Package chemaxon.struc

Class RxnMolecule

java.lang.Object
chemaxon.struc.MoleculeGraph
chemaxon.struc.Molecule
chemaxon.struc.RxnMolecule
All Implemented Interfaces:
MoleculeWithValence<MolAtom>, chemaxon.core.structure.MoleculeForBuilder, chemaxon.core.structure.ReactionForBuilder, chemaxon.struc.MObjectContainer, MTransformable, StereoConstants, Serializable
@PublicApi public class RxnMolecule extends Molecule implements chemaxon.struc.MObjectContainer, chemaxon.core.structure.ReactionForBuilder
Reaction.
Since:
Marvin 2.9
See Also:

  • Field Details

    • TYPE_COUNT

      public static final int TYPE_COUNT
      Number of structure types. Currently 3: REACTANTS, PRODUCTS, AGENTS.
      See Also:

    • REACTANTS

      public static final int REACTANTS
      "Reactant" structure type.
      See Also:

    • PRODUCTS

      public static final int PRODUCTS
      "Product" structure type.
      See Also:

    • AGENTS

      public static final int AGENTS
      "Agent" structure type.
      See Also:

    • RGROUPED

      public static final int RGROUPED
      Add R-groups to component structure.
      Since:
      Marvin 3.1
      See Also:

    • TYPE_MASK

      public static final int TYPE_MASK
      Component type mask.
      Since:
      Marvin 3.1
      See Also:

    • REGULAR_SINGLE

      public static final int REGULAR_SINGLE
      Regular single reaction arrow type.
      Since:
      Marvin 5.1, 02/28/2008
      See Also:

    • TWO_HEADED_SINGLE

      public static final int TWO_HEADED_SINGLE
      Two headed single reaction arrow type.
      Since:
      Marvin 5.1, 02/28/2008
      See Also:

    • REGULAR_DOUBLE

      public static final int REGULAR_DOUBLE
      Regular double reaction arrow type.
      Since:
      Marvin 5.1, 02/28/2008
      See Also:

    • TWO_HEADED_DOUBLE

      public static final int TWO_HEADED_DOUBLE
      Two headed double reaction arrow type.
      Since:
      Marvin 5.1, 02/28/2008
      See Also:

    • RESONANCE

      public static final int RESONANCE
      Resonance arrow, the same as the two-headed single reaction arrow.
      Since:
      Marvin 5.2 27/01/2009
      See Also:

    • RETROSYNTHETIC

      public static final int RETROSYNTHETIC
      Retrosynthetic arrow, the same as the regular double reaction arrow.
      Since:
      Marvin 5.2 27/01/2009
      See Also:

    • EQUILIBRIUM

      public static final int EQUILIBRIUM
      Resonance arrow, the same as the two-headed double reaction arrow.
      Since:
      Marvin 5.2 27/01/2009
      See Also:

  • Constructor Details

    • RxnMolecule

      public RxnMolecule()
      Create a reaction.

  • Method Details

    • createReaction

      public static RxnMolecule createReaction(Molecule mol, DPoint3[] arw, int art)
      Creates a reaction.
      Parameters:
      mol - contains the atoms of reactants and products
      arw - two-element array containing the endpoints of the reaction arrow
      art - the arrow type
      Returns:
      the reaction

    • createReaction

      public static RxnMolecule createReaction(MoleculeGraph mol, DPoint3[] arw)
      Creates a reaction.
      Parameters:
      mol - contains the atoms of reactants and products
      arw - two-element array containing the endpoints of the reaction arrow
      Returns:
      the reaction

    • determineArrowDistance

      public static double determineArrowDistance(double x, double y, double z, DPoint3[] ar)
      Project the point (x,y,z) to the line of the reaction arrow 'ar'. Return the signed distance of the projected point from the start-point of the arrow divided by the arrow length.
      Parameters:
      x - is the x coordinate of the point
      y - is the y coordinate of the point
      z - is the z coordinate of the point
      ar - is the reaction arrow
      Returns:
      the signed distance of the projected point from the start-point of the arrow divided by the arrow length

    • determineType

      public static int determineType(double x, double y, double z, DPoint3[] ar)
      Determines whether a point should be in a reactant, in a product or in an agent.
      Parameters:
      x - point x coordinate
      y - point y coordinate
      z - point z coordinate
      ar - reaction arrow
      Returns:
      REACTANTS, PRODUCTS or AGENTS

    • getReaction

      public static RxnMolecule getReaction(MoleculeGraph g)
      Returns the reaction represented by the given molecule if exists, otherwise null. The corresponding reaction molecule is either the molecule itself or its root structure.
      Parameters:
      g - the molecule graph
      Returns:
      the corresponding reaction molecule

    • add

      public void add(MolAtom a)
      Adds an atom to a reactant, product or agent structure. If a neighbour of the atom is in a reactant, product or agent, then adds the atom to that structure. Otherwise creates a new reactant or product.
      Overrides:
      add in class MoleculeGraph
      Parameters:
      a - the new atom

    • add

      public void add(MolBond e)
      Adds a bond to a reactant, product, agent. If an endpoint of the edge is in a reactant, product or agent, then adds the edge to that structure.
      Overrides:
      add in class Molecule
      Parameters:
      e - the new edge

    • addComponent

      public void addComponent(Molecule m, int type) throws IllegalArgumentException
      Adds a reactant, product or agent. If atoms in the specified structure are already part of some other reactants, products or agents then removes them from those structures.
      Parameters:
      m - the reactant, product or agent
      type - REACTANTS, PRODUCTS or AGENTS
      Throws:
      IllegalArgumentException - if m is of a subclass of Molecule for which the embedding in an RxnMolecule is not supported

    • addComponent

      public void addComponent(Molecule m, int type, boolean beNew) throws IllegalArgumentException
      Adds a reactant, product or agent. If atoms in the specified structure are already part of some other reactants, products or agents then removes them from those structures.
      Parameters:
      m - the reactant, product or agent
      type - REACTANTS, PRODUCTS or AGENTS
      beNew - m should be a new structure if true
      Throws:
      IllegalArgumentException - if m is of a subclass of Molecule for which the embedding in an RxnMolecule is not supported

    • addSgroup

      public void addSgroup(Sgroup sg, boolean setparent)
      Adds an S-group to this object.
      Overrides:
      addSgroup in class Molecule
      Parameters:
      sg - the S-group to add.
      setparent - if true then the parent of the S-group is set to the root or that R-group member of this molecule which contains the S-group and the S-group is removed from the old parent molecule.

    • canBeReactionComponent

      public boolean canBeReactionComponent()
      Tests whether an object of this class can be a reaction component. This implementation returns false, RxnMolecules cannot be embedded in each other.
      Overrides:
      canBeReactionComponent in class Molecule
      Returns:
      true if it can be a reactant, product or agent, false if adding it to an RxnMolecule is not supported
      Since:
      Marvin 4.1.13, 09/19/2007

    • clearForImport

      public void clearForImport(String fmt)
      Clear the edges vector and the properties.
      Overrides:
      clearForImport in class Molecule
      Parameters:
      fmt - input file format. See the text formats on the File Formats in Marvin page.
      See Also:

    • clearObjects

      public void clearObjects()
      Deletes the graphical objects from this.
      Specified by:
      clearObjects in interface chemaxon.struc.MObjectContainer
      Overrides:
      clearObjects in class Molecule

    • clone

      public RxnMolecule clone()
      Make an identical copy of the reaction structure. Document is not cloned!
      Overrides:
      clone in class Molecule
      Returns:
      the copy

    • clonecopy

      public void clonecopy(int[] iatoms, MoleculeGraph g)
      Copies the specified nodes and edges of this graph to another one. The RxnMolecule implementation of this method is incomplete.
      Overrides:
      clonecopy in class Molecule
      Parameters:
      iatoms - array of atom indices to copy
      g - the target graph
      Since:
      Marvin 5.0.2, 03/11/2008

    • clonecopy

      public void clonecopy(MoleculeGraph g)
      Make another molecule identical to this one.
      Overrides:
      clonecopy in class Molecule
      Parameters:
      g - the target structure

    • clonelesscopy

      @Deprecated public void clonelesscopy(MoleculeGraph g)
      Deprecated.
      as of Marvin 6.3.
      Not supported feature.
      Copy to selection. Make another molecule identical to this one, but do not clone atoms, bonds, and the props.
      Overrides:
      clonelesscopy in class Molecule
      Parameters:
      g - the target structure

    • cloneMoleculeWithDocument

      public RxnMolecule cloneMoleculeWithDocument()
      Description copied from class: Molecule
      Makes an identical copy of the molecule and its document. If the molecule does not have a parent, then copies non-molecular data: graphics objects, electron flows, text boxes, atom and bond sets (color, font and thickness). Otherwise (root, rgroup, component molecule) creates a new document.
      Overrides:
      cloneMoleculeWithDocument in class Molecule
      Returns:
      the copy

    • contains

      public boolean contains(MolAtom node)
      Checks if a reactant, agent or product structure contains the specified node.
      Overrides:
      contains in class Molecule
      Parameters:
      node - the node object
      Returns:
      true if the graph contains the object, false otherwise

    • contains

      public boolean contains(MolBond edge)
      Checks if a reactant, agent or product structure contains the specified edge.
      Overrides:
      contains in class MoleculeGraph
      Parameters:
      edge - the edge object
      Returns:
      true if the graph contains the object, false otherwise
      See Also:

    • determineType

      public int determineType(double x, double y, double z)
      Determines whether a point should be in a reactant, in a product or in an agent.
      Parameters:
      x - point x coordinate
      y - point y coordinate
      z - point z coordinate
      Returns:
      REACTANTS, PRODUCTS or AGENTS

    • fixProperties

      public void fixProperties()
      Description copied from class: MoleculeGraph
      Delegates to tracker's fixProperties().
      Overrides:
      fixProperties in class MoleculeGraph

    • fuse

      public void fuse(MoleculeGraph graph, boolean check)
      Add the atoms and bonds of another molecule.
      Overrides:
      fuse in class MoleculeGraph
      Parameters:
      graph - the other molecule
      check - true if a containment check should be performed to ensure that only those nodes and edges 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

    • fuse

      public void fuse(RxnMolecule rxnMol)
      Fuse and RxnMolecule to this RxnMolecule. Adds the reactants of the parameter to the reactants, the agents of the parameter to the agents and the products of the parameter to the products.
      Since:
      Marvin 6.2, 09/23/2013

    • getAgent

      public Molecule getAgent(int i)
      Gets an agent.
      Parameters:
      i - agent index
      Returns:
      an agent

    • getAgentCount

      public int getAgentCount()
      Gets the number of agents.
      Returns:
      the number of agents

    • getAgents

      public Molecule[] getAgents()
      Gets all agents in an array.
      Returns:
      the agents
      Since:
      Marvin 5.3

    • getAllFragments

      public List<Molecule> getAllFragments()
      Gets the list of reaction fragments (product, reactant, agent components) that build up this reaction.
      Returns:
      the list of fragments (Molecule)
      Since:
      Marvin 5.0, 12/06/2007
      See Also:

    • getAllObjects

      public List<MObject> getAllObjects()
      Specified by:
      getAllObjects in interface chemaxon.struc.MObjectContainer
      Overrides:
      getAllObjects in class Molecule

    • getArrowAsProperty

      public MPropertyContainer getArrowAsProperty()
      Gets the properties (type, endpoint coordinates) of the reaction arrow in this reaction.
      Returns:
      the properties

    • getAtom

      public MolAtom getAtom(int i)
      Gets a node.
      Overrides:
      getAtom in class MoleculeGraph
      Parameters:
      i - node index
      Returns:
      the node object

    • getAtomCount

      public int getAtomCount()
      Returns the number of nodes in the graph union.
      Overrides:
      getAtomCount in class MoleculeGraph
      Returns:
      the number of nodes

    • getAtomCount

      public int getAtomCount(int atomicNumber)
      Gets the number of atoms with the given atomic number in the unified molecule graph of the reaction. When atomicNumber is 1, sum includes only explicit Hydrogen atoms (but also D and T isotopes).
      Overrides:
      getAtomCount in class MoleculeGraph
      Parameters:
      atomicNumber - atomic number of atoms looked for
      Returns:
      number of atoms with the given atomic number
      Since:
      Marvin 5.5, 27/01/2011

    • getAtomIterator

      public IteratorFactory.AtomIterator getAtomIterator()
      Returns an iterator over the atoms in this molecule in proper sequence.
      Overrides:
      getAtomIterator in class MoleculeGraph
      Returns:
      an iterator over the atoms in this molecule in proper sequencer
      Since:
      Marvin 6.2, 2013.09.09.

    • getBond

      public MolBond getBond(int i)
      Gets an edge.
      Overrides:
      getBond in class MoleculeGraph
      Parameters:
      i - edge index in the graph union
      Returns:
      the edge object

    • getBondCount

      public int getBondCount()
      Gets the number of edges in the graph union.
      Overrides:
      getBondCount in class MoleculeGraph
      Returns:
      the number of edges

    • getBondIterator

      public IteratorFactory.BondIterator getBondIterator()
      Returns an iterator over the bonds in this molecule in proper sequence.
      Overrides:
      getBondIterator in class MoleculeGraph
      Returns:
      an iterator over the bonds in this molecule in proper sequence
      Since:
      Marvin 6.2, 2013.09.09.

    • getBondTable

      public BondTable getBondTable()
      Gets the bond table for the graph union. If there is no bond table for the molecule, then create it. btab.elementAt(i, j) will be the index of the bond between atoms i and j, or -1 if there is no bond.
      Overrides:
      getBondTable in class MoleculeGraph
      Returns:
      the btab array
      Since:
      Marvin 5.4

    • getCenter

      public DPoint3 getCenter(int type, int i)
      Gets the geometrical center of a reaction component.
      Parameters:
      type - REACTANTS, PRODUCTS or AGENTS
      i - reactant, product or agent index
      Returns:
      the center of mass

    • getComponent

      public Molecule getComponent(int typeFlag, int i)
      Gets a reactant, product or agent.

      Warning! The RGROUPED flag returns an RgMolecule object having the same atom objects as the original reactant/product/agent. The parent of the atom objects is unchanged (it is the original reactant/product/agent).

      Parameters:
      typeFlag - REACTANTS, PRODUCTS or AGENTS, can be combined with RGROUPED
      i - reactant, product or agent index
      Returns:
      a reactant, product or agent
      Since:
      Marvin 4.1, 11/19/2005

    • getComponent

      public Molecule getComponent(long id)
      Gets a reactant, product or agent.

      Warning! The RGROUPED flag returns an RgMolecule object having the same atom objects as the original reactant/product/agent. The parent of the atom objects is unchanged (it is the original reactant/product/agent).

      Parameters:
      id - the reaction component ID
      Returns:
      a reactant, product or agent
      Since:
      Marvin 4.1, 11/19/2005
      See Also:

    • getComponentCount

      public int getComponentCount(int type)
      Gets the number of reactants, products or agents.
      Parameters:
      type - REACTANTS, PRODUCTS or AGENTS
      Returns:
      the number of reactants, products or agents
      Since:
      Marvin 4.1, 11/19/2005

    • getComponentFlags

      public int getComponentFlags(long id)
      Gets the reaction component type flags from the ID.
      Parameters:
      id - the reaction component ID or -1
      Returns:
      the reaction component type or -1
      Since:
      Marvin 4.1, 11/19/2005

    • getComponentID

      public long getComponentID(MolAtom atom)
      Gets the reaction component ID of an atom.
      Parameters:
      atom - the atom
      Returns:
      the reaction component ID or -1 if not found
      Since:
      Marvin 4.1, 11/19/2005

    • getComponentID

      public long getComponentID(MolBond bond)
      Gets the reaction component ID of a bond.
      Parameters:
      bond - the bond
      Returns:
      the reaction component ID or -1 if not found
      Since:
      Marvin 4.1, 11/19/2005

    • getComponentID

      public long getComponentID(Molecule molecule)
      Gets the ID of a reaction component.
      Parameters:
      molecule - the reaction component
      Returns:
      the reaction component ID or -1 if not found
      Since:
      Marvin 4.1, 11/19/2005

    • getComponentIndex

      public int getComponentIndex(long id)
      Gets the reactant, product or agent index from the ID.
      Parameters:
      id - the reaction component ID or -1
      Returns:
      the reaction component index or -1
      Since:
      Marvin 4.1, 11/19/2005

    • getComponentType

      public int getComponentType(long id)
      Gets the reaction component type from the ID.
      Parameters:
      id - the reaction component ID or -1
      Returns:
      the reaction component type or -1
      Since:
      Marvin 4.1, 11/19/2005

    • getCtab

      public int[][] getCtab()
      Gets the connection table for the graph union. If there is no connection table for the molecule, then create it. ctab[i][j] will be the index of the jth neighbor of the ith atom.
      Overrides:
      getCtab in class MoleculeGraph
      Returns:
      the ctab array

    • getFormula

      public String getFormula()
      Gets the molecular formula in Hill order.
      Overrides:
      getFormula in class MoleculeGraph
      Returns:
      the formula

    • getGraphUnion

      public MoleculeGraph getGraphUnion()
      Gets a graph containing all the atoms and bonds.
      Overrides:
      getGraphUnion in class MoleculeGraph
      Returns:
      the unified structure
      Since:
      Marvin 3.0, 11/11/2002
      See Also:

    • getItsArrow

      public MRArrow getItsArrow()
      Gets the reaction arrow of this reaction. If the arrow is not yet set creates one.
      Returns:
      the reaction arrow of this reaction
      Since:
      Marvin 5.0, 12/06/2007

    • getLocalParity

      public int getLocalParity(int i)
      Computes the local parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those. The molecule symmetry is not checked, so even an atom with same ligands can have parity. Leaves the imported parity unchanged. Contracted sgroups must be expanded to achieve consistent result.
      Overrides:
      getLocalParity in class MoleculeGraph
      Parameters:
      i - the index of the atom whose parity is to be determined
      Returns:
      PARITY_ODD or PARITY_EVEN for atoms of odd or even parity, PARITY_EITHER for atoms with wiggly bond 0 for atoms whose parity is unspecified or not known.
      Throws:
      SecurityException - the Parity module cannot be loaded because of security reasons (firewall)
      See Also:

    • getMass

      public double getMass()
      Calculates the molecular weight of the molecule. Always returns 0 for reactions
      Overrides:
      getMass in class MoleculeGraph
      Returns:
      the molecular weight

    • getMSLogic

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public Map<MRArrow,RxnMolecule> getMSLogic()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Multi-step reactions not supported. Method performs no operations.
      Multi-step reactions not supported. Method always returns null.
      Returns:
      returns the hash that stores the mapping.

    • getObjectCount

      public int getObjectCount()
      Specified by:
      getObjectCount in interface chemaxon.struc.MObjectContainer
      Overrides:
      getObjectCount in class Molecule

    • getParity

      public int getParity(int i)
      Computes the parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those. Leaves the imported parity unchanged.
      Overrides:
      getParity in class MoleculeGraph
      Parameters:
      i - the index of the atom whose parity is to be determined
      Returns:
      0 for nonchiral, PARITY_ODD or PARITY_EVEN for atoms of odd or even parity, PARITY_ODD|PARITY_EVEN for atoms whose parity is unspecified or cannot be assigned -as they are defined in MolAtom
      Throws:
      SecurityException - the Parity module cannot be loaded because of security reasons (firewall)
      See Also:

    • getProduct

      public Molecule getProduct(int i)
      Gets a product.
      Parameters:
      i - product index
      Returns:
      a product

    • getProductCount

      public int getProductCount()
      Gets the number of products.
      Returns:
      the number of products

    • getProducts

      public Molecule[] getProducts()
      Gets all products in an array.
      Returns:
      the products
      Since:
      Marvin 5.3

    • getReactant

      public Molecule getReactant(int i)
      Gets a reactant.
      Parameters:
      i - reactant index
      Returns:
      a reactant

    • getReactantCount

      public int getReactantCount()
      Gets the number of reactants.
      Returns:
      the number of reactants

    • getReactants

      public Molecule[] getReactants()
      Gets all reactants in an array.
      Returns:
      the reactants
      Since:
      Marvin 5.3

    • getReactionArrow

      public DPoint3[] getReactionArrow()
      Gets a two-element array containing the endpoints of the reaction arrow.
      Returns:
      the arrow

    • getReactionArrow

      public MRArrow getReactionArrow(boolean generate)
      Gets the reaction arrow of this reaction with the possibility to generate an arrow if the arrow is not yet set.
      Parameters:
      generate - if true then arrow is generated in case when the arrow is not yet set.
      Returns:
      the arrow of this reaction, null if the arrow is not set and the generate parameter was false.

    • getReactionArrowList

      public List<MRArrow> getReactionArrowList()
      Gets the list of the reaction arrows of this reaction.
      Returns:
      the list of MRArrow-s
      Since:
      Marvin 5.0
      See Also:

    • getReactionArrowType

      public int getReactionArrowType()
      Gets the reaction arrow type.
      Returns:
      the reaction arrow type, REGULAR_SINGLE if no reaction arrow is set.
      Since:
      Marvin 3.5
      See Also:

    • getReactionArrowTypeName

      public String getReactionArrowTypeName()
      Gets the reaction arrow type name. Used in molecule export.
      Returns:
      the reaction arrow type name:
      • "DEFAULT" for arrow type RxnMolecule.REGULAR_SINGLE or in case if no reaction arrow is set.
      • "RESONANCE" for arrow type RxnMolecule.RESONANCE or RxnMolecule.TWO_HEADED_SINGLE
      • "RETROSYNTHETIC" for arrow type RxnMolecule.RETROSYNTHETIC or RxnMolecule.REGULAR_DOUBLE
      • "EQUILIBRIUM" for arrow type RxnMolecule.EQUILIBRIUM or RxnMolecule.TWO_HEADED_DOUBLE
      Since:
      Marvin 3.5

    • getType

      public int getType(MoleculeGraph selection)
      Checks whether the atoms in the selection are all in reactants, products or agents.
      Parameters:
      selection - the molecule graph containing the selection
      Returns:
      REACTANTS, PRODUCTS or AGENTS or -1 if not of the same type or there is an atom which is not contained in any component

    • hasAtomSet

      public boolean hasAtomSet()
      Tests whether the molecule graph has atom sets.
      Overrides:
      hasAtomSet in class Molecule
      Returns:
      true if there are atom sets, false otherwise
      Since:
      Marvin 4.0, 03/02/2005

    • hasBondSet

      public boolean hasBondSet()
      Tests whether the molecule graph has atom sets.
      Overrides:
      hasBondSet in class MoleculeGraph
      Returns:
      true if there are atom sets, false otherwise
      Since:
      Marvin 4.0, 03/02/2005

    • indexOf

      public int indexOf(MolAtom node)
      Gets the index of the specified node in the graph union.
      Overrides:
      indexOf in class MoleculeGraph
      Parameters:
      node - the node
      Returns:
      the index, or -1 if not found
      Since:
      Marvin 2.7

    • indexOf

      public int indexOf(MolBond edge)
      Gets the index of the specified edge in the graph union.
      Overrides:
      indexOf in class MoleculeGraph
      Parameters:
      edge - the edge
      Returns:
      the index, or -1 if not found
      Since:
      Marvin 2.7
      See Also:

    • isAtom

      @Deprecated @SubjectToRemoval(date=JUL_01_2025) public boolean isAtom()
      Deprecated.
      As of Marvin 14.7.7, no replacement.
      Not supported feature.
      A reaction molecule cannot represent an atom.
      Overrides:
      isAtom in class MoleculeGraph
      Returns:
      false

    • isBond

      @Deprecated @SubjectToRemoval(date=JUL_01_2025) public boolean isBond()
      Deprecated.
      As of Marvin 14.7.7, no replacement.
      Not supported feature.
      A reaction molecule cannot represent a bond.
      Overrides:
      isBond in class MoleculeGraph
      Returns:
      false

    • isEmpty

      public boolean isEmpty()
      Ask if the reaction is empty or not.
      Overrides:
      isEmpty in class Molecule
      Returns:
      true if there are no reactants, products or agents

    • isIncompleteReaction

      public boolean isIncompleteReaction()
      Check whether the reaction is incomplete or not.
      Returns:
      true if something is missing, false if it seems to be okay
      Since:
      Marvin 3.5

    • isMergedComponent

      public boolean isMergedComponent(MoleculeGraph m)
      Check whether given molecule is reaction component with a set of intentionally merged fragments or not.
      Parameters:
      m - the molecule to check
      Returns:
      true if merged

    • isQuery

      public boolean isQuery()
      Indicates if the molecule has query features: query atoms or query bonds.
      Overrides:
      isQuery in class MoleculeGraph
      Returns:
      true if any of the components has query features
      Since:
      Marvin 6.0 26/01/2013
      See Also:

    • isReaction

      public boolean isReaction()
      Checks if the structure represents a reaction or not.
      Overrides:
      isReaction in class Molecule
      Returns:
      true
      Since:
      Marvin 3.0

    • isSingleStepReaction

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public boolean isSingleStepReaction()
      Deprecated, for removal: This API element is subject to removal in a future version.
      Multi-step reactions not supported. Method always returns true.
      Returns:
      true

    • mergeAtoms

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void mergeAtoms(MolAtom that, MolAtom node)
      Deprecated, for removal: This API element is subject to removal in a future version.
      As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
      Merges bonds of an atom with another atom, then add the atom to the molecule.
      Overrides:
      mergeAtoms in class Molecule
      Parameters:
      that - the atom
      node - the other atom

    • mergeComponentParts

      public void mergeComponentParts(MoleculeGraph m, int type, boolean isMergeStored) throws IllegalArgumentException
      Finds those component parts that are contained in the molecule graph m and creates a new component containing all atoms of m, splitting them from the previous merges.
      Parameters:
      m - molecule graph that contains atoms of the fragments to merge
      type - type of component parts to merge (only parts of components of the same type can be merged)
      isMergeStored - if true then merged component remains merged until not splitted intentionnaly
      Throws:
      IllegalArgumentException
      See Also:

    • newInstance

      public MoleculeGraph newInstance()
      Creates a new RxnMolecule object. The dimension and the origin coordinates will be the same as in the original molecule.
      Overrides:
      newInstance in class Molecule
      Returns:
      the new reaction

    • rebuildStructures

      public void rebuildStructures()
      For each structure (reactant or product) determines whether it should be a reactant or a product depending on its the relative position to the reaction arrow. Rebuilds the reactant and product vectors accordingly.

    • rebuildStructures

      public void rebuildStructures(DPoint3[] arw, int art)
      Sets the reaction arrow. For each reaction component (reactant or product) determines whether it should be a reactant or a product depending on its the relative position to the reaction arrow. Rebuilds the reactant and product vectors accordingly.
      Parameters:
      arw - is the new reaction arrow
      art - is the new reaction arrow type

    • recalcReactionArrow

      public void recalcReactionArrow()
      Recalculates the coordinates of the reaction arrow from the reactants and products, forced recalculation.

    • regenBonds

      public void regenBonds()
      Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
      Overrides:
      regenBonds in class MoleculeGraph

    • removeAll

      public void removeAll()
      Remove all the atoms and bonds from the root structure, and from all the R-groups.
      Overrides:
      removeAll in class Molecule

    • removeAllBonds

      public void removeAllBonds()
      Removes all bonds from the reactants, products and agents.
      Overrides:
      removeAllBonds in class Molecule

    • removeAtom

      public void removeAtom(int iu, int cleanupFlags)
      Removes an atom from the reactants, products or agents. This method is for internal use only. Use MoleculeGraph.removeAtom(MolAtom) instead unless you are sure what you are doing.
      Overrides:
      removeAtom in class Molecule
      Parameters:
      iu - atom index in the graph union
      cleanupFlags - extra clean-up methods
      Since:
      Marvin 3.1
      See Also:

    • removeAtom

      public void removeAtom(MolAtom node, int cleanupFlags)
      Removes an atom from the reactants, products or agents. This method is for internal use only. Use MoleculeGraph.removeAtom(MolAtom) instead unless you are sure what you are doing.
      Overrides:
      removeAtom in class Molecule
      Parameters:
      node - the atom
      cleanupFlags - extra clean-up methods
      Since:
      Marvin 3.1
      See Also:

    • removeComponent

      public Molecule removeComponent(int flags, int i)
      Removes a reactant, product or agent.

      Warning! The RGROUPED flag returns an RgMolecule object having the same atom objects as the original reactant/product/agent. The parent of the atom objects is unchanged (it is the original reactant/product/agent).

      Parameters:
      flags - REACTANTS, PRODUCTS or AGENTS, can be combined with RGROUPED
      i - reactant, product or agent index
      Returns:
      the removed reactant, product or agent
      Since:
      Marvin 4.1, 11/19/2005

    • removeEmptyComponents

      public void removeEmptyComponents()
      Checks all the componentes and removes those that are empty (node count is zero).

    • removeObject

      public void removeObject(MObject o)
      Removes a graphical object from this.
      Specified by:
      removeObject in interface chemaxon.struc.MObjectContainer
      Overrides:
      removeObject in class Molecule
      Parameters:
      o - the graphical object

    • removeReactionArrow

      public void removeReactionArrow()
      Removes the reaction arrow of this reacion.

    • replaceBond

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void replaceBond(MolBond olde, MolBond newe)
      Deprecated, for removal: This API element is subject to removal in a future version.
      as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and add(MolBond) for adding a new bond to the molecule.
      Replaces an edge by another one.
      Overrides:
      replaceBond in class MoleculeGraph
      Parameters:
      olde - the old edge
      newe - the new edge
      Since:
      Marvin 4.1, 11/24/2005

    • revalidateCoordDependentProps

      public void revalidateCoordDependentProps()
      Revalidate coordinate dependent properties. This method should be called at molecule import, after all atomic coordinates and bonds are parsed.
      Overrides:
      revalidateCoordDependentProps in class MoleculeGraph
      Since:
      Marvin 4.1, 08/03/2006

    • selectAllObjects

      public void selectAllObjects(boolean s)
      Specified by:
      selectAllObjects in interface chemaxon.struc.MObjectContainer
      Overrides:
      selectAllObjects in class Molecule

    • setAbsStereo

      public void setAbsStereo(boolean c)
      Sets the absolute stereoconfiguration flag for all the structures.
      Overrides:
      setAbsStereo in class MoleculeGraph
      Parameters:
      c - the absolute stereoconfiguration flag
      See Also:

    • setAtom

      @Deprecated public void setAtom(int iu, MolAtom node)
      Deprecated.
      As of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(MolAtom) and add(MolAtom) to modify the structure.
      Sets the node at the specified index.
      Overrides:
      setAtom in class MoleculeGraph
      Parameters:
      iu - node index in the graph union
      node - new node reference

    • setBond

      @Deprecated public void setBond(int iu, MolBond edge)
      Deprecated.
      as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and add(MolBond) for adding a new bond to the molecule.
      Sets the edge at the specified index.
      Overrides:
      setBond in class MoleculeGraph
      Parameters:
      iu - edge index in the graph union
      edge - new node reference

    • setDim

      public void setDim(int d)
      Sets the dimension for all the structures.
      Overrides:
      setDim in class Molecule
      Parameters:
      d - 0, 2 or 3
      See Also:

    • setLocation

      public void setLocation(DPoint3 p)
      Set the origin of the molecule. The MolAtom coordinates are relative to this origin.
      Overrides:
      setLocation in class MoleculeGraph
      Parameters:
      p - the origin
      See Also:

    • setMSLogic

      @Deprecated(forRemoval=true) @SubjectToRemoval(date=JUL_01_2025) public void setMSLogic(Map<MRArrow,RxnMolecule> ms)
      Deprecated, for removal: This API element is subject to removal in a future version.
      Multi-step reactions not supported. Method performs no operations.
      Multi-step reactions not supported. Method performs no operations. Method declaration kept for compatibility reasons.
      Parameters:
      ms - mapping store.

    • setReactionArrow

      public void setReactionArrow(DPoint3... points)
      Sets the endpoint coordinates of the reaction arrow. Sets the stored reaction arrow to its calculated value if no argument passed.
      Parameters:
      points - endpoint coordinates of the reaction arrow
      Throws:
      IllegalArgumentException - if argument contains one point only.

    • setReactionArrow

      public void setReactionArrow(MRArrow arrow)
      Sets the reaction arrow.

    • setReactionArrow0

      public void setReactionArrow0(DPoint3... points)
      Sets the reaction arrow. Sets the stored reaction arrow 'arrowPoints' to its calculated value if no argument passed.
      Parameters:
      points - is the new reaction arrow.
      Throws:
      IllegalArgumentException - if argument contains one point only.

    • setReactionArrowEndPoints

      public void setReactionArrowEndPoints(DPoint3[] points)
      Sets the endpoints of the reaction arrow in this reaction. If the arrow is not yet set creates one with the given endpoint coordinates.
      Parameters:
      points - the endpoint coordinates of the arrow
      Since:
      Marvin 5.0, 12/06/2007

    • setReactionArrowType

      public void setReactionArrowType(int type)
      Sets the reaction arrow type.
      Parameters:
      type - the reaction arrow type
      Since:
      Marvin 3.5

    • setReactionArrowType

      public void setReactionArrowType(String name)
      Sets the reaction arrow type from type name. Used in molecule import.
      Parameters:
      name - the reaction arrow type name
      Throws:
      IllegalArgumentException - for invalid type name
      Since:
      Marvin 3.5

    • setSgroupParent

      public void setSgroupParent(MolAtom a, Sgroup sg, boolean set)
      Sets or unsets an S-group as a parent of an atom in reactants, products or agents.
      Overrides:
      setSgroupParent in class Molecule
      Parameters:
      a - the atom
      sg - the S-group
      set - set (true) or unset (false)
      Throws:
      IllegalArgumentException - neither reactants, nor products or agents contain the atom
      Since:
      Marvin 3.0

    • simplifyIncompleteReactionToMolecule

      public Molecule simplifyIncompleteReactionToMolecule()
      Simplify a reaction to a molecule if possible. If the reaction is incomplete and it only contains one reactant, one product or one agent, then that object is returned. Otherwise, simplification is impossible and this is returned.
      Returns:
      a reactant, product, agent or this
      Since:
      Marvin 4.0
      See Also:

    • simplifyToMolecule

      public Molecule simplifyToMolecule()
      Simplifies this RxnMolecule by moving the atoms and bonds from the reactants, products, and agents to a Molecule. Clears reactans, products, agents.
      Returns:
      the simplified molecule
      Since:
      Marvin 5.0

    • sortBondsAccordingTo

      public void sortBondsAccordingTo(MolBond[] order)
      Sort edges in the same order as they appear in the specified array.
      Overrides:
      sortBondsAccordingTo in class MoleculeGraph
      Parameters:
      order - the array
      Since:
      Marvin 3.5, 09/02/2004

    • splitAllDisconnectedComponents

      public void splitAllDisconnectedComponents()
      Replaces all disconnected reaction components by its connected fragments in the structure array.
      Since:
      Marvin 5.4, 07/07/2010
      See Also:

    • splitComponentParts

      public void splitComponentParts(MoleculeGraph m, int type) throws IllegalArgumentException
      Finds those component parts that are contained in the molecule graph m and creates separate components from the fragments contained in m, splitting them from the previous merges.
      Parameters:
      m - molecule graph that contains atoms of the fragments to split
      type - type of component parts to merge (only parts of components of the same type can be merged)
      Throws:
      IllegalArgumentException

    • splitDisconnectedComponent

      public void splitDisconnectedComponent(int type, int index)
      Replaces a disconnected reaction component by its connected fragments in the structure array.
      Parameters:
      type - is the structure type: REACTANTS, PRODUCTS or AGENTS
      index - is the structure index
      Since:
      Marvin 4.1, 11/19/2005

    • splitDisconnectedComponent

      public void splitDisconnectedComponent(long id)
      Replaces a disconnected reaction component by its connected fragments in the structure array.
      Parameters:
      id - the reaction component ID
      Since:
      Marvin 4.1, 11/19/2005
      See Also:

    • stereoClean

      public boolean stereoClean()
      Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D. Take care of expanding the molecule if neccessary.
      Overrides:
      stereoClean in class MoleculeGraph
      Returns:
      true if succesful
      See Also:

    • toString

      public String toString()
      Overrides Object.toString() to ease debugging.
      Overrides:
      toString in class MoleculeGraph
      Returns:
      a string representation of the object

    • transform

      public void transform(CTransform3D t, boolean incg)
      Apply a transformation matrix to the atomic coordinates and the reaction arrow.
      Overrides:
      transform in class Molecule
      Parameters:
      t - the transformation matrix
      incg - increase grinvCC or not

    • updateComponentRoles

      public void updateComponentRoles()
      Updates fragment roles in the molecule. roles are like: - nodes that are sources only: are REACTANTS - nodes that are sinks only: are PRODUCTS - all other nodes: are AGENTS For single step reactions: if the reaction is stored as single step, does nothing. If the single reaction is stored in the hash, transforms it into a single step one.

    • addAtomToFragment

      protected void addAtomToFragment(MolAtom a)
      Description copied from class: Molecule
      Adds an atom to a fragment. S-groups are added only if all atoms are already in the molecule.
      Overrides:
      addAtomToFragment in class Molecule
      Parameters:
      a - the atom reference

    • checkSgroupConsistency

      protected void checkSgroupConsistency()
      Checks the consistency of S-groups.
      Overrides:
      checkSgroupConsistency in class Molecule
      Throws:
      RuntimeException - if inconsistency found
      Since:
      Marvin 5.0, 11/06/2007

    • createGearch

      protected chemaxon.struc.gearch.MoleculeGraphGearch createGearch()
      Overrides:
      createGearch in class Molecule

    • fillSelectionMolecule

      protected void fillSelectionMolecule(SelectionMolecule s)
      Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
      Overrides:
      fillSelectionMolecule in class Molecule
      Parameters:
      s - the selection molecule
      Since:
      Marvin 3.0, 11/05/2002

    • fuse0

      protected void fuse0(MoleculeGraph graph, boolean check)
      Add those nodes and edges of a graph that are not already elements. If the graph has an atom connected to a reactant or product, then also adds the graph to that structure. Handles one connected component.
      Overrides:
      fuse0 in class Molecule
      Parameters:
      graph - the structure to fuse into this one
      check - true if a containment check should be performed to ensure that only those nodes and edges 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

    • getSubGraphCount

      protected final int getSubGraphCount()
      Gets the number of all "submolecules".
      Overrides:
      getSubGraphCount in class MoleculeGraph
      Returns:
      the number of submolecules
      Since:
      Marvin 4.1.2
      See Also:

    • getSubGraphs

      protected final void getSubGraphs(MoleculeGraph[] arr, int off)
      Gets all "submolecules".
      Overrides:
      getSubGraphs in class MoleculeGraph
      Parameters:
      arr - the output array
      off - offset
      Since:
      Marvin 4.1.2
      See Also:

    • isRealAtomParent

      protected boolean isRealAtomParent()
      Reaction molecules cannot be real node parents.
      Overrides:
      isRealAtomParent in class MoleculeGraph
      Returns:
      false
      Since:
      Marvin 3.0

    • makeItSimilar

      protected void makeItSimilar(MoleculeGraph g)
      Copies some properties of this molecule to the other one specified as argument. Copies the reaction arrow.
      Overrides:
      makeItSimilar in class Molecule
      Parameters:
      g - the molecule to change

    • removeBond

      protected void removeBond(int iu, int cleanupFlags)
      Removes an edge from a reactant, agent or product.
      Overrides:
      removeBond in class Molecule
      Parameters:
      iu - edge index in the graph union
      cleanupFlags - extra clean-up methods
      Since:
      Marvin 3.1
      See Also:

    • removeBond

      protected void removeBond(MolBond edge, int cleanupFlags)
      Removes a bond from the reactants, products or agents.
      Overrides:
      removeBond in class Molecule
      Parameters:
      edge - the edge
      cleanupFlags - extra clean-up methods
      Since:
      Marvin 3.1
      See Also:

    • setSupergraph

      protected void setSupergraph(MoleculeGraph molecule)
      Sets the given molecule as the supergraph of this graph and its components.
      Overrides:
      setSupergraph in class MoleculeGraph
      Parameters:
      molecule - the molecule
      Since:
      Marvin 14.7.7, Jul 2, 2014

    • transformReactionArrow

      protected void transformReactionArrow(CTransform3D t)
      Apply a transformation matrix to the reaction arrow.
      Parameters:
      t - the transformation matrix