From: <sh...@us...> - 2007-05-07 08:17:57
|
Revision: 8306 http://svn.sourceforge.net/cdk/?rev=8306&view=rev Author: shk3 Date: 2007-05-07 01:17:51 -0700 (Mon, 07 May 2007) Log Message: ----------- changed the charge classes to be able to add to an existing charge (reused unused parameter for that) Modified Paths: -------------- trunk/cdk/src/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java trunk/cdk/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java Modified: trunk/cdk/src/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java 2007-05-05 15:47:17 UTC (rev 8305) +++ trunk/cdk/src/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java 2007-05-07 08:17:51 UTC (rev 8306) @@ -98,11 +98,11 @@ * Main method which assigns Gasteiger Marisili partial sigma charges * *@param ac AtomContainer - *@param setCharge boolean flag to set charge on atoms + *@param addCharge true=add charge to existing charge, false=reset charge *@return AtomContainer with partial charges *@exception Exception Possible Exceptions */ - public IAtomContainer assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac, boolean setCharge) throws Exception { + public IAtomContainer assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer ac, boolean addCharge) throws Exception { // if (setCharge) { // atomTypeCharges.setCharges(ac); // not necessary initial charge @@ -170,7 +170,11 @@ } for (int i = 0; i < ac.getAtomCount(); i++) { - ac.getAtom(i).setCharge(gasteigerFactors[STEP_SIZE * i + i + 5]); + if(addCharge){ + ac.getAtom(i).setCharge(ac.getAtom(i).getCharge()+gasteigerFactors[STEP_SIZE * i + i + 5]); + }else{ + ac.getAtom(i).setCharge(gasteigerFactors[STEP_SIZE * i + i + 5]); + } } return ac; } Modified: trunk/cdk/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java =================================================================== --- trunk/cdk/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2007-05-05 15:47:17 UTC (rev 8305) +++ trunk/cdk/src/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java 2007-05-07 08:17:51 UTC (rev 8306) @@ -103,11 +103,11 @@ * * *@param ac AtomContainer - *@param setCharge boolean flag to set charge on atoms + *@param addCharge true=add charge to existing charge, false=reset charge *@return AtomContainer with partial charges *@exception Exception Possible Exceptions */ - public IAtomContainer assignGasteigerPiPartialCharges(IAtomContainer ac, boolean setCharge) throws Exception { + public IAtomContainer assignGasteigerPiPartialCharges(IAtomContainer ac, boolean addCharge) throws Exception { // logger.debug("smiles1: "+(new SmilesGenerator()).createSMILES((IMolecule) ac)); IAtomContainerSet setHI = null; @@ -268,7 +268,11 @@ double chargeT = 0.0; chargeT = charge + gasteigerFactors[k][STEP_SIZE * i + i + 5]; // logger.debug("i<|"+chargeT+"=c:" +charge + "+g: "+gasteigerFactors[k][STEP_SIZE * i + i + 5]); - ac.getAtom(i).setCharge(chargeT); + if(addCharge){ + ac.getAtom(i).setCharge(ac.getAtom(i).getCharge()+chargeT); + }else{ + ac.getAtom(i).setCharge(chargeT); + } } } This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site. |