/** * Helper to get an ordered list of R-group numbers for a certain IRGroupQuery. * @param RgroupQuery * @return an ordered list of R-group numbers in rgroupQuery. */ private List<Integer> sortRGroupNumbers () { List<Integer> rNumbers = new ArrayList<Integer>(); if (rGroupQuery!=null) { for (Iterator<Integer> itr = rGroupQuery.getRGroupDefinitions().keySet().iterator(); itr.hasNext(); ) { rNumbers.add(itr.next()); } Collections.sort(rNumbers); } return rNumbers; }
/** * Method to check whether a given atom is part of one of the substitutes. * @param atom */ public boolean isAtomPartOfSubstitute(IAtom atom) { if (rGroupQuery!=null && rGroupQuery.getRGroupDefinitions()!=null) { for (Iterator<Integer> itr = rGroupQuery.getRGroupDefinitions().keySet().iterator(); itr.hasNext(); ) { RGroupList rgpList =rGroupQuery.getRGroupDefinitions().get(itr.next()); if(rgpList!=null && rgpList.getRGroups()!=null) { for (RGroup rgrp: rgpList.getRGroups() ) { if(rgrp.getGroup().contains(atom)) { return true; } } } } } return false; }
List<Integer> rgrpToRemove=new ArrayList<Integer>(); if (rGroupQuery!=null){ Map<Integer,RGroupList> def = rGroupQuery.getRGroupDefinitions(); for(Iterator<Integer> itr= def.keySet().iterator();itr.hasNext();) { for (RGroup rgrp :rGroupQuery.getRGroupDefinitions().get(rgrpNum).getRGroups()) { atomCount+=rgrp.getGroup().getAtomCount(); rGroupQuery.getRGroupDefinitions().remove(rgrpNum);
Map<Integer,RGroupList> def = rGroupQuery.getRGroupDefinitions(); for(Iterator<Integer> itr= def.keySet().iterator();itr.hasNext();) { int rgrpNum=itr.next();
if (_existingRgroupLists!=null) { redoRgroupLists = new HashMap<Integer,RGroupList>(); for (Iterator<Integer> itr=rgrpHandler.getrGroupQuery().getRGroupDefinitions().keySet().iterator(); itr.hasNext();) { int rNum=itr.next(); redoRgroupLists.put(rNum, rgrpHandler.getrGroupQuery().getRGroupDefinitions().get(rNum)); for (Iterator<Integer> rnumItr= hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().keySet().iterator(); rnumItr.hasNext();) { for (RGroup rgrp: hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().get(rnumItr.next()).getRGroups()) { if(rgrp.equals(undoRGroup)) { redoRGroupApo= new HashMap <RGroup,Map<Integer,IAtom>>();
/** * See restores what was saved by makeHash(). */ public void restoreFromHash(Map<Integer,Map<Integer,Integer>> mash, IAtomContainerSet mset) { if(rGroupQuery!=null) { int rootHash = mash.get(-1).get(0); rGroupQuery.setRootStructure(findContainer(rootHash,mset)); Map<Integer,RGroupList> def = rGroupQuery.getRGroupDefinitions(); for (Iterator<Integer>rgpHashItr=mash.keySet().iterator(); rgpHashItr.hasNext();) { int rgpHash = rgpHashItr.next(); restore: for(Iterator<Integer> itr= def.keySet().iterator();itr.hasNext();) { int rgrpNum=itr.next(); List<RGroup> rgpList = def.get(rgrpNum).getRGroups(); for(RGroup rgp : rgpList) { if (rgp!=null && rgp.hashCode()==rgpHash) { rgp.setGroup(findContainer(mash.get(rgpHash).get(0),mset)); if (rgp.getGroup()!=null) { rgp.setFirstAttachmentPoint(findAtom(mash.get(rgpHash).get(1),rgp.getGroup())); rgp.setSecondAttachmentPoint(findAtom(mash.get(rgpHash).get(2),rgp.getGroup())); } break restore; } } } } } }
for(Iterator<Integer> rNums=redoRgroupLists.keySet().iterator(); rNums.hasNext();){ int rNum= rNums.next(); rgrpQ.getRGroupDefinitions().put(rNum, redoRgroupLists.get(rNum)); for (Iterator<Integer> rnumItr= hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().keySet().iterator(); rnumItr.hasNext();) { for (RGroup rgrp: hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().get(rnumItr.next()).getRGroups()) { if(rgrp.equals(redoRGroup)) { IAtom apo1=redoRGroupApo.get(redoRGroup).get(1);
private void constructPanel() { rNumbers= new ArrayList<Integer>(); for (Iterator<Integer> rnumItr=hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().keySet().iterator(); rnumItr.hasNext();) { rNumbers.add(rnumItr.next()); } Collections.sort(rNumbers); for(Integer r : rNumbers) { JPanel rgrpPanel = this.addTab("R"+r); JTextField occurrenceField = new JTextField(20); occurrenceField.setName("occurrence"); addField(GT.get("Occurrence"), occurrenceField, rgrpPanel,DEF_INSET); String[] trueFalseStrings = { GT.get("True"), GT.get("False")}; JComboBox<?> restHBox= new JComboBox<Object>(trueFalseStrings); restHBox.setName("restH"); addField(GT.get("Rest H"), restHBox, rgrpPanel,DEF_INSET); List<String> otherRnums = new ArrayList<String>(); otherRnums.add(GT.get("None")); for (Iterator<Integer> rnumItr=hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().keySet().iterator(); rnumItr.hasNext();) { int r_=rnumItr.next(); if (r_!= r) { otherRnums.add("R"+r_); } } String[] ifThenStrings=(String[])(otherRnums.toArray(new String[otherRnums.size()])); JComboBox<?> ifThenBox = new JComboBox<Object>(ifThenStrings); ifThenBox.setName("ifThen"); addField(GT.get("If R" + r + " then "), ifThenBox, rgrpPanel,DEF_INSET); panels.add(rgrpPanel); } }
public void setChemObject(IChemObject object) { if (object instanceof IRGroupQuery) { source = object; IRGroupQuery rgroupQuery = (IRGroupQuery)source; for (int i=0; i< rNumbers.size(); i++) { int r = rNumbers.get(i); JPanel rgrpPanel = panels.get(i); RGroupList rgrpList = rgroupQuery.getRGroupDefinitions().get(r); JTextField occurrenceField = (JTextField) (rgrpPanel.getComponent(1)); String occ=rgrpList.getOccurrence(); occurrenceField.setText(occ); JComboBox<?> restHBox = (JComboBox<?>) (rgrpPanel.getComponent(3)); boolean restH=rgrpList.isRestH(); String restHString= restH? GT.get("True"): GT.get("False"); restHBox.setSelectedItem(restHString); JComboBox<?> ifThenBox = (JComboBox<?>) (rgrpPanel.getComponent(5)); int ifThenR = rgrpList.getRequiredRGroupNumber(); String ifThenRString= ifThenR==0?GT.get("None"):"R"+ifThenR; ifThenBox.setSelectedItem(ifThenRString); } } else { throw new IllegalArgumentException("Argument must be a IRGroupQuery"); } }
int r = rNumbers.get(i); JPanel rgrpPanel = panels.get(i); RGroupList rgrpList = rgroupQuery.getRGroupDefinitions().get(r); int r = rNumbers.get(i); JPanel rgrpPanel = panels.get(i); RGroupList rgrpList = rgroupQuery.getRGroupDefinitions().get(r);
for(Iterator<Integer> rNums=existingRgroupLists.keySet().iterator(); rNums.hasNext();){ int rNum= rNums.next(); rgrpQ.getRGroupDefinitions().put(rNum, existingRgroupLists.get(rNum)); for (Iterator<Integer> rnumItr= hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().keySet().iterator(); rnumItr.hasNext();) { for (RGroup rgrp: hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().get(rnumItr.next()).getRGroups()) { if(rgrp.equals(undoRGroup)) { IAtom apo1=existingRGroupApo.get(undoRGroup).get(1); hub.setRGroupHandler(rgrpHandler); rgrpQ.getRootStructure().setProperty(CDKConstants.TITLE, RGroup.ROOT_LABEL); for (Iterator<Integer> rnumItr= hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().keySet().iterator(); rnumItr.hasNext();) { int rNum=rnumItr.next(); for (RGroup rgrp: hub.getRGroupHandler().getrGroupQuery().getRGroupDefinitions().get(rNum).getRGroups()) { rgrp.getGroup().setProperty(CDKConstants.TITLE,RGroup.makeLabel(rNum));
for (Integer rgrpNum : rGroupQuery.getRGroupDefinitions().keySet()) { RGroupList rgList = rGroupQuery.getRGroupDefinitions().get(rgrpNum); int restH = rgList.isRestH() ? 1 : 0; String logLine = "M LOG" + MDLV2000Writer.formatMDLInt(1, 3) + MDLV2000Writer.formatMDLInt(rgrpNum, 4) for (Integer rgrpNum : rGroupQuery.getRGroupDefinitions().keySet()) { List<RGroup> rgrpList = rGroupQuery.getRGroupDefinitions().get(rgrpNum).getRGroups(); if (rgrpList != null && rgrpList.size() != 0) { rgpBlock.append("$RGP").append(LSEP);;
if (rGroupQuery.getRGroupDefinitions().keySet()!=null) { apo: for(Iterator<Integer> itr =rGroupQuery.getRGroupDefinitions().keySet().iterator();itr.hasNext();) { for (RGroup rgrp :rGroupQuery.getRGroupDefinitions().get(itr.next()).getRGroups()) { if(rgrp.getGroup()==ac) { acDetachedFromRGroup=false;
Map<Integer,RGroupList> def = rGroupQuery.getRGroupDefinitions(); for(Iterator<Integer> itr= def.keySet().iterator();itr.hasNext();) { int rgrpNum=itr.next();
IAtom apoAtom = (IAtom) eventSource; apoLoop: for (Iterator<Integer> rnumItr=rGroupHandler.getrGroupQuery().getRGroupDefinitions().keySet().iterator(); rnumItr.hasNext();) { for (RGroup rgrp: rGroupHandler.getrGroupQuery().getRGroupDefinitions().get(rnumItr.next()).getRGroups()) { if(rgrp.getGroup().contains(apoAtom)) { existingRGroupApo= new HashMap <RGroup,Map<Integer,IAtom>>(); if (rgrpQuery.getRGroupDefinitions()==null) { rgrpQuery.setRGroupDefinitions(new HashMap<Integer, RGroupList>()); if (rgrpQuery.getRGroupDefinitions().get(rNum)==null) { RGroupList rList = new RGroupList(rNum); rList.setRGroups(new ArrayList<RGroup>()); rgrpQuery.getRGroupDefinitions().put(rNum, rList); for(Iterator<Integer> itr=rgrpQuery.getRGroupDefinitions().keySet().iterator();itr.hasNext();) { int rgrpNum=itr.next(); RGroupList rgrpList = rgrpQuery.getRGroupDefinitions().get(rgrpNum); if(rgrpList!=null) { existingRgroupLists.put(rgrpNum, makeClone(rgrpList)); rgrpQuery.getRGroupDefinitions().get(rNum).getRGroups().add(rgrp);
/** * Creates a {@link org.openscience.cdk.interfaces.IAtomContainerSet} from a * provided {@link org.openscience.cdk.isomorphism.matchers.IRGroupQuery). * The root structure becomes the atom container as position zero, the * substitutes follow on position 1..n, ordered by R-group number. * * @param chemModel * @param RgroupQuery * @throws CDKException */ public IAtomContainerSet getMoleculeSet (IChemModel chemModel) throws CDKException { if (rGroupQuery==null || rGroupQuery.getRootStructure() == null || rGroupQuery.getRootStructure().getAtomCount()==0) throw new CDKException( "The R-group is empty"); IAtomContainerSet moleculeSet = chemModel.getBuilder().newInstance(IAtomContainerSet.class); moleculeSet.addAtomContainer(rGroupQuery.getRootStructure()); chemModel.setMoleculeSet(moleculeSet); for (int rgrpNum : sortRGroupNumbers()) { RGroupList rgrpList = rGroupQuery.getRGroupDefinitions().get(rgrpNum); for (RGroup rgrp : rgrpList.getRGroups()) { chemModel.getMoleculeSet().addAtomContainer(rgrp.getGroup()); } } return moleculeSet; }
double listXRight=xLeft; RGroupList rgrpList = rGroupQuery.getRGroupDefinitions().get(rgrpNum); for (RGroup rgrp : rgrpList.getRGroups()) {