From: <raj...@us...> - 2007-06-22 22:35:28
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Revision: 8375 http://svn.sourceforge.net/cdk/?rev=8375&view=rev Author: rajarshi Date: 2007-06-22 15:15:36 -0700 (Fri, 22 Jun 2007) Log Message: ----------- Generified Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java trunk/cdk/src/org/openscience/cdk/charges/MMFF94PartialCharges.java trunk/cdk/src/org/openscience/cdk/charges/Polarizability.java Modified: trunk/cdk/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2007-06-22 19:37:58 UTC (rev 8374) +++ trunk/cdk/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2007-06-22 22:15:36 UTC (rev 8375) @@ -371,19 +371,18 @@ ac.getBuilder() ); - java.util.List atoms = ac.getConnectedAtomsList(ac.getAtom(atom1)); - for(int i = 0 ; i < atoms.size() ; i++){ - double covalentradius = 0; - String symbol = ((IAtom)atoms.get(i)).getSymbol(); - IAtomType type = factory.getAtomType(symbol); - covalentradius = type.getCovalentRadius(); + java.util.List<IAtom> atoms = ac.getConnectedAtomsList(ac.getAtom(atom1)); + for (IAtom atom : atoms) { + double covalentradius = 0; + String symbol = atom.getSymbol(); + IAtomType type = factory.getAtomType(symbol); + covalentradius = type.getCovalentRadius(); - double charge = ds[STEP_SIZE * atom1 + atom1 + 5]; - double sumI = CoulombForceConstant*charge/(covalentradius*covalentradius); -// logger.debug("sum_("+sumI+") = CFC("+CoulombForceConstant+")*charge("+charge+"/ret("+covalentradius); - sum += sumI; - } - } catch (CDKException e) { + double charge = ds[STEP_SIZE * atom1 + atom1 + 5]; + // logger.debug("sum_("+sumI+") = CFC("+CoulombForceConstant+")*charge("+charge+"/ret("+covalentradius); + sum += CoulombForceConstant * charge / (covalentradius * covalentradius); + } + } catch (CDKException e) { logger.debug(e); } Modified: trunk/cdk/src/org/openscience/cdk/charges/MMFF94PartialCharges.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/charges/MMFF94PartialCharges.java 2007-06-22 19:37:58 UTC (rev 8374) +++ trunk/cdk/src/org/openscience/cdk/charges/MMFF94PartialCharges.java 2007-06-22 22:15:36 UTC (rev 8375) @@ -23,12 +23,14 @@ */ package org.openscience.cdk.charges; +import org.openscience.cdk.interfaces.IAtom; +import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IMolecule; +import org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator; + import java.util.Hashtable; import java.util.Vector; -import org.openscience.cdk.interfaces.IAtomContainer; -import org.openscience.cdk.interfaces.IMolecule; -import org.openscience.cdk.modeling.builder3d.ForceFieldConfigurator; /** * The calculation of the MMFF94 partial charges. * Charges are stored as atom properties: @@ -83,45 +85,44 @@ double sumOfFormalCharges = 0; double sumOfBondIncrements = 0; org.openscience.cdk.interfaces.IAtom thisAtom = null; - java.util.List neighboors = null; + java.util.List<IAtom> neighboors; Vector data = null; Vector bondData = null; Vector dataNeigh = null; - java.util.Iterator atoms = ac.atoms(); + java.util.Iterator<IAtom> atoms = ac.atoms(); while(atoms.hasNext()) { //logger.debug("ATOM "+i+ " " +atoms[i].getSymbol()); - thisAtom = (org.openscience.cdk.interfaces.IAtom)atoms.next(); + thisAtom = atoms.next(); data = (Vector) parameterSet.get("data"+thisAtom.getAtomTypeName()); neighboors = ac.getConnectedAtomsList(thisAtom); formalCharge = thisAtom.getCharge(); - theta = ((Double)data.get(5)).doubleValue(); + theta = (Double) data.get(5); charge = formalCharge * (1 - (neighboors.size() * theta)); sumOfFormalCharges = 0; sumOfBondIncrements = 0; - for(int n = 0; n < neighboors.size(); n++) { - org.openscience.cdk.interfaces.IAtom neighbour = (org.openscience.cdk.interfaces.IAtom)neighboors.get(n); - dataNeigh = (Vector) parameterSet.get("data"+neighbour.getAtomTypeName()); - if (parameterSet.containsKey("bond"+thisAtom.getAtomTypeName()+";"+neighbour.getAtomTypeName())) { - bondData = (Vector) parameterSet.get("bond"+thisAtom.getAtomTypeName()+";"+neighbour.getAtomTypeName()); - sumOfBondIncrements -= ((Double) bondData.get(4)).doubleValue(); - } - else if (parameterSet.containsKey("bond"+neighbour.getAtomTypeName()+";"+thisAtom.getAtomTypeName())) { - bondData = (Vector) parameterSet.get("bond"+neighbour.getAtomTypeName()+";"+thisAtom.getAtomTypeName()); - sumOfBondIncrements += ((Double) bondData.get(4)).doubleValue(); - } - else { - // Maybe not all bonds have pbci in mmff94.prm, i.e. C-N - sumOfBondIncrements += ( theta - ((Double)dataNeigh.get(5)).doubleValue() ); - } - - - dataNeigh = (Vector) parameterSet.get("data"+neighbour.getID()); - formalChargeNeigh = neighbour.getCharge(); - sumOfFormalCharges += formalChargeNeigh; - } - charge += sumOfFormalCharges * theta; + for (IAtom neighboor : neighboors) { + IAtom neighbour = (IAtom) neighboor; + dataNeigh = (Vector) parameterSet.get("data" + neighbour.getAtomTypeName()); + if (parameterSet.containsKey("bond" + thisAtom.getAtomTypeName() + ";" + neighbour.getAtomTypeName())) { + bondData = (Vector) parameterSet.get("bond" + thisAtom.getAtomTypeName() + ";" + neighbour.getAtomTypeName()); + sumOfBondIncrements -= (Double) bondData.get(4); + } else + if (parameterSet.containsKey("bond" + neighbour.getAtomTypeName() + ";" + thisAtom.getAtomTypeName())) { + bondData = (Vector) parameterSet.get("bond" + neighbour.getAtomTypeName() + ";" + thisAtom.getAtomTypeName()); + sumOfBondIncrements += (Double) bondData.get(4); + } else { + // Maybe not all bonds have pbci in mmff94.prm, i.e. C-N + sumOfBondIncrements += (theta - (Double) dataNeigh.get(5)); + } + + + dataNeigh = (Vector) parameterSet.get("data" + neighbour.getID()); + formalChargeNeigh = neighbour.getCharge(); + sumOfFormalCharges += formalChargeNeigh; + } + charge += sumOfFormalCharges * theta; charge += sumOfBondIncrements; - thisAtom.setProperty("MMFF94charge", new Double(charge)); + thisAtom.setProperty("MMFF94charge", charge); //logger.debug( "CHARGE :"+thisAtom.getProperty("MMFF94charge") ); } return ac; Modified: trunk/cdk/src/org/openscience/cdk/charges/Polarizability.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/charges/Polarizability.java 2007-06-22 19:37:58 UTC (rev 8374) +++ trunk/cdk/src/org/openscience/cdk/charges/Polarizability.java 2007-06-22 22:15:36 UTC (rev 8375) @@ -23,18 +23,19 @@ */ package org.openscience.cdk.charges; -import java.util.Vector; - -import org.openscience.cdk.Atom; import org.openscience.cdk.AtomContainer; import org.openscience.cdk.Bond; import org.openscience.cdk.CDKConstants; import org.openscience.cdk.Molecule; import org.openscience.cdk.graph.PathTools; +import org.openscience.cdk.interfaces.IAtom; import org.openscience.cdk.interfaces.IAtomContainer; +import org.openscience.cdk.interfaces.IBond; import org.openscience.cdk.tools.HydrogenAdder; import org.openscience.cdk.tools.LoggingTool; +import java.util.Vector; + /** * Calculation of the polarizability of a molecule by the method of Kang and * Jhon and Gasteiger based on {@cdk.cite KJ81} and {@cdk.cite GH82} @@ -111,8 +112,8 @@ int influenceSphereCutOff) { double polarizabilitiy = 0; Molecule acH = new Molecule(atomContainer); - Vector startAtom = new Vector(1); - startAtom.add(0, (Atom) atom); + Vector<IAtom> startAtom = new Vector<IAtom>(1); + startAtom.add(0, atom); double bond; try { HydrogenAdder hAdder = new HydrogenAdder(); @@ -246,11 +247,11 @@ *@return The numberOfHydrogen value */ private int getNumberOfHydrogen(IAtomContainer atomContainer, org.openscience.cdk.interfaces.IAtom atom) { - java.util.List bonds = atomContainer.getConnectedBondsList(atom); + java.util.List<IBond> bonds = atomContainer.getConnectedBondsList(atom); org.openscience.cdk.interfaces.IAtom connectedAtom; int hCounter = 0; - for (int i = 0; i < bonds.size(); i++) { - connectedAtom = ((org.openscience.cdk.interfaces.IBond)bonds.get(i)).getConnectedAtom(atom); + for (IBond bond : bonds) { + connectedAtom = bond.getConnectedAtom(atom); if (connectedAtom.getSymbol().equals("H")) { hCounter += 1; } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |