org.biojava.nbio.structure.secstruc.SecStrucState Maven / Gradle / Ivy

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/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package org.biojava.nbio.structure.secstruc;

import java.util.Locale;

import org.biojava.nbio.structure.Atom;
import org.biojava.nbio.structure.Group;
import org.biojava.nbio.structure.StructureTools;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

/**
 * This class extends the basic container for secondary structure annotation,
 * including all the information used in the DSSP algorithm.
 *
 * @author Andreas Prlic
 * @author Aleix Lafita
 *
 */
public class SecStrucState extends SecStrucInfo {

	private static final long serialVersionUID = -5549430890272724340L;

	private static final Logger logger = LoggerFactory
			.getLogger(SecStrucState.class);

	private double phi;
	private double psi;
	private double omega;
	private float kappa;

	private HBond accept1; // from CO of partner to NH of this
	private HBond accept2; // this is the donor of accept partner
	private HBond donor1; // from CO of this to NH of partner
	private HBond donor2; // this is the acceptor of donor partner

	// Symbols: starting '>', ending '<', or both 'X'.
	// Number means bracketed n-turn residue without h-bond
	private char[] turn;
	private boolean bend;

	private BetaBridge bridge1;
	private BetaBridge bridge2;

	public SecStrucState(Group g, String ass, SecStrucType t) {
		super(g, ass, t);

		phi = 360;
		psi = 360;
		omega = 360;

		accept1 = new HBond();
		accept2 = new HBond();
		donor1 = new HBond();
		donor2 = new HBond();

		bridge1 = null;
		bridge2 = null;

		turn = new char[3];
		turn[0] = ' ';
		turn[1] = ' ';
		turn[2] = ' ';

		bend = false;
		kappa = 360;
	}

	public boolean isBend() {
		return bend;
	}

	public void setBend(boolean bend) {
		this.bend = bend;
	}

	public float getKappa() {
		return kappa;
	}

	public void setKappa(float kappa) {
		this.kappa = kappa;
	}

	public char[] getTurn() {
		return turn;
	}

	/**
	 * Set the turn column corresponding to 3,4 or 5 helix patterns. If starting
	 * > or ending < was set and the opposite is being set, the value will be
	 * converted to X. If a number was set, it will be overwritten by the new
	 * character.
	 *
	 * @param c
	 *            character in the column
	 * @param t
	 *            turn of the helix {3,4,5}
	 */
	public void setTurn(char c, int t) {
		if (turn[t - 3] == 'X')
			return;
		else if (turn[t - 3] == '<' && c == '>' || turn[t - 3] == '>'
				&& c == '<') {
			turn[t - 3] = 'X';
		} else if (turn[t - 3] == '<' || turn[t - 3] == '>')
			return;
		else
			turn[t - 3] = c;
	}

	public HBond getAccept1() {
		return accept1;
	}

	public void setAccept1(HBond accept1) {
		this.accept1 = accept1;
	}

	public HBond getAccept2() {
		return accept2;
	}

	public void setAccept2(HBond accept2) {
		this.accept2 = accept2;
	}

	public HBond getDonor1() {
		return donor1;
	}

	public void setDonor1(HBond donor1) {
		this.donor1 = donor1;
	}

	public HBond getDonor2() {
		return donor2;
	}

	public void setDonor2(HBond donor2) {
		this.donor2 = donor2;
	}

	public double getPhi() {
		return phi;
	}

	public void setPhi(double phi) {
		this.phi = phi;
	}

	public double getPsi() {
		return psi;
	}

	public void setPsi(double psi) {
		this.psi = psi;
	}

	public double getOmega() {
		return omega;
	}

	public void setOmega(double omega) {
		this.omega = omega;
	}

	public BetaBridge getBridge1() {
		return bridge1;
	}

	public BetaBridge getBridge2() {
		return bridge2;
	}

	/**
	 * Adds a Bridge to the residue. Each residue can only store two bridges. If
	 * the residue contains already two Bridges, the Bridge will not be added
	 * and the method returns false.
	 *
	 * @param bridge
	 * @return false if the Bridge was not added, true otherwise
	 */
	public boolean addBridge(BetaBridge bridge) {
		if (bridge1 == null) {
			bridge1 = bridge;
			return true;
		} else if (bridge1.equals(bridge)) {
			return true;
		} else if (bridge2 == null) {
			bridge2 = bridge;
			return true;
		} else if (bridge2.equals(bridge)) {
			return true;
		} else { //no space left, cannot add the bridge
			logger.info("Residue forms more than 2 beta Bridges, "
					+ "DSSP output might differ in Bridges column.");
			return false;
		}
	}

	public void setBridge1(BetaBridge bridge1) {
		this.bridge1 = bridge1;
	}

	public void setBridge2(BetaBridge bridge2) {
		this.bridge2 = bridge2;
	}

	public String printDSSPline(int index) {

		StringBuffer buf = new StringBuffer();

		// #
		if (index < 9)
			buf.append("    ");
		else if (index < 99)
			buf.append("   ");
		else if (index < 999)
			buf.append("  ");
		else
			buf.append(" ");
		buf.append(index + 1);

		// RESIDUE
		int resnum = parent.getResidueNumber().getSeqNum();
		if (resnum < 10)
			buf.append("    ");
		else if (resnum < 100)
			buf.append("   ");
		else
			buf.append("  ");
		buf.append(resnum);
		Character insCode = parent.getResidueNumber().getInsCode();
		if (insCode != null)
			buf.append(insCode);
		else
			buf.append(" ");
		buf.append(parent.getChainId());
		if (parent.getChainId().length() == 1)
			buf.append(" ");

		// AA
		char aaLetter = StructureTools.get1LetterCode(parent.getPDBName());
		buf.append(aaLetter).append("  ");

		// STRUCTURE
		buf.append(type).append(" ");

		for (int t = 0; t < 3; t++) {
			buf.append(turn[t]);
		}

		buf.append("  ");

		if (isBend())
			buf.append('S');
		else
			buf.append(" ");

		buf.append(" ");

		int bp1 = 0;
		if (bridge1 != null) {
			if (bridge1.partner1 != index)
				bp1 = bridge1.partner1 + 1;
			else
				bp1 = bridge1.partner2 + 1;
		}
		// TODO a clever way to do this?
		if (bp1 < 10)
			buf.append("   ").append(bp1);
		else if (bp1 < 100)
			buf.append("  ").append(bp1);
		else if (bp1 < 1000)
			buf.append(" ").append(bp1);
		else
			buf.append(bp1);

		int bp2 = 0;
		if (bridge2 != null) {
			if (bridge2.partner1 != index)
				bp2 = bridge2.partner1 + 1;
			else
				bp2 = bridge2.partner2 + 1;
		}
		if (bp2 < 10)
			buf.append("   ").append(bp2);
		else if (bp2 < 100)
			buf.append("  ").append(bp2);
		else if (bp2 < 1000)
			buf.append(" ").append(bp2);
		else
			buf.append(bp2);

		// beta-sheet label TODO
		buf.append(" ");

		// ACC TODO
		buf.append("     ");

		// N-H-->O
		int p1 = accept1.getPartner();
		double e1 = (accept1.getEnergy() / 1000.0);
		if (e1 < 0.0)
			p1 -= index;
		buf.append(String.format(Locale.US, "%6d,%4.1f", p1, e1));

		// O-->H-N
		int p2 = donor1.getPartner();
		double e2 = (donor1.getEnergy() / 1000.0);
		if (e2 < 0.0)
			p2 -= index;
		buf.append(String.format(Locale.US, "%6d,%4.1f", p2, e2));

		// N-H-->O
		int p3 = accept2.getPartner();
		double e3 = (accept2.getEnergy() / 1000.0);
		if (e3 < 0.0)
			p3 -= index;
		buf.append(String.format(Locale.US, "%6d,%4.1f", p3, e3));

		// O-->H-N
		int p4 = donor2.getPartner();
		double e4 = (donor2.getEnergy() / 1000.0);
		if (e4 < 0.0)
			p4 -= index;
		buf.append(String.format(Locale.US, "%6d,%4.1f", p4, e4));

		// TCO TODO
		buf.append("        ");

		// KAPPA
		buf.append(String.format(Locale.US, "%6.1f", kappa));

		// ALPHA TODO
		buf.append("      ");

		// PHI PSI
		buf.append(String.format(Locale.US, "%6.1f %6.1f ", phi, psi));

		// X-CA Y-CA Z-CA
		Atom ca = parent.getAtom("CA");
		buf.append(String.format(Locale.US, "%6.1f %6.1f %6.1f", ca.getX(), ca.getY(),
				ca.getZ()));

		return buf.toString();
	}

}