chemaxon.struc

Class SelectionMolecule

java.lang.Object

chemaxon.struc.MoleculeGraph

chemaxon.struc.SelectionMolecule

All Implemented Interfaces:

chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>, chemaxon.core.structure.MoleculeForBuilder, chemaxon.core.structure.RootStructureForBuilder, chemaxon.core.structure.StructureForBuilder, Incomplecule, MTransformable, StereoConstants, Serializable

public class SelectionMolecule
extends MoleculeGraph

A selection object which can contain atoms and bonds without real parent relationship (the real parent of atoms and bonds is another MoleculeGraph ancestor).

Since:

Marvin 3.0

Version:

5.3, 05/26/2009

Author:

Peter Csizmadia

See Also:

Serialized Form

Property Summary

Properties inherited from class chemaxon.struc.MoleculeGraph

hasSelfReferringProperty

Nested Class Summary

Nested classes/interfaces inherited from class chemaxon.struc.MoleculeGraph

MoleculeGraph.ValenceCheckState

Field Summary

Fields inherited from class chemaxon.struc.MoleculeGraph

AROM_AMBIGUOUS, AROM_BASIC, AROM_GENERAL, AROM_LOOSE, AROM_SUBSTRUCTURE, atomCount, AUTO_UNGROUP, bondCount, btab, CACHE_REMOVE_ALL, CACHE_REMOVE_AROMATAMODULE, CACHE_REMOVE_CACHEMEMORY, CACHE_REMOVE_GRINVMODULE, CACHE_REMOVE_PARITYMODULE, CACHE_REMOVE_SSSRMODULE, CACHE_REMOVE_TABS, cacheMemory, ctab, DEAROM_GENERAL, DEAROM_HUCKELCHECK, DEAROM_HUCKELCHECK_EX, DIM_MASK, FRAG_BASIC, FRAG_KEEPING_MULTICENTERS, FRAG_KEEPING_SGROUPS, FRAG_TYPE_COUNT, gearch, GRINV_DONT_STORE, GRINV_NOHYDROGEN, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_USEMAPS, GRINV_VALUE_OPTIONS, grinvCC, INITIAL_CAPACITY, INVALID_LINKNODE_MESSAGE, MIN_RING_SIZE_FOR_TRANS_DB, OMIT_POSTCLEAN, orix, oriy, oriz, parentGraph, propertyContainer, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_FIXCOMPONENT, RMCLEANUP_MOBJECT, RMCLEANUP_NONE, RMCLEANUP_PARENTDOC, RMCLEANUP_STEREO, superGraph, theAtoms, theBonds, useOnlyFirstAtomInStereoCalculation, VALENCE_CHECK, VALENCE_CHECK_AMBIGUOUS

Fields inherited from interface chemaxon.struc.StereoConstants

ANTI, ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_M, CHIRALITY_MASK, CHIRALITY_P, CHIRALITY_r, CHIRALITY_R, CHIRALITY_s, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS

Constructor Summary

Constructors

Constructor and Description
SelectionMolecule()

Method Summary

Methods

Modifier and Type	Method and Description
void	add(MolAtom atom) Adds an atom to the molecule.
void	add(MolAtom atom, boolean addBonds) Adds an atom to the molecule.
void	add(MolBond bond) Adds a bond to the graph.
void	add(MolBond bond, boolean checkParallel) Add a bond to the molecule.
protected void	addAtom0(MolAtom atom) Adds an atom.
protected void	addAtomWithBonds(MolAtom atom) Adds an atom to the molecule.
protected int	addAtomWithoutChangingIt(MolAtom atom) Adds an atom without setting its parentGraph and index fields.
protected void	addBond0(MolBond bond) Adds a bond.
protected void	checkBondConsistency() Empty implementation, bond consistency is not checked in case of selections.
SelectionMolecule	clone() Create a clone of this SelectionMolecule.
void	clonecopy(MoleculeGraph graph) Copies the clones of atoms and bonds of this graph to another one.
protected boolean	clonecopyMoleculeGraphWithoutSgroups(int[] iatoms, MolBond[] cbonds, int nb, MoleculeGraph g) Copies the specified atoms and bonds of this graph to another one.
protected chemaxon.struc.gearch.MoleculeGraphGearch	createGearch()
protected void	fuse0(MoleculeGraph g, boolean check) Adds those atoms and bonds of a graph to this one that are not already elements.
Integer[]	getLigands(Integer atom)
protected boolean	isGrinvCCValid() Tests whether the graph invariant change count is valid.
protected boolean	isRealAtomParent() Selection molecules are not real atom parents.
protected void	regenCtabs() Regenerates connection table and bond table.
void	removeAtom(int i) Removes an atom and its bonds from the graph.
void	removeAtom(MolAtom atom) Removes an atom and its bonds.
void	removeBond(int i) Removes a bond from the graph.
void	removeBond(MolBond bond) Removes a bond by reference.
protected void	setAtom0(int i, MolAtom atom) Sets the atom at the specified index.
void	setBond(int i, MolBond bond) Deprecated. as of Marvin 6.2. Use removeBond(MolBond) for bond removal and add(MolBond) for adding a new bond to the molecule.
void	swapAtoms(int i, int j) Swap two atoms.
void	transform(CTransform3D t) Apply a transformation matrix to the atomic coordinates.

Methods inherited from class chemaxon.struc.MoleculeGraph

addAtomsAndBondsTo, addAtomToFragment, addBondWithoutChangingIt, addExplicitHydrogens, addExplicitHydrogens, addExplicitLonePairs, addSimpleAtomWithoutChangingIt, adjustMultiChiralFlag, aromatize, aromatize, aromatize, aromatize, arrangeComponents, bondlength, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcHybridization, calcOutRect, calcOutRect, calcOutRectCenter, calcOutRectCenter, calcWidth, canBeCT, canBeCT, canBeCT, checkConsistency, clean, clean, clear, clearCachedInfo, clearForImport, cloneAtoms, clonecopy, clonelesscopy, connectOriginalBondsToNewAtom, contains, contains, contains, createBHtab, createCHtab, createDehydrogenizedReadOnlyGraph, createSmolecule, dearomatize, dearomatize, findAtom, findAtomClone, findBasicFrags, findBond, findComponentIds, findComponentIds, findFrag, findFrag, findFragById, findFrags, findFrags, findInArray, fixSelfReferringProperty, fuse, fuse, getAromaticAndAliphaticRings, getAtom, getAtomArray, getAtomCount, getAtomCount, getAtomicNumber, getAtomIterator, getAtomReferenceList, getBond, getBondArray, getBondCount, getBondIterator, getBonds, getBondTable, getBtab, getCharge, getChirality, getCSSR, getCtab, getDesiredLength, getDesiredLength, getDim, getDocument, getDocumentForChild, getEnclosingCube, getExactMass, getExplicitHcount, getExplicitLonePairCount, getEZStereo, getFlags, getForefather, getFormalCharge, getFormula, getFragCount, getFragCount, getFragIds, getFreeAttachmentPoints, getGraphUnion, getGrinv, getGrinv, getGrinv, getGrinv, getGrinvCC, getGrinvOptions, getImplicitHcount, getImplicitHCount, getLigand, getLigandAtno, getLigandBondType, getLigandCount, getLocalParity, getLocation, getLock, getLonePairCount, getMass, getMaxRgroupAttachmentPointOrder, getName, getParent, getParentDocument, getParity, getParityType, getPoints, getPossibleAttachmentPoints, getRadicalCount, getSmallestRingSizeForIdx, getSSSR, getSSSRBonds, getSSSRBondsAsBitSet, getSSSRBondSet, getSSSRBondSetInLong, getSSSRIdxesForAtoms, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphCount, getSubGraphs, getSubGraphs, getTotalCharge, getValenceCheckOptions, getValenceCheckState, getValenceProperty, getVisibleCoords, hasAtomSet, hasBondSet, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, implicitizeHydrogens, implicitizeHydrogens0, incGrinvCC, incGrinvCC, incGrinvCCOnly, indexOf, indexOf, insertAtom, insertBond, insertBondInOrder, insertNullAtoms, insertNullBonds, isAbsStereo, isAcceptedSpecialLigand, isAtom, isAtomInRing, isBond, isBondParallelWith, isEmpty, isLargeMolecule, isMolecule, isMultiChiral, isolate, isolate, isOnlyFirstAtomInStereoCalculation, isQuery, isRing, isRingBond, isSelfReference, isSimilarTo, isSymmetric, isValenceCheckEnabled, isValidLinkNode, makeItSimilar, mergeAtoms, mergeFrags, moveTo, newInstance, pack, partialClean, partialClean, partialClean, properties, qpropCheck, regenBonds, regenGearch, removeAll, removeAllBonds, removeAtom, removeAtom, removeBond, removeBond, removeExplicitLonePairs, removeIsolatedAtoms, removeIsolatedBonds, replaceAtom, replaceBond, resetCtab, resetGrinvInParents, restoreCache, revalidateCoordDependentProps, saveCache, setAbsStereo, setAtom, setAtomSetSeqs, setBondSetSeqs, setChirality, setChirality, setDim, setFlags, setFlags, setGrinvCC, setGrinvOptions, setLinkNodeDefaultOuters, setLocalParity, setLocalParity, setLocation, setParity, setParity, setParity, setSupergraph, setValenceCheckEnabled, setValenceCheckOptions, setValenceCheckState, smol, sortBondsAccordingTo, stereoClean, sumConservedQuantities, toString, transform, updateDim, useOnlyFirstAtomInStereoCalculation, valenceCheck, valenceCheck

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Detail

SelectionMolecule

public SelectionMolecule()

Method Detail

isRealAtomParent

protected boolean isRealAtomParent()

Selection molecules are not real atom parents. However, in some special cases a selection molecule can be an atom parent.

Overrides:

isRealAtomParent in class MoleculeGraph

Returns:

false

Since:

Marvin 3.0

setBond

@Deprecated
public void setBond(int i,
                      MolBond bond)

Deprecated. as of Marvin 6.2. Use removeBond(MolBond) for bond removal and add(MolBond) for adding a new bond to the molecule.

Sets the bond at the specified index.

Overrides:

setBond in class MoleculeGraph

Parameters:

i - bond index

bond - the bond reference

add

public void add(MolBond bond)

Adds a bond to the graph. If the bond doesn't have parent molecule then the bond is also added to its end-points.

Overrides:

add in class MoleculeGraph

Parameters:

bond - the bond object

add

public void add(MolBond bond,
       boolean checkParallel)

Add a bond to the molecule. If the second parameter is true, there an exception thrown when there is already a bond between the given MolAtoms. There is no checking if either is SgroupAtom. If the molecule graph is a superGraph, the bond is also added to its endpoints (two MolAtom objects).

Overrides:

add in class MoleculeGraph

Parameters:

bond - the bond object

checkParallel -

add

public void add(MolAtom atom)

Adds an atom to the molecule. It doesn't add the bonds of the atom to the molecule.

Overrides:

add in class MoleculeGraph

Parameters:

atom - the atom object

add

public void add(MolAtom atom,
       boolean addBonds)

Adds an atom to the molecule. It the second parameter is true, then adds the bonds of the atom to the molecule, if the bond's other atom is already added.

Parameters:

atom -

addBonds -

Since:

Marvin 6.1, 04/30/2013

addAtomWithBonds

protected void addAtomWithBonds(MolAtom atom)

Adds an atom to the molecule. Adds the bonds of the atom to the molecule, if the bond's other atom is already added.

Parameters:

atom -

Since:

Marvin 6.1, 04/30/2013

swapAtoms

public void swapAtoms(int i,
             int j)

Swap two atoms.

Parameters:

i - index of the first atom

j - index of the second atom

Since:

Marvin 3.3, 11/04/2003

removeAtom

public void removeAtom(MolAtom atom)

Removes an atom and its bonds.

Overrides:

removeAtom in class MoleculeGraph

Parameters:

atom - the atom

removeAtom

public void removeAtom(int i)

Removes an atom and its bonds from the graph.

Overrides:

removeAtom in class MoleculeGraph

Parameters:

i - the atom index

removeBond

public void removeBond(MolBond bond)

Removes a bond by reference.

Overrides:

removeBond in class MoleculeGraph

Parameters:

bond - the bond

removeBond

public void removeBond(int i)

Removes a bond from the graph.

Overrides:

removeBond in class MoleculeGraph

Parameters:

i - the bond index

addAtom0

protected void addAtom0(MolAtom atom)

Adds an atom.

Overrides:

addAtom0 in class MoleculeGraph

Parameters:

atom - the atom reference

setAtom0

protected void setAtom0(int i,
            MolAtom atom)

Sets the atom at the specified index.

Overrides:

setAtom0 in class MoleculeGraph

Parameters:

i - atom index

atom - new atom reference

addBond0

protected void addBond0(MolBond bond)

Adds a bond.

Overrides:

addBond0 in class MoleculeGraph

Parameters:

bond - the bond reference

regenCtabs

protected void regenCtabs()

Regenerates connection table and bond table.

Overrides:

regenCtabs in class MoleculeGraph

Since:

Marvin 3.5.2, 12/16/2004

fuse0

protected void fuse0(MoleculeGraph g,
         boolean check)

Adds those atoms and bonds of a graph to this one that are not already elements.

Overrides:

fuse0 in class MoleculeGraph

Parameters:

g - the graph

check - true if a containment check should be performed to ensure that only those atoms and bonds are added that are not already elements - false if the graph is known to be disjoint from this graph and this check can be safely skipped

Since:

Marvin 5.0

transform

public void transform(CTransform3D t)

Apply a transformation matrix to the atomic coordinates.

Specified by:

transform in interface MTransformable

Overrides:

transform in class MoleculeGraph

Parameters:

t - the transformation matrix

clonecopy

public void clonecopy(MoleculeGraph graph)

Copies the clones of atoms and bonds of this graph to another one.

Overrides:

clonecopy in class MoleculeGraph

Parameters:

graph - the target graph

clonecopyMoleculeGraphWithoutSgroups

protected boolean clonecopyMoleculeGraphWithoutSgroups(int[] iatoms,
                                           MolBond[] cbonds,
                                           int nb,
                                           MoleculeGraph g)

Copies the specified atoms and bonds of this graph to another one.

Overrides:

clonecopyMoleculeGraphWithoutSgroups in class MoleculeGraph

Parameters:

iatoms - array of atoms indices to copy

cbonds - array of bonds to copy or null to copy bonds in cbonds only

nb - number of bonds

g - the target graph

Returns:

false if the bonds array contains all bond end points, true if there is at least one external bond

Since:

Marvin 5.0.2, 03/07/2008

clone

public SelectionMolecule clone()

Create a clone of this SelectionMolecule.

Overrides:

clone in class MoleculeGraph

Returns:

the cloned SelectionMolecule

isGrinvCCValid

protected boolean isGrinvCCValid()

Tests whether the graph invariant change count is valid.

Overrides:

isGrinvCCValid in class MoleculeGraph

Returns:

false

Since:

Marvin 5.0, 11/30/2007

checkBondConsistency

protected void checkBondConsistency()

Empty implementation, bond consistency is not checked in case of selections.

Overrides:

checkBondConsistency in class MoleculeGraph

Since:

Marvin 5.0, 11/06/2007

createGearch

protected chemaxon.struc.gearch.MoleculeGraphGearch createGearch()

Overrides:

createGearch in class MoleculeGraph

getLigands

public Integer[] getLigands(Integer atom)

addAtomWithoutChangingIt

protected final int addAtomWithoutChangingIt(MolAtom atom)

Adds an atom without setting its parentGraph and index fields.

Overrides:

addAtomWithoutChangingIt in class MoleculeGraph

Parameters:

atom - the atom reference

Returns:

the new atom index