/*
* 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/
*
* Created on Nov 14, 2007
*
*/
package org.biojava.nbio.structure.io;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;
import org.biojava.nbio.structure.Bond;
import org.biojava.nbio.structure.PDBRecord;
/**
* A simple bean to store disulfide bridge information, the SSBOND records in the PDB files.
*
* The two residues specified here are CYS residues that form a Disulfide bridge.
*
*
*
* @author Andreas Prlic
*
*/
public class SSBondImpl implements PDBRecord, Serializable, Cloneable {
private static final long serialVersionUID = -8663681100691188647L;
private int serNum;
private String chainID1;
private String chainID2;
private String resnum1;
private String resnum2;
private String insCode1;
private String insCode2;
public SSBondImpl(){
serNum = 0;
}
@Override
public String toPDB(){
StringBuffer buf = new StringBuffer();
toPDB(buf);
return buf.toString();
}
/**
* Append the PDB representation of this SSBOND to the provided StringBuffer
*
* @param buf a StringBuffer to print the PDB representation to
*/
@Override
public void toPDB(StringBuffer buf){
/*12 - 14 LString(3) "CYS" Residue name.
16 Character chainID1 Chain identifier.
18 - 21 Integer seqNum1 Residue sequence number.
22 AChar icode1 Insertion code.
26 - 28 LString(3) "CYS" Residue name.
30 Character chainID2 Chain identifier.
32 - 35 Integer seqNum2 Residue sequence number.
36 AChar icode2 Insertion code.
60 - 65 SymOP sym1 Symmetry oper for 1st resid
67 - 72 SymOP sym2 Symmetry oper for 2nd resid
*/
//01234567890123456789012345678901234567890123456789012345678901234567890123456789
//SSBOND 1 CYS 5 CYS 55 5PTI 67
//SSBOND 2 CYS 14 CYS 38
//SSBOND 3 CYS 30 CYS 51
buf.append("SSBOND ");
buf.append(String.format("%3d", serNum));
buf.append(String.format(" CYS %s %4s%1s ", chainID1, resnum1, insCode1));
buf.append(String.format(" CYS %s %4s%1s ", chainID2, resnum2, insCode2));
}
public String getInsCode1() {
return insCode1;
}
public void setInsCode1(String insCode1) {
this.insCode1 = insCode1;
}
public String getInsCode2() {
return insCode2;
}
public void setInsCode2(String insCode2) {
this.insCode2 = insCode2;
}
public int getSerNum() {
return serNum;
}
/** get serial number of this SSBOND in PDB file
*
* @param serNum
*/
public void setSerNum(int serNum) {
this.serNum = serNum;
}
@Override
public SSBondImpl clone() {
SSBondImpl nbond = new SSBondImpl();
nbond.setChainID1(chainID1);
nbond.setChainID2(chainID2);
nbond.setResnum1(resnum1);
nbond.setResnum2(resnum2);
return nbond;
}
public String getChainID1() {
return chainID1;
}
public void setChainID1(String chainID1) {
this.chainID1 = chainID1;
}
public String getChainID2() {
return chainID2;
}
public void setChainID2(String chainID2) {
this.chainID2 = chainID2;
}
public String getResnum1() {
return resnum1;
}
public void setResnum1(String resnum1) {
this.resnum1 = resnum1;
}
public String getResnum2() {
return resnum2;
}
public void setResnum2(String resnum2) {
this.resnum2 = resnum2;
}
@Override
public String toString() {
String s = "[SSBOND:\n";
s += "Atom 1:\n";
s += "\tChain: " + chainID1 + "\n";
s += "\tResidue #: " + resnum1 + "\n";
s += "\tIns. Code: " + insCode1 + "\n";
s += "Atom 2:\n";
s += "\tChain: " + chainID2 + "\n";
s += "\tResidue #: " + resnum2 + "\n";
s += "\tIns. Code: " + insCode2 + "\n";
s += "]";
return s;
}
/* (non-Javadoc)
* @see java.lang.Object#hashCode()
*/
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + ((chainID1 == null) ? 0 : chainID1.hashCode());
result = prime * result + ((chainID2 == null) ? 0 : chainID2.hashCode());
result = prime * result + ((insCode1 == null) ? 0 : insCode1.hashCode());
result = prime * result + ((insCode2 == null) ? 0 : insCode2.hashCode());
result = prime * result + ((resnum1 == null) ? 0 : resnum1.hashCode());
result = prime * result + ((resnum2 == null) ? 0 : resnum2.hashCode());
return result;
}
/* (non-Javadoc)
* @see java.lang.Object#equals(java.lang.Object)
*/
@Override
public boolean equals(Object obj) {
if (this == obj)
return true;
if (obj == null)
return false;
if (getClass() != obj.getClass())
return false;
SSBondImpl other = (SSBondImpl) obj;
if (chainID1 == null) {
if (other.chainID1 != null)
return false;
} else if (!chainID1.equals(other.chainID1))
return false;
if (chainID2 == null) {
if (other.chainID2 != null)
return false;
} else if (!chainID2.equals(other.chainID2))
return false;
if (insCode1 == null) {
if (other.insCode1 != null)
return false;
} else if (!insCode1.equals(other.insCode1))
return false;
if (insCode2 == null) {
if (other.insCode2 != null)
return false;
} else if (!insCode2.equals(other.insCode2))
return false;
if (resnum1 == null) {
if (other.resnum1 != null)
return false;
} else if (!resnum1.equals(other.resnum1))
return false;
if (resnum2 == null) {
if (other.resnum2 != null)
return false;
} else if (!resnum2.equals(other.resnum2))
return false;
return true;
}
public static List<SSBondImpl> getSsBondListFromBondList(List<Bond> bonds) {
List<SSBondImpl> l = new ArrayList<>();
for (int i=0; i<bonds.size(); i++) {
SSBondImpl ssbond = toSsBond(bonds.get(i));
ssbond.setSerNum(i + 1);
l.add(ssbond);
}
return l;
}
/**
* Converts the given {@link Bond} object into a {@link SSBondImpl}.
*
* @return
* @throws IllegalArgumentException if this Bond is not between two CYS residues
*/
public static SSBondImpl toSsBond(Bond bond) {
if (!bond.getAtomA().getGroup().getPDBName().equals("CYS") ||
!bond.getAtomB().getGroup().getPDBName().equals("CYS") ) {
throw new IllegalArgumentException("Trying to create a SSBond from a Bond between 2 groups that are not CYS");
}
SSBondImpl ssbond = new SSBondImpl();
ssbond.setChainID1(bond.getAtomA().getGroup().getChainId());
ssbond.setChainID2(bond.getAtomB().getGroup().getChainId());
ssbond.setResnum1(String.valueOf(bond.getAtomA().getGroup().getResidueNumber().getSeqNum()));
ssbond.setResnum2(String.valueOf(bond.getAtomB().getGroup().getResidueNumber().getSeqNum()));
Character iCode1 = bond.getAtomA().getGroup().getResidueNumber().getInsCode();
if (iCode1 == null) iCode1 = ' ';
Character iCode2 = bond.getAtomB().getGroup().getResidueNumber().getInsCode();
if (iCode2 == null) iCode2 = ' ';
ssbond.setInsCode1(String.valueOf(iCode1));
ssbond.setInsCode2(String.valueOf(iCode2));
return ssbond;
}
}