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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/
*
* Created on 05.03.2004
* @author Andreas Prlic
*
*/
package org.biojava.bio.structure;
import java.io.Serializable;
import java.util.HashMap;
import java.util.Map;
import org.biojava.bio.structure.io.PDBParseException;
/**
*
* AminoAcid inherits most from Hetatom. Adds a few AminoAcid
* specific methods.
* @author Andreas Prlic
* @author Jules Jacobsen
* @since 1.4
* @version %I% %G%
*
*/
public class AminoAcidImpl
extends HetatomImpl
implements AminoAcid, Serializable
{
/**
*
*/
private static final long serialVersionUID = -6018854413829044230L;
/** this is an Amino acid. type is "amino". */
public static final String type = GroupType.AMINOACID;
/* IUPAC amino acid residue names
*/
Character amino_char ;
Map<String,String> secstruc;
String recordType; // allows to distinguish between AAs that have been created from SEQRES records and ATOM records
/*
* inherits most from Hetero and has just a few extensions.
*/
public AminoAcidImpl() {
super();
amino_char = null;
secstruc = new HashMap<String,String>();
recordType = ATOMRECORD;
}
public String getType(){ return type;}
/** set the secondary structure data for this amino acid. the data
* is a Map with the following indeces (@see Secstruc)
*
* @param secstr a Map object specifying the sec struc value
* @see #getSecStruc
*/
public void setSecStruc(Map<String,String> secstr) {
this.secstruc = secstr ;
}
/** get secondary structure data .
*
* @return a Map object representing the sec struc value
*
* @see #setSecStruc
*/
public Map<String,String> getSecStruc(){
return secstruc ;
}
/** get N atom.
*
* @return an Atom object
* @throws StructureException ...
*/
public Atom getN() throws StructureException {return getAtom("N"); }
/** get CA atom.
* @return an Atom object
* @throws StructureException ...
*/
public Atom getCA() throws StructureException {return getAtom(" CA "); }
/** get C atom.
* @return an Atom object
* @throws StructureException ...
*/
public Atom getC() throws StructureException {return getAtom("C"); }
/** get O atom.
* @return an Atom object
* @throws StructureException ...
*/
public Atom getO() throws StructureException {return getAtom("O"); }
/** get CB atom.
* @return an Atom object
* @throws StructureException ...
*/
public Atom getCB() throws StructureException {return getAtom("CB"); }
/** returns the name of the AA, in single letter code.
*
* @return a Character object representing the amino type value
* @see #setAminoType
*/
public Character getAminoType() {
return amino_char;
}
/** set the name of the AA, in single letter code .
*
* @param aa a Character object specifying the amino type value
* @see #getAminoType
*/
public void setAminoType(Character aa){
amino_char = aa ;
}
public void setRecordType(String recordName) {
recordType = recordName;
}
public String getRecordType() {
return recordType;
}
/** string representation. */
public String toString(){
String str = "AminoAcid "+ recordType + ":"+ pdb_name + " " + amino_char +
" " + residueNumber + " "+ pdb_flag + " " + recordType ;
if (pdb_flag) {
str = str + " atoms: "+atoms.size();
}
if ( altLocs != null)
str += " has altLocs :" + altLocs.size();
return str ;
}
/** set three character name of AminoAcid.
*
* @param s a String specifying the PDBName value
* @see #getPDBName()
* @throws PDBParseException ...
*/
public void setPDBName(String s)
throws PDBParseException
{
if (s != null && s.length() != 3) {
throw new PDBParseException("amino acid name is not of length 3! (" + s +")");
}
pdb_name =s ;
}
/** returns and identical copy of this Group object .
* @return and identical copy of this Group object
*/
public Object clone(){
AminoAcidImpl n = new AminoAcidImpl();
n.setPDBFlag(has3D());
n.setResidueNumber(getResidueNumber());
try {
n.setPDBName(getPDBName());
} catch (PDBParseException e) {
e.printStackTrace();
}
n.setAminoType(getAminoType());
n.setRecordType(recordType);
// copy the atoms
for (int i=0;i<atoms.size();i++){
Atom atom = (Atom)atoms.get(i);
n.addAtom((Atom)atom.clone());
}
return n;
}
}
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