fixed an issue with missing bonds

src/main/java/com/actelion/research/chem/Molecule.java

@@ -3607,7 +3607,7 @@ public void setAtomCustomLabel(int atom, String label) {
 				label = null;
 			else {
 				int atomicNo = getAtomicNoFromLabel(label);
-				if ((atomicNo != 0 && label.equals(cAtomLabel[atomicNo]))
+				if ((atomicNo != 0 && atomicNo == mAtomicNo[atom])
 				 || label.equals("?")) {
 					setAtomicNo(atom, atomicNo);
 					label = null;

src/main/java/com/actelion/research/chem/io/pdb/converter/AminoAcids.java

@@ -0,0 +1,122 @@
+/*
+ * Copyright (c) 1997 - 2016
+ * Actelion Pharmaceuticals Ltd.
+ * Gewerbestrasse 16
+ * CH-4123 Allschwil, Switzerland
+ *
+ * All rights reserved.
+ *
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice, this
+ *    list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ * 3. Neither the name of the the copyright holder nor the
+ *    names of its contributors may be used to endorse or promote products
+ *    derived from this software without specific prior written permission.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
+ * ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
+ * WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+ * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR
+ * ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
+ * (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
+ * LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
+ * ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
+ * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
+ * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+ *
+ * @author Modest v. Korff, Thomas Sander
+ */
+
+package com.actelion.research.chem.io.pdb.converter;
+
+import com.actelion.research.chem.*;
+import com.actelion.research.chem.io.pdb.parser.AtomRecord;
+
+import java.util.*;
+
+public class AminoAcids {
+	private static final String[][] AA_TEMPLATES = {
+            { "gGX`BDdwMULPGzILwXM[jD", "Alanine", "ala" },
+            { "dctd@BE]ADf{UYjjihp`GzBfMvCS]Plw^OMtbK]hrwUj}tRfwnbXp", "Arginine", "arg" },
+            { "diEL@BDDyInvZjZL`OtiL[lFfzaYn|^{iFLO]Hi`", "Asparagine", "asn" },
+            { "diFB@BANEInvZjZLHA~eIc]`twTKMwcw]Hqa{iEL", "Aspartic Acid", "asp" },
+            { "gNxhMV@aI[jihj@?SHF{ac]PinpP", "Cysteine", "Cys" },
+            { "defB@BAAeInufjihr@?QdqnpZ[jEf{qyndQ{mFMO]hi`","Glutamic Acid", "glu" },
+            { "deeL@BdDEInufjihp`GzLfMvCS]Plw^OMtbO]hqi{mEL", "Glutamine", "gln" },
+            { "gJX`BDdvu@OtbYnpP", "Glycine", "gly" },
+            { "dmwD@ByPQInvVUZjejL`OtyL[lFfzaYn|^{iFLO]Hii{mFLo]hi`", "Histidine", "his" },
+            { "diFD@BADf{ejjdrU@_iRXwXMMuBw]xqn{oELO]Hq`", "Isoleucine", "ile" },
+            { "diFD@BADf{Yjjhr@?RdqnpZ[jEf{q{ndTp}tcF@", "Leucine", "leu" },
+            { "deeD@BdDR[mUjjjL`OtYL[lFfzaYn|^[iDV{QenkP", "Lysine", "lys" },
+            { "diFD`JxPBDivzjihI@?RdAndX[oEF{QqnhR[lD", "Methionine", "met" },
+            { "dcND@BADf{YU]Zj@@cHC}ASF{AinhV[oGnzQSCwRLZ^{QSKwZL[Vzm@", "Phenylalanine", "phe" },
+            { "daFD@BADfyVyjjhr@?PdqnpZ[jEfzQyn|P", "Proline", "pro" },
+            { "gNy`BDtf{ZjfHC}Lf[lFmuBv{q@", "Serine", "ser" },
+            { "dazL@BAFR[nZjdrT`_hRXwXMMuBw]xqn{oEL", "Threonine", "thr" },
+            { "foAP`@BZ@aInvYWejsfjiB@bFB@OttfF{AhwTKF{qywRJXW]Hqi]vbfUwZN[W]hqc]uZfmwUnYw]Di`", "Tryptophane", "trp" },
+            { "dknL@BACR[me]]Zj@BHr@?RTqnpZ[jEf{q{ndTp}tcFgntTr}vcFunkS[hd", "Tyrosine", "tyr" },
+            { "dazD@BADf{fjjL`OtIL[lFfza[n|Tw]wcF@", "Valine", "val" }
+    };
+
+    private static TreeMap<String,StereoMolecule> sShortLabelMap;
+
+    public static StereoMolecule getStructure(String label) {
+        return ensureAAMap().get(label.toLowerCase());
+    }
+
+    public static Molecule3D createResidue(String label, List<AtomRecord> atomRecordList) {
+        StereoMolecule mol = getStructure(label);
+        if (mol != null) {
+            Molecule3D aminoAcid = new Molecule3D(mol);
+            Map<String,AtomRecord> recordMap = new HashMap<>();
+            for(AtomRecord record : atomRecordList)
+                recordMap.put(record.getAtomName(), record);
+
+            for (int atom=0; atom<aminoAcid.getAllAtoms(); atom++) {
+                String atomName = mol.getAtomLabel(atom);
+                String customLabel = mol.getAtomCustomLabel(atom);
+                if (customLabel != null && customLabel.startsWith("]"))
+                    atomName = atomName.concat(customLabel.substring(1));
+
+                AtomRecord record = recordMap.get(atomName);
+                if (record != null) {
+                    Coordinates coords3d = new Coordinates(record.getX(), record.getY(), record.getZ());
+                    aminoAcid.setAtomName(atom, record.getAtomName());
+                    aminoAcid.setAtomAmino(atom, record.getResName());
+                    aminoAcid.setAtomSequence(atom, record.getSerialId());
+                    aminoAcid.setResSequence(atom, record.getResNum());
+                    aminoAcid.setAtomAmino(atom, record.getResName());
+                    aminoAcid.setAtomChainId(atom, record.getChainID());
+                    aminoAcid.setAtomX(atom, coords3d.x);
+                    aminoAcid.setAtomY(atom, coords3d.y);
+                    aminoAcid.setAtomZ(atom, coords3d.z);
+                }
+            };
+
+            for (int atom=0; atom<aminoAcid.getAllAtoms(); atom++)
+                if (aminoAcid.getAtomName(atom) == null)
+                    aminoAcid.markAtomForDeletion(atom);
+            aminoAcid.deleteMarkedAtomsAndBonds();
+
+            return aminoAcid;
+        }
+        return null;
+    }
+
+    private static TreeMap<String,StereoMolecule> ensureAAMap() {
+        if (sShortLabelMap == null) {
+            sShortLabelMap = new TreeMap<>();
+            for (String[] template : AA_TEMPLATES) {
+                StereoMolecule mol = new IDCodeParserWithoutCoordinateInvention().getCompactMolecule(template[0]);
+                mol.setName(template[1]);
+                sShortLabelMap.put(template[2], mol);
+            }
+        }
+        return sShortLabelMap;
+    }
+}

src/main/java/com/actelion/research/chem/io/pdb/parser/ProteinSynthesizer.java

@@ -6,12 +6,8 @@
 
 public class ProteinSynthesizer {
 
-	private Molecule3D protein;
-	private int terminalC=-1;
-
-	public ProteinSynthesizer() {
-	}
-
+	private Molecule3D mProtein;
+	private int mTerminalC =-1;
 
 	/**
 	 * an amino acid is added to the protein structure and a peptide coupling is performed, 
@@ -27,42 +23,40 @@ public boolean addResidue(Molecule3D residue) {
 				newTerminalN = atom;
 			if(residue.getAtomicNo(atom)==6 && residue.getAtomCustomLabel(atom)==null)
 				newTerminalC = atom;
-
 		}
-		if(protein==null) { // first residue
-			protein = residue;
-			terminalC = newTerminalC;
+		if(mProtein ==null) { // first residue
+			mProtein = residue;
+			mTerminalC = newTerminalC;
 			coupled = true;
 		}
-		else if(newTerminalN>-1 && terminalC>-1) { //coupling should be performed
-			Coordinates coordsC = protein.getCoordinates(terminalC);
+		else if(newTerminalN>-1 && mTerminalC >-1) { //coupling should be performed
+			Coordinates coordsC = mProtein.getCoordinates(mTerminalC);
 			Coordinates coordsN = residue.getCoordinates(newTerminalN);
 			if(coordsC.distanceSquared(coordsN)<Residue.BOND_CUTOFF_SQ) {
 				boolean notFound = true;
-				for(int i=0;i<protein.getConnAtoms(terminalC) && notFound;i++) {
-					int a = protein.getConnAtom(terminalC, i);
-					int b = protein.getBond(terminalC, a);
-					if(protein.getAtomicNo(a)==8 && protein.getBondOrder(b)==1) {
+				for(int i = 0; i< mProtein.getConnAtoms(mTerminalC) && notFound; i++) {
+					int a = mProtein.getConnAtom(mTerminalC, i);
+					int b = mProtein.getBond(mTerminalC, a);
+					if(mProtein.getAtomicNo(a)==8 && mProtein.getBondOrder(b)==1) {
 						notFound=false;
-						toDelete = protein.getConnAtom(terminalC, i);
+						toDelete = mProtein.getConnAtom(mTerminalC, i);
 					}
 				}
 
 				if(toDelete>=0) {
-					protein.deleteAtom(toDelete);
-					int[] atomMap = protein.addMolecule(residue);
-					protein.addBond(terminalC, atomMap[newTerminalN], 1);
-					terminalC = protein.getAllAtoms()-(residue.getAllAtoms()-newTerminalC);
+					mProtein.deleteAtom(toDelete);
+					int[] atomMap = mProtein.addMolecule(residue);
+					mProtein.addBond(mTerminalC, atomMap[newTerminalN], 1);
+					mTerminalC = mProtein.getAllAtoms()-(residue.getAllAtoms()-newTerminalC);
 					coupled = true;
 				}
 			}
 		}
-		protein.ensureHelperArrays(Molecule.cHelperNeighbours);
+		mProtein.ensureHelperArrays(Molecule.cHelperNeighbours);
 		return coupled;
 	}
 
-	public Molecule3D retrieveProtein() {
-		return protein;
+	public Molecule3D getProtein() {
+		return mProtein;
 	}
-
 }