com.actelion.research.chem.prediction.GlobularityCalculator Maven / Gradle / Ivy

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package com.actelion.research.chem.prediction;

import com.actelion.research.calc.SingularValueDecomposition;
import com.actelion.research.chem.Coordinates;
import com.actelion.research.chem.StereoMolecule;
import com.actelion.research.chem.conf.Conformer;
import com.actelion.research.chem.conf.ConformerSet;
import com.actelion.research.chem.conf.ConformerSetGenerator;
import org.openmolecules.chem.conf.gen.ConformerGenerator;

import java.util.Arrays;

public class GlobularityCalculator {
	private static final boolean MINIMIZE = false;

	/**
	 * Generates conformers from a 2D- or 3D-molecule and then calculates the globularity
	 * (flat=0, round=1) from the conformer's atom coordinates.
	 * @param mol molecule used to generate conformers
	 * @param maxConformerCount maximum number of conformers to generate
	 * @return globularity (flat=0, round=1)
	 */
	public static double assessGlobularity(StereoMolecule mol, int maxConformerCount) {
		ConformerSet cs = new ConformerSetGenerator(maxConformerCount, ConformerGenerator.STRATEGY_LIKELY_RANDOM, MINIMIZE,0).generateConformerSet(mol);
		return assessGlobularity(cs);
		}

	/**
	 * Generates conformers from a 2D- or 3D-molecule and then calculates the globularity
	 * (flat=0, round=1) from the conformer's atom coordinates.
	 * @param cs conformer set from which to calculate and average the globularity
	 * @return globularity (flat=0, round=1)
	 */
	public static double assessGlobularity(ConformerSet cs) {
		if (cs == null || cs.size() == 0)
			return Double.NaN;

		double globularity = 0.0;
		for (Conformer conf:cs)
			globularity += assessGlobularityFromSVD(conf);

		return globularity / cs.size();
		}

	/**
	 * Calculates the globularity of a conformer (flat=0, round=1) from 3D coordinates
	 * @param conf
	 * @return
	 */
	public static double assessGlobularityFromSVD(Conformer conf) {
		int atomCount = conf.getSize();
		Coordinates cog = new Coordinates();	// center of gravity
		for (int i=0; i c.x)
				xmin = c.x;
			if (xmax < c.x)
				xmax = c.x;
			if (ymin > c.y)
				ymin = c.y;
			if (ymax < c.y)
				ymax = c.y;
			if (zmin > c.z)
				zmin = c.z;
			if (zmax < c.z)
				zmax = c.z;
			}
		double dx = xmax - xmin;
		double dy = ymax - ymin;
		double dz = zmax - zmin;

		return dx == 0.0 ? Double.NaN : dz / dx;
		}
	}