RepeatingUnitSgroup (Marvin API documentation (c) 1998-2019 ChemAxon Ltd.)

java.lang.Object
- chemaxon.struc.Sgroup
- - chemaxon.struc.sgroup.RepeatingUnitSgroup

All Implemented Interfaces:

java.io.Serializable
```
@PublicAPI
public class RepeatingUnitSgroup
extends Sgroup
```
Source-based and structure-based representation of repeating unit groups (polymers and repeating units with repetition ranges).

Source and structure structure-based representation of polymers.
The polymer structure consists of structural fragments. These fragments are enclosed by polymer brackets. The meaning of an SRU bracket is that the fragment within the brackets can repeat with itself. The fragment within the bracket is called repeating unit. Each SRU S-group has two or more dedicated bonds, called crossing bonds, that cross the brackets. The crossing bonds of an SRU show how the repeating units may connect in several ways to each other within the polymer. Depending on the number of crossing bonds and brackets we differentiate the following polymers and connectivities within the polymer:
- Polymers with two crossing bonds.
  If the polymer has one crossing bond on each bracket of the SRU there are three possibilities for the repeating pattern:
  - head-to-tail
  - head-to-head
  - either/unknown
- Ladder-Type Polymers
  Polymers with paired brackets and with two crossing bonds on each bracket are called ladder-type polymers. Here it must be specified how the two crossing bonds on each bracket connect to the corresponding bonds of the adjoining repeating units. Additionally to the head-to-tail, head-to-head connectivity information there is a flip information to specify whether the repeating unit flips around the polymer backbone when it connects to the adjoining SRU. This information is handled only in case of brackets with exactly two crossing bonds on both side (head and tail side). We differentiate the following polymer connectivities:
  - head-to-tail with no flip
  - head-to-tail with flip
  - head-to-head with no flip
  - head-to-head with flip
  - either/unknown
- Polymers with three or more brackets.
  If the polymer has three or more bonds with a separated bracket on each bond, the polymer always has the either/unknown repeating pattern.
The end groups of polymers are often unknown or unspecified which are represented by star atoms (*).
Repeating units with repetition ranges.
Implemented S-group types:
- Sgroup.ST_ANY
- Sgroup.ST_SRU
- Sgroup.ST_COPOLYMER
- Sgroup.ST_CROSSLINK
- Sgroup.ST_GRAFT
- Sgroup.ST_MODIFICATION
Since:

Marvin 5.0, 10/13/2006

Version:

5.3, 09/25/2009

Author:

Erika Biro

See Also:

Serialized Form

Field Summary
- Fields inherited from class chemaxon.struc.Sgroup
  atomSet, brackets, CHARGE_ON_ATOMS, CHARGE_ON_GROUP, parentSgroup, PR_ATSYMS, RA_IN_EXPAND, RA_REMOVE_EXCEPT_RU, SCN_EITHER_UNKNOWN, SCN_HEAD_TO_HEAD, SCN_HEAD_TO_TAIL, SGROUP_TYPE_COUNT, sgroupGraph, sgroupType, SORT_CHILD_PARENT, SORT_PARENT_CHILD, SST_ALTERNATING, SST_BLOCK, SST_RANDOM, ST_AMINOACID, ST_ANY, ST_COMPONENT, ST_COPOLYMER, ST_CROSSLINK, ST_DATA, ST_FORMULATION, ST_GENERIC, ST_GRAFT, ST_MER, ST_MIXTURE, ST_MODIFICATION, ST_MONOMER, ST_MULTICENTER, ST_MULTIPLE, ST_SRU, ST_SUPERATOM, XSTATE_C, XSTATE_NONE, XSTATE_X, XSTATE_XC

Constructor Summary

Constructors
Modifier	Constructor and Description
	`RepeatingUnitSgroup(Molecule parent, int type)` Constructs an SRU S-group.
	`RepeatingUnitSgroup(Molecule parent, java.lang.String connectivity, int type)` Constructs an SRU S-group with connectivity.
`protected`	`RepeatingUnitSgroup(RepeatingUnitSgroup sg, Molecule m, Sgroup psg)` Copy constructor.
`protected`	`RepeatingUnitSgroup(RepeatingUnitSgroup sg, Molecule m, Sgroup psg, int[] atomIndexMap)` Copy constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`void`	`addCrossingBonds(java.util.List<MolBond> crsList, java.util.List<MolBond> list)` Sets the crossing bonds (head and tail) of a ladder-type polymer.
`void`	`addStarAtoms()` Changes terminal carbon atoms to star atoms (*).
`protected Sgroup`	`cloneSgroup(Molecule m, Sgroup psg, int[] atomIndexMap)` Gets a new Sgroup instance.
`boolean`	`containsLadderTypePolymer()` Decides whether the structure of this sgroup contains a ladder-type repeating unit.
`boolean`	`equalsHead(MolBond[] bonds)` Decides whether the head bonds equal the given bonds.
`boolean`	`equalsTail(MolBond[] bonds)` Decides whether the tail bonds equal the given bonds.
`MolBond[]`	`findCrossingBonds()` Finds the crossing bonds.
`MolBond[]`	`getBondConnectionInfo()` Gets a bond triplet which stores the crossing bond and flip information.
`MolBond[]`	`getBondCorrespondence()` Gets four bonds that store the crossing bond and flip information.
`MolBond[]`	`getHeadCrossingBonds()` Gets the head crossing bonds.
`MolBond`	`getOtherCrossingBond(MolBond b)` Gets the other bond if a bond is a crossing bond in a ladder-type polimer bracket.
`java.lang.String`	`getSuperscript()` Gets the superscript for Sru S-groups.
`MolBond[]`	`getTailCrossingBonds()` Gets the tail crossing bonds.
`java.lang.String`	`internalsToString()` Print state to a String.
`static boolean`	`isAcceptablePolymerGraph(MoleculeGraph molGraph)` Checks if the given molecular graph can be the graph of a polymer SRU
`static boolean`	`isAcceptableRSRUGraph(MoleculeGraph molGraph)` Checks if the given molecular graph can be the graph of an RSRU
`static boolean`	`isAcceptableSru(java.lang.String s)`
`boolean`	`isCrossingBond(MolBond b)` Decides whether the bond is a crossing bond in a ladder-type polymer bracket.
`boolean`	`isFlipped()` Decides whether this sgroup is flipped.
`boolean`	`isStarAtom(MolAtom atom)` Decides whether an atom is a star atom in this S-group.
`void`	`mergeBrackets(MolBond b1, MolBond b2)` Sets the crossing bonds of this sgroup so that they will share a common bracket.
`void`	`removeStarAtoms()` Changes terminal star atoms (*) to carbon atoms (C).
`void`	`setBondCorrespondence(MolBond[] b)` Sets the crossing bonds (head and tail) of a ladder-type polymer.
`void`	`setFlipped(boolean flipped)` Sets the flip property of this sgroup.
`void`	`setHeadCrossingBonds(MolBond[] b)` Sets the head crossing bonds.
`void`	`setTailCrossingBonds(MolBond[] tailCrossingBonds)` Sets the tail crossing bonds.
`void`	`swapHeadTail()` Swaps the head and tail bonds of this sru if both are set.

Methods inherited from class chemaxon.struc.Sgroup
add, addBracket, addChildSgroup, areChildSgroupsVisible, checkBondConsistency, checkBonds, checkConsistencyInEmbeddings, checkSgroupGraphConsistency, clearObjects, cloneSgroup, cloneStructure, contains, containsAllAtomsOf, contract, countAllAtoms, createMolecule, createMolecule, expand, findSmallestSgroupContaining, findSmallestSgroupOf, getAtom, getAtomArray, getAtomCount, getAtomSymbolListAsString, getAttach, getBondArray, getBracketCount, getBrackets, getChargeLocation, getChildSgroup, getChildSgroupCount, getChildSgroups, getConnectivity, getCrossingAtoms, getId, getParentMolecule, getParentSgroup, getSgroupGraph, getSgroupType, getSubscript, getSubType, getTotalCharge, getType, getXState, hasAtom, hasBrackets, indexOf, indexOf, initBrackets, isBracketCrossingBond, isBracketVisible, isDescendantOf, isEmpty, isOrderedComponentSgroup, isPartSelected, isRemovable, isSelected, isTotalSelected, isVisible, removeAtom, removeAtom, removeAtom, removeBond, removeBonds, removeChildSgroup, removeGroupedAtom, removeObject, replaceAtom, replaceAtom, selectAllObjects, setAtom, setChargeLocation, setConnectivity, setGUIStateRecursively, setGUIStateRecursively, setId, setParentMolecule, setSgroupGraph, setSubscript, setSubType, setXState, setXState, setXState0, sort, toString, toString, transformByParent

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - RepeatingUnitSgroup
```
public RepeatingUnitSgroup(Molecule parent,
                           int type)
```
    Constructs an SRU S-group.
    Parameters:
    
    parent - the parent molecule
    type - type of the repeating unit sgroup. Possible values:
    
    Sgroup.ST_ANY
    Sgroup.ST_SRU
    Sgroup.ST_COPOLYMER
    Sgroup.ST_CROSSLINK
    Sgroup.ST_GRAFT
    Sgroup.ST_MODIFICATION
  - RepeatingUnitSgroup
```
public RepeatingUnitSgroup(Molecule parent,
                           java.lang.String connectivity,
                           int type)
```
    Constructs an SRU S-group with connectivity. The connectivity string returned by getSuperscript() can be used to create another SRU S-group with the same connectivity data.
    Parameters:
    
    parent - the parent molecule
    connectivity - the connectivity information possibilities:
    
    "htn" or "ht,n" or "ht" - head to tail & no flip,
    "htf" or "ht,f" - head to tail & flip,
    "hhn" or "hh,n" or "hh" - head to head & no flip,
    "hhf" or "hh,f" - head to head & flip,
    "eun" or "eu,n" or "eu" - either/unknown.
    type - type of the repeating unit sgroup. Possible values:
    
    Sgroup.ST_ANY
    Sgroup.ST_SRU
    Sgroup.ST_COPOLYMER
    Sgroup.ST_CROSSLINK
    Sgroup.ST_GRAFT
    Sgroup.ST_MODIFICATION
    See Also:
    
    Sgroup.SCN_HEAD_TO_TAIL, Sgroup.SCN_HEAD_TO_HEAD, Sgroup.SCN_EITHER_UNKNOWN
  - RepeatingUnitSgroup
```
protected RepeatingUnitSgroup(RepeatingUnitSgroup sg,
                              Molecule m,
                              Sgroup psg,
                              int[] atomIndexMap)
```
    Copy constructor.
    
    Parameters:
    
    sg - the S-group to copy
    
    m - the new parent molecule
    
    psg - the new parent S-group or null
    
    atomIndexMap - indices of cloned atoms in the original molecule in the case of partial cloning, or null otherwise
    
    Since:
    
    Marvin 4.1
  - RepeatingUnitSgroup
```
protected RepeatingUnitSgroup(RepeatingUnitSgroup sg,
                              Molecule m,
                              Sgroup psg)
```
    Copy constructor.
    
    Parameters:
    
    sg - the S-group to copy
    
    m - the new parent molecule
    
    psg - the new parent S-group or null
    
    Since:
    
    Marvin 4.1
- Method Detail
  - cloneSgroup
```
protected Sgroup cloneSgroup(Molecule m,
                             Sgroup psg,
                             int[] atomIndexMap)
```
    Gets a new Sgroup instance.
    
    Overrides:
    
    cloneSgroup in class Sgroup
    
    Parameters:
    
    m - the new parent molecule
    
    psg - the new parent S-group
    
    atomIndexMap - indices of cloned atoms in the original molecule or null
    
    Returns:
    
    the new object
    
    Since:
    
    Marvin 5.0.2, 03/07/2008
  - getSuperscript
```
public java.lang.String getSuperscript()
```
    Gets the superscript for Sru S-groups. This contains the connectivity data.
    Overrides:
    
    getSuperscript in class Sgroup
    
    Returns:
    the superscript:
    
    "ht" - head to tail & no flip,
    "ht,f" - head to tail & flip,
    "hh" - head to head & no flip,
    "hh,f" - head to head & flip,
    "eu" - either/unknown.
  - isAcceptableSru
```
public static boolean isAcceptableSru(java.lang.String s)
```
  - isAcceptablePolymerGraph
```
public static boolean isAcceptablePolymerGraph(MoleculeGraph molGraph)
```
    Checks if the given molecular graph can be the graph of a polymer SRU
    
    Parameters:
    
    molGraph - the molecular graph to check
    
    Returns:
    
    true if the molecular graph is acceptable for a polymer SRU
  - isAcceptableRSRUGraph
```
public static boolean isAcceptableRSRUGraph(MoleculeGraph molGraph)
```
    Checks if the given molecular graph can be the graph of an RSRU
    
    Parameters:
    
    molGraph - the molecular graph to check
    
    Returns:
    
    true if the molecular graph is acceptable for an RSRU
  - addStarAtoms
```
public void addStarAtoms()
```
    Changes terminal carbon atoms to star atoms (*).
  - removeStarAtoms
```
public void removeStarAtoms()
```
    Changes terminal star atoms (*) to carbon atoms (C).
  - isStarAtom
```
public boolean isStarAtom(MolAtom atom)
```
    Decides whether an atom is a star atom in this S-group.
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    true if the atom is star atom false otherwise
  - findCrossingBonds
```
public MolBond[] findCrossingBonds()
```
    Finds the crossing bonds.
    
    Overrides:
    
    findCrossingBonds in class Sgroup
    
    Returns:
    
    the attachment bonds
    
    Since:
    
    Marvin 5.0
  - mergeBrackets
```
public void mergeBrackets(MolBond b1,
                          MolBond b2)
```
    Sets the crossing bonds of this sgroup so that they will share a common bracket.
    
    Parameters:
    
    b1 - first bond
    
    b2 - second bond
  - isCrossingBond
```
public boolean isCrossingBond(MolBond b)
```
    Decides whether the bond is a crossing bond in a ladder-type polymer bracket.
    
    Parameters:
    
    b - the bond
    
    Returns:
    
    true if the bond is a crossing bond in a ladder-type polymer bracket, false otherwise
  - getOtherCrossingBond
```
public MolBond getOtherCrossingBond(MolBond b)
```
    Gets the other bond if a bond is a crossing bond in a ladder-type polimer bracket.
    
    Parameters:
    
    b - the bond which crosses a ladder-type bracket
    
    Returns:
    
    the other bond if the given bond is in a ladder-type polimer bracket, null otherwise.
  - isFlipped
```
public boolean isFlipped()
```
    Decides whether this sgroup is flipped.
    
    Returns:
    
    true if the sgroup is flipped, false otherwise
    
    See Also:
    
    flipped
  - setFlipped
```
public void setFlipped(boolean flipped)
```
    Sets the flip property of this sgroup.
    
    Parameters:
    
    flipped - the value of flip property
    
    See Also:
    
    flipped
  - getBondConnectionInfo
```
public MolBond[] getBondConnectionInfo()
```
    Gets a bond triplet which stores the crossing bond and flip information.
    
    Returns:
    
    array of bonds In case of ladder-type sru sgroups: 0. and 1. bond in the array are the crossing bond-pair that share a common bracket, 2. bond in the array is a crossing bond in repeating unit that attaches to the 0. item of this array. Null if the this sgroup contains a non ladder-type polymer.
  - getBondCorrespondence
```
public MolBond[] getBondCorrespondence()
```
    Gets four bonds that store the crossing bond and flip information.
    
    Returns:
    
    array of bonds In case of ladder-type sru sgroups: 0. and 2. bond in the array are the crossing bond-pair that share a common bracket, 1. bond in the array is a crossing bond in repeating unit that attaches to the 0. item of this array, 3. bond in the array is a crossing bond in repeating unit that attaches to the 2. item of this array. Null if the this sgroup contains a non ladder-type polymer.
  - setBondCorrespondence
```
public void setBondCorrespondence(MolBond[] b)
```
    Sets the crossing bonds (head and tail) of a ladder-type polymer. If head and tail crossing bonds are not yet set then adds the bonds from the bond array. If only head is already set, sets the tail bonds. Here the head bonds should be in the array, otherwise does nothing. Calculates the flip property according the connection given in the array.
    
    Parameters:
    
    b - array of four bonds. The order of bonds should be the following: 0. and 2. bond belong to the same bracket, 1. and 3. as well. When the sru connects to the adjoining sru, it does via 0. and 1. bond, 2. and 3. bond.
  - equalsTail
```
public boolean equalsTail(MolBond[] bonds)
```
    Decides whether the tail bonds equal the given bonds.
    
    Parameters:
    
    bonds - the bonds to compare with
    
    Returns:
    
    true if the bonds equal with the tail bonds (order is not important)
  - equalsHead
```
public boolean equalsHead(MolBond[] bonds)
```
    Decides whether the head bonds equal the given bonds.
    
    Parameters:
    
    bonds - the bonds to compare with
    
    Returns:
    
    true if the bonds equal with the head bonds (order is not important)
  - addCrossingBonds
```
public void addCrossingBonds(java.util.List<MolBond> crsList,
                             java.util.List<MolBond> list)
```
    Sets the crossing bonds (head and tail) of a ladder-type polymer.
    
    Parameters:
    
    crsList - list that contains a pair of crossing bonds that share a common bracket (0. and 1. item of this list) and a crossing bond that connects to the 0. item of this list.
    
    list - list of all crossing bonds that share a common bracket
    
    See Also:
    
    headCrossingBonds, tailCrossingBonds
  - getHeadCrossingBonds
```
public MolBond[] getHeadCrossingBonds()
```
    Gets the head crossing bonds.
    
    Returns:
    
    exactly two head crossing bonds if this sgroup contains a ladder-type polymer, null otherwise
  - setHeadCrossingBonds
```
public void setHeadCrossingBonds(MolBond[] b)
```
    Sets the head crossing bonds. Exactly two or null head crossing bonds should be specified.
    
    Parameters:
    
    b - the head crossing bonds.
  - getTailCrossingBonds
```
public MolBond[] getTailCrossingBonds()
```
    Gets the tail crossing bonds.
    
    Returns:
    
    the tail crossing bonds if this sgroup contains a ladder-type polymer, null otherwise
  - setTailCrossingBonds
```
public void setTailCrossingBonds(MolBond[] tailCrossingBonds)
```
    Sets the tail crossing bonds. Exactly two or null head crossing bonds should be given.
    
    Parameters:
    
    tailCrossingBonds - the tail crossing bonds.
  - swapHeadTail
```
public void swapHeadTail()
```
    Swaps the head and tail bonds of this sru if both are set.
  - containsLadderTypePolymer
```
public boolean containsLadderTypePolymer()
```
    Decides whether the structure of this sgroup contains a ladder-type repeating unit.
    
    Returns:
    
    true if this sgroup contains a ladder-type repeating unit.
  - internalsToString
```
public java.lang.String internalsToString()
```
    Print state to a String. This method is intended for internal use only!
    
    Returns:
    
    Internal state as a multi line String

Class RepeatingUnitSgroup

Field Summary

Fields inherited from class chemaxon.struc.Sgroup

Constructor Summary

Method Summary

Methods inherited from class chemaxon.struc.Sgroup

Methods inherited from class java.lang.Object

Constructor Detail

RepeatingUnitSgroup

RepeatingUnitSgroup

RepeatingUnitSgroup

RepeatingUnitSgroup

Method Detail

cloneSgroup

getSuperscript

isAcceptableSru

isAcceptablePolymerGraph

isAcceptableRSRUGraph

addStarAtoms

removeStarAtoms

isStarAtom

findCrossingBonds

mergeBrackets

isCrossingBond

getOtherCrossingBond

isFlipped

setFlipped

getBondConnectionInfo

getBondCorrespondence

setBondCorrespondence

equalsTail

equalsHead

addCrossingBonds

getHeadCrossingBonds

setHeadCrossingBonds

getTailCrossingBonds

setTailCrossingBonds

swapHeadTail

containsLadderTypePolymer

internalsToString