as the comparison

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

selectRefAtom(index)

Select the current atom in the reference structure

Parameters:

index (int) – The index of the atom to select

mapPair(ref_index, comp_index, advance=True, guess=False, generate=True)

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.

• generate (bool) – Whether to regenerate the 2D picture

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

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

markAtomsInWS()

Mark selected atoms for guess in the WS.

markSuggestedAtomsInWS(ref_idx, comp_idx)

Pick reference atom in the WS and mark suggested comparison atom.

Parameters:

• ref_idx (int) – Index of the atom to pick in the reference WS

• comp_idx (int or None) – If int, mark atom in the comparison WS structure

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

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

highlightCompAtom(comp_index)

Highlight an atom in the Comparision structure

Parameters:

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

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

guessOrder()

Make a guess at the new order of the Comparison atoms

guessAccepted()

User has accepted the guess, make the atoms truly mapped

guessRejected()

User has rejected the guess remove it

isInGuessMode()

Is the panel currently in guess mode?

Return type:

bool

Returns:

True if the panel is in guess mode, False if not

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.

doneReordering()

Check if the reordering process is done

Return type:

bool

Returns:

True if all the atoms in one of the structures are mapped

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.

resetMap()

Reset only the map, keeping the structures

reset(reset_structures=True)

Reset the frame

Parameters:

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

class schrodinger.application.matsci.reordergui.ReorderAtomPanel(**kwargs)

Bases: 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.

setPanelOptions()

Override the generic parent class to set panel options

layOut()

Lay out the widgets for this panel

loadStructures()

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

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.

class schrodinger.application.matsci.reordergui.ReorderAtomsDialog(master, struct1, struct2, modality=WindowModality.NonModal, struct1_atomic_constraints=None, default_guess_method='SMARTS patterns of whole molecule or unique atoms', enable_2d_structure=True, **kwargs)

Bases: SDialog

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

__init__(master, struct1, struct2, modality=WindowModality.NonModal, struct1_atomic_constraints=None, default_guess_method='SMARTS patterns of whole molecule or unique atoms', enable_2d_structure=True, **kwargs)

Create a ReorderAtomDialog instance. See parent for **kwargs docs.

Parameters:

• master (QWidget) – The parent widget

• struct1 (schrodinger.structure.Structure) – The reference structure. This structure will not be reordered.

• struct2 (schrodinger.structure.Structure) – The comparison structure. A copy of this structure will be reordered when the user clicks OK

• modality (int) – The modality of the dialog. Default is Qt.NonModal, other options may be Qt.WindowModal or Qt.ApplicationModal.

• struct1_atomic_constraints (list) – List of constraints in text format

• default_guess_method (str) – Default guess method

layOut()

Lay out the custom widgets in this dialog.

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

reject()

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

Return type:

int

Returns:

QDialog.Reject

schrodinger.application.matsci.reordergui.panel()

Top-level function for bringing up the panel.

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