/*
* 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 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 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("%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("%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("%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("%6d,%4.1f", p4, e4));
// TCO TODO
buf.append(" ");
// KAPPA
buf.append(String.format("%6.1f", kappa));
// ALPHA TODO
buf.append(" ");
// PHI PSI
buf.append(String.format("%6.1f %6.1f ", phi, psi));
// X-CA Y-CA Z-CA
Atom ca = parent.getAtom("CA");
buf.append(String.format("%6.1f %6.1f %6.1f", ca.getX(), ca.getY(),
ca.getZ()));
return buf.toString();
}
}