Class Molecule

    • Constructor Detail

      • Molecule

        public Molecule​(Molecule p,
                        int na,
                        int nb)
        Construct a molecule or fragment with the specified number of atoms and bonds.
        Parameters:
        p - the molecule that contains the created fragment
        na - no reallocation needed until the number of atoms is less than this value
        nb - no reallocation needed until the number of bonds is less than this value
      • Molecule

        public Molecule​(Molecule p,
                        MolAtom a)
        Construct a molecule consisting of a single atom (node).
        Parameters:
        p - the parent structure
        a - the atom
      • Molecule

        public Molecule​(Molecule p,
                        MolBond b)
        Construct a molecule consisting of a single bond (edge).
        Parameters:
        p - the parent structure
        b - the bond
      • Molecule

        public Molecule()
        Construct a 2 dimensional molecule.
    • Method Detail

      • getStartPosition

        public long getStartPosition()
        Gets the starting position of this molecule in the input file.
        Returns:
        the starting position
      • setStartPosition

        public void setStartPosition​(long off)
        Sets the starting position of this molecule in the input file.
        Parameters:
        off - the starting position
      • getEndPosition

        public long getEndPosition()
        Gets the end position of this molecule in the input file.
        Returns:
        the end position
      • setEndPosition

        public void setEndPosition​(long off)
        Sets the end position of this molecule in the input file.
        Parameters:
        off - the end position
      • setName

        public void setName​(String s)
        Sets the molecule name/title.
        Parameters:
        s - the molecule name, empty string or null (null is equivalent to empty string)
        Since:
        Marvin 2.7
      • getComment

        public String getComment()
        Gets the comment.
        Returns:
        the comment or empty string
        Since:
        Marvin 2.9
      • setComment

        public void setComment​(String s)
        Sets the comment.
        Parameters:
        s - the comment, empty string or null (null is equivalent to empty string)
        Since:
        Marvin 2.9
      • getId

        public String getId()
      • setId

        public void setId​(String id)
      • hasId

        public boolean hasId​(String id)
      • getInputFormat

        public final String getInputFormat()
        Gets the input file format. Set by the import module if the molecule is from a file.
        Returns:
        "mrv", "mol", "mol:V3", "csmol", "sdf", "cssdf", "rdf", "csrdf", "smiles", "sybyl", "mol2", "pdb", "xyz" or "cube" or "inchi" or null if not imported from any format
        Since:
        Marvin 2.7
      • setInputFormat

        public void setInputFormat​(String format)
        Sets the input file format.
        Parameters:
        format - the input format
        Since:
        Marvin 2.7
        See Also:
        getInputFormat()
      • clearProperties

        public void clearProperties()
        Clears RDfile/SDfile properties.
      • getPropertyCount

        public int getPropertyCount()
        Gets the total number of RDfile/SDfile properties.
        Returns:
        number of properties
        Since:
        Marvin 2.7
      • getPropertyKey

        public String getPropertyKey​(int i)
        Gets an RDfile/SDfile property key.
        Parameters:
        i - property index
        Returns:
        the property name
        Since:
        Marvin 2.7
      • getProperty

        @Deprecated
        public String getProperty​(String key)
        Deprecated.
        As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
        Usage:
         
                     String property = MPropHandler.convertToString(mol.properties(), key);
                     
        Gets an RDfile/SDfile property.
        Parameters:
        key - property name
        Returns:
        the value of the property, or null if the key is not found
      • getPropertyObject

        public Object getPropertyObject​(String key)
        Gets an RDfile/SDfile property object.
        Parameters:
        key - property name
        Returns:
        the value of the property, or null if the key is not found
        Since:
        Marvin 3.1.2
      • setProperty

        public void setProperty​(String key,
                                String value)
        Sets an RDfile/SDfile property. Setting null value removes the property.
        Parameters:
        key - the property name
        value - the value or null
      • setPropertyObject

        public void setPropertyObject​(String key,
                                      Object value)
        Sets an RDfile/SDfile property object. Setting null value removes the property.
        Parameters:
        key - the property name
        value - the value or null
        Since:
        Marvin 3.1.2
      • residueTypeOf

        public static int residueTypeOf​(String name)
        Gets the residue identifier for a residue name.
        Parameters:
        name - residue name
        Returns:
        the residue type
      • residueSymbolOf

        public static String residueSymbolOf​(int id)
        Gets the name of a residue.
        Parameters:
        id - the residue identifier
        Returns:
        the residue symbol
      • setAtom0

        protected void setAtom0​(int i,
                                MolAtom newAtom)
        Sets the atom at the specified index. Overridden because Sgroups must be set correctly in RgMolecule.clone() and RxnMolecule.clone().
        Overrides:
        setAtom0 in class MoleculeGraph
        Parameters:
        i - the atom index
        newAtom - the atom
      • removeAll

        public void removeAll()
        Removes all the atoms and bonds.
        Overrides:
        removeAll in class MoleculeGraph
      • isEmpty

        public boolean isEmpty()
        Tests whether the molecule is empty.
        Overrides:
        isEmpty in class MoleculeGraph
        Returns:
        true if the molecule graph does not contain any atoms, bonds or non-empty S-groups, false otherwise
        Since:
        Marvin 4.1.1, 09/06/2006
      • dearomatize

        public boolean dearomatize()
        Dearomatize molecule.
        Overrides:
        dearomatize in class MoleculeGraph
        Returns:
        true if success, else false.
        Throws:
        SecurityException - cannot load module because of a security problem (firewall)
      • clonecopy

        public void clonecopy​(MoleculeGraph g)
        Makes another molecule identical to this one.
        Overrides:
        clonecopy in class MoleculeGraph
        Parameters:
        g - the target molecule
      • addSgroupClones

        protected final void addSgroupClones​(Molecule origparentm,
                                             Molecule origm,
                                             Molecule newm)
        Adds the S-groups of a child molecule clone to the new parent molecule clone.
        Parameters:
        origparentm - the original parent molecule
        origm - the original child molecule
        newm - the new child molecule (clone of the original)
        Since:
        Marvin 3.4
      • clonecopy

        public void clonecopy​(int[] iatoms,
                              MoleculeGraph g)
        Copies the specified atoms and bonds of this molecule to another one.
        Overrides:
        clonecopy in class MoleculeGraph
        Parameters:
        iatoms - array of atom indices to copy or null
        g - the target molecule graph
        Since:
        Marvin 5.0.2, 03/11/2008
      • clonecopyWithoutSgroups

        protected void clonecopyWithoutSgroups​(Molecule m)
        Copies the all the contents except the S-groups into another molecule object.
        Parameters:
        m - the target molecule
        Since:
        Marvin 3.4
      • cloneAtoms

        protected int cloneAtoms​(int[] cnodes,
                                 MoleculeGraph graph)
        Copies the specified atoms.
        Overrides:
        cloneAtoms in class MoleculeGraph
        Parameters:
        cnodes - array of atom indices to copy or null
        graph - the target molecule graph
        Returns:
        the atom count
        Since:
        Marvin 6.0, 2013.02.25.
      • clonelesscopy

        @Deprecated
        public void clonelesscopy​(MoleculeGraph g)
        Deprecated.
        as of Marvin 6.3.
        Not supported feature.
        Copies to selection. Makes another molecule identical to this one, but does not clone atoms, bonds, and the properties.
        Overrides:
        clonelesscopy in class MoleculeGraph
        Parameters:
        g - the target molecule object (the selection)
      • cloneMoleculeWithDocument

        public Molecule cloneMoleculeWithDocument()
        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.
        Returns:
        the copy
        Since:
        Marvin 4.1, 01/16/2006
      • cloneMolecule

        @Deprecated
        public Molecule cloneMolecule()
        Deprecated.
        as of Marvin 2014.09.01.0 use clone() instead
        Makes an identical copy of the molecule. It also clones the atoms and bonds of the Molecule. Note that it does not clone the corresponding MDocument, hence the atom and bond formatting (color, font, thickness) is lost.
        Returns:
        the copy
        Since:
        Marvin 3.5.1, 11/20/2004
      • clone

        public Molecule clone()
        Makes an identical copy of the molecule. It also clones the atoms and bonds of the Molecule. Note, that it does not clone the corresponding MDocument, hence the atom and bond formatting (color, font, thickness) is lost.
        Overrides:
        clone in class MoleculeGraph
        Returns:
        the copy
      • toFormat

        @Deprecated
        public final String toFormat​(String fmt)
        Deprecated.
        As of Marvin 5.7, replaced by MolExporter.exportToFormat(Molecule, String).
        To get exact replacement use:
                     try {
                         String out = MolExporter.exportToFormat(this, fmt);
                     } catch (IOException e) {
                         throw new IllegalArgumentException(e);
                     }
                     
        Creates a string representation of the molecule. The format descriptor string can also contain export options. Format and options are separated by a colon, multiple options can be separated by commas. See the text formats and their options on the File Formats in Marvin page. Examples:
         s1 = mol.toFormat("mol");
         s2 = mol.toFormat("smiles:a-H"); // aromatize and remove Hydrogens
         
        Parameters:
        fmt - the format descriptor string
        Returns:
        string representation of the molecule in the specified format
        Throws:
        IllegalArgumentException - Invalid format string.
        SecurityException - Export module cannot be loaded because of security reasons (firewall).
        See Also:
        toObject(java.lang.String)
      • toBinFormat

        @Deprecated
        public final byte[] toBinFormat​(String fmt)
        Deprecated.
        Creates a binary representation of the molecule. Works with all the text formats that are supported by the toFormat method, and also with the binary image formats (jpeg, msbmp, png). When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples:
         
         byte[] d1 = mol.toBinFormat("mol");
         byte[] d2 = mol.toBinFormat("smiles:a-H"); // aromatize and remove H
         byte[] d3 = mol.toBinFormat("png:w300,h300,b32,#00ffff00");
         byte[] d4 = mol.toBinFormat("jpeg:w300,h300,Q95,#ffff00,spacefill");
         
        Parameters:
        fmt - the format descriptor string
        Returns:
        a binary representation of the molecule in the specified format
        Throws:
        IllegalArgumentException - Invalid format string.
        SecurityException - Export module cannot be loaded because of security reasons (firewall).
        Since:
        Marvin 2.7.11
        See Also:
        toObject(java.lang.String)
      • toObject

        @Deprecated
        public Object toObject​(String fmt)
        Deprecated.
        As of Marvin 5.7, replaced by MolExporter.exportToObject(Molecule, String).
        Creates a String, byte[] array or Image representation of the molecule. When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples:
         import java.awt.Image;
         ...
         String s1 = (String)mol.toObject("mol");
         String s2 = (String)mol.toObject("smiles:a-H"); // aromatize, remove H
         Image img = (Image)mol.toObject("image:w300,h300,#ffff00");
         byte[] d3 = (byte[])mol.toObject("png:w300,h300,b32,#00ffff00");
         byte[] d4 = (byte[])mol.toObject("jpeg:w300,h300,Q95,#ffff00,spacefill");
         
        Parameters:
        fmt - the format descriptor string
        Returns:
        a String, a byte[] array or an Image
        Throws:
        IllegalArgumentException - Invalid format string.
        SecurityException - Export module cannot be loaded because of security reasons (firewall).
        Since:
        Marvin 2.8.1
        See Also:
        toFormat(java.lang.String), toBinFormat(java.lang.String)
      • reuseAtom

        public MolAtom reuseAtom​(int z,
                                 int i)
        Reuse an atom or create a new one. If an atom is reused, all its properties except the corners are initialized.
        Parameters:
        z - the atomic number
        i - the atom index
        Returns:
        the atom reference
        Since:
        Marvin 2.6
      • endReuse

        public void endReuse​(int n)
        End reusing atoms.
        Parameters:
        n - number of atoms
        Since:
        Marvin 2.6
      • newInstance

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

        public SelectionMolecule newSelectionMolecule()
        Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
        Returns:
        an empty selection molecule
        Since:
        Marvin 4.1, 11/24/2005
      • makeItSimilar

        protected void makeItSimilar​(MoleculeGraph g)
        Copies some properties of this molecule to the other one specified as argument. Copies the input format.
        Overrides:
        makeItSimilar in class MoleculeGraph
        Parameters:
        g - the molecule to change
      • getSimplifiedMolecule

        public final Molecule getSimplifiedMolecule()
        Gets the simplified molecule object. It returns this usually. In case of RgMolecule, it returns the simply modified root structure if there are no R-groups present. In this case the RgMolecule will be inconsistent. It can simplify the molecule only if there is no parent document containing other objects.
        Returns:
        the simplified molecule
        Since:
        Marvin 3.0.1
      • getMostSimplifiedMolecule

        protected Molecule getMostSimplifiedMolecule()
        Gets the simplified molecule object even if there is a parent document with other objects. It returns this usually. In case of RgMolecule, it returns the root structure if there are no R-groups present.
        Returns:
        this in the default implementation
        Since:
        Marvin 4.1.13, 09/20/2007
      • isReaction

        public boolean isReaction()
        Checks if the structure represents a reaction or not.
        Returns:
        false
        Since:
        Marvin 3.0
      • canBeReactionComponent

        public boolean canBeReactionComponent()
        Tests whether an object of this class can be a reaction component. This implementation returns true
        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
      • isSgroup

        @Deprecated
        public boolean isSgroup()
        Deprecated.
        As of Marvin 14.7.7, no replacement.
        Not supported feature.
        Checks if the structure represents an S-group or not.
        Returns:
        true if the structure is an S-group, false otherwise
        Since:
        Marvin 3.0
      • getSgroupLigands

        public MolAtom[] getSgroupLigands()
        Gets the S-group's ligands if the structure represents an S-group.
        Returns:
        the array of ligands if the structure is an S-group with ligands, null otherwise
        Since:
        Marvin 3.0
      • findExpandableSgroup

        public final Sgroup findExpandableSgroup()
        Finds a contracted residue.
        Returns:
        the S-group if found, null if all S-groups are expanded
        Since:
        Marvin 3.0
      • findContractableSgroup

        public final Sgroup findContractableSgroup()
        Finds an expanded residue.
        Returns:
        the S-group if found, null if all S-groups are contracted
        Since:
        Marvin 3.0
      • getSgroupArray

        public final Sgroup[] getSgroupArray()
        Gets the array of S-groups.

        Warning! Expansion or contraction of an S-group in this array may invalidate other array elements. Examples:

        • contracting a MultipleSgroup removes any embedded SuperatomSgroup except those inside the repeating unit,
        • expanding a MultipleSgroup adds n-1 new clones for each embedded SuperatomSgroup in the repeating unit.
        Returns:
        an array containing all the S-groups
        Since:
        Marvin 3.0
      • getSgroupCount

        public final int getSgroupCount()
        Gets the number of S-groups.
        Returns:
        the number of S-groups
        Since:
        Marvin 3.0
      • countExpandableContractableSgroups

        public final int countExpandableContractableSgroups()
        Counts the expandable and contractable S-groups.
        Returns:
        the number of expandable/contractable S-groups
        Since:
        Marvin 5.0, 02/28/2007
      • countOrderedComponentSgroups

        public final int countOrderedComponentSgroups()
        Counts the ordered component S-groups.
        Returns:
        the number of ordered component S-groups.
        Since:
        Marvin 4.1.6, 02/28/2007
      • getSgroup

        public final Sgroup getSgroup​(int i)
        Gets an S-group.
        Parameters:
        i - S-group index
        Since:
        Marvin 3.0
      • getSortedSgroups

        public final Sgroup[] getSortedSgroups()
        Gets the sorted S-groups in parent-child order.

        Warning! Expansion or contraction of an S-group in this array may invalidate other array elements. Examples:

        • contracting a MultipleSgroup removes any embedded SuperatomSgroup except those inside the repeating unit,
        • expanding a MultipleSgroup adds n-1 new clones for each embedded SuperatomSgroup in the repeating unit.
        Returns:
        array containing the S-groups
        Since:
        Marvin 3.4, 05/04/2004
      • getRootSgroups

        public final Sgroup[] getRootSgroups()
        Gets root s-groups (groups that are not embedded into another s-group).
        Returns:
        array containing the root s-groups (empty array if there are no s-groups)
        Since:
        Marvin 5.3.3, 31/03/2010
      • sortSgroupXBonds

        @Deprecated
        public void sortSgroupXBonds()
        Deprecated.
        As of Marvin 5.12, no replacement.
        Crossing bonds of a SuperatomSgroup do not need to be sorted any more. It is not advised to sort them anyway because then the indexes of bonds change in the parent molecule.
        Sorts superatom S-group crossing bonds in attachment point number order.
        Since:
        Marvin 5.0, 12/07/2007
      • indexOf

        public final int indexOf​(Sgroup sg)
        Gets the array index of an S-group.
        Parameters:
        sg - the S-group
        Since:
        Marvin 3.0
      • findSgroupOf

        public final Sgroup findSgroupOf​(MolAtom a)
        Finds the smallest S-group related to the specified atom.
        Parameters:
        a - the atom
        Returns:
        the S-group or null if not found
        Since:
        Marvin 3.0
      • findSgroupContaining

        public final Sgroup findSgroupContaining​(MolAtom a)
        Finds the largest S-group that contains the specified atom.
        Parameters:
        a - the atom
        Returns:
        the S-group or null if not found
        Since:
        Marvin 3.0
      • findSmallestSgroupContaining

        public final Sgroup findSmallestSgroupContaining​(MolAtom a)
        Finds the smallest S-group that contains the specified atom.
        Parameters:
        a - the atom
        Returns:
        the S-group or null if not found
        Since:
        Marvin 3.4
      • findAllSgroupContaining

        public Sgroup[] findAllSgroupContaining​(MolAtom a)
        Finds all smallest S-groups containing the specified atom. There can be more groups containing the same atom and not embedding each other because of the data S-groups: they are not in the embedding hierarchy.
        Parameters:
        a - the atom
        Returns:
        the array of S-groups
        Since:
        Marvin 5.0.1
      • contains

        public boolean contains​(MolAtom atom)
        Checks if the molecule graph contains the specified atom. If the atom is not found in the graph, looks in the sgroupgraphs of contracted Expandable-Sgroups.
        Overrides:
        contains in class MoleculeGraph
        Parameters:
        atom - the atom
        Returns:
        true if the graph or an sgroupgraph contains the object, false otherwise
      • setSgroupParent

        public void setSgroupParent​(MolAtom a,
                                    Sgroup sg,
                                    boolean set)
        Sets or unsets an S-group as a parent of an atom.
        Parameters:
        a - the atom
        sg - the S-group
        set - set (true) or unset (false)
        Throws:
        IllegalArgumentException - molecule does not contain the atom
        Since:
        Marvin 3.0
      • reparentSgroups

        protected final void reparentSgroups​(Molecule p)
        Change parents of all S-groups in this molecule.
        Parameters:
        p - the new parent
        Throws:
        IllegalArgumentException - molecule does not contain the atom
        Since:
        Marvin 3.0
      • mergeAtoms

        @Deprecated
        public void mergeAtoms​(MolAtom that,
                               MolAtom node)
        Deprecated.
        As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
        Merges bonds of an atom with another atom, then adds the atom to the molecule.
        Overrides:
        mergeAtoms in class MoleculeGraph
        Parameters:
        that - the atom
        node - the other atom
      • addAtom0

        protected void addAtom0​(MolAtom node)
        Adds an atom.
        Overrides:
        addAtom0 in class MoleculeGraph
        Parameters:
        node - the atom reference
      • addAtomToFragment

        protected void addAtomToFragment​(MolAtom atom)
        Adds an atom to a fragment. S-groups are added only if all atoms are already in the molecule.
        Overrides:
        addAtomToFragment in class MoleculeGraph
        Parameters:
        atom - the atom reference
      • addBond0

        protected void addBond0​(MolBond bond)
        Adds a bond.
        Overrides:
        addBond0 in class MoleculeGraph
        Parameters:
        bond - the bond reference
      • fuse0

        protected void fuse0​(MoleculeGraph graph,
                             boolean check)
        Adds those atoms and bonds of a molecule graph to this one that are not already elements.
        Overrides:
        fuse0 in class MoleculeGraph
        Parameters:
        graph - the molecule 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 moleclue graph is known to be disjoint from this one and this check can be safely skipped
        Since:
        Marvin 5.0
      • contractSgroups

        public final boolean contractSgroups()
        Contracts all S-groups.
        Returns:
        true if the operation was successful, false if nothing changed
        Since:
        Marvin 3.0
      • expandSgroups

        public final boolean expandSgroups()
        Expands all S-groups.
        Returns:
        true if the operation was successful, false if nothing changed
        Since:
        Marvin 3.0
        See Also:
        expandSgroups(int)
      • isExpandable

        public final boolean isExpandable​(int opts)
        Tests if the molecule is expandable with the specified options.
        Parameters:
        opts - expansion options
        Returns:
        true if an S-group is GUI-contractable, false otherwise
        Since:
        Marvin 4.0.2, 10/26/2005
        See Also:
        Expandable.DEFAULT_OPTIONS, Expandable.LEAVE_COORDS_UNCHANGED
      • setGUIContracted

        @Deprecated
        public final void setGUIContracted​(boolean contract)
        Deprecated.
        as of Marvin 6.2, use expandSgroups(int) or contractSgroups(int) instead with option parameter Expandable.LEAVE_COORDS_UNCHANGED
        S-group expansion or contraction is performed depending on the parameter contract.
        If contract is set to:
        • false, then expansion happens to the contracted groups with no coordinate generation.
        • true, then contraction is performed for those s-groups that were expanded the way that was explained in the previous point.
        Parameters:
        contract - true for contraction, false for expansion
        Since:
        Marvin 3.4, 05/04/2004
      • setGUIContracted

        @Deprecated
        public final void setGUIContracted​(boolean contract,
                                           int opts)
        Deprecated.
        as of Marvin 6.2, use expandSgroups(int) or contractSgroups(int) instead with option parameter Expandable.LEAVE_COORDS_UNCHANGED
        S-group expansion or contraction is performed depending on the parameter contract.
        If contract is set to:
        • false, then expansion happens to the contracted groups with no coordinate generation.
        • true, then contraction is performed for those s-groups that were expanded the way that was explained in the previous point.
        Parameters:
        contract - true for contraction, false for expansion
        opts - for further expand options
        Since:
        Marvin 3.4, 05/04/2004
      • isGUIContracted

        @Deprecated
        public final boolean isGUIContracted()
        Deprecated.
        as of Marvin 6.2 replaced by hasContractedSgroup()
        Tests if the molecule has contracted S-groups or not.
        Returns:
        true there is at least one contracted S-group, false otherwise
        Since:
        Marvin 3.4.1, 07/26/2004
      • hasContractedSgroup

        public boolean hasContractedSgroup()
        Tests if the molecule has contracted S-groups or not.
        Returns:
        true there is at least one contracted S-group, false otherwise
        Since:
        Marvin 6.2, 2013/09/25
      • ungroupSgroup

        public final boolean ungroupSgroup​(Sgroup sg)
        Ungroups the specified S-group and expands it if it is an Expandable S-group. Ungroups and expands the child S-groups also if they are Expandable S-groups. Calls a recursive ungroup.
        Parameters:
        sg - the S-group
        Returns:
        true if the operation was successful, false if nothing changed
        Since:
        Marvin 3.4
        See Also:
        RECURSIVE_UNGROUP, ungroupSgroup(int)
      • ungroupSgroup

        public final boolean ungroupSgroup​(Sgroup sg,
                                           int opts)
        Expand and ungroup the specified S-group.
        Parameters:
        sg - the S-group
        opts - option to specify the ungroup type
        Returns:
        true if the operation was successful, false if nothing changed
        Since:
        Marvin 5.1.2
        See Also:
        RECURSIVE_UNGROUP, DEFAULT_UNGROUP, ungroupSgroup(int, int)
      • ungroupSgroup

        @Deprecated
        public final boolean ungroupSgroup​(int i)
        Deprecated.
        as of Marvin 6.3. use ungroupSgroup(Sgroup) instead.
        Ungroups the specified S-group and expands it if it is an Expandable S-group. Ungroups and expands the child S-groups also if they are Expandable S-groups.
        Parameters:
        i - the S-group index
        Returns:
        true if the operation was successful, false if nothing changed
        Since:
        Marvin 3.4
        See Also:
        ungroupSgroup(chemaxon.struc.Sgroup), RECURSIVE_UNGROUP
      • ungroupSgroups

        @Deprecated
        public final boolean ungroupSgroups​(int type)
        Deprecated.
        as of Marvin 6.3. use ungroupSgroups(EnumSet) instead.
        Ungroups all S-groups of a specified type in this molecule. Performs expand before ungroup if the type is an expandable S-group type.
        Parameters:
        type - the S-group type that specifies which S-groups to ungroup.
        Returns:
        true if the operation was successful, false if nothing changed.
        Since:
        Marvin 5.2
        See Also:
        ungroupSgroup(Sgroup sg)
      • ungroupSgroups

        public final boolean ungroupSgroups​(EnumSet<SgroupType> types)
        Ungroups all S-groups of the specified types in this molecule. Performs expand before ungroup if a type is an expandable S-group type. NOTE that giving SgroupType.SUPERATOM as parameter will leave the SgroupType.AMINOACID typed S-groups in unchanged state while the former method (ungroupSgroups(int)) ungrouped the AminoAcidSgroups as well.
        Parameters:
        types - the S-group types that specifies which S-group types to ungroup.
        Returns:
        true if the operation was successful, false if nothing changed.
        Since:
        Marvin 6.3
        See Also:
        SgroupType
      • ungroupSgroup

        @Deprecated
        public final boolean ungroupSgroup​(int i,
                                           int opts)
        Deprecated.
        as of Marvin 6.3. use ungroupSgroup(Sgroup) instead.
        Ungroups the specified S-group and expands it if it is an Expandable S-group. Ungroups and expands the child S-groups also if they are Expandable S-groups according to the specified option.
        Parameters:
        i - the S-group index
        opts - option to specify the ungroup type
        Returns:
        true if the operation was successful, false if nothing changed
        Since:
        Marvin 5.1
        See Also:
        RECURSIVE_UNGROUP, DEFAULT_UNGROUP, ungroupSgroup(chemaxon.struc.Sgroup)
      • ungroupSgroups

        public final boolean ungroupSgroups()
        Expands and ungroups all S-groups.
        Returns:
        true if the operation was successful, false if nothing changed
        Since:
        Marvin 3.0
      • addSgroupsOf

        protected final void addSgroupsOf​(Molecule m)
        Adds S-groups to this object and its parent.
      • removeSgroupsOf

        protected final void removeSgroupsOf​(Molecule m,
                                             int rmflags)
        Removes S-groups that are contained in a given molecule but not contained in another molecule.
        Parameters:
        m - the molecule whose S-groups are to remove
        rmflags - removal flags
        Since:
        Marvin 4.1.7
        See Also:
        RMSG_DEFAULT, RMSG_KEEP_CHILDREN, RMSG_KEEP_PARENT
      • removeSgroupsOf

        protected final void removeSgroupsOf​(Molecule m)
        Removes S-groups from this object and its parent.
      • removeAllSgroups

        protected void removeAllSgroups()
        Removes all S-groups.
      • removeSgroupFromList

        protected void removeSgroupFromList​(Sgroup sg)
        Removes an S-group from the sgroupVector.
        Since:
        Marvin 4.1, 07/28/2006
      • rearrangeSgroups

        public void rearrangeSgroups​(int[] newIndexes)
        Orders S-groups in the vector of S-groups in the given order corresponding to the given new indexes.
        Parameters:
        newIndexes - array of new S-group indexes, ith element of the array contains the new index of the ith s-group in the s-group vector
        Throws:
        IllegalArgumentException - if newIndexes are not in the range [0..getSgroupCount()] or not all values in this range are contained.
        Since:
        Marvin 5.12, 2012.11.12.
      • addSgroup

        public void addSgroup​(Sgroup sg,
                              boolean setparent)
        Adds an S-group to this object.
        Parameters:
        sg - the S-group to add.
        setparent - if true then the parent of the S-group is set to this molecule and the S-group is removed from the old parent molecule.
        Since:
        Marvin 5.2
      • removeAtomFromChildren

        protected void removeAtomFromChildren​(Sgroup sgroup,
                                              MolAtom atom)
        Removes the parameter atom from the parameter S-group and it's descendants.
      • getGraphUnionAsSelection

        protected final SelectionMolecule getGraphUnionAsSelection()
        Gets a selection molecule containing all the atoms and bonds. Returns the same object until the unified structure is (or might be) changed, then recreates it.
        Returns:
        a selection molecule object containing the unified structure
        Since:
        Marvin 3.0, 11/05/2002
        See Also:
        SelectionMolecule
      • bondlength

        public double bondlength()
        Calculate the regular bond length for the unified structure.
        Overrides:
        bondlength in class MoleculeGraph
        Returns:
        the regular bond length
      • convertToFrags

        public final Molecule[] convertToFrags()
        Converts this molecule to its disconnected fragments, expanding all S-groups and keeping disconnected Multicenter S-groups in the same fragment, but ungroupping and separating fragments in all other types of S-groups.

        Warning: Atoms are removed from the original molecule object to the created fragments, therefore the original molecule becomes inconsistent.

        The original atom order is preserved in the returned fragments. Fragment order is also determined by the original atom order. The first fragment is the one containing atom 0, the second fragment is the one containing the smallest indexed atom not in the first fragment, etc.

        Returns:
        array of fragments
        Since:
        Marvin 3.1
        See Also:
        MoleculeGraph.findFrags(Class, int)
      • findFrags

        public <C extends MoleculeGraph> C[] findFrags​(Class<C> cl,
                                                       int fragmentationType)
        Determines the disconnected fragments and puts them into an array. Atoms are removed from the original molecule object unless the fragment class is SelectionMolecule.class. The original atom order is preserved in the returned fragments. Fragment order is also determined by the original atom order. The first fragment is the one containing atom 0, the second fragment is the one containing the smallest indexed atom not in the first fragment, etc. If not using the FRAG_KEEPING_SGROUPS option and an S-group would contain more fragments, then it won't be added to any of them, and its parent-child relations with other S-groups will be removed. Fragmentation is performed depending on fragmentation type:
        Overrides:
        findFrags in class MoleculeGraph
        Type Parameters:
        C - the class of the fragments
        Parameters:
        cl - create fragment objects of this class
        fragmentationType - determines the type of fragmentation
        Returns:
        array of fragments
        Since:
        Marvin 5.6
        See Also:
        MoleculeGraph.FRAG_BASIC, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, MoleculeGraph.FRAG_KEEPING_SGROUPS
      • findFrags

        public final SelectionMolecule[] findFrags()
        Determines the disconnected fragments and puts them into an array. Multicenter S-groups are kept in one fragment.

        The original atom order is preserved in the returned fragments. Fragment order is also determined by the original atom order. The first fragment is the one containing atom 0, the second fragment is the one containing the smallest indexed atom not in the first fragment, etc.

        Returns:
        array of fragments
        Since:
        Marvin 3.0
      • fillSelectionMolecule

        protected void fillSelectionMolecule​(SelectionMolecule s)
        Adds all atoms and bonds to the specified molecule.
        Parameters:
        s - the selection molecule
        Since:
        Marvin 3.0, 11/05/2002
      • clearExtraLabels

        public void clearExtraLabels()
        Clears extra atom labels.
      • checkConsistency

        @Deprecated
        public void checkConsistency()
        Deprecated.
        As of Marvin 5.7, no replacement.
        Not intended for public use, it was intended only for internal debugging.
        Checks the internal consistency of the structure. Use this method for debugging.
        Overrides:
        checkConsistency in class MoleculeGraph
        Throws:
        RuntimeException - if inconsistency found
        Since:
        Marvin 5.0, 11/06/2007
      • checkSgroupConsistency

        protected void checkSgroupConsistency()
        Checks the internal consisitency of S-groups.
        Throws:
        RuntimeException - if inconsistency found
        Since:
        Marvin 5.0, 11/06/2007
      • getVisibleCoords

        public double[] getVisibleCoords​(MolAtom ma)
        Returns the coordinates of the given atom (contained in the molecule). If the atom is part of a contracted superatom sgroup, its coordinates may be false, so this method returns the coordinates of the corresponding sgroup atom instead.
        Overrides:
        getVisibleCoords in class MoleculeGraph
        Parameters:
        ma - The atom to be queried.
        Returns:
        The real coordinates of ma.
        Since:
        Marvin 4.0 8/07/2005
      • transform

        public void transform​(CTransform3D t,
                              boolean incg)
        Apply a transformation matrix to the atomic coordinates and Data Sgroup coordinates.
        Overrides:
        transform in class MoleculeGraph
        Parameters:
        t - the transformation matrix
        incg - graph invariants are changed (true) or not (false)
        Since:
        Marvin 4.0 2/09/2005
      • findContainingMulticenterSgroup

        public MulticenterSgroup findContainingMulticenterSgroup​(MolAtom atom)
        Gets the containing multicenter S-group of a multicenter atom.
        Parameters:
        atom - the multicenter atom.
        Returns:
        the containing multicenter S-group, null if none of the multicenter sgroups contains the multicenter atom.
        Since:
        Marvin 5.0 04/20/2007
        See Also:
        MulticenterSgroup, MolAtom.MULTICENTER
      • createGearch

        protected chemaxon.struc.gearch.MoleculeGraphGearch createGearch()
        Overrides:
        createGearch in class MoleculeGraph
      • clearObjects

        public void clearObjects()
        Specified by:
        clearObjects in interface chemaxon.struc.MObjectContainer
      • getObjectCount

        public int getObjectCount()
        Specified by:
        getObjectCount in interface chemaxon.struc.MObjectContainer
      • removeObject

        public void removeObject​(MObject mo)
        Specified by:
        removeObject in interface chemaxon.struc.MObjectContainer
      • selectAllObjects

        public void selectAllObjects​(boolean s)
        Specified by:
        selectAllObjects in interface chemaxon.struc.MObjectContainer
      • getAllObjects

        public List<MObject> getAllObjects()
        Specified by:
        getAllObjects in interface chemaxon.struc.MObjectContainer
      • replaceSgroup

        public void replaceSgroup​(Sgroup sgroup,
                                  Sgroup newSgroup)
        Replaces an S-group with a new sgroup in the molecule. Sets parent - child relations of the new sgroup according to the parent - child relations of the old sgroup.
        Parameters:
        sgroup - the sgroup to replace
        newSgroup - the sgroup to replace with
      • add

        public void add​(MolBond bond)
        Adds a bond to the molecule. 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
      • replaceAtom

        public void replaceAtom​(int i,
                                MolAtom newAtom)
        Replaces the atom on the given index with the parameter atom and removes the parameter atom from its original parent molecule if needed. Sets the sgroup hierarchy.
        Overrides:
        replaceAtom in class MoleculeGraph
        Parameters:
        i - the index of the original atom
        newAtom - the atom which will replace the original
      • getBonds

        protected MolBond[] getBonds​(MolAtom atom)
        Returns the bonds attached to the given atom.
        Overrides:
        getBonds in class MoleculeGraph
        Parameters:
        atom - the atom
        Returns:
        the bonds attached to the given atom in this molecule
        Since:
        Marvin 6.2
      • getSgroupIterator

        public IteratorFactory.SgroupIterator getSgroupIterator()
        Returns an iterator over the s-groups in this molecule in proper sequence.
        Returns:
        an iterator over the s-groups in this molecule in proper sequence
        Since:
        Marvin 6.2, 2013.09.09.
      • connectOriginalBondsToNewAtom

        protected void connectOriginalBondsToNewAtom​(MolAtom newAtom,
                                                     MolAtom orig,
                                                     MolBond[] bonds)
        Description copied from class: MoleculeGraph
        Sets the original connections to the new atom.
        Overrides:
        connectOriginalBondsToNewAtom in class MoleculeGraph
        Parameters:
        newAtom - the atom which replace the original
        orig - the original atom
        bonds - the original atoms bonds (before any modification)
      • hasAtomSet

        public boolean hasAtomSet()
        Description copied from class: MoleculeGraph
        Tests whether the molecule graph has atom sets.
        Overrides:
        hasAtomSet in class MoleculeGraph
        Returns:
        true if there are atom sets, false otherwise