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Changing reaction center for some reactions

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commit a40d21096503e62c3b26732f883b88e5c764c1b2 1 parent 196eddb
miguelrojasch authored committed
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8 ...k.reaction/src/org/openscience/cdk/reaction/type/RadicalChargeSiteInitiationReaction.java
@@ -142,7 +142,9 @@ public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws
while (bondis.hasNext()) {
IBond bondi = bondis.next();
- if(bondi.getFlag(CDKConstants.REACTIVE_CENTER)&& bondi.getOrder() == IBond.Order.SINGLE){
+ if(bondi.getFlag(CDKConstants.REACTIVE_CENTER)
+// && bondi.getOrder() == IBond.Order.SINGLE
+ ){
IAtom atomj = bondi.getConnectedAtom(atomi);
if(atomj.getFlag(CDKConstants.REACTIVE_CENTER) && atomj.getFormalCharge() == 0){
@@ -214,7 +216,7 @@ private void setActiveCenters(IMolecule reactant) throws CDKException {
while (bondis.hasNext()) {
IBond bondi = bondis.next();
- if(bondi.getOrder() == IBond.Order.SINGLE){
+// if(bondi.getOrder() == IBond.Order.SINGLE){
IAtom atomj = bondi.getConnectedAtom(atomi);
if(atomj.getFormalCharge() == 0){
@@ -239,7 +241,7 @@ private void setActiveCenters(IMolecule reactant) throws CDKException {
}
}
}
- }
+// }
}
}
}
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8 ...cience.cdk.reaction/src/org/openscience/cdk/reaction/type/RadicalSiteHrGammaReaction.java
@@ -156,7 +156,8 @@ public IReactionSet initiate(IMoleculeSet reactants, IMoleculeSet agents) throws
Iterator<IAtom> atomis = reactant.atoms().iterator();
while(atomis.hasNext()){
IAtom atomi = atomis.next();
- if(atomi.getFlag(CDKConstants.REACTIVE_CENTER) && atomi.getSymbol().equals("C")
+ if(atomi.getFlag(CDKConstants.REACTIVE_CENTER)
+// && atomi.getSymbol().equals("C")
&& reactant.getConnectedSingleElectronsCount(atomi) == 1) {
hcg.getSpheres((Molecule) reactant, atomi, 4, true);
@@ -214,8 +215,9 @@ private void setActiveCenters(IMolecule reactant) throws CDKException {
Iterator<IAtom> atomis = reactant.atoms().iterator();
while(atomis.hasNext()){
IAtom atomi = atomis.next();
- if(atomi.getSymbol().equals("C")
- && reactant.getConnectedSingleElectronsCount(atomi) == 1) {
+ if(
+// atomi.getSymbol().equals("C")&&
+ reactant.getConnectedSingleElectronsCount(atomi) == 1) {
hcg.getSpheres((Molecule) reactant, atomi, 4, true);
Iterator<IAtom> atomls = hcg.getNodesInSphere(4).iterator();
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