com.actelion.research.chem.conf.TorsionDescriptorHelper Maven / Gradle / Ivy

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There is a newer version: 2024.12.1
package com.actelion.research.chem.conf;

import com.actelion.research.chem.Molecule;
import com.actelion.research.chem.StereoMolecule;

public class TorsionDescriptorHelper {
	private static final int SYMMETRY_360 = 0;  // 0 -> 359 degrees
	private static final int SYMMETRY_180 = 1;  // 0 -> 179 (equal to 180 -> 359)
	private static final int SYMMETRY_120 = 2;  // 0 -> 119 (equals 120 -> 239 and 240 -> 359)
	private static final int SYMMETRY_60  = 3;  // 0 -> 59 (60 -> 119, 120 -> 179, 180 -> 239, 240 -> 299, 300 -> 359)

	private static double[] SYMMETRY_REDUNDANCY_ANGLE = { 2*Math.PI, Math.PI, 2*Math.PI/3, Math.PI/3};

	private static final int HALF_SYMMETRY_C1 = 0;  // three distinct terminal neighbors
	private static final int HALF_SYMMETRY_D1 = 1;  // e.g. single terminal neighbor or two equal sp3 neighbors
	private static final int HALF_SYMMETRY_D2 = 2;  // two equal sp2 neighbors
	private static final int HALF_SYMMETRY_D3 = 3;  // for simplicity reasons this is covered by D1

	private static final int[][] SYMMETRY =
		  { { SYMMETRY_360, SYMMETRY_360, SYMMETRY_360, SYMMETRY_120 },
			{ SYMMETRY_360, SYMMETRY_360, SYMMETRY_180, SYMMETRY_120 },
			{ SYMMETRY_360, SYMMETRY_180, SYMMETRY_180, SYMMETRY_60  },
			{ SYMMETRY_120, SYMMETRY_120, SYMMETRY_60 , SYMMETRY_120 } };

	private StereoMolecule mMol;
	private int[] mRotatableBond;
	private int[][] mAtomSequence;
	private int[][] mRearAtom;
	private int[] mSymmetryClass;

	public TorsionDescriptorHelper(StereoMolecule mol) {
		mMol = mol;
		mMol.ensureHelperArrays(Molecule.cHelperSymmetrySimple);
		mRotatableBond = findRotatableBonds(mol);
		findAtomSequences();
		}

	public TorsionDescriptorHelper(StereoMolecule mol, int[] rotatableBond) {
		mMol = mol;
		mMol.ensureHelperArrays(Molecule.cHelperSymmetrySimple);
		mRotatableBond = rotatableBond;
		findAtomSequences();
		}

	/**
	 * Creates a TorsionDescriptor from the coordinates of the molecule passed to the constructor
	 * using the default method to detect rotatable bonds.
	 * The torsion descriptor is not canonical, unless the passed molecule is canonical.
	 * Rotatable bonds need to carry at least one external non-hydrogen neighbor on each side.
	 */
	public TorsionDescriptor getTorsionDescriptor() {
		float[] torsion = new float[mRotatableBond.length];
		float[] maxTorsion = new float[mRotatableBond.length];

		for (int i=0; i= 0.
	 * @param angle
	 * @param symmetryClass
	 * @return angle within native range of symmetry type
	 */
	private static double getNormalizedTorsion(double angle, int symmetryClass) {
		double limit = SYMMETRY_REDUNDANCY_ANGLE[symmetryClass] / 2;

		while (angle < -limit)
			angle += 2*Math.PI;

		while (angle >= limit)
			angle -= SYMMETRY_REDUNDANCY_ANGLE[symmetryClass];

		return angle;
		}
	}