Package schrodinger :: Package application :: Package matsci :: Module reordergui :: Class ReorderAtomFrame

Class ReorderAtomFrame

PyQt4.QtGui.QFrame --+
                     |
                    ReorderAtomFrame

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.

Instance Methods

[hide private]

__init__(self, parent=None, by_element=True, by_smiles=True, by_smarts=True, by_superposition=True, layout=None, reference_structure=None, comparison_structure=None)
Create a ReorderAtomFrame widget

setStructures(self, reference, comparison)
Set the reference and comparison structures

guessMode(self, guessmode)
Set the current guess mode - affects label texts and enabling/disabling widgets and user interaction signals.

selectRefAtom(self, index)
Select the current atom in the reference structure

mapPair(self, 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.

unmapPair(self, ref_index, comp_index)
Create a mapping between an atom in the Comparison structure to an atom in the Reference structure.

mapCompAtom(self, comp_index, ref_index=None, auto=True, advance=True)
Map an atom in the Comparison structure to an atom in the Reference structure

autoMap(self)
Automatically map no-brainer atoms based on the current mapping.

int

compAtomFromRefAtom(self, index)
Get the atom in the Comparison structure that is mapped to the given index in the Reference structure

int

refAtomFromCompAtom(self, index)
Get the atom in the Reference structure that is mapped to the given index in the Comparison structure

highlightCompAtom(self, comp_index)
Highlight an atom in the Comparision structure

highlightRefAtom(self, ref_index)
Highlight an atom in the Reference structure

highlightMapPair(self, ref_index, comp_index)
Highlight the mapped pair of atoms

guessOrder(self)
Make a guess at the new order of the Comparison atoms

guessAccepted(self)
User has accpeted the guess, make the atoms truly mapped

guessRejected(self)
User has rejected the guess remove it

bool

isInGuessMode(self)
Is the panel currently in guess mode?

finishGuess(self)
Finish guess mode after the user has accepted or rejected the guess.

bool

doneReordering(self)
Check if the reordering process is done

schrodinger.structure.Structure, list or (None, None)

getReorderedStructure(self)
Get a reordered version of the comparison structure

resetMap(self)
Reset only the map, keeping the structures

reset(self, reset_structures=True)
Reset the frame

Method Details

[hide private]

init(self, parent=None, by_element=True, by_smiles=True, by_smarts=True, by_superposition=True, layout=None, reference_structure=None, comparison_structure=None)
(Constructor)

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
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

setStructures(self, 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(self, 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(self, index)

Select the current atom in the reference structure

Parameters:

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

mapPair(self, 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.

unmapPair(self, 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(self, 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

autoMap(self)

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(self, 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

Returns: int

The index of the Comparison atom mapped to the given Reference atom

refAtomFromCompAtom(self, 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

Returns: int

The index of the Reference atom mapped to the given Comparison atom

highlightCompAtom(self, comp_index)

Highlight an atom in the Comparision structure

Parameters:

comp_index (int) - The index of the comparison atom to highlight

highlightRefAtom(self, ref_index)

Highlight an atom in the Reference structure

Parameters:

ref_index (int) - The index of the reference atom to highlight

highlightMapPair(self, 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

isInGuessMode(self)

Is the panel currently in guess mode?

Returns: bool: True if the panel is in guess mode, False if not

finishGuess(self)

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(self)

Check if the reordering process is done

Returns: bool: True if all the atoms in one of the structures are mapped

getReorderedStructure(self)

Get a reordered version of the comparison structure

Returns: schrodinger.structure.Structure, list or (None, None): 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.

reset(self, reset_structures=True)

Reset the frame

Parameters:

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

Class ReorderAtomFrame

__init__(self, parent=None, by_element=True, by_smiles=True, by_smarts=True, by_superposition=True, layout=None, reference_structure=None, comparison_structure=None) (Constructor)

setStructures(self, reference, comparison)

guessMode(self, guessmode)

selectRefAtom(self, index)

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

unmapPair(self, ref_index, comp_index)

mapCompAtom(self, comp_index, ref_index=None, auto=True, advance=True)

autoMap(self)

compAtomFromRefAtom(self, index)

refAtomFromCompAtom(self, index)

highlightCompAtom(self, comp_index)

highlightRefAtom(self, ref_index)

highlightMapPair(self, ref_index, comp_index)

isInGuessMode(self)

finishGuess(self)

doneReordering(self)

getReorderedStructure(self)

reset(self, reset_structures=True)

init(self, parent=None, by_element=True, by_smiles=True, by_smarts=True, by_superposition=True, layout=None, reference_structure=None, comparison_structure=None)
(Constructor)