Package chemaxon.marvin.util
Class CleanUtil
- java.lang.Object
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- chemaxon.marvin.util.CleanUtil
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- All Implemented Interfaces:
HybridizationStateConsts
@PublicAPI public class CleanUtil extends Object implements HybridizationStateConsts
Utility methods for cleaning.- Since:
- Marvin 4.1, 01/31/2006
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Field Summary
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Fields inherited from interface chemaxon.struc.HybridizationStateConsts
HS_S, HS_SP, HS_SP2, HS_SP3, HS_UNKNOWN
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Constructor Summary
Constructors Constructor Description CleanUtil()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method 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 nicelystatic 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 boolean
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.
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Method Detail
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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
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arrangeComponents
public static boolean arrangeComponents(MoleculeGraph mol, boolean obj)
Arranges molecule components (reactants, agents, products, R-group definitions, data, brackets) nicely.- Parameters:
mol
- the moleculeobj
- also arrange other object attached to the molecule (like data, brackets)- Returns:
true
if components have been rearranged,false
if no components found
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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 moleculeobj
- 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
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arrangeReaction
public static void arrangeReaction(RxnMolecule m)
Arranges reaction components nicely- Parameters:
m
- the reaction molecule
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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
- moleculesdist
- use CCLENGTH distance for the moleculescol
- number of colums (if -1 calculate it)
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arrangeDataSgroupData
public static void arrangeDataSgroupData(MoleculeGraph m)
Arrange data attached to DataSgroup. Set it to the right down corner.
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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
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arrangeSgBrackets
public static void arrangeSgBrackets(MoleculeGraph m)
Arrange sgroup brackets in the molecule.- Parameters:
m
- molecule
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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 moleculep
- the point
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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 moleculemol2
- the transformed substructuresa
- additional transformed atom or nullxbonds
- additional bonds between mol1 and mol2, or null- Returns:
- the badness
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createSavedCoordsArray
public static double[] createSavedCoordsArray(MoleculeGraph g)
Creates an empty array for the atomic coordinates of a structure.- Parameters:
g
- the structure
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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 structurecoords
- array for the coordinates
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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 structurecoords
- array containing the coordinates
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createRotationAboutBond
public static CTransform3D createRotationAboutBond(MolBond b, double phi)
Creates a rotation transformation about a bond.- Parameters:
b
- the bondphi
- rotation angle
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setCTWigglyBond
public static boolean setCTWigglyBond(MoleculeGraph m)
Convert crossed double bonds to wiggly type.- Parameters:
m
- molecule
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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 bondbond
- the index of the double bond to- Returns:
- true if the wiggly representation could be set successfully
- Since:
- Marvin 5.2
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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
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setCTCrossedBond
public static boolean setCTCrossedBond(MoleculeGraph m)
Convert wiggly type double bonds to crossed.- Parameters:
m
- molecule
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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
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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.
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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 calculatedligand
- the ligand atom whoose optimal position is calculated- Since:
- Marvin 5.4
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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 calculatedligand
- the ligand atom whoose optimal position is calculatedbondlength
- the requested bond length between the atom and its ligand, use -1 for automatic bond length determination according atom types.- Since:
- Marvin 5.4
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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.
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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 segmentp2
- the second endpoint of the segmentk
- the ratio- Returns:
- the division point
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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 sgroupp2
- the other endpoint of the bond- Returns:
- bracket points
- See Also:
RepeatingUnitSgroup
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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 forbtype
- the type of the brackets to generate- See Also:
MBracket.T_ROUND
,MBracket.T_SQUARE
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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 forbtype
- the type of the brackets to generateextraSpace
- calculate with extra space at atom labels- See Also:
MBracket.T_ROUND
,MBracket.T_SQUARE
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