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Switched from + to , in logger.debug() calls

Signed-off-by: Egon Willighagen <egonw@users.sourceforge.net>
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1 parent 9b48adb commit 52691c37b721beb13b3774f540ba161dfcfc7d3d @jonalv jonalv committed with egonw Mar 10, 2011
Showing with 646 additions and 646 deletions.
  1. +7 −7 src/main/org/openscience/cdk/atomtype/MM2AtomTypeMatcher.java
  2. +4 −4 src/main/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java
  3. +2 −2 src/main/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java
  4. +10 −10 src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
  5. +5 −5 src/main/org/openscience/cdk/charges/InductivePartialCharges.java
  6. +2 −2 src/main/org/openscience/cdk/charges/MMFF94PartialCharges.java
  7. +1 −1 src/main/org/openscience/cdk/config/AtomTypeFactory.java
  8. +1 −1 src/main/org/openscience/cdk/debug/DebugAdductFormula.java
  9. +19 −19 src/main/org/openscience/cdk/debug/DebugAminoAcid.java
  10. +6 −6 src/main/org/openscience/cdk/debug/DebugAtom.java
  11. +20 −20 src/main/org/openscience/cdk/debug/DebugAtomContainer.java
  12. +7 −7 src/main/org/openscience/cdk/debug/DebugAtomContainerSet.java
  13. +5 −5 src/main/org/openscience/cdk/debug/DebugAtomType.java
  14. +20 −20 src/main/org/openscience/cdk/debug/DebugBioPolymer.java
  15. +4 −4 src/main/org/openscience/cdk/debug/DebugBond.java
  16. +5 −5 src/main/org/openscience/cdk/debug/DebugChemFile.java
  17. +4 −4 src/main/org/openscience/cdk/debug/DebugChemModel.java
  18. +4 −4 src/main/org/openscience/cdk/debug/DebugChemObject.java
  19. +4 −4 src/main/org/openscience/cdk/debug/DebugChemSequence.java
  20. +19 −19 src/main/org/openscience/cdk/debug/DebugCrystal.java
  21. +4 −4 src/main/org/openscience/cdk/debug/DebugElectronContainer.java
  22. +5 −5 src/main/org/openscience/cdk/debug/DebugElement.java
  23. +18 −18 src/main/org/openscience/cdk/debug/DebugFragmentAtom.java
  24. +4 −4 src/main/org/openscience/cdk/debug/DebugIsotope.java
  25. +4 −4 src/main/org/openscience/cdk/debug/DebugLonePair.java
  26. +4 −4 src/main/org/openscience/cdk/debug/DebugMapping.java
  27. +3 −3 src/main/org/openscience/cdk/debug/DebugMolecularFormula.java
  28. +1 −1 src/main/org/openscience/cdk/debug/DebugMolecularFormulaSet.java
  29. +19 −19 src/main/org/openscience/cdk/debug/DebugMolecule.java
  30. +7 −7 src/main/org/openscience/cdk/debug/DebugMoleculeSet.java
  31. +19 −19 src/main/org/openscience/cdk/debug/DebugMonomer.java
  32. +1 −1 src/main/org/openscience/cdk/debug/DebugPDBAtom.java
  33. +20 −20 src/main/org/openscience/cdk/debug/DebugPolymer.java
  34. +18 −18 src/main/org/openscience/cdk/debug/DebugPseudoAtom.java
  35. +10 −10 src/main/org/openscience/cdk/debug/DebugReaction.java
  36. +4 −4 src/main/org/openscience/cdk/debug/DebugReactionScheme.java
  37. +5 −5 src/main/org/openscience/cdk/debug/DebugReactionSet.java
  38. +19 −19 src/main/org/openscience/cdk/debug/DebugRing.java
  39. +4 −4 src/main/org/openscience/cdk/debug/DebugSingleElectron.java
  40. +19 −19 src/main/org/openscience/cdk/debug/DebugStrand.java
  41. +3 −3 src/main/org/openscience/cdk/dict/Dictionary.java
  42. +2 −2 src/main/org/openscience/cdk/dict/OWLFile.java
  43. +2 −2 src/main/org/openscience/cdk/dict/OWLReact.java
  44. +1 −1 src/main/org/openscience/cdk/fingerprint/FingerprinterTool.java
  45. +1 −1 src/main/org/openscience/cdk/fragment/ExhaustiveFragmenter.java
  46. +1 −1 src/main/org/openscience/cdk/geometry/GeometryTools.java
  47. +2 −2 src/main/org/openscience/cdk/geometry/surface/NumericalSurface.java
  48. +1 −1 src/main/org/openscience/cdk/graph/AtomContainerPermutor.java
  49. +1 −1 src/main/org/openscience/cdk/graph/invariant/HuLuIndexTool.java
  50. +9 −9 src/main/org/openscience/cdk/io/CIFReader.java
  51. +1 −1 src/main/org/openscience/cdk/io/CTXReader.java
  52. +17 −17 src/main/org/openscience/cdk/io/CrystClustReader.java
  53. +1 −1 src/main/org/openscience/cdk/io/Gaussian03Reader.java
  54. +4 −4 src/main/org/openscience/cdk/io/Gaussian98Reader.java
  55. +3 −3 src/main/org/openscience/cdk/io/GhemicalMMReader.java
  56. +1 −1 src/main/org/openscience/cdk/io/MDLRXNReader.java
  57. +1 −1 src/main/org/openscience/cdk/io/MDLRXNV3000Reader.java
  58. +8 −8 src/main/org/openscience/cdk/io/MDLReader.java
  59. +8 −8 src/main/org/openscience/cdk/io/MDLV2000Reader.java
  60. +11 −11 src/main/org/openscience/cdk/io/MDLV3000Reader.java
  61. +3 −3 src/main/org/openscience/cdk/io/PCCompoundASNReader.java
  62. +5 −5 src/main/org/openscience/cdk/io/PMPReader.java
  63. +1 −1 src/main/org/openscience/cdk/io/SMILESReader.java
  64. +1 −1 src/main/org/openscience/cdk/io/SMILESWriter.java
  65. +9 −9 src/main/org/openscience/cdk/io/ShelXReader.java
  66. +2 −2 src/main/org/openscience/cdk/io/VASPReader.java
  67. +2 −2 src/main/org/openscience/cdk/io/cml/CDKConvention.java
  68. +4 −4 src/main/org/openscience/cdk/io/cml/CMLCoreModule.java
  69. +1 −1 src/main/org/openscience/cdk/io/cml/CMLHandler.java
  70. +3 −3 src/main/org/openscience/cdk/io/cml/PDBConvention.java
  71. +2 −2 src/main/org/openscience/cdk/io/cml/PMPConvention.java
  72. +8 −8 src/main/org/openscience/cdk/io/iterator/event/EventCMLHandler.java
  73. +22 −22 src/main/org/openscience/cdk/layout/AtomPlacer.java
  74. +3 −3 src/main/org/openscience/cdk/layout/HydrogenPlacer.java
  75. +12 −12 src/main/org/openscience/cdk/layout/OverlapResolver.java
  76. +25 −25 src/main/org/openscience/cdk/layout/RingPlacer.java
  77. +22 −22 src/main/org/openscience/cdk/layout/StructureDiagramGenerator.java
  78. +6 −6 src/main/org/openscience/cdk/layout/TemplateHandler.java
  79. +1 −1 src/main/org/openscience/cdk/libio/cml/QSARCustomizer.java
  80. +1 −1 src/main/org/openscience/cdk/modeling/builder3d/ModelBuilder3D.java
  81. +5 −5 src/main/org/openscience/cdk/pharmacophore/PharmacophoreMatcher.java
  82. +2 −2 src/main/org/openscience/cdk/protein/ProteinPocketFinder.java
  83. +4 −4 src/main/org/openscience/cdk/qsar/DescriptorEngine.java
  84. +1 −1 src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_G3R.java
  85. +1 −1 src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GDR.java
  86. +1 −1 src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR.java
  87. +1 −1 src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GHR_topol.java
  88. +1 −1 src/main/org/openscience/cdk/qsar/descriptors/atomic/RDFProtonDescriptor_GSR.java
  89. +2 −2 src/main/org/openscience/cdk/qsar/descriptors/protein/TaeAminoAcidDescriptor.java
  90. +1 −1 src/main/org/openscience/cdk/renderer/JCPAction2D.java
  91. +5 −5 src/main/org/openscience/cdk/ringsearch/AllRingsFinder.java
  92. +7 −7 src/main/org/openscience/cdk/ringsearch/FiguerasSSSRFinder.java
  93. +1 −1 src/main/org/openscience/cdk/smiles/DeduceBondSystemTool.java
  94. +5 −5 src/main/org/openscience/cdk/smiles/SmilesParser.java
  95. +5 −5 src/main/org/openscience/cdk/structgen/RandomGenerator.java
  96. +13 −13 src/main/org/openscience/cdk/structgen/VicinitySampler.java
  97. +1 −1 src/main/org/openscience/cdk/structgen/stochastic/PartialFilledStructureMerger.java
  98. +3 −3 src/main/org/openscience/cdk/templates/AminoAcids.java
  99. +2 −2 src/main/org/openscience/cdk/tools/HOSECodeGenerator.java
  100. +1 −1 src/main/org/openscience/cdk/tools/ProteinBuilderTool.java
  101. +34 −34 src/main/org/openscience/cdk/tools/SaturationChecker.java
  102. +2 −2 src/main/org/openscience/cdk/validate/DictionaryValidator.java
View
14 src/main/org/openscience/cdk/atomtype/MM2AtomTypeMatcher.java
@@ -127,7 +127,7 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atomIn
if (oRingSize != null) {
atomRingSize = (Integer) oRingSize;
}
- logger.debug(" Symbol:" + atom.getSymbol() +" HoseCode>" + atomSphericalMatcher + " ");
+ logger.debug(" Symbol:" , atom.getSymbol() ," HoseCode>" , atomSphericalMatcher , " ");
if (atom instanceof IPseudoAtom) {
return factory.getAtomTypes("DU")[0];
@@ -139,10 +139,10 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atomIn
Matcher mat1=null;
IBond.Order tmpMaxBondOrder = IBond.Order.SINGLE;
maxBondOrder = atomContainer.getMaximumBondOrder(atom);
- logger.debug("Atom maxBond"+maxBondOrder+" ChemicalGroupConstant "+atomChemicalGroupConstant);
+ logger.debug("Atom maxBond",maxBondOrder," ChemicalGroupConstant ",atomChemicalGroupConstant);
for (int j = 0; j < atomTypeIds.length; j++){
tmpMaxBondOrder = factory.getAtomType(atomTypeIds[j]).getMaxBondOrder();
- logger.debug(j + "ATOM TYPE "+ tmpMaxBondOrder + " " +getSphericalMatcher(atomTypeIds[j]));
+ logger.debug(j , "ATOM TYPE ", tmpMaxBondOrder , " " ,getSphericalMatcher(atomTypeIds[j]));
p1 =Pattern.compile(getSphericalMatcher(atomTypeIds[j]));
mat1 = p1.matcher(atomSphericalMatcher);
if (mat1.matches()) {
@@ -291,17 +291,17 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atomIn
}
}
atomTypeFlag = true;
- logger.debug(" MATCH AtomTypeID:"+j+ " " + ID);
+ logger.debug(" MATCH AtomTypeID:",j, " " , ID);
break;
}//IF
}//for end
if (atomTypeFlag) {
atomTypeFlag = false;
- logger.debug("ID in factory true:"+ID);
+ logger.debug("ID in factory true:",ID);
return factory.getAtomType(ID);
} else {
- logger.debug("NoSuchAtomTypeException: Atom is unkown with Symbol:" + atom.getSymbol() + " does not MATCH AtomType. HoseCode:" + atomSphericalMatcher);
- logger.debug("ID in factory false:"+ID);
+ logger.debug("NoSuchAtomTypeException: Atom is unkown with Symbol:" , atom.getSymbol() , " does not MATCH AtomType. HoseCode:" , atomSphericalMatcher);
+ logger.debug("ID in factory false:",ID);
return factory.getAtomType("DU");
}
}
View
8 src/main/org/openscience/cdk/atomtype/MMFF94AtomTypeMatcher.java
@@ -121,8 +121,8 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atomIn
org.openscience.cdk.Atom atom = (org.openscience.cdk.Atom)atomInterface;
//logger.debug("****** Configure MMFF94 AtomType via findMatching ******");
- //logger.debug(" Symbol:" + atom.getSymbol() +" HoseCode>" + atom.getSphericalMatcher() + " ");
- logger.debug(" Symbol:" + atom.getSymbol() +" HoseCode>" + atom.getProperty(CDKConstants.SPHERICAL_MATCHER) + " ");
+ //logger.debug(" Symbol:" , atom.getSymbol() ," HoseCode>" , atom.getSphericalMatcher() , " ");
+ logger.debug(" Symbol:" , atom.getSymbol() ," HoseCode>" , atom.getProperty(CDKConstants.SPHERICAL_MATCHER) , " ");
//System.out.print("IN MMFF94AtomTypeMatcher Symbol:" + atom.getSymbol() +" HoseCode>" + atom.getProperty(CDKConstants.SPHERICAL_MATCHER) + " ");
if (atom instanceof IPseudoAtom) {
@@ -139,7 +139,7 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atomIn
for (int j = 0; j < atomTypeIds.length; j++){
tmpMaxBondOrder = factory.getAtomType(atomTypeIds[j]).getMaxBondOrder();
String atomSphericalMatcher = (String)factory.getAtomType(atomTypeIds[j]).getProperty(CDKConstants.SPHERICAL_MATCHER);
- logger.debug(j + " ATOM TYPE "+ tmpMaxBondOrder + " " +atomSphericalMatcher);
+ logger.debug(j , " ATOM TYPE ", tmpMaxBondOrder , " " ,atomSphericalMatcher);
p1 =Pattern.compile(atomSphericalMatcher);
mat1 = p1.matcher((String)atom.getProperty(CDKConstants.SPHERICAL_MATCHER));
if (mat1.matches()) {
@@ -330,7 +330,7 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atomIn
}
atomTypeFlag = true;
- logger.debug(" MATCH AtomTypeID:"+j+ " " + ID);
+ logger.debug(" MATCH AtomTypeID:",j, " " , ID);
break;
}//IF
}//for end
View
4 src/main/org/openscience/cdk/charges/GasteigerMarsiliPartialCharges.java
@@ -176,7 +176,7 @@ public IAtomContainer assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer a
q_old[j] = q;
gasteigerFactors[STEP_SIZE * j + j + 4] = gasteigerFactors[STEP_SIZE * j + j + 2] * q * q + gasteigerFactors[STEP_SIZE * j + j + 1] * q + gasteigerFactors[STEP_SIZE * j + j];
-// logger.debug("g4: "+gasteigerFactors[STEP_SIZE * j + j + 4]);
+// logger.debug("g4: ",gasteigerFactors[STEP_SIZE * j + j + 4]);
}
if(!isDifferent)/* automatically break the maximum iterations*/
break out;
@@ -204,7 +204,7 @@ public IAtomContainer assignGasteigerMarsiliSigmaPartialCharges(IAtomContainer a
}
q = (gasteigerFactors[STEP_SIZE * atom1 + atom1 + 4] - gasteigerFactors[STEP_SIZE * atom2 + atom2 + 4]) / deoc;
-// logger.debug("qq: "+q);
+// logger.debug("qq: ",q);
gasteigerFactors[STEP_SIZE * atom1 + atom1 + 5] -= (q*alpha);
gasteigerFactors[STEP_SIZE * atom2 + atom2 + 5] += (q*alpha);
}
View
20 src/main/org/openscience/cdk/charges/GasteigerPEPEPartialCharges.java
@@ -290,7 +290,7 @@ public IAtomContainer assignGasteigerPiPartialCharges(IAtomContainer ac, boolean
double[] Wt = new double[iSet.getAtomContainerCount()-1];
for(int i = 1; i < iSet.getAtomContainerCount() ; i++){
Wt[i-1]= getTopologicalFactors(iSet.getAtomContainer(i),ac);
- logger.debug(", W:"+Wt[i-1]);
+ logger.debug(", W:",Wt[i-1]);
try {
acCloned = (IAtomContainer)iSet.getAtomContainer(i).clone();
@@ -326,11 +326,11 @@ public IAtomContainer assignGasteigerPiPartialCharges(IAtomContainer ac, boolean
double q1 = gasteigerFactors[k][STEP_SIZE * j + j + 5];
electronegativity[count] = gasteigerFactors[k][STEP_SIZE * j + j + 2] * q1 * q1 + gasteigerFactors[k][STEP_SIZE * j + j + 1] * q1 + gasteigerFactors[k][STEP_SIZE * j + j];
- logger.debug("e:"+electronegativity[count] +",q1: "+q1+", c:"+gasteigerFactors[k][STEP_SIZE * j + j + 2] +", b:"+gasteigerFactors[k][STEP_SIZE * j + j + 1] + ", a:"+gasteigerFactors[k][STEP_SIZE * j + j]);
+ logger.debug("e:",electronegativity[count] ,",q1: ",q1,", c:",gasteigerFactors[k][STEP_SIZE * j + j + 2] ,", b:",gasteigerFactors[k][STEP_SIZE * j + j + 1] , ", a:",gasteigerFactors[k][STEP_SIZE * j + j]);
count++;
}
}
- logger.debug("Atom1:"+atom1+",Atom2:"+atom2);
+ logger.debug("Atom1:",atom1,",Atom2:",atom2);
/*diferency of electronegativity 1 lower*/
double max1 = Math.max(electronegativity[0], electronegativity[1]);
double min1 = Math.min(electronegativity[0], electronegativity[1]);
@@ -341,20 +341,20 @@ public IAtomContainer assignGasteigerPiPartialCharges(IAtomContainer ac, boolean
DX = gasteigerFactors[k][STEP_SIZE * atom2 + atom2 + 3];
double Dq = (max1-min1)/DX;
- logger.debug("Dq : "+Dq+ " = ("+ max1+"-"+min1+")/"+DX);
+ logger.debug("Dq : ",Dq, " = (", max1,"-",min1,")/",DX);
double epN1 = getElectrostaticPotentialN(iac,atom1,gasteigerFactors[k]);
double epN2 = getElectrostaticPotentialN(iac,atom2,gasteigerFactors[k]);
double SumQN = Math.abs(epN1 - epN2);
- logger.debug("sum("+SumQN+") = ("+epN1+") - ("+epN2+")");
+ logger.debug("sum(",SumQN,") = (",epN1,") - (",epN2,")");
/* electronic weight*/
double WE = Dq + fE*SumQN;
- logger.debug("WE : "+WE+" = Dq("+Dq+")+fE("+fE+")*SumQN("+SumQN);
+ logger.debug("WE : ",WE," = Dq(",Dq,")+fE(",fE,")*SumQN(",SumQN);
int iTE = iter+1;
/* total topological*/
double W = WE*Wt[k-1]*fS/(iTE);
- logger.debug("W : "+W+" = WE("+WE+")*Wt("+Wt[k-1]+")*fS("+fS+")/iter("+iTE+"), atoms: "+atom1+", "+atom2);
+ logger.debug("W : ",W," = WE(",WE,")*Wt(",Wt[k-1],")*fS(",fS,")/iter(",iTE,"), atoms: ",atom1,", ",atom2);
/*iac == new structure, ac == old structure*/
/* atom1 */
@@ -390,7 +390,7 @@ public IAtomContainer assignGasteigerPiPartialCharges(IAtomContainer ac, boolean
double charge = ac.getAtom(i).getCharge();
double chargeT = 0.0;
chargeT = charge + gasteigerFactors[k][STEP_SIZE * i + i + 5];
- logger.debug("i<|"+ac.getAtom(i).getSymbol()+", "+chargeT+"=c:" +charge + "+g: "+gasteigerFactors[k][STEP_SIZE * i + i + 5]);
+ logger.debug("i<|",ac.getAtom(i).getSymbol(),", ",chargeT,"=c:" ,charge , "+g: ",gasteigerFactors[k][STEP_SIZE * i + i + 5]);
ac.getAtom(i).setCharge(chargeT);
}
}
@@ -582,7 +582,7 @@ private double getElectrostaticPotentialN(IAtomContainer ac, int atom1, double[]
covalentradius = type.getCovalentRadius();
double charge = ds[STEP_SIZE * atom1 + atom1 + 5];
- logger.debug("sum_("+sum+") = CFC("+CoulombForceConstant+")*charge("+charge+"/ret("+covalentradius);
+ logger.debug("sum_(",sum,") = CFC(",CoulombForceConstant,")*charge(",charge,"/ret(",covalentradius);
sum += CoulombForceConstant * charge / (covalentradius * covalentradius);
}
} catch (CDKException e) {
@@ -645,7 +645,7 @@ private double getTopologicalFactors(IAtomContainer atomContainer,IAtomContainer
} catch (CDKException e) {
e.printStackTrace();
}
- logger.debug("return "+fQ*fB*fPlus*fA+"= sp:"+fQ+", dc:"+fB+", fPlus:"+fPlus+", fA:"+fA);
+ logger.debug("return ",fQ*fB*fPlus*fA,"= sp:",fQ,", dc:",fB,", fPlus:",fPlus,", fA:",fA);
return fQ*fB*fPlus*fA;
}
View
10 src/main/org/openscience/cdk/charges/InductivePartialCharges.java
@@ -105,7 +105,7 @@ public IAtomContainer assignInductivePartialCharges(IAtomContainer ac) throws Ex
double[] startEE = getPaulingElectronegativities(ac, true);
for (int e = 0; e < atoms.length; e++) {
ElEn[e] = startEE[e];
- //logger.debug("INDU: initial EE "+startEE[e]);
+ //logger.debug("INDU: initial EE ",startEE[e]);
}
//double tmp1 = 0;
//double tmp2 = 0;
@@ -120,7 +120,7 @@ public IAtomContainer assignInductivePartialCharges(IAtomContainer ac) throws Ex
}
//tmp1 = pCh[a + (s * atoms.length)];
//tmp2 = ElEn[a + (s * atoms.length)];
- //logger.debug("DONE step " + s + ", atom " + atoms[a].getSymbol() + ", ch " + tmp1 + ", ee " + tmp2);
+ //logger.debug("DONE step " , s , ", atom " , atoms[a].getSymbol() , ", ch " , tmp1 , ", ee " , tmp2);
}
}
return ac;
@@ -295,7 +295,7 @@ private double getAtomicChargeIncrement(IAtomContainer ac, int atomPosition, dou
double incrementedCharge = 0;
double radiusTarget = 0;
target = ac.getAtom(atomPosition);
- //logger.debug("ATOM "+target.getSymbol()+" AT POSITION "+atomPosition);
+ //logger.debug("ATOM ",target.getSymbol()," AT POSITION ",atomPosition);
allAtoms = AtomContainerManipulator.getAtomArray(ac);
double tmp = 0;
double radius = 0;
@@ -334,11 +334,11 @@ private double getAtomicChargeIncrement(IAtomContainer ac, int atomPosition, dou
tmp = tmp / (calculateSquaredDistanceBetweenTwoAtoms(target, allAtoms[a]));
incrementedCharge += tmp;
//if(actualStep==1)
- //logger.debug("INDU: particular atom "+symbol+ ", radii: "+ radius+ " - " + radiusTarget+", dist: "+calculateSquaredDistanceBetweenTwoAtoms(target, allAtoms[a]));
+ //logger.debug("INDU: particular atom ",symbol, ", radii: ", radius, " - " , radiusTarget,", dist: ",calculateSquaredDistanceBetweenTwoAtoms(target, allAtoms[a]));
}
}
incrementedCharge = 0.172 * incrementedCharge;
- //logger.debug("Increment: " +incrementedCharge);
+ //logger.debug("Increment: " ,incrementedCharge);
return incrementedCharge;
}
View
4 src/main/org/openscience/cdk/charges/MMFF94PartialCharges.java
@@ -91,7 +91,7 @@ public IAtomContainer assignMMFF94PartialCharges(IAtomContainer ac) throws Excep
Object dataNeigh = null;
java.util.Iterator<IAtom> atoms = ac.atoms().iterator();
while(atoms.hasNext()) {
- //logger.debug("ATOM "+i+ " " +atoms[i].getSymbol());
+ //logger.debug("ATOM ",i, " " ,atoms[i].getSymbol());
thisAtom = atoms.next();
data = parameterSet.get("data"+thisAtom.getAtomTypeName());
neighboors = ac.getConnectedAtomsList(thisAtom);
@@ -123,7 +123,7 @@ public IAtomContainer assignMMFF94PartialCharges(IAtomContainer ac) throws Excep
charge += sumOfFormalCharges * theta;
charge += sumOfBondIncrements;
thisAtom.setProperty("MMFF94charge", charge);
- //logger.debug( "CHARGE :"+thisAtom.getProperty("MMFF94charge") );
+ //logger.debug( "CHARGE :",thisAtom.getProperty("MMFF94charge") );
}
return ac;
}
View
2 src/main/org/openscience/cdk/config/AtomTypeFactory.java
@@ -318,7 +318,7 @@ public IAtomType getAtomType(String identifier) throws NoSuchAtomTypeException
}
IAtomType[] atomTypes = (IAtomType[])atomList.toArray(new IAtomType[atomList.size()]);
if (atomTypes.length > 0)
- logger.debug("Atomtype for symbol ", symbol, " has this number of types: " + atomTypes.length);
+ logger.debug("Atomtype for symbol ", symbol, " has this number of types: " , atomTypes.length);
else
logger.debug("No atomtype for symbol ", symbol);
return atomTypes;
View
2 src/main/org/openscience/cdk/debug/DebugAdductFormula.java
@@ -124,7 +124,7 @@ public void removeMolecularFormula(int position) {
}
public int size() {
- logger.debug("Getting the size of this adduct: " + super.size());
+ logger.debug("Getting the size of this adduct: " , super.size());
return super.size();
}
View
38 src/main/org/openscience/cdk/debug/DebugAminoAcid.java
@@ -75,7 +75,7 @@ public void setAtoms(IAtom[] atoms) {
// }
public void setAtom(int number, IAtom atom) {
- logger.debug("Setting atom at: pos=" + number, " atom=" + atom);
+ logger.debug("Setting atom at: pos=" , number, " atom=" , atom);
super.setAtom(number, atom);
}
@@ -100,7 +100,7 @@ public ISingleElectron getSingleElectron(int number) {
}
// public void setElectronContainer(int number, IElectronContainer electronContainer) {
-// logger.debug("Setting electron container at: pos=" + number, " electron container=" +electronContainer);
+// logger.debug("Setting electron container at: pos=" , number, " electron container=" ,electronContainer);
// super.setElectronContainer(number, electronContainer);
// }
@@ -155,7 +155,7 @@ public int getAtomNumber(IAtom atom) {
}
public int getBondNumber(IAtom atom1, IAtom atom2) {
- logger.debug("Getting bond number: atom1=" + atom1, " atom2=" + atom2);
+ logger.debug("Getting bond number: atom1=" , atom1, " atom2=" , atom2);
return super.getBondNumber(atom1, atom2);
}
@@ -180,7 +180,7 @@ public IElectronContainer getElectronContainer(int number) {
}
public IBond getBond(IAtom atom1, IAtom atom2) {
- logger.debug("Getting bond for atoms: atom1=" + atom1, " atom2=" + atom2);
+ logger.debug("Getting bond for atoms: atom1=" , atom1, " atom2=" , atom2);
return super.getBond(atom1, atom2);
}
@@ -231,12 +231,12 @@ public List getConnectedBondsList(IAtom atom) {
}
public List getConnectedLonePairsList(IAtom atom) {
- logger.debug("Getting lone pairs at atom: atom=" + atom, " lone pairs=" + super.getConnectedLonePairsCount(atom));
+ logger.debug("Getting lone pairs at atom: atom=" , atom, " lone pairs=" , super.getConnectedLonePairsCount(atom));
return super.getConnectedLonePairsList(atom);
}
public List getConnectedSingleElectronsList(IAtom atom) {
- logger.debug("Getting single electrons at atom: atom=" + atom, " single electrons=" + super.getConnectedSingleElectronsCount(atom));
+ logger.debug("Getting single electrons at atom: atom=" , atom, " single electrons=" , super.getConnectedSingleElectronsCount(atom));
return super.getConnectedSingleElectronsList(atom);
}
@@ -341,37 +341,37 @@ public void removeAtom(IAtom atom) {
}
public IBond removeBond(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeBond(pos);
}
public IBond removeBond(IAtom atom1, IAtom atom2) {
- logger.debug("Removing bond: atom1=" + atom1 + " atom2=" + atom2);
+ logger.debug("Removing bond: atom1=" , atom1 , " atom2=" , atom2);
return super.removeBond(atom1, atom2);
}
public void removeBond(IBond bond) {
- logger.debug("Removing bond=" + bond);
+ logger.debug("Removing bond=" , bond);
super.removeBond(bond);
}
public ILonePair removeLonePair(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeLonePair(pos);
}
public void removeLonePair(ILonePair ec) {
- logger.debug("Removing bond=" + ec);
+ logger.debug("Removing bond=" , ec);
super.removeLonePair(ec);
}
public ISingleElectron removeSingleElectron(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeSingleElectron(pos);
}
public void removeSingleElectron(ISingleElectron ec) {
- logger.debug("Removing bond=" + ec);
+ logger.debug("Removing bond=" , ec);
super.removeSingleElectron(ec);
}
@@ -397,12 +397,12 @@ public void removeAllBonds() {
public void addBond(int atom1, int atom2, IBond.Order order,
IBond.Stereo stereo) {
- logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo);
+ logger.debug("Adding bond: atom1=" , atom1 , " atom2=" , atom2, " order=" , order , " stereo=" , stereo);
super.addBond(atom1, atom2, order, stereo);
}
public void addBond(int atom1, int atom2, IBond.Order order) {
- logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order);
+ logger.debug("Adding bond: atom1=" , atom1 , " atom2=" , atom2, " order=" , order);
super.addBond(atom1, atom2, order);
}
@@ -467,7 +467,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -477,7 +477,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -497,12 +497,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
12 src/main/org/openscience/cdk/debug/DebugAtom.java
@@ -61,12 +61,12 @@ public DebugAtom(String symbol) {
public DebugAtom(String symbol, Point2d point2d) {
super(symbol, point2d);
- logger.debug("Instantiated a DebugAtom: symbol= ", symbol + " point2d=" + point2d);
+ logger.debug("Instantiated a DebugAtom: symbol= ", symbol , " point2d=" , point2d);
}
public DebugAtom(String symbol, Point3d point3d) {
super(symbol, point3d);
- logger.debug("Instantiated a DebugAtom: symbol= ", symbol + " point3d=" + point3d);
+ logger.debug("Instantiated a DebugAtom: symbol= ", symbol , " point3d=" , point3d);
}
public DebugAtom(IElement element) {
@@ -312,7 +312,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -322,7 +322,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -342,12 +342,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
40 src/main/org/openscience/cdk/debug/DebugAtomContainer.java
@@ -86,7 +86,7 @@ public void setAtoms(IAtom[] atoms) {
// }
public void setAtom(int number, IAtom atom) {
- logger.debug("Setting atom at: pos=" + number, " atom=" + atom);
+ logger.debug("Setting atom at: pos=" , number, " atom=" , atom);
super.setAtom(number, atom);
}
@@ -111,7 +111,7 @@ public ISingleElectron getSingleElectron(int number) {
}
// public void setElectronContainer(int number, IElectronContainer electronContainer) {
-// logger.debug("Setting electron container at: pos=" + number, " electron container=" +electronContainer);
+// logger.debug("Setting electron container at: pos=" , number, " electron container=" ,electronContainer);
// super.setElectronContainer(number, electronContainer);
// }
@@ -166,7 +166,7 @@ public int getAtomNumber(IAtom atom) {
}
public int getBondNumber(IAtom atom1, IAtom atom2) {
- logger.debug("Getting bond number: atom1=" + atom1, " atom2=" + atom2);
+ logger.debug("Getting bond number: atom1=" , atom1, " atom2=" , atom2);
return super.getBondNumber(atom1, atom2);
}
@@ -191,7 +191,7 @@ public IElectronContainer getElectronContainer(int number) {
}
public IBond getBond(IAtom atom1, IAtom atom2) {
- logger.debug("Getting bond for atoms: atom1=" + atom1, " atom2=" + atom2);
+ logger.debug("Getting bond for atoms: atom1=" , atom1, " atom2=" , atom2);
return super.getBond(atom1, atom2);
}
@@ -242,12 +242,12 @@ public List getConnectedBondsList(IAtom atom) {
}
public List getConnectedLonePairsList(IAtom atom) {
- logger.debug("Getting lone pairs at atom: atom=" + atom, " lone pairs=" + super.getConnectedLonePairsCount(atom));
+ logger.debug("Getting lone pairs at atom: atom=" , atom, " lone pairs=" , super.getConnectedLonePairsCount(atom));
return super.getConnectedLonePairsList(atom);
}
public List getConnectedSingleElectronsList(IAtom atom) {
- logger.debug("Getting single electrons at atom: atom=" + atom, " single electrons=" + super.getConnectedSingleElectronsCount(atom));
+ logger.debug("Getting single electrons at atom: atom=" , atom, " single electrons=" , super.getConnectedSingleElectronsCount(atom));
return super.getConnectedSingleElectronsList(atom);
}
@@ -352,37 +352,37 @@ public void removeAtom(IAtom atom) {
}
public IBond removeBond(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeBond(pos);
}
public IBond removeBond(IAtom atom1, IAtom atom2) {
- logger.debug("Removing bond: atom1=" + atom1 + " atom2=" + atom2);
+ logger.debug("Removing bond: atom1=" , atom1 , " atom2=" , atom2);
return super.removeBond(atom1, atom2);
}
public void removeBond(IBond bond) {
- logger.debug("Removing bond=" + bond);
+ logger.debug("Removing bond=" , bond);
super.removeBond(bond);
}
public ILonePair removeLonePair(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeLonePair(pos);
}
public void removeLonePair(ILonePair ec) {
- logger.debug("Removing bond=" + ec);
+ logger.debug("Removing bond=" , ec);
super.removeLonePair(ec);
}
public ISingleElectron removeSingleElectron(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeSingleElectron(pos);
}
public void removeSingleElectron(ISingleElectron ec) {
- logger.debug("Removing bond=" + ec);
+ logger.debug("Removing bond=" , ec);
super.removeSingleElectron(ec);
}
@@ -408,12 +408,12 @@ public void removeAllBonds() {
public void addBond(int atom1, int atom2, IBond.Order order,
IBond.Stereo stereo) {
- logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo);
+ logger.debug("Adding bond: atom1=" , atom1 , " atom2=" , atom2, " order=" , order , " stereo=" , stereo);
super.addBond(atom1, atom2, order, stereo);
}
public void addBond(int atom1, int atom2, IBond.Order order) {
- logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order);
+ logger.debug("Adding bond: atom1=" , atom1 , " atom2=" , atom2, " order=" , order);
super.addBond(atom1, atom2, order);
}
@@ -478,7 +478,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -488,7 +488,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -508,12 +508,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
@@ -537,7 +537,7 @@ public Object clone() throws CloneNotSupportedException {
try {
clone = super.clone();
} catch (Exception exception) {
- logger.error("Could not clone DebugAtomContainer: " + exception.getMessage(), exception);
+ logger.error("Could not clone DebugAtomContainer: " , exception.getMessage(), exception);
logger.debug(exception);
}
return clone;
View
14 src/main/org/openscience/cdk/debug/DebugAtomContainerSet.java
@@ -72,7 +72,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -82,7 +82,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -102,12 +102,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
@@ -167,12 +167,12 @@ public void replaceAtomContainer(int position, IAtomContainer container) {
}
public boolean setMultiplier(IAtomContainer container, Double multiplier) {
- logger.debug("Setting multiplier for atomcontainer: ", container, ""+multiplier);
+ logger.debug("Setting multiplier for atomcontainer: ", container, "",multiplier);
return super.setMultiplier(container, multiplier);
}
public void setMultiplier(int position, Double multiplier) {
- logger.debug("Setting multiplier for atomcontainer at pos: ", ""+position, ""+multiplier);
+ logger.debug("Setting multiplier for atomcontainer at pos: ", "",position, "",multiplier);
super.setMultiplier(position, multiplier);
}
@@ -187,7 +187,7 @@ public boolean setMultipliers(Double[] newMultipliers) {
}
public void addAtomContainer(IAtomContainer atomContainer, double multiplier) {
- logger.debug("Adding atom container with multiplier: ", ""+multiplier, atomContainer);
+ logger.debug("Adding atom container with multiplier: ", "",multiplier, atomContainer);
super.addAtomContainer(atomContainer, multiplier);
}
View
10 src/main/org/openscience/cdk/debug/DebugAtomType.java
@@ -54,7 +54,7 @@ public DebugAtomType(String elementSymbol) {
public DebugAtomType(String identifier, String elementSymbol) {
super(elementSymbol); // cannot use super(identifier, elementSymbol); that gives a NPE
- logger.debug("Instantiated a DebugAtomType: identifier= " + identifier + " symbol= ", elementSymbol);
+ logger.debug("Instantiated a DebugAtomType: identifier= " , identifier , " symbol= ", elementSymbol);
this.setSymbol(elementSymbol);
this.setAtomTypeName(identifier);
}
@@ -110,7 +110,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -120,7 +120,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -140,12 +140,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
40 src/main/org/openscience/cdk/debug/DebugBioPolymer.java
@@ -78,7 +78,7 @@ public void setAtoms(IAtom[] atoms) {
// }
public void setAtom(int number, IAtom atom) {
- logger.debug("Setting atom at: pos=" + number, " atom=" + atom);
+ logger.debug("Setting atom at: pos=" , number, " atom=" , atom);
super.setAtom(number, atom);
}
@@ -103,7 +103,7 @@ public ISingleElectron getSingleElectron(int number) {
}
// public void setElectronContainer(int number, IElectronContainer electronContainer) {
-// logger.debug("Setting electron container at: pos=" + number, " electron container=" +electronContainer);
+// logger.debug("Setting electron container at: pos=" , number, " electron container=" ,electronContainer);
// super.setElectronContainer(number, electronContainer);
// }
@@ -158,7 +158,7 @@ public int getAtomNumber(IAtom atom) {
}
public int getBondNumber(IAtom atom1, IAtom atom2) {
- logger.debug("Getting bond number: atom1=" + atom1, " atom2=" + atom2);
+ logger.debug("Getting bond number: atom1=" , atom1, " atom2=" , atom2);
return super.getBondNumber(atom1, atom2);
}
@@ -183,7 +183,7 @@ public IElectronContainer getElectronContainer(int number) {
}
public IBond getBond(IAtom atom1, IAtom atom2) {
- logger.debug("Getting bond for atoms: atom1=" + atom1, " atom2=" + atom2);
+ logger.debug("Getting bond for atoms: atom1=" , atom1, " atom2=" , atom2);
return super.getBond(atom1, atom2);
}
@@ -234,12 +234,12 @@ public List getConnectedBondsList(IAtom atom) {
}
public List getConnectedLonePairsList(IAtom atom) {
- logger.debug("Getting lone pairs at atom: atom=" + atom, " lone pairs=" + super.getConnectedLonePairsCount(atom));
+ logger.debug("Getting lone pairs at atom: atom=" , atom, " lone pairs=" , super.getConnectedLonePairsCount(atom));
return super.getConnectedLonePairsList(atom);
}
public List getConnectedSingleElectronsList(IAtom atom) {
- logger.debug("Getting single electrons at atom: atom=" + atom, " single electrons=" + super.getConnectedSingleElectronsCount(atom));
+ logger.debug("Getting single electrons at atom: atom=" , atom, " single electrons=" , super.getConnectedSingleElectronsCount(atom));
return super.getConnectedSingleElectronsList(atom);
}
@@ -344,37 +344,37 @@ public void removeAtom(IAtom atom) {
}
public IBond removeBond(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeBond(pos);
}
public IBond removeBond(IAtom atom1, IAtom atom2) {
- logger.debug("Removing bond: atom1=" + atom1 + " atom2=" + atom2);
+ logger.debug("Removing bond: atom1=" , atom1 , " atom2=" , atom2);
return super.removeBond(atom1, atom2);
}
public void removeBond(IBond bond) {
- logger.debug("Removing bond=" + bond);
+ logger.debug("Removing bond=" , bond);
super.removeBond(bond);
}
public ILonePair removeLonePair(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeLonePair(pos);
}
public void removeLonePair(ILonePair ec) {
- logger.debug("Removing bond=" + ec);
+ logger.debug("Removing bond=" , ec);
super.removeLonePair(ec);
}
public ISingleElectron removeSingleElectron(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeSingleElectron(pos);
}
public void removeSingleElectron(ISingleElectron ec) {
- logger.debug("Removing bond=" + ec);
+ logger.debug("Removing bond=" , ec);
super.removeSingleElectron(ec);
}
@@ -400,12 +400,12 @@ public void removeAllBonds() {
public void addBond(int atom1, int atom2, IBond.Order order,
IBond.Stereo stereo) {
- logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo);
+ logger.debug("Adding bond: atom1=" , atom1 , " atom2=" , atom2, " order=" , order , " stereo=" , stereo);
super.addBond(atom1, atom2, order, stereo);
}
public void addBond(int atom1, int atom2, IBond.Order order) {
- logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order);
+ logger.debug("Adding bond: atom1=" , atom1 , " atom2=" , atom2, " order=" , order);
super.addBond(atom1, atom2, order);
}
@@ -470,7 +470,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -480,7 +480,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -500,12 +500,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
@@ -529,7 +529,7 @@ public Object clone() throws CloneNotSupportedException {
try {
clone = super.clone();
} catch (Exception exception) {
- logger.error("Could not clone DebugAtom: " + exception.getMessage(), exception);
+ logger.error("Could not clone DebugAtom: " , exception.getMessage(), exception);
logger.debug(exception);
}
return clone;
View
8 src/main/org/openscience/cdk/debug/DebugBond.java
@@ -110,7 +110,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -120,7 +120,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -140,12 +140,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
10 src/main/org/openscience/cdk/debug/DebugChemFile.java
@@ -76,7 +76,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -86,7 +86,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -106,12 +106,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
@@ -135,7 +135,7 @@ public Object clone() throws CloneNotSupportedException {
try {
clone = super.clone();
} catch (Exception exception) {
- logger.error("Could not clone DebugAtom: " + exception.getMessage(), exception);
+ logger.error("Could not clone DebugAtom: " , exception.getMessage(), exception);
logger.debug(exception);
}
return clone;
View
8 src/main/org/openscience/cdk/debug/DebugChemModel.java
@@ -75,7 +75,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -85,7 +85,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -105,12 +105,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
8 src/main/org/openscience/cdk/debug/DebugChemObject.java
@@ -81,7 +81,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -91,7 +91,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -111,12 +111,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
8 src/main/org/openscience/cdk/debug/DebugChemSequence.java
@@ -72,7 +72,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -82,7 +82,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -102,12 +102,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
38 src/main/org/openscience/cdk/debug/DebugCrystal.java
@@ -85,7 +85,7 @@ public void setAtoms(IAtom[] atoms) {
// }
public void setAtom(int number, IAtom atom) {
- logger.debug("Setting atom at: pos=" + number, " atom=" + atom);
+ logger.debug("Setting atom at: pos=" , number, " atom=" , atom);
super.setAtom(number, atom);
}
@@ -110,7 +110,7 @@ public ISingleElectron getSingleElectron(int number) {
}
// public void setElectronContainer(int number, IElectronContainer electronContainer) {
-// logger.debug("Setting electron container at: pos=" + number, " electron container=" +electronContainer);
+// logger.debug("Setting electron container at: pos=" , number, " electron container=" ,electronContainer);
// super.setElectronContainer(number, electronContainer);
// }
@@ -165,7 +165,7 @@ public int getAtomNumber(IAtom atom) {
}
public int getBondNumber(IAtom atom1, IAtom atom2) {
- logger.debug("Getting bond number: atom1=" + atom1, " atom2=" + atom2);
+ logger.debug("Getting bond number: atom1=" , atom1, " atom2=" , atom2);
return super.getBondNumber(atom1, atom2);
}
@@ -190,7 +190,7 @@ public IElectronContainer getElectronContainer(int number) {
}
public IBond getBond(IAtom atom1, IAtom atom2) {
- logger.debug("Getting bond for atoms: atom1=" + atom1, " atom2=" + atom2);
+ logger.debug("Getting bond for atoms: atom1=" , atom1, " atom2=" , atom2);
return super.getBond(atom1, atom2);
}
@@ -241,12 +241,12 @@ public List getConnectedBondsList(IAtom atom) {
}
public List getConnectedLonePairsList(IAtom atom) {
- logger.debug("Getting lone pairs at atom: atom=" + atom, " lone pairs=" + super.getConnectedLonePairsCount(atom));
+ logger.debug("Getting lone pairs at atom: atom=" , atom, " lone pairs=" , super.getConnectedLonePairsCount(atom));
return super.getConnectedLonePairsList(atom);
}
public List getConnectedSingleElectronsList(IAtom atom) {
- logger.debug("Getting single electrons at atom: atom=" + atom, " single electrons=" + super.getConnectedSingleElectronsCount(atom));
+ logger.debug("Getting single electrons at atom: atom=" , atom, " single electrons=" , super.getConnectedSingleElectronsCount(atom));
return super.getConnectedSingleElectronsList(atom);
}
@@ -351,37 +351,37 @@ public void removeAtom(IAtom atom) {
}
public IBond removeBond(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeBond(pos);
}
public IBond removeBond(IAtom atom1, IAtom atom2) {
- logger.debug("Removing bond: atom1=" + atom1 + " atom2=" + atom2);
+ logger.debug("Removing bond: atom1=" , atom1 , " atom2=" , atom2);
return super.removeBond(atom1, atom2);
}
public void removeBond(IBond bond) {
- logger.debug("Removing bond=" + bond);
+ logger.debug("Removing bond=" , bond);
super.removeBond(bond);
}
public ILonePair removeLonePair(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeLonePair(pos);
}
public void removeLonePair(ILonePair ec) {
- logger.debug("Removing bond=" + ec);
+ logger.debug("Removing bond=" , ec);
super.removeLonePair(ec);
}
public ISingleElectron removeSingleElectron(int pos) {
- logger.debug("Removing bond at " + pos);
+ logger.debug("Removing bond at " , pos);
return super.removeSingleElectron(pos);
}
public void removeSingleElectron(ISingleElectron ec) {
- logger.debug("Removing bond=" + ec);
+ logger.debug("Removing bond=" , ec);
super.removeSingleElectron(ec);
}
@@ -407,12 +407,12 @@ public void removeAllBonds() {
public void addBond(int atom1, int atom2, IBond.Order order,
IBond.Stereo stereo) {
- logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order + " stereo=" + stereo);
+ logger.debug("Adding bond: atom1=" , atom1 , " atom2=" , atom2, " order=" , order , " stereo=" , stereo);
super.addBond(atom1, atom2, order, stereo);
}
public void addBond(int atom1, int atom2, IBond.Order order) {
- logger.debug("Adding bond: atom1=" + atom1 + " atom2=" + atom2, " order=" + order);
+ logger.debug("Adding bond: atom1=" , atom1 , " atom2=" , atom2, " order=" , order);
super.addBond(atom1, atom2, order);
}
@@ -477,7 +477,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -487,7 +487,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -507,12 +507,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
8 src/main/org/openscience/cdk/debug/DebugElectronContainer.java
@@ -81,7 +81,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -91,7 +91,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -111,12 +111,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
10 src/main/org/openscience/cdk/debug/DebugElement.java
@@ -57,7 +57,7 @@ public DebugElement(String symbol) {
public DebugElement(String symbol, int atomicNumber) {
super(symbol, atomicNumber);
- logger.debug("Instantiated a DebugElement: symbol= ", symbol + " atomic number= " + atomicNumber);
+ logger.debug("Instantiated a DebugElement: symbol= ", symbol , " atomic number= " , atomicNumber);
}
public DebugElement(IElement element) {
@@ -111,7 +111,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -121,7 +121,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -141,12 +141,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
36 src/main/org/openscience/cdk/debug/DebugFragmentAtom.java
@@ -66,7 +66,7 @@ public boolean isExpanded() {
}
public void setExpanded(boolean bool) {
- logger.debug("Setting the isExpanded state: " + bool);
+ logger.debug("Setting the isExpanded state: " , bool);
super.setExpanded(bool);
}
@@ -101,20 +101,20 @@ public Integer getImplicitHydrogenCount() {
}
public void setPoint2d(Point2d point2d) {
- logger.debug("Setting point2d: x=" + point2d.x +
- ", y=" + point2d.y);
+ logger.debug("Setting point2d: x=" , point2d.x ,
+ ", y=" , point2d.y);
super.setPoint2d(point2d);
}
public void setPoint3d(Point3d point3d) {
- logger.debug("Setting point3d: x=" + point3d.x +
- ", y=" + point3d.y, ", z=" + point3d.z);
+ logger.debug("Setting point3d: x=" , point3d.x ,
+ ", y=" , point3d.y, ", z=" , point3d.z);
super.setPoint3d(point3d);
}
public void setFractionalPoint3d(Point3d point3d) {
- logger.debug("Setting fractional point3d: x=" + point3d.x +
- ", y=" + point3d.y, ", z=" + point3d.z);
+ logger.debug("Setting fractional point3d: x=" , point3d.x ,
+ ", y=" , point3d.y, ", z=" , point3d.z);
super.setFractionalPoint3d(point3d);
}
@@ -128,8 +128,8 @@ public Point2d getPoint2d() {
if (point2d == null) {
logger.debug("Getting point2d: null");
} else {
- logger.debug("Getting point2d: x=" + point2d.x +
- ", y=" + point2d.y);
+ logger.debug("Getting point2d: x=" , point2d.x ,
+ ", y=" , point2d.y);
}
return point2d;
}
@@ -139,8 +139,8 @@ public Point3d getPoint3d() {
if (point3d == null) {
logger.debug("Getting point3d: null");
} else {
- logger.debug("Getting point3d: x=" + point3d.x +
- ", y=" + point3d.y, ", z=" + point3d.z);
+ logger.debug("Getting point3d: x=" , point3d.x ,
+ ", y=" , point3d.y, ", z=" , point3d.z);
}
return point3d;
}
@@ -150,8 +150,8 @@ public Point3d getFractionalPoint3d() {
if (point3d == null) {
logger.debug("Getting fractional point3d: null");
} else {
- logger.debug("Getting fractional point3d: x=" + point3d.x +
- ", y=" + point3d.y, ", z=" + point3d.z);
+ logger.debug("Getting fractional point3d: x=" , point3d.x ,
+ ", y=" , point3d.y, ", z=" , point3d.z);
}
return point3d;
}
@@ -318,7 +318,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -328,7 +328,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -348,12 +348,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
@@ -377,7 +377,7 @@ public Object clone() throws CloneNotSupportedException {
try {
clone = super.clone();
} catch (Exception exception) {
- logger.error("Could not clone DebugAtom: " + exception.getMessage(), exception);
+ logger.error("Could not clone DebugAtom: " , exception.getMessage(), exception);
logger.debug(exception);
}
return clone;
View
8 src/main/org/openscience/cdk/debug/DebugIsotope.java
@@ -119,7 +119,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -129,7 +129,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -149,12 +149,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
8 src/main/org/openscience/cdk/debug/DebugLonePair.java
@@ -107,7 +107,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -117,7 +117,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -137,12 +137,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "=" + flag_value);
+ logger.debug("Setting flag: ", flag_type , "=" , flag_value);
super.setFlag(flag_type, flag_value);
}
public boolean getFlag(int flag_type) {
- logger.debug("Setting flag: ", flag_type + "=" + super.getFlag(flag_type));
+ logger.debug("Setting flag: ", flag_type , "=" , super.getFlag(flag_type));
return super.getFlag(flag_type);
}
View
8 src/main/org/openscience/cdk/debug/DebugMapping.java
@@ -76,7 +76,7 @@ public void notifyChanged(IChemObjectChangeEvent evt) {
}
public void setProperty(Object description, Object property) {
- logger.debug("Setting property: ", description + "=" + property);
+ logger.debug("Setting property: ", description , "=" , property);
super.setProperty(description, property);
}
@@ -86,7 +86,7 @@ public void removeProperty(Object description) {
}
public Object getProperty(Object description) {
- logger.debug("Getting property: ", description + "=" + super.getProperty(description));
+ logger.debug("Getting property: ", description , "=" , super.getProperty(description));
return super.getProperty(description);
}
@@ -106,12 +106,12 @@ public void setID(String identifier) {
}
public void setFlag(int flag_type, boolean flag_value) {
- logger.debug("Setting flag: ", flag_type + "="