Tool for re-organizing the list of atoms of an IAtomContainer More...

Collaboration diagram for denoptim.utils.AtomOrganizer:

Public Member Functions
	AtomOrganizer ()

void	setScheme (int scheme)

ArrayList< Integer >	getNewToOldOrder (int seed)
	Returns the list of indexes that allow to map the new atom position with the old one. More...

ArrayList< Integer >	getOldToNewOrder (int seed)
	Returns the list of indexes that allow to map the old atom position with the new one. More...

IAtomContainer	reorderStartingFrom (int seed, IAtomContainer mol) throws DENOPTIMException
	Reorder the atoms in `mol starting with atom seed` More...

Static Public Member Functions
static IAtomContainer	makeReorderedCopy (IAtomContainer original, List< Integer > newToOldOrder, List< Integer > oldToNewOrder) throws DENOPTIMException
	Produces a new container that looks very similar to the original one, but has a different atom order. More...

Private Member Functions
void	branchOrienterReordering (int seed, int flag, IAtomContainer mol)
	Reorders atoms according to the branch-oriented scheme. More...

void	exploreMolecule (int seed, int flag, IAtomContainer mol, int ap)
	Method meant for recursion on all atoms connected to a starting point. More...

void	layerOrientedReordering (int seed, int flag, IAtomContainer mol)
	Reorders atoms according to the layer-oriented scheme. More...

void	addAtomToLayer (int atmidx, int ap, int layer, int doneFlag)
	Set the layer membership of an antom. More...

void	processAtom (int atmidx, int ap, int doneFlag)
	Perform all the operation to report an atom in the new order. More...

List< IAtom >	prioritizeAtomList (List< IAtom > inList, IAtomContainer mol)
	Change the order of atoms in a list according to the priority rules defined in the comparator `ConnectedLigandComparator.` More...

int	getFreeAtomsFlag (IAtomContainer mol)
	Generates a vector of boolean flags. More...

void	deleteAtomsFlag (int flagID)
	Destroy a vector of flags. More...

Private Attributes
ArrayList< ArrayList< Boolean > >	flags

Map< Integer, ArrayList< Integer > >	atomOrders

Map< Integer, ArrayList< Integer > >	oldToNewOrder

Map< Integer, Map< Integer, Set< Integer > > >	layers

int	lidx

int	scheme = 1

Detailed Description

Tool for re-organizing the list of atoms of an IAtomContainer

Author: Marco Foscato

Definition at line 47 of file AtomOrganizer.java.

Constructor & Destructor Documentation

◆ AtomOrganizer()

denoptim.utils.AtomOrganizer.AtomOrganizer ( )

Definition at line 69 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.atomOrders, denoptim.utils.AtomOrganizer.flags, denoptim.utils.AtomOrganizer.layers, denoptim.utils.AtomOrganizer.lidx, and denoptim.utils.AtomOrganizer.oldToNewOrder.

Member Function Documentation

◆ addAtomToLayer()

void denoptim.utils.AtomOrganizer.addAtomToLayer	(	int	atmidx,
		int	ap,
		int	layer,
		int	doneFlag
	)

private

Set the layer membership of an antom.

Parameters

atmidx	index of the atom.
ap	index of the seed atom (starting point).
layer	index of the leyer which `atmidx belongs to.`
doneFlag	`index of the flag reminding which atom is already done.`

Definition at line 479 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.flags, and denoptim.utils.AtomOrganizer.layers.

Referenced by denoptim.utils.AtomOrganizer.layerOrientedReordering().

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◆ branchOrienterReordering()

void denoptim.utils.AtomOrganizer.branchOrienterReordering	(	int	seed,
		int	flag,
		IAtomContainer	mol
	)

private

Reorders atoms according to the branch-oriented scheme.

Atoms connected to the seed (starting point) are listed according to the priority rules defined in ConnectedLigandComparator.

Parameters


  
    seed index of the first atom. The starting point. 
    flag index of the flag used to specify that an atom was processed. 
    mol molecular object.

Definition at line 314 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.exploreMolecule(), and denoptim.utils.AtomOrganizer.processAtom().

Referenced by denoptim.utils.AtomOrganizer.reorderStartingFrom().

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◆ deleteAtomsFlag()

void denoptim.utils.AtomOrganizer.deleteAtomsFlag ( int flagID )

private

Destroy a vector of flags.

Parameters

flagID the index of the vector to be destroyed

Definition at line 592 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.flags.

Referenced by denoptim.utils.AtomOrganizer.layerOrientedReordering(), and denoptim.utils.AtomOrganizer.reorderStartingFrom().

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◆ exploreMolecule()

void denoptim.utils.AtomOrganizer.exploreMolecule	(	int	seed,
		int	flag,
		IAtomContainer	mol,
		int	ap
	)

private

Method meant for recursion on all atoms connected to a starting point.

Definition at line 329 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.exploreMolecule(), denoptim.utils.AtomOrganizer.flags, denoptim.utils.AtomOrganizer.prioritizeAtomList(), and denoptim.utils.AtomOrganizer.processAtom().

Referenced by denoptim.utils.AtomOrganizer.branchOrienterReordering(), and denoptim.utils.AtomOrganizer.exploreMolecule().

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◆ getFreeAtomsFlag()

int denoptim.utils.AtomOrganizer.getFreeAtomsFlag ( IAtomContainer mol )

private

Generates a vector of boolean flags.

The size of the vector equals the number of atoms in the IAtomContainer. All flags are initialized to false.

Parameters

mol	molecular object for which the vector of flags has to be generated.

Returns: an integer index referring to the vector of flags.

Definition at line 568 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.flags.

Referenced by denoptim.utils.AtomOrganizer.layerOrientedReordering(), and denoptim.utils.AtomOrganizer.reorderStartingFrom().

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◆ getNewToOldOrder()

ArrayList< Integer > denoptim.utils.AtomOrganizer.getNewToOldOrder ( int seed )

Returns the list of indexes that allow to map the new atom position with the old one.

Namely,

int oldAtmIdx = getNewToOldOrder().get(newAtmIdx);

Returns: the atom ordering list.

Definition at line 97 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.atomOrders.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree().

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◆ getOldToNewOrder()

ArrayList< Integer > denoptim.utils.AtomOrganizer.getOldToNewOrder ( int seed )

Returns the list of indexes that allow to map the old atom position with the new one.

Namely,

int newAtmIdx = getOldToNewOrder().get(seed).get(oldAtmIdx);

Returns: the atom ordering list.

Definition at line 119 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.oldToNewOrder.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree().

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◆ layerOrientedReordering()

void denoptim.utils.AtomOrganizer.layerOrientedReordering	(	int	seed,
		int	flag,
		IAtomContainer	mol
	)

private

Reorders atoms according to the layer-oriented scheme.

Atoms connected to the seed (starting point) are listed according to the distance from the seed atom (distance = number of bonds). All atoms directly connected to the seed, belong to the 1st layer; all atoms connected to the atoms of the 1st layer belong to the 2nd layer and so on. Within each layer atoms are listed according to priority rules that are defined in the ConnectedLigandComparator.

Parameters


  
    seed index of the first atom. The starting point. 
    flag index of the flag uset to specify that an atom was processed. 
    mol molecular object.

Definition at line 398 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.addAtomToLayer(), denoptim.utils.AtomOrganizer.deleteAtomsFlag(), denoptim.utils.AtomOrganizer.flags, denoptim.utils.AtomOrganizer.getFreeAtomsFlag(), denoptim.utils.AtomOrganizer.layers, denoptim.utils.AtomOrganizer.lidx, denoptim.utils.AtomOrganizer.prioritizeAtomList(), and denoptim.utils.AtomOrganizer.processAtom().

Referenced by denoptim.utils.AtomOrganizer.reorderStartingFrom().

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◆ makeReorderedCopy()

static IAtomContainer denoptim.utils.AtomOrganizer.makeReorderedCopy	(	IAtomContainer	original,
		List< Integer >	newToOldOrder,
		List< Integer >	oldToNewOrder
	)		throws DENOPTIMException

static

Produces a new container that looks very similar to the original one, but has a different atom order.

Only selected properties of the original container are projected into the new one, namely

Parameters

original	the container to reorganize.
newToOldOrder	list of atom indexes in the original atom container. The list is supposed to work so that oldIndex = newToOldOrder.get(newIndex); Indexes are 0-based.
oldToNewOrder	list of atom indexes in the new atom container. The list is supposed to work so that newIndex = oldToNewOrder.get(oldIndex); Indexes are 0-based.

Returns: a new container that collects new atoms and new bonds that reflect the original molecule but with a different order of atoms.

Exceptions

DENOPTIMException

Definition at line 208 of file AtomOrganizer.java.

References denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXID, denoptim.constants.DENOPTIMConstants.ATMPROPVERTEXPATH, denoptim.utils.MoleculeUtils.makeSameAtomAs(), denoptim.constants.DENOPTIMConstants.MOLERRORTAG, denoptim.utils.AtomOrganizer.oldToNewOrder, denoptim.constants.DENOPTIMConstants.RCAPROPAPCTORCA, denoptim.constants.DENOPTIMConstants.RCAPROPCHORDBNDTYP, and denoptim.constants.DENOPTIMConstants.RCAPROPRINGUSER.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.buildMulti3DStructure(), and denoptim.utils.AtomOrganizer.reorderStartingFrom().

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◆ prioritizeAtomList()

List< IAtom > denoptim.utils.AtomOrganizer.prioritizeAtomList	(	List< IAtom >	inList,
		IAtomContainer	mol
	)

private

Change the order of atoms in a list according to the priority rules defined in the comparator ConnectedLigandComparator.

Parameters

inList	initial list of atoms.
mol	molecular object which the atoms belongs to.

Returns: the ordered list of atoms.

Definition at line 536 of file AtomOrganizer.java.

Referenced by denoptim.utils.AtomOrganizer.exploreMolecule(), and denoptim.utils.AtomOrganizer.layerOrientedReordering().

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◆ processAtom()

void denoptim.utils.AtomOrganizer.processAtom	(	int	atmidx,
		int	ap,
		int	doneFlag
	)

private

Perform all the operation to report an atom in the new order.

Parameters

atmidx	the index of the atom to be reported
ap	the index of the seed atom (starting point) identifying the reordered list of atoms
doneFlag	index of the flag reminding which atom is already done.

Definition at line 511 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.atomOrders, denoptim.utils.AtomOrganizer.flags, and denoptim.utils.AtomOrganizer.oldToNewOrder.

Referenced by denoptim.utils.AtomOrganizer.branchOrienterReordering(), denoptim.utils.AtomOrganizer.exploreMolecule(), and denoptim.utils.AtomOrganizer.layerOrientedReordering().

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◆ reorderStartingFrom()

IAtomContainer denoptim.utils.AtomOrganizer.reorderStartingFrom	(	int	seed,
		IAtomContainer	mol
	)		throws DENOPTIMException

Reorder the atoms in mol starting with atom seed

Parameters

seed	index of the atom being the seed of the new order
mol	molecule with the original order of atoms

Returns: an IAtomContainer with the new order of atoms

Definition at line 140 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.atomOrders, denoptim.utils.AtomOrganizer.branchOrienterReordering(), denoptim.utils.AtomOrganizer.deleteAtomsFlag(), denoptim.utils.AtomOrganizer.getFreeAtomsFlag(), denoptim.utils.AtomOrganizer.layerOrientedReordering(), denoptim.utils.AtomOrganizer.makeReorderedCopy(), denoptim.utils.AtomOrganizer.oldToNewOrder, and denoptim.utils.AtomOrganizer.scheme.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree().

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◆ setScheme()

void denoptim.utils.AtomOrganizer.setScheme ( int scheme )

Definition at line 80 of file AtomOrganizer.java.

References denoptim.utils.AtomOrganizer.scheme.

Referenced by denoptim.molecularmodeling.MultiMolecularModelBuilder.build3DTree().

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Member Data Documentation

◆ atomOrders

Map<Integer, ArrayList<Integer> > denoptim.utils.AtomOrganizer.atomOrders

private

Definition at line 56 of file AtomOrganizer.java.

Referenced by denoptim.utils.AtomOrganizer.AtomOrganizer(), denoptim.utils.AtomOrganizer.getNewToOldOrder(), denoptim.utils.AtomOrganizer.processAtom(), and denoptim.utils.AtomOrganizer.reorderStartingFrom().

◆ flags

ArrayList<ArrayList<Boolean> > denoptim.utils.AtomOrganizer.flags

private

Definition at line 54 of file AtomOrganizer.java.

Referenced by denoptim.utils.AtomOrganizer.addAtomToLayer(), denoptim.utils.AtomOrganizer.AtomOrganizer(), denoptim.utils.AtomOrganizer.deleteAtomsFlag(), denoptim.utils.AtomOrganizer.exploreMolecule(), denoptim.utils.AtomOrganizer.getFreeAtomsFlag(), denoptim.utils.AtomOrganizer.layerOrientedReordering(), and denoptim.utils.AtomOrganizer.processAtom().

◆ layers

Map<Integer, Map<Integer, Set<Integer> > > denoptim.utils.AtomOrganizer.layers

private

Definition at line 59 of file AtomOrganizer.java.

Referenced by denoptim.utils.AtomOrganizer.addAtomToLayer(), denoptim.utils.AtomOrganizer.AtomOrganizer(), and denoptim.utils.AtomOrganizer.layerOrientedReordering().

◆ lidx

int denoptim.utils.AtomOrganizer.lidx

private

Definition at line 61 of file AtomOrganizer.java.

Referenced by denoptim.utils.AtomOrganizer.AtomOrganizer(), and denoptim.utils.AtomOrganizer.layerOrientedReordering().

◆ oldToNewOrder

Map<Integer, ArrayList<Integer> > denoptim.utils.AtomOrganizer.oldToNewOrder

private

Definition at line 57 of file AtomOrganizer.java.

Referenced by denoptim.utils.AtomOrganizer.AtomOrganizer(), denoptim.utils.AtomOrganizer.getOldToNewOrder(), denoptim.utils.AtomOrganizer.makeReorderedCopy(), denoptim.utils.AtomOrganizer.processAtom(), and denoptim.utils.AtomOrganizer.reorderStartingFrom().

◆ scheme

int denoptim.utils.AtomOrganizer.scheme = 1

private

Definition at line 65 of file AtomOrganizer.java.

Referenced by denoptim.utils.AtomOrganizer.reorderStartingFrom(), and denoptim.utils.AtomOrganizer.setScheme().

The documentation for this class was generated from the following file:

/github/workspace/src/main/java/denoptim/utils/AtomOrganizer.java

seed	index of the first atom. The starting point.
flag	index of the flag used to specify that an atom was processed.
mol	molecular object.

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ AtomOrganizer()

Member Function Documentation

◆ addAtomToLayer()

◆ branchOrienterReordering()

◆ deleteAtomsFlag()

◆ exploreMolecule()

◆ getFreeAtomsFlag()

◆ getNewToOldOrder()

◆ getOldToNewOrder()

◆ layerOrientedReordering()

◆ makeReorderedCopy()

◆ prioritizeAtomList()

◆ processAtom()

◆ reorderStartingFrom()

◆ setScheme()

Member Data Documentation

◆ atomOrders

◆ flags

◆ layers

◆ lidx

◆ oldToNewOrder

◆ scheme