CleanUtil (JChem Base API documentation (c) 1998-2019 ChemAxon Ltd.)

java.lang.Object
- chemaxon.marvin.util.CleanUtil

All Implemented Interfaces:

HybridizationStateConsts
```
@PublicAPI
public class CleanUtil
extends java.lang.Object
implements HybridizationStateConsts
```
Utility methods for cleaning.

Since:

Marvin 4.1, 01/31/2006

Version:

5.3, 04/27/2009

Author:

Peter Csizmadia, Andras Volford

Field Summary
- Fields inherited from interface chemaxon.struc.HybridizationStateConsts
  HS_S, HS_SP, HS_SP2, HS_SP3, HS_UNKNOWN

Constructor Summary

Constructors
Constructor and Description

CleanUtil()

Constructors
Constructor and Description
`CleanUtil()`

Method Summary

All Methods Static Methods Concrete Methods
Modifier and Type	Method and Description
`static boolean`	`arrangeComponents(MoleculeGraph mol)` Arranges molecule components (reactants, agents, products, R-group definitions) nicely.
`static boolean`	`arrangeComponents(MoleculeGraph mol, boolean obj)` Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
`static boolean`	`arrangeComponents(MoleculeGraph mol, boolean obj, boolean frags)` Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
`static void`	`arrangeDataSgroupData(MoleculeGraph m)` Arrange data attached to DataSgroup.
`static void`	`arrangeMolecules(MoleculeGraph[] mo, int dist, int col)` Arrange molecules nicely If we have more molecules try to arrange them in a 2D square lattice.
`static void`	`arrangeReaction(RxnMolecule m)` Arranges reaction components nicely
`static void`	`arrangeRelativeDataSgroupData(MoleculeGraph m)` Arrange data attached to DataSgroup.
`static void`	`arrangeSgBrackets(MoleculeGraph m)` Arrange sgroup brackets in the molecule.
`static double`	`calcBadness(MoleculeGraph mol1, MoleculeGraph mol2, MolAtom sa, MolBond[] xbonds)` Calculates a "badness" value for the atomic coordinates.
`static DPoint3[]`	`calcBracketEndPoints(DPoint3[] q, DPoint3 p1, double c)` Calculates the bracket endpoints from the base line of the bracket.
`static DPoint3`	`calcDividingPoint(DPoint3 p1, DPoint3 p2, double k)` Calculates the division point of a segment with a given ratio.
`static DPoint3[]`	`calcSimplePolymerBracket(DPoint3 p1, DPoint3 p2, double ratio)` Calculates the points of a simple polymer bracket that belongs to a bond.
`static void`	`createBracket(Sgroup sg, DPoint3[] q, int btype)`
`static CTransform3D`	`createRotationAboutBond(MolBond b, double phi)` Creates a rotation transformation about a bond.
`static double[]`	`createSavedCoordsArray(MoleculeGraph g)` Creates an empty array for the atomic coordinates of a structure.
`static void`	`generateBracketCoords(Sgroup sg, int btype)` Generates brackets with coordinates for a specified S-group.
`static void`	`generateBracketCoords(Sgroup sg, int btype, boolean extraSpace)` Generates brackets with coordinates for a specified S-group.
`static boolean`	`hasWiggly(MolAtom a)` Check if at least one wiggly bond starts from this atom.
`static boolean[]`	`isNonPreferredStereoAtom(MoleculeGraph m)` Check if the atoms in the molecule is in SP2 hybridization state and has wedge whose getAtom1 is the specified atom, but wiggly bonds next to double bonds are allowed.
`static boolean`	`removeCTflagFromSmallRings(MoleculeGraph m)` Remove CIS\|TRANS flag from bonds in rings smaller than size 8.
`static void`	`restoreCoords(MoleculeGraph g, double[] coords)` Restores atomic coordinates.
`static void`	`saveCoords(MoleculeGraph g, double[] coords)` Saves atomic coordinates.
`static void`	`setBestLigandPosition(MolAtom atom, MolAtom ligand)` Calculates and sets an optimal position for a ligand atom.
`static void`	`setBestLigandPosition(MolAtom atom, MolAtom ligand, double bondlength)` Calculates and sets an optimal position for a ligand atom.
`static void`	`setCTCrossedBond(MoleculeGraph m)` Convert wiggly type double bonds to crossed.
`static boolean`	`setCTWigglyBond(MoleculeGraph m)` Convert crossed double bonds to wiggly type.
`static boolean`	`setCTWigglyBond(MoleculeGraph m, int bond)` Convert crossed double bond to wiggly type.
`static double`	`sumDistanceSquare(MoleculeGraph mol, DPoint3 p)` Calculates the sum of the distance square for each atom from a point.

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

- Constructor Detail
  - CleanUtil
```
public CleanUtil()
```
- Method Detail
  - arrangeComponents
```
public static boolean arrangeComponents(MoleculeGraph mol)
```
    Arranges molecule components (reactants, agents, products, R-group definitions) nicely. Also arranges attached data, Sgroup brackets.
    
    Parameters:
    
    mol - the molecule
    
    Returns:
    
    true if components have been rearranged, false if no components found
  - arrangeComponents
```
public static boolean arrangeComponents(MoleculeGraph mol,
                                        boolean obj)
```
    Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
    
    Parameters:
    
    mol - the molecule
    
    obj - also arrange other object attached to the molecule (like data, brackets)
    
    Returns:
    
    true if components have been rearranged, false if no components found
  - arrangeComponents
```
public static boolean arrangeComponents(MoleculeGraph mol,
                                        boolean obj,
                                        boolean frags)
```
    Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.
    
    Parameters:
    
    mol - the molecule
    
    obj - also arrange other object attached to the molecule (like data, brackets)
    
    frags - also arrange fragments in root / main molecule
    
    Returns:
    
    true if components have been rearranged, false if no components found
    
    Since:
    
    Marvin 5.4.1
  - arrangeReaction
```
public static void arrangeReaction(RxnMolecule m)
```
    Arranges reaction components nicely
    
    Parameters:
    
    m - the reaction molecule
  - arrangeMolecules
```
public static void arrangeMolecules(MoleculeGraph[] mo,
                                    int dist,
                                    int col)
```
    Arrange molecules nicely If we have more molecules try to arrange them in a 2D square lattice. Also arrange the DataSgroup values close to the atoms if relative arrangement needed.
    
    Parameters:
    
    mo - molecules
    
    dist - use CCLENGTH distance for the molecules
    
    col - number of colums (if -1 calculate it)
  - arrangeDataSgroupData
```
public static void arrangeDataSgroupData(MoleculeGraph m)
```
    Arrange data attached to DataSgroup. Set it to the right down corner.
  - arrangeRelativeDataSgroupData
```
public static void arrangeRelativeDataSgroupData(MoleculeGraph m)
```
    Arrange data attached to DataSgroup. Keeps the position of the data label if it is relative.
    
    Parameters:
    
    m - molecule
  - arrangeSgBrackets
```
public static void arrangeSgBrackets(MoleculeGraph m)
```
    Arrange sgroup brackets in the molecule.
    
    Parameters:
    
    m - molecule
  - sumDistanceSquare
```
public static double sumDistanceSquare(MoleculeGraph mol,
                                       DPoint3 p)
```
    Calculates the sum of the distance square for each atom from a point.
    
    Parameters:
    
    mol - the molecule
    
    p - the point
  - calcBadness
```
public static double calcBadness(MoleculeGraph mol1,
                                 MoleculeGraph mol2,
                                 MolAtom sa,
                                 MolBond[] xbonds)
```
    Calculates a "badness" value for the atomic coordinates.
    
    Parameters:
    
    mol1 - the original molecule
    
    mol2 - the transformed substructure
    
    sa - additional transformed atom or null
    
    xbonds - additional bonds between mol1 and mol2, or null
    
    Returns:
    
    the badness
  - createSavedCoordsArray
```
public static double[] createSavedCoordsArray(MoleculeGraph g)
```
    Creates an empty array for the atomic coordinates of a structure.
    
    Parameters:
    
    g - the structure
  - saveCoords
```
public static void saveCoords(MoleculeGraph g,
                              double[] coords)
```
    Saves atomic coordinates. This method can be called before trying a coordinate transformation.
    
    Parameters:
    
    g - the structure
    
    coords - array for the coordinates
  - restoreCoords
```
public static void restoreCoords(MoleculeGraph g,
                                 double[] coords)
```
    Restores atomic coordinates. This method can be called after trying a coordinate transformation.
    
    Parameters:
    
    g - the structure
    
    coords - array containing the coordinates
  - createRotationAboutBond
```
public static CTransform3D createRotationAboutBond(MolBond b,
                                                   double phi)
```
    Creates a rotation transformation about a bond.
    
    Parameters:
    
    b - the bond
    
    phi - rotation angle
  - setCTWigglyBond
```
public static boolean setCTWigglyBond(MoleculeGraph m)
```
    Convert crossed double bonds to wiggly type.
    
    Parameters:
    
    m - molecule
  - setCTWigglyBond
```
public static boolean setCTWigglyBond(MoleculeGraph m,
                                      int bond)
```
    Convert crossed double bond to wiggly type. Set wiggly bond to the endpoint of the given double bond.
    
    Parameters:
    
    m - a molecule that contains a double bond to convert it to a wiggly represented up-o-down stereo double bond
    
    bond - the index of the double bond to
    
    Returns:
    
    true if the wiggly representation could be set successfully
    
    Since:
    
    Marvin 5.2
  - hasWiggly
```
public static boolean hasWiggly(MolAtom a)
```
    Check if at least one wiggly bond starts from this atom. (The which first atom of the bond should be the given atom.)
    
    Parameters:
    
    a - atom
    
    Returns:
    
    true if has wiggly bond starting from this atom
  - setCTCrossedBond
```
public static void setCTCrossedBond(MoleculeGraph m)
```
    Convert wiggly type double bonds to crossed.
    
    Parameters:
    
    m - molecule
  - isNonPreferredStereoAtom
```
public static boolean[] isNonPreferredStereoAtom(MoleculeGraph m)
```
    Check if the atoms in the molecule is in SP2 hybridization state and has wedge whose getAtom1 is the specified atom, but wiggly bonds next to double bonds are allowed.
    
    Parameters:
    
    m - molecule
    
    Returns:
    
    true for SP2 atom which has wedge with narrow end else false.
    
    Since:
    
    Marvin 5.0
  - removeCTflagFromSmallRings
```
public static boolean removeCTflagFromSmallRings(MoleculeGraph m)
```
    Remove CIS|TRANS flag from bonds in rings smaller than size 8. Remove TRANS flag from bonds in rings smaller than size 8, but give warning. Suppose that the stereo info stored already in the flags.
    
    Parameters:
    
    m - molecule
    
    Returns:
    
    false if TRANS stereoinformation is removed, otherwise true.
  - setBestLigandPosition
```
public static void setBestLigandPosition(MolAtom atom,
                                         MolAtom ligand)
```
    Calculates and sets an optimal position for a ligand atom.
    
    Parameters:
    
    atom - the atom whose ligand atom's position is calculated
    
    ligand - the ligand atom whoose optimal position is calculated
    
    Since:
    
    Marvin 5.4
  - setBestLigandPosition
```
public static void setBestLigandPosition(MolAtom atom,
                                         MolAtom ligand,
                                         double bondlength)
```
    Calculates and sets an optimal position for a ligand atom.
    
    Parameters:
    
    atom - the atom whose ligand atom's position is calculated
    
    ligand - the ligand atom whoose optimal position is calculated
    
    bondlength - the requested bond length between the atom and its ligand, use -1 for automatic bond length determination according atom types.
    
    Since:
    
    Marvin 5.4
  - calcBracketEndPoints
```
public static DPoint3[] calcBracketEndPoints(DPoint3[] q,
                                             DPoint3 p1,
                                             double c)
```
    Calculates the bracket endpoints from the base line of the bracket. Another point is neccessary to calculate in the plane where the end points will be.
    
    Parameters:
    
    q - endpoints of the base line in the bracket.
    
    p1 - point to fix the plane in which the bracket endpoints will be.
    
    c - expected length of the bracket internal segment
    
    Returns:
    
    bracket endpoints.
  - calcDividingPoint
```
public static DPoint3 calcDividingPoint(DPoint3 p1,
                                        DPoint3 p2,
                                        double k)
```
    Calculates the division point of a segment with a given ratio.
    
    Parameters:
    
    p1 - the first endpoint of the segment
    
    p2 - the second endpoint of the segment
    
    k - the ratio
    
    Returns:
    
    the division point
  - calcSimplePolymerBracket
```
public static DPoint3[] calcSimplePolymerBracket(DPoint3 p1,
                                                 DPoint3 p2,
                                                 double ratio)
```
    Calculates the points of a simple polymer bracket that belongs to a bond.
    
    Parameters:
    
    p1 - endpoint of the bond that belongs to the sgroup
    
    p2 - the other endpoint of the bond
    
    Returns:
    
    bracket points
    
    See Also:
    
    RepeatingUnitSgroup
  - createBracket
```
public static void createBracket(Sgroup sg,
                                 DPoint3[] q,
                                 int btype)
```
  - generateBracketCoords
```
public static void generateBracketCoords(Sgroup sg,
                                         int btype)
```
    Generates brackets with coordinates for a specified S-group.
    
    Parameters:
    
    sg - the S-group to generate the brackets and coordinates for
    
    btype - the type of the brackets to generate
    
    See Also:
    
    MBracket.T_ROUND, MBracket.T_SQUARE
  - generateBracketCoords
```
public static void generateBracketCoords(Sgroup sg,
                                         int btype,
                                         boolean extraSpace)
```
    Generates brackets with coordinates for a specified S-group.
    
    Parameters:
    
    sg - the S-group to generate the brackets and coordinates for
    
    btype - the type of the brackets to generate
    
    extraSpace - calculate with extra space at atom labels
    
    See Also:
    
    MBracket.T_ROUND, MBracket.T_SQUARE

Class CleanUtil

Field Summary

Fields inherited from interface chemaxon.struc.HybridizationStateConsts

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

CleanUtil

Method Detail

arrangeComponents

arrangeComponents

arrangeComponents

arrangeReaction

arrangeMolecules

arrangeDataSgroupData

arrangeRelativeDataSgroupData

arrangeSgBrackets

sumDistanceSquare

calcBadness

createSavedCoordsArray

saveCoords

restoreCoords

createRotationAboutBond

setCTWigglyBond

setCTWigglyBond

hasWiggly

setCTCrossedBond

isNonPreferredStereoAtom

removeCTflagFromSmallRings

setBestLigandPosition

setBestLigandPosition

calcBracketEndPoints

calcDividingPoint

calcSimplePolymerBracket

createBracket

generateBracketCoords

generateBracketCoords