org.openscience.cdk.geometry

Class GeometryUtil

• ```public final class GeometryUtil
extends Object```
A set of static utility classes for geometric calculations and operations. This class is extensively used, for example, by JChemPaint to edit molecule. All methods in this class change the coordinates of the atoms. Use GeometryTools if you use an external set of coordinates (e. g. renderingCoordinates from RendererModel)
Author:
seb, Stefan Kuhn, Egon Willighagen, Ludovic Petain, Christian Hoppe, Niels Out, John May
Source code:
master
• Nested Class Summary

Nested Classes
Modifier and Type Class and Description
`static class ` `GeometryUtil.CoordinateCoverage`
Provides the coverage of coordinates for this molecule.
• Method Summary

All Methods
Modifier and Type Method and Description
`static javax.vecmath.Vector2d` ```calculatePerpendicularUnitVector(javax.vecmath.Point2d point1, javax.vecmath.Point2d point2)```
Determines the normalized vector orthogonal on the vector p1->p2.
`static void` ```center(IAtomContainer atomCon, double[] areaDim)```
Centers the molecule in the given area.
`static double[]` ```distanceCalculator(double[] coords, double dist)```
`static int[]` ```distanceCalculator(int[] coords, double dist)```
Gets the coordinates of two points (that represent a bond) and calculates for each the coordinates of two new points that have the given distance vertical to the bond.
`static List<IAtom>` ```findClosestInSpace(IAtomContainer container, IAtom startAtom, int max)```
Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.
`static javax.vecmath.Point2d` `get2DCenter(IAtomContainer container)`
Returns the geometric center of all the atoms in the atomContainer.
`static javax.vecmath.Point2d` `get2DCenter(IRingSet ringSet)`
Returns the geometric center of all the rings in this ringset.
`static javax.vecmath.Point2d` `get2DCenter(Iterable<IAtom> atoms)`
Calculates the center of the given atoms and returns it as a Point2d.
`static javax.vecmath.Point2d` `get2DCenter(Iterator<IAtom> atoms)`
Calculates the center of the given atoms and returns it as a Point2d.
`static javax.vecmath.Point2d` `get2DCentreOfMass(IAtomContainer ac)`
Calculates the center of mass for the `Atom`s in the AtomContainer for the 2D coordinates.
`static GeometryUtil.CoordinateCoverage` `get2DCoordinateCoverage(IAtomContainer container)`
Determines the coverage of this `IAtomContainer`'s 2D coordinates.
`static double[]` `get2DDimension(IAtomContainer atomCon)`
Returns the dimension of a molecule (width/height).
`static javax.vecmath.Point3d` `get3DCenter(IAtomContainer ac)`
Returns the geometric center of all the atoms in this atomContainer.
`static javax.vecmath.Point3d` `get3DCentreOfMass(IAtomContainer ac)`
Calculates the center of mass for the `Atom`s in the AtomContainer.
`static GeometryUtil.CoordinateCoverage` `get3DCoordinateCoverage(IAtomContainer container)`
Determines the coverage of this `IAtomContainer`'s 3D coordinates.
`static double` ```getAllAtomRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, Map<Integer,Integer> mappedAtoms, boolean Coords3d)```
Return the RMSD between the 2 aligned molecules.
`static double` ```getAngle(double xDiff, double yDiff)```
Gets the angle attribute of the GeometryTools class.
`static double` ```getAngleRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, Map<Integer,Integer> mappedAtoms)```
Return the variation of each angle value between the 2 aligned molecules.
`static int` ```getBestAlignmentForLabel(IAtomContainer container, IAtom atom)```
Determines the best alignment for the label of an atom in 2D space.
`static int` ```getBestAlignmentForLabelXY(IAtomContainer container, IAtom atom)```
Determines the best alignment for the label of an atom in 2D space.
`static int[]` `getBondCoordinates(IBond bond)`
Writes the coordinates of the atoms participating the given bond into an array.
`static double` `getBondLengthAverage(IAtomContainer container)`
An average of all 2D bond length values is produced.
`static double` `getBondLengthAverage(IReaction reaction)`
`static double` `getBondLengthAverage3D(IAtomContainer container)`
An average of all 3D bond length values is produced, using point3ds in atoms.
`static double` `getBondLengthMedian(IAtomContainer container)`
Calculate the median bond length of an atom container.
`static double` ```getBondLengthMedian(Iterable<IBond> bonds, int cap)```
Calculate the median bond length of some bonds.
`static double` ```getBondLengthRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, Map<Integer,Integer> mappedAtoms, boolean Coords3d)```
Return the RMSD of bonds length between the 2 aligned molecules.
`static IAtom` ```getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon)```
Returns the atom of the given molecule that is closest to the given coordinates.
`static IAtom` ```getClosestAtom(double xPosition, double yPosition, IAtomContainer atomCon, IAtom toignore)```
Returns the atom of the given molecule that is closest to the given coordinates and is not the atom.
`static IAtom` ```getClosestAtom(IAtomContainer atomCon, IAtom atom)```
Returns the atom of the given molecule that is closest to the given atom (excluding itself).
`static IAtom` ```getClosestAtom(int xPosition, int yPosition, IAtomContainer atomCon)```
Returns the atom of the given molecule that is closest to the given coordinates.
`static IBond` ```getClosestBond(double xPosition, double yPosition, IAtomContainer atomCon)```
Returns the bond of the given molecule that is closest to the given coordinates.
`static IBond` ```getClosestBond(int xPosition, int yPosition, IAtomContainer atomCon)```
Returns the bond of the given molecule that is closest to the given coordinates.
`static double` ```getHeavyAtomRMSD(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, Map<Integer,Integer> mappedAtoms, boolean hetAtomOnly, boolean Coords3d)```
Return the RMSD of the heavy atoms between the 2 aligned molecules.
`static double` `getLength2D(IBond bond)`
Returns the geometric length of this bond in 2D space.
`static double[]` `getMinMax(IAtomContainer container)`
Returns the minimum and maximum X and Y coordinates of the atoms in the AtomContainer.
`static double[]` `getMinMax(Iterable<IAtom> atoms)`
Returns the minimum and maximum X and Y coordinates of the atoms.
`static double` `getNormalizationFactor(IAtomContainer container)`
Calculates the normalization factor in order to get an average bond length of 1.5.
`static double` ```getScaleFactor(IAtomContainer container, double bondLength)```
Determines the scale factor for displaying a structure loaded from disk in a frame.
`static boolean` `has2DCoordinates(IAtom atom)`
Determines if this Atom contains 2D coordinates.
`static boolean` `has2DCoordinates(IAtomContainer container)`
Determines if all this `IAtomContainer`'s atoms contain 2D coordinates.
`static boolean` `has2DCoordinates(IBond bond)`
Determines if this Bond contains 2D coordinates.
`static boolean` `has2DCoordinates(IReaction reaction)`
Determine if all parts of a reaction have coodinates
`static int` `has2DCoordinatesNew(IAtomContainer container)`
`static boolean` `has3DCoordinates(IAtomContainer container)`
Determines if all this `IAtomContainer`'s atoms contain 3D coordinates.
`static boolean` `has3DCoordinates(IChemModel chemModel)`
Determines if this model contains 3D coordinates for all atoms.
`static Map<Integer,Integer>` ```mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer, IAtomContainer secondAtomContainer, double searchRadius, Map<Integer,Integer> mappedAtoms)```
Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomcontainer.
`static void` `normalize(javax.vecmath.Point3d point)`
Normalizes a point.
`static void` ```reflect(Collection<IAtom> atoms, IBond bond)```
Reflect a collection of atoms in the line formed by the specified bond.
`static void` ```reflect(Collection<IAtom> atoms, javax.vecmath.Point2d beg, javax.vecmath.Point2d end)```
Reflect a collection of atoms in the line formed by the two specified points (beg,end).
`static void` ```rotate(IAtomContainer atomCon, javax.vecmath.Point2d center, double angle)```
Rotates a molecule around a given center by a given angle.
`static void` ```rotate(IAtom atom, javax.vecmath.Point3d p1, javax.vecmath.Point3d p2, double angle)```
Rotates a 3D point about a specified line segment by a specified angle.
`static void` ```scaleMolecule(IAtomContainer atomCon, double scaleFactor)```
Multiplies all the coordinates of the atoms of the given molecule with the scalefactor.
`static void` ```scaleMolecule(IAtomContainer atomCon, double[] areaDim, double fillFactor)```
Scales a molecule such that it fills a given percentage of a given dimension.
`static double[]` ```shiftContainer(IAtomContainer container, double[] bounds, double[] last, double gap)```
Shift the container horizontally to the right to make its bounds not overlap with the other bounds.
`static double[]` ```shiftReactionVertical(IReaction reaction, double[] bounds, double[] last, double gap)```
Shift the containers in a reaction vertically upwards to not overlap with the reference rectangle.
`static void` ```sortBy2DDistance(IAtom[] atoms, javax.vecmath.Point2d point)```
Sorts a Vector of atoms such that the 2D distances of the atom locations from a given point are smallest for the first atoms in the vector.
`static void` ```translate2D(IAtomContainer atomCon, double transX, double transY)```
Translates the given molecule by the given Vector.
`static void` ```translate2D(IAtomContainer atomCon, javax.vecmath.Vector2d vector)```
Translates a molecule from the origin to a new point denoted by a vector.
`static void` ```translate2DCenterTo(IAtomContainer container, javax.vecmath.Point2d p)```
Translates the geometric 2DCenter of the given AtomContainer container to the specified Point2d p.
`static void` ```translate2DCentreOfMassTo(IAtomContainer atomCon, javax.vecmath.Point2d p)```
Translates a molecule from the origin to a new point denoted by a vector.
`static void` `translateAllPositive(IAtomContainer atomCon)`
Adds an automatically calculated offset to the coordinates of all atoms such that all coordinates are positive and the smallest x or y coordinate is exactly zero.
• Methods inherited from class java.lang.Object

`clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait`
• Method Detail

• translateAllPositive

`public static void translateAllPositive(IAtomContainer atomCon)`
Adds an automatically calculated offset to the coordinates of all atoms such that all coordinates are positive and the smallest x or y coordinate is exactly zero. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`atomCon` - AtomContainer for which all the atoms are translated to positive coordinates
• translate2D

```public static void translate2D(IAtomContainer atomCon,
double transX,
double transY)```
Translates the given molecule by the given Vector. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`atomCon` - The molecule to be translated
`transX` - translation in x direction
`transY` - translation in y direction
• scaleMolecule

```public static void scaleMolecule(IAtomContainer atomCon,
double fillFactor)```
Scales a molecule such that it fills a given percentage of a given dimension. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`atomCon` - The molecule to be scaled {width, height}
`areaDim` - The dimension to be filled {width, height}
`fillFactor` - The percentage of the dimension to be filled
• scaleMolecule

```public static void scaleMolecule(IAtomContainer atomCon,
double scaleFactor)```
Multiplies all the coordinates of the atoms of the given molecule with the scalefactor. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`atomCon` - The molecule to be scaled
`scaleFactor` - Description of the Parameter
• center

```public static void center(IAtomContainer atomCon,
Centers the molecule in the given area. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`atomCon` - molecule to be centered
`areaDim` - dimension in which the molecule is to be centered, array containing {width, height}
• translate2D

```public static void translate2D(IAtomContainer atomCon,
javax.vecmath.Vector2d vector)```
Translates a molecule from the origin to a new point denoted by a vector. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`atomCon` - molecule to be translated
`vector` - dimension that represents the translation vector
• rotate

```public static void rotate(IAtomContainer atomCon,
javax.vecmath.Point2d center,
double angle)```
Rotates a molecule around a given center by a given angle.
Parameters:
`atomCon` - The molecule to be rotated
`center` - A point giving the rotation center
`angle` - The angle by which to rotate the molecule, in radians
• reflect

```public static void reflect(Collection<IAtom> atoms,
javax.vecmath.Point2d beg,
javax.vecmath.Point2d end)```
Reflect a collection of atoms in the line formed by the two specified points (beg,end).
Parameters:
`atoms` - the atoms
`beg` - the begin point of a line
`end` - the end point of a line
• reflect

```public static void reflect(Collection<IAtom> atoms,
IBond bond)```
Reflect a collection of atoms in the line formed by the specified bond.
Parameters:
`atoms` - the atoms
`bond` - the bond at which to reflect
• rotate

```public static void rotate(IAtom atom,
javax.vecmath.Point3d p1,
javax.vecmath.Point3d p2,
double angle)```
Rotates a 3D point about a specified line segment by a specified angle. The code is based on code available here. Positive angles are anticlockwise looking down the axis towards the origin. Assume right hand coordinate system.
Parameters:
`atom` - The atom to rotate
`p1` - The first point of the line segment
`p2` - The second point of the line segment
`angle` - The angle to rotate by (in degrees)
• normalize

`public static void normalize(javax.vecmath.Point3d point)`
Normalizes a point.
Parameters:
`point` - The point to normalize
• get2DDimension

`public static double[] get2DDimension(IAtomContainer atomCon)`
Returns the dimension of a molecule (width/height).
Parameters:
`atomCon` - of which the dimension should be returned
Returns:
array containing {width, height}
• getMinMax

`public static double[] getMinMax(Iterable<IAtom> atoms)`
Returns the minimum and maximum X and Y coordinates of the atoms. The output is returned as:
```   minmax[0] = minX;
minmax[1] = minY;
minmax[2] = maxX;
minmax[3] = maxY;
```
Parameters:
`atoms` - the atoms.
Returns:
An four int array as defined above.
• getMinMax

`public static double[] getMinMax(IAtomContainer container)`
Returns the minimum and maximum X and Y coordinates of the atoms in the AtomContainer. The output is returned as:
```   minmax[0] = minX;
minmax[1] = minY;
minmax[2] = maxX;
minmax[3] = maxY;
```
See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`container` - Description of the Parameter
Returns:
An four int array as defined above.
• translate2DCentreOfMassTo

```public static void translate2DCentreOfMassTo(IAtomContainer atomCon,
javax.vecmath.Point2d p)```
Translates a molecule from the origin to a new point denoted by a vector. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`atomCon` - molecule to be translated
`p` - Description of the Parameter
• get2DCenter

`public static javax.vecmath.Point2d get2DCenter(Iterable<IAtom> atoms)`
Calculates the center of the given atoms and returns it as a Point2d. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`atoms` - The vector of the given atoms
Returns:
The center of the given atoms as Point2d
• get2DCenter

`public static javax.vecmath.Point2d get2DCenter(Iterator<IAtom> atoms)`
Calculates the center of the given atoms and returns it as a Point2d. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`atoms` - The Iterator of the given atoms
Returns:
The center of the given atoms as Point2d
• get2DCenter

`public static javax.vecmath.Point2d get2DCenter(IRingSet ringSet)`
Returns the geometric center of all the rings in this ringset. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`ringSet` - Description of the Parameter
Returns:
the geometric center of the rings in this ringset
• get2DCentreOfMass

`public static javax.vecmath.Point2d get2DCentreOfMass(IAtomContainer ac)`
Calculates the center of mass for the `Atom`s in the AtomContainer for the 2D coordinates. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`ac` - AtomContainer for which the center of mass is calculated
Returns:
Null, if any of the atomcontainer `IAtom`'s masses are null
Keywords:
center of mass
• get2DCenter

`public static javax.vecmath.Point2d get2DCenter(IAtomContainer container)`
Returns the geometric center of all the atoms in the atomContainer. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`container` - Description of the Parameter
Returns:
the geometric center of the atoms in this atomContainer
• get3DCentreOfMass

`public static javax.vecmath.Point3d get3DCentreOfMass(IAtomContainer ac)`
Calculates the center of mass for the `Atom`s in the AtomContainer.
Parameters:
`ac` - AtomContainer for which the center of mass is calculated
Returns:
The center of mass of the molecule, or `NULL` if the molecule does not have 3D coordinates or if any of the atoms do not have a valid atomic mass
Dictionary pointer(s):
calculate3DCenterOfMass in the Blue Obelisk Chemoinformatics Dictionary [blue-obelisk:calculate3DCenterOfMass]
Keywords:
center of mass
• get3DCenter

`public static javax.vecmath.Point3d get3DCenter(IAtomContainer ac)`
Returns the geometric center of all the atoms in this atomContainer. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`ac` - Description of the Parameter
Returns:
the geometric center of the atoms in this atomContainer
• getAngle

```public static double getAngle(double xDiff,
double yDiff)```
Gets the angle attribute of the GeometryTools class.
Parameters:
`xDiff` - Description of the Parameter
`yDiff` - Description of the Parameter
Returns:
The angle value
• distanceCalculator

```public static int[] distanceCalculator(int[] coords,
double dist)```
Gets the coordinates of two points (that represent a bond) and calculates for each the coordinates of two new points that have the given distance vertical to the bond.
Parameters:
`coords` - The coordinates of the two given points of the bond like this [point1x, point1y, point2x, point2y]
`dist` - The vertical distance between the given points and those to be calculated
Returns:
The coordinates of the calculated four points
• distanceCalculator

```public static double[] distanceCalculator(double[] coords,
double dist)```
• getBondCoordinates

`public static int[] getBondCoordinates(IBond bond)`
Writes the coordinates of the atoms participating the given bond into an array. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`bond` - The given bond
Returns:
The array with the coordinates
• getClosestAtom

```public static IAtom getClosestAtom(int xPosition,
int yPosition,
IAtomContainer atomCon)```
Returns the atom of the given molecule that is closest to the given coordinates. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`xPosition` - The x coordinate
`yPosition` - The y coordinate
`atomCon` - The molecule that is searched for the closest atom
Returns:
The atom that is closest to the given coordinates
• getClosestAtom

```public static IAtom getClosestAtom(IAtomContainer atomCon,
IAtom atom)```
Returns the atom of the given molecule that is closest to the given atom (excluding itself).
Parameters:
`atomCon` - The molecule that is searched for the closest atom
`atom` - The atom to search around
Returns:
The atom that is closest to the given coordinates
• getClosestAtom

```public static IAtom getClosestAtom(double xPosition,
double yPosition,
IAtomContainer atomCon,
IAtom toignore)```
Returns the atom of the given molecule that is closest to the given coordinates and is not the atom. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`xPosition` - The x coordinate
`yPosition` - The y coordinate
`atomCon` - The molecule that is searched for the closest atom
`toignore` - This molecule will not be returned.
Returns:
The atom that is closest to the given coordinates
• getClosestAtom

```public static IAtom getClosestAtom(double xPosition,
double yPosition,
IAtomContainer atomCon)```
Returns the atom of the given molecule that is closest to the given coordinates. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`xPosition` - The x coordinate
`yPosition` - The y coordinate
`atomCon` - The molecule that is searched for the closest atom
Returns:
The atom that is closest to the given coordinates
• getClosestBond

```public static IBond getClosestBond(int xPosition,
int yPosition,
IAtomContainer atomCon)```
Returns the bond of the given molecule that is closest to the given coordinates. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`xPosition` - The x coordinate
`yPosition` - The y coordinate
`atomCon` - The molecule that is searched for the closest bond
Returns:
The bond that is closest to the given coordinates
• getClosestBond

```public static IBond getClosestBond(double xPosition,
double yPosition,
IAtomContainer atomCon)```
Returns the bond of the given molecule that is closest to the given coordinates. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`xPosition` - The x coordinate
`yPosition` - The y coordinate
`atomCon` - The molecule that is searched for the closest bond
Returns:
The bond that is closest to the given coordinates
• sortBy2DDistance

```public static void sortBy2DDistance(IAtom[] atoms,
javax.vecmath.Point2d point)```
Sorts a Vector of atoms such that the 2D distances of the atom locations from a given point are smallest for the first atoms in the vector. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`point` - The point from which the distances to the atoms are measured
`atoms` - The atoms for which the distances to point are measured
• getScaleFactor

```public static double getScaleFactor(IAtomContainer container,
double bondLength)```
Determines the scale factor for displaying a structure loaded from disk in a frame. An average of all bond length values is produced and a scale factor is determined which would scale the given molecule such that its See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`container` - The AtomContainer for which the ScaleFactor is to be calculated
`bondLength` - The target bond length
Returns:
The ScaleFactor with which the AtomContainer must be scaled to have the target bond length
• getBondLengthAverage

`public static double getBondLengthAverage(IAtomContainer container)`
An average of all 2D bond length values is produced. Bonds which have Atom's with no coordinates are disregarded. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`container` - The AtomContainer for which the average bond length is to be calculated
Returns:
the average bond length
• getLength2D

`public static double getLength2D(IBond bond)`
Returns the geometric length of this bond in 2D space. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`bond` - Description of the Parameter
Returns:
The geometric length of this bond
• has2DCoordinates

`public static boolean has2DCoordinates(IAtomContainer container)`
Determines if all this `IAtomContainer`'s atoms contain 2D coordinates. If any atom is null or has unset 2D coordinates this method will return false.
Parameters:
`container` - the atom container to examine
Returns:
indication that all 2D coordinates are available
`IAtom.getPoint2d()`
• has2DCoordinates

`public static boolean has2DCoordinates(IReaction reaction)`
Determine if all parts of a reaction have coodinates
Parameters:
`reaction` - a reaction
Returns:
the reaction has coordinates
• has2DCoordinates

`public static boolean has2DCoordinates(IAtom atom)`
Determines if this Atom contains 2D coordinates. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`atom` - Description of the Parameter
Returns:
boolean indication that 2D coordinates are available
• has2DCoordinates

`public static boolean has2DCoordinates(IBond bond)`
Determines if this Bond contains 2D coordinates. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`bond` - Description of the Parameter
Returns:
boolean indication that 2D coordinates are available
• has3DCoordinates

`public static boolean has3DCoordinates(IAtomContainer container)`
Determines if all this `IAtomContainer`'s atoms contain 3D coordinates. If any atom is null or has unset 3D coordinates this method will return false. If the provided container is null false is returned.
Parameters:
`container` - the atom container to examine
Returns:
indication that all 3D coordinates are available
`IAtom.getPoint3d()`
• calculatePerpendicularUnitVector

```public static javax.vecmath.Vector2d calculatePerpendicularUnitVector(javax.vecmath.Point2d point1,
javax.vecmath.Point2d point2)```
Determines the normalized vector orthogonal on the vector p1->p2.
Parameters:
`point1` - Description of the Parameter
`point2` - Description of the Parameter
Returns:
Description of the Return Value
• getNormalizationFactor

`public static double getNormalizationFactor(IAtomContainer container)`
Calculates the normalization factor in order to get an average bond length of 1.5. It takes only into account Bond's with two atoms. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`container` - Description of the Parameter
Returns:
The normalizationFactor value
• getBestAlignmentForLabel

```public static int getBestAlignmentForLabel(IAtomContainer container,
IAtom atom)```
Determines the best alignment for the label of an atom in 2D space. It returns 1 if left aligned, and -1 if right aligned. See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`container` - Description of the Parameter
`atom` - Description of the Parameter
Returns:
The bestAlignmentForLabel value
• getBestAlignmentForLabelXY

```public static int getBestAlignmentForLabelXY(IAtomContainer container,
IAtom atom)```
Determines the best alignment for the label of an atom in 2D space. It returns 1 if right (=default) aligned, and -1 if left aligned. returns 2 if top aligned, and -2 if H is aligned below the atom See comment for center(IAtomContainer atomCon, Dimension areaDim, HashMap renderingCoordinates) for details on coordinate sets
Parameters:
`container` - Description of the Parameter
`atom` - Description of the Parameter
Returns:
The bestAlignmentForLabel value
• findClosestInSpace

```public static List<IAtom> findClosestInSpace(IAtomContainer container,
IAtom startAtom,
int max)
throws CDKException```
Returns the atoms which are closes to an atom in an AtomContainer by distance in 3d.
Parameters:
`container` - The AtomContainer to examine
`startAtom` - the atom to start from
`max` - the number of neighbours to return
Returns:
the average bond length
Throws:
`CDKException` - Description of the Exception
• mapAtomsOfAlignedStructures

```public static Map<Integer,Integer> mapAtomsOfAlignedStructures(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms)
throws CDKException```
Returns a Map with the AtomNumbers, the first number corresponds to the first (or the largest AtomContainer) atomcontainer. It is recommend to sort the atomContainer due to their number of atoms before calling this function. The molecules needs to be aligned before! (coordinates are needed)
Parameters:
`firstAtomContainer` - the (largest) first aligned AtomContainer which is the reference
`secondAtomContainer` - the second aligned AtomContainer
`searchRadius` - the radius of space search from each atom
Returns:
a Map of the mapped atoms
Throws:
`CDKException` - Description of the Exception
• getBondLengthRMSD

```public static double getBondLengthRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean Coords3d)```
Return the RMSD of bonds length between the 2 aligned molecules.
Parameters:
`firstAtomContainer` - the (largest) first aligned AtomContainer which is the reference
`secondAtomContainer` - the second aligned AtomContainer
`mappedAtoms` - Map: a Map of the mapped atoms
`Coords3d` - boolean: true if moecules has 3D coords, false if molecules has 2D coords
Returns:
double: all the RMSD of bonds length
• getAngleRMSD

```public static double getAngleRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms)```
Return the variation of each angle value between the 2 aligned molecules.
Parameters:
`firstAtomContainer` - the (largest) first aligned AtomContainer which is the reference
`secondAtomContainer` - the second aligned AtomContainer
`mappedAtoms` - Map: a Map of the mapped atoms
Returns:
double: the value of the RMSD
• getAllAtomRMSD

```public static double getAllAtomRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean Coords3d)
throws CDKException```
Return the RMSD between the 2 aligned molecules.
Parameters:
`firstAtomContainer` - the (largest) first aligned AtomContainer which is the reference
`secondAtomContainer` - the second aligned AtomContainer
`mappedAtoms` - Map: a Map of the mapped atoms
`Coords3d` - boolean: true if molecules has 3D coords, false if molecules has 2D coords
Returns:
double: the value of the RMSD
Throws:
`CDKException` - if there is an error in getting mapped atoms
• getHeavyAtomRMSD

```public static double getHeavyAtomRMSD(IAtomContainer firstAtomContainer,
IAtomContainer secondAtomContainer,
Map<Integer,Integer> mappedAtoms,
boolean hetAtomOnly,
boolean Coords3d)```
Return the RMSD of the heavy atoms between the 2 aligned molecules.
Parameters:
`firstAtomContainer` - the (largest) first aligned AtomContainer which is the reference
`secondAtomContainer` - the second aligned AtomContainer
`mappedAtoms` - Map: a Map of the mapped atoms
`hetAtomOnly` - boolean: true if only hetero atoms should be considered
`Coords3d` - boolean: true if molecules has 3D coords, false if molecules has 2D coords
Returns:
double: the value of the RMSD
• getBondLengthAverage3D

`public static double getBondLengthAverage3D(IAtomContainer container)`
An average of all 3D bond length values is produced, using point3ds in atoms. Atom's with no coordinates are disregarded.
Parameters:
`container` - The AtomContainer for which the average bond length is to be calculated
Returns:
the average bond length
• shiftContainer

```public static double[] shiftContainer(IAtomContainer container,
double[] bounds,
double[] last,
double gap)```
Shift the container horizontally to the right to make its bounds not overlap with the other bounds. To avoid dependence on Java AWT, rectangles are described by arrays of double. Each rectangle is specified by {minX, minY, maxX, maxY}.
Parameters:
`container` - the `IAtomContainer` to shift to the right
`bounds` - the bounds of the `IAtomContainer` to shift
`last` - the bounds that is used as reference
`gap` - the gap between the two rectangles
Returns:
the rectangle of the `IAtomContainer` after the shift
• getBondLengthAverage

`public static double getBondLengthAverage(IReaction reaction)`
• getBondLengthMedian

`public static double getBondLengthMedian(IAtomContainer container)`
Calculate the median bond length of an atom container.
Parameters:
`container` - structure representation
Returns:
median bond length
Throws:
`IllegalArgumentException` - unset coordinates or no bonds
• getBondLengthMedian

```public static double getBondLengthMedian(Iterable<IBond> bonds,
int cap)```
Calculate the median bond length of some bonds.
Parameters:
`bonds` - the bonds
Returns:
median bond length
Throws:
`IllegalArgumentException` - unset coordinates or no bonds
• has3DCoordinates

`public static boolean has3DCoordinates(IChemModel chemModel)`
Determines if this model contains 3D coordinates for all atoms.
Parameters:
`chemModel` - the ChemModel to consider
Returns:
Boolean indication that 3D coordinates are available for all atoms.
• shiftReactionVertical

```public static double[] shiftReactionVertical(IReaction reaction,
double[] bounds,
double[] last,
double gap)```
Shift the containers in a reaction vertically upwards to not overlap with the reference rectangle. The shift is such that the given gap is realized, but only if the reactions are actually overlapping. To avoid dependence on Java AWT, rectangles are described by arrays of double. Each rectangle is specified by {minX, minY, maxX, maxY}.
Parameters:
`reaction` - the reaction to shift
`bounds` - the bounds of the reaction to shift
`last` - the bounds of the last reaction
Returns:
the rectangle of the shifted reaction