moving generation of atom tags to chem.soft.-agnostic code

src/main/java/autocompchem/atom/AtomUtils.java

@@ -345,15 +345,7 @@ public static String getSymbolOrLabel(IAtom atm)
     	} 
     	else if (atm instanceof PseudoAtom) 
     	{
-	    	if (isPsaudoAtmWithLabel(atm,AtomConstants.DUMMYATMLABEL))
-	    	{
-	    		res = AtomConstants.DUMMYATMLABEL;
-	    	}
-	    	else if (isPsaudoAtmWithLabel(atm,
-	    			AtomConstants.ATTACHMENTPOINTLABEL))
-	    	{
-	    		res = AtomConstants.ATTACHMENTPOINTLABEL;
-	    	}
+    		res = ((PseudoAtom) atm).getLabel();
     	}
     	else if (atm instanceof Atom)
     	{
@@ -418,18 +410,14 @@ public static Integer countExplicitHydrogens(IAtom atm, IAtomContainer mol)
     public static Point3d getCoords3d(IAtom atom)
     {
         Point3d p3d = new Point3d();
-        try {
-            Point2d atp2d = new Point2d();
-            atp2d = atom.getPoint2d();
-            p3d.x = atp2d.x;
-            p3d.y = atp2d.y;
-            p3d.z = 0.0000;
-        } catch (Throwable t) {
-            Point3d atp3d = new Point3d();
-            atp3d = atom.getPoint3d();
-            p3d.x = atp3d.x;
-            p3d.y = atp3d.y;
-            p3d.z = atp3d.z;            
+        if (atom.getPoint3d()!=null)
+        {
+        	Point3d atp3d = atom.getPoint3d();
+        	p3d = new Point3d(atp3d.x, atp3d.y, atp3d.z);
+        } else if (atom.getPoint2d()!=null)
+        {
+        	Point2d atp2d = atom.getPoint2d();
+        	p3d = new Point3d(atp2d.x, atp2d.y, 0);
         }
         return p3d;
     }

src/main/java/autocompchem/chemsoftware/ChemSoftInputWriter.java

@@ -515,8 +515,12 @@ private void produceSingleJobInputFiles(List<IAtomContainer> mols,
 		molSpecJob.setParameter(ChemSoftConstants.PAROUTFILEROOT, 
 				outFileNameRoot, true);
 
-		// Add atom coordinates to the so-far molecule-agnostic job
-		setChemicalSystem(molSpecJob, mols);
+		// Add atom coordinates to the so-far possible molecule-agnostic job
+		if (useAtomTags)
+			setChemicalSystem(molSpecJob, makeAtomContainersWithAtomTags(mols));
+		else
+			setChemicalSystem(molSpecJob, mols);
+
 		// We keep a copy of the agnostic chemical system definition in the job 
 		// parameters
 		setChemicalSystemAsJobParam(molSpecJob, mols);
@@ -543,7 +547,7 @@ private void produceSingleJobInputFiles(List<IAtomContainer> mols,
 			}
     	}
 
-		// These calls take care also of the sub-jobs/directives
+		// This call takes care also of the sub-jobs/directives
 		molSpecJob.processDirectives(mols, this.getMyJob());
 
 		// Ensure a value of charge and spin has been defined
@@ -570,6 +574,19 @@ private void produceSingleJobInputFiles(List<IAtomContainer> mols,
 		}
     }
 
+//------------------------------------------------------------------------------
+
+    private List<IAtomContainer> makeAtomContainersWithAtomTags(
+    		List<IAtomContainer> mols)
+    {
+    	List<IAtomContainer> molsWithAtomTags = new ArrayList<IAtomContainer>();
+    	for (IAtomContainer iac : mols)
+    	{
+    		molsWithAtomTags.add(MolecularUtils.makeSimpleCopyWithAtomTags(iac));
+    	}
+    	return molsWithAtomTags;
+    }
+
 //------------------------------------------------------------------------------
 
     private void setChemicalSystemAsJobParam(CompChemJob job, 

src/main/java/autocompchem/chemsoftware/Directive.java

@@ -47,6 +47,7 @@
 import autocompchem.modeling.basisset.BasisSetGenerator;
 import autocompchem.modeling.constraints.ConstraintsGenerator;
 import autocompchem.modeling.constraints.ConstraintsSet;
+import autocompchem.molecule.MolecularUtils;
 import autocompchem.molecule.conformation.ConformationalSpace;
 import autocompchem.molecule.conformation.ConformationalSpaceGenerator;
 import autocompchem.molecule.intcoords.zmatrix.ZMatrix;
@@ -1231,6 +1232,8 @@ private void performACCTask(List<IAtomContainer> mols, ParameterStorage params,
             				ChemSoftConstants.PARMULTIGEOMID).getValueAsString());
             	}
 
+            	boolean useAtomTags = params.contains(ChemSoftConstants.PARUSEATMTAGS);
+
             	switch (coordsType)
             	{    
                 	case ZMAT:
@@ -1244,6 +1247,7 @@ private void performACCTask(List<IAtomContainer> mols, ParameterStorage params,
                         Worker w = WorkerFactory.createWorker(zmatMakerTask,
                         		masterJob);
                         ZMatrixHandler zmh = (ZMatrixHandler) w;
+                        //TODO-gg make it use atom tags upon request
                         ZMatrix zmat = zmh.makeZMatrix();
                         if (params.contains(ZMatrixConstants.SELECTORMODE))
                         {
@@ -1290,6 +1294,10 @@ private void performACCTask(List<IAtomContainer> mols, ParameterStorage params,
                 	default:
                 	{
                 		IAtomContainer mol = mols.get(geometryId);
+                		if (useAtomTags)
+                		{
+                			mol = MolecularUtils.makeSimpleCopyWithAtomTags(mol);
+                		}
                 		((IValueContainer) dirComp).setValue(mol);
                 		break;
                 	}

src/main/java/autocompchem/chemsoftware/nwchem/NWChemInputWriter.java

@@ -272,22 +272,10 @@ private ArrayList<String> getTextForInput(Directive d)
 				break;
 
 			case IATOMCONTAINER:
-            	boolean useTags = false;
-            	if (data.getTaskParams()!=null 
-            			&& data.getTaskParams().contains(
-            					ChemSoftConstants.PARUSEATMTAGS))
-            	{
-            		useTags = true;
-            	}
 				IAtomContainer mol = (IAtomContainer) data.getValue();
 				for (IAtom atm : mol.atoms())
 				{
 					String atmId = AtomUtils.getSymbolOrLabel(atm);
-					if (useTags)
-					{
-						// Convention is to use 1-based indexing here
-						atmId = atmId + (mol.indexOf(atm)+1);
-					}
 					Point3d p3d = AtomUtils.getCoords3d(atm);
 					ddLines.add(String.format(Locale.ENGLISH," %3s", atmId)
 							+ String.format(Locale.ENGLISH," %10.6f",p3d.x)

src/main/java/autocompchem/molecule/MolecularUtils.java

@@ -30,13 +30,19 @@
 import javax.vecmath.Point3d;
 import javax.vecmath.Vector3d;
 
+import org.openscience.cdk.Atom;
+import org.openscience.cdk.Bond;
 import org.openscience.cdk.CDKConstants;
+import org.openscience.cdk.DefaultChemObjectBuilder;
+import org.openscience.cdk.PseudoAtom;
 import org.openscience.cdk.aromaticity.Kekulization;
 import org.openscience.cdk.exception.CDKException;
 import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
 import org.openscience.cdk.interfaces.IBond;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 import org.openscience.cdk.interfaces.IBond.Order;
+import org.openscience.cdk.tools.periodictable.PeriodicTable;
 
 import autocompchem.atom.AtomUtils;
 import autocompchem.geometry.DistanceMatrix;
@@ -58,6 +64,9 @@ public class MolecularUtils
     //TODO move to constants
     @SuppressWarnings("unused")
         private static double linearBendThld = 175.0;
+
+	private static IChemObjectBuilder chemBuilder = 
+    		DefaultChemObjectBuilder.getInstance();
 
 
 //------------------------------------------------------------------------------
@@ -807,7 +816,50 @@ public static void ensureNoUnsetBondOrders(IAtomContainer mol)
 			}
 		}
 	}
-
+
+//------------------------------------------------------------------------------
+
+	/**
+	 * Makes a simplified copy of the given {@link IAtomContainer} considering
+	 * only the list of atoms as elements/labels and points in 3D, set of bonds,
+	 * and container title/name, 
+	 * without any further property of atoms, bonds, or of the container, and
+	 * sets the atom label to be an atom tag, i.e., a string that allows to 
+	 * identify the atom (e.g., "C3"). The tag is generated by concatenating
+	 * the elemental symbol (or initial {@link PseudoAtom} label) with the
+	 * 1-based index of the atom in the given container.
+	 * @param iac the original atom container to copy and decorate with atom 
+	 * tags.
+	 * @return the copy of the original container with the atom tags.
+	 */
+	public static IAtomContainer makeSimpleCopyWithAtomTags(IAtomContainer iac)
+	{
+		IAtomContainer iacWithTags = chemBuilder.newAtomContainer();
+		int iAtm = 0;
+		for (IAtom origAtm : iac.atoms())
+    	{
+    		iAtm++;
+    		String atomTag = AtomUtils.getSymbolOrLabel(origAtm) + iAtm;
+	    	IAtom atmWithTag = new PseudoAtom(atomTag);
+	    	Point3d p3d = AtomUtils.getCoords3d(origAtm);
+	    	atmWithTag.setPoint3d(new Point3d(p3d.x, p3d.y, p3d.z));
+	    	iacWithTags.addAtom(atmWithTag);
+    	}
+		for (IBond origBnd : iac.bonds())
+		{
+			IAtom[] atomsInNewBond = new IAtom[origBnd.getAtomCount()];
+			for (int i=0; i<origBnd.getAtomCount(); i++)
+			{
+				atomsInNewBond[i] = iacWithTags.getAtom(
+						iac.indexOf(origBnd.getAtom(i)));
+			}
+			IBond newBond = new Bond(atomsInNewBond, origBnd.getOrder());
+			iacWithTags.addBond(newBond);
+		}
+		iacWithTags.setTitle(MolecularUtils.getNameIDOrNull(iac));
+		return iacWithTags;
+	}
+
 //------------------------------------------------------------------------------
 
 }

src/test/java/autocompchem/atom/AtomUtilsTest.java

@@ -24,10 +24,17 @@
 
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
+import javax.vecmath.Point2d;
+import javax.vecmath.Point3d;
+
 import org.junit.jupiter.api.Test;
 import org.openscience.cdk.Atom;
+import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.PseudoAtom;
 import org.openscience.cdk.interfaces.IAtom;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+
+import autocompchem.molecule.MolecularUtils;
 
 /**
  * Unit Test for atom utilities
@@ -38,6 +45,9 @@
 public class AtomUtilsTest 
 {
 
+	private static IChemObjectBuilder chemBuilder = 
+    		DefaultChemObjectBuilder.getInstance();
+
 //------------------------------------------------------------------------------
 
     @Test
@@ -81,6 +91,33 @@ public void testGetSymbolOrLabel() throws Exception
     			"Return label for attachment points");
     }
 
+//------------------------------------------------------------------------------
+
+    @Test
+    public void testGetCoords3d() throws Exception
+    {
+    	IAtom atm = chemBuilder.newAtom();
+    	assertTrue(closeEnough(AtomUtils.getCoords3d(atm), new Point3d(0,0,0)));
+
+    	atm.setPoint2d(new Point2d(1.2, 2.3));
+    	assertTrue(closeEnough(AtomUtils.getCoords3d(atm), 
+    			new Point3d(1.2, 2.3,0)));
+
+    	atm.setPoint3d(new Point3d(1.2, 2.3, -3.4));
+    	assertTrue(closeEnough(AtomUtils.getCoords3d(atm), 
+    			new Point3d(1.2, 2.3,  -3.4)));
+    }
+
+//------------------------------------------------------------------------------
+
+    private boolean closeEnough(Point3d pA, Point3d pB)
+    {
+    	if (pA==null | pB==null)
+    		return false;
+
+    	return pA.distance(pB) < 0.0002;
+    }
+
 //------------------------------------------------------------------------------
 
 }

src/test/java/autocompchem/molecule/MolecularUtilsTest.java

@@ -1,5 +1,6 @@
 package autocompchem.molecule;
 
+import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 
 /*   
@@ -25,10 +26,13 @@
 
 import org.junit.jupiter.api.Test;
 import org.openscience.cdk.Atom;
-import org.openscience.cdk.AtomContainer;
+import org.openscience.cdk.DefaultChemObjectBuilder;
 import org.openscience.cdk.PseudoAtom;
+import org.openscience.cdk.interfaces.IAtom;
 import org.openscience.cdk.interfaces.IAtomContainer;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
 
+import autocompchem.atom.AtomUtils;
 import autocompchem.geometry.DistanceMatrix;
 
 /**
@@ -39,13 +43,43 @@
 
 public class MolecularUtilsTest 
 {
+
+	private static IChemObjectBuilder chemBuilder = 
+    		DefaultChemObjectBuilder.getInstance();
+
+//------------------------------------------------------------------------------
+
+	@Test
+	public void testMakeSimpleCopyWithAtomTags() throws Exception
+	{
+		IAtomContainer mol = chemBuilder.newAtomContainer();
+    	mol.addAtom(new Atom("H"));
+    	mol.addAtom(new Atom("C"));
+    	mol.addAtom(new Atom("O"));
+    	mol.addAtom(new Atom("Ru"));
+    	mol.addAtom(new PseudoAtom("Du"));
+    	mol.addAtom(new PseudoAtom("Xx")); 
+
+    	IAtomContainer tagged = MolecularUtils.makeSimpleCopyWithAtomTags(mol);
+
+    	assertEquals(mol.getAtomCount(),tagged.getAtomCount());
+    	for (int iAtm=0; iAtm<mol.getAtomCount(); iAtm++)
+    	{
+    		IAtom atm = tagged.getAtom(iAtm);
+    		IAtom origAtm = mol.getAtom(iAtm);
+    		// NB: so far there is only one format for atom tags, so we can
+    		// hard-code the expected tag.
+    		String expectedTag = AtomUtils.getSymbolOrLabel(origAtm)+(iAtm+1);
+    		assertEquals(expectedTag, AtomUtils.getSymbolOrLabel(atm));
+    	}
+	}
 
 //------------------------------------------------------------------------------
 
 	@Test
 	public void testElementalSymbols() throws Exception
     {
-    	IAtomContainer mol = new AtomContainer();
+		IAtomContainer mol = chemBuilder.newAtomContainer();
     	mol.addAtom(new Atom("H"));
     	mol.addAtom(new Atom("C"));
     	mol.addAtom(new Atom("O"));
@@ -72,7 +106,7 @@ public void testElementalSymbols() throws Exception
 	@Test
 	public void testMinInterelementalBondDistance() throws Exception
     {
-    	IAtomContainer mol = new AtomContainer();
+		IAtomContainer mol = chemBuilder.newAtomContainer();
     	mol.addAtom(new Atom("C",new Point3d(0,0,0.0)));
     	mol.addAtom(new Atom("C",new Point3d(1.0,0,0)));
     	mol.addAtom(new Atom("C",new Point3d(2.0,0,0)));
@@ -92,8 +126,7 @@ public void testMinInterelementalBondDistance() throws Exception
     @Test
     public void testInteratormicDistanceMatrix() throws Exception
     {
-
-    	IAtomContainer mol = new AtomContainer();
+		IAtomContainer mol = chemBuilder.newAtomContainer();
     	mol.addAtom(new Atom("C",new Point3d(0,0,0.0)));
     	mol.addAtom(new Atom("C",new Point3d(0,3.0,0)));
     	mol.addAtom(new Atom("C",new Point3d(4.0,0,0)));

test/t87.check

@@ -16,7 +16,7 @@ if [ $n -ne 2 ] ; then echo NOT Passes ERROR 3 ; exit -1 ; fi
 n=0;n=$(grep -c -i "Ru.*nelec 28" t87-mol.nw)
 if [ $n -ne 1 ] ; then echo NOT Passes ERROR 4 ; exit -1 ; fi
 
-n=0;n=$(grep -c -i "Ru.*\\s*[0-9\-]*\.[0-9]*\\s*[0-9\-]*\.[0-9]*\\s*[0-9\-]*\.[0-9]*" t87-mol.nw)
+n=0;n=$(grep -c -i "Ru1.*\\s*2.7141[0-9]*\\s*-1\.3069[0-9]*\\s*-0\.6133[0-9]*" t87-mol.nw)
 if [ $n -ne 1 ] ; then echo NOT Passes ERROR 5 ; exit -1 ; fi
 
 n=0;n=$(grep -c -i "fix atom " t87-mol.nw)

test/t87.params

@@ -4,4 +4,5 @@
 VERBOSITY: 2
 TASK: PrepareInputNWChem
 INPUTGEOMETRIESFILE: ../t87-mol.sdf
+USEATOMTAGS:
 JOBDETAILSFILE: ../t87-jobDetails.json