| /dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/main/java/uk/ac/cam/ch/wwmm/opsin/ |
| H A D | Ring.java | 28 Atom atom1 = bond.getFromAtom(); in Ring()
119 if (bond2.getFromAtom() == atom){ in makeCyclicLists()
126 atom = bond2.getFromAtom(); in makeCyclicLists()
|
| H A D | FragmentManager.java | 149 if (bond.getFromAtom().getFrag() == parentFrag && bond.getToAtom().getFrag() == parentFrag){ in incorporateFragment()
317 if (bond.getFromAtom().getFrag() == frag){ in removeFragment()
321 fragToInterFragmentBond.get(bond.getFromAtom().getFrag()).remove(bond); in removeFragment()
468 …Bond newBond = createBond(oldToNewAtomMap.get(bond.getFromAtom()), oldToNewAtomMap.get(bond.getToA… in copyAndRelabelFragment()
533 Atom originalFromAtom = bond.getFromAtom(); in cloneElement()
593 fragToInterFragmentBond.get(bond.getFromAtom().getFrag()).remove(bond); in removeInterFragmentBondIfPresent()
602 fragToInterFragmentBond.get(bond.getFromAtom().getFrag()).add(bond); in addInterFragmentBond()
669 bond.getFromAtom().getFrag().removeBond(bond); in removeBond()
670 bond.getFromAtom().removeBond(bond); in removeBond()
|
| H A D | StereoAnalyser.java | 98 Atom a1 = bond.getFromAtom(); in getOrderedStereoAtoms()
239 Atom fromAtom = bond.getFromAtom(); in addGhostAtoms()
619 Atom a1 = bond.getFromAtom(); in findStereoBonds()
628 neighbours2.remove(bond.getFromAtom()); in findStereoBonds()
|
| H A D | AmbiguityChecker.java | 51 relevantAtoms.add(b.getFromAtom()); in allBondsEquivalent()
63 String s1 = getAtomEnviron(analyser, b.getFromAtom()); in bondToCanonicalEnvironString()
|
| H A D | SuffixApplier.java | 187 if (bond.getFromAtom().getFrag() == suffixFrag) { in resolveSuffixes()
188 bond.getFromAtom().addChargeAndProtons(chargeChange, protonChange); in resolveSuffixes()
214 if (bond.getFromAtom().getFrag() == suffixFrag) { in resolveSuffixes()
215 suffixFrag.addOutAtom(bond.getFromAtom(), outValency, true); in resolveSuffixes()
|
| H A D | Bond.java | 90 Atom getFromAtom() { in getFromAtom() method in Bond
|
| H A D | SMILESFragmentBuilder.java | 804 List<Bond> fromAtomBonds = centralBond.getFromAtom().getBonds(); in addBondStereoElements()
812 Atom atom2 = centralBond.getFromAtom(); in addBondStereoElements()
827 upSecond = followingBond.getFromAtom() != atom3; in addBondStereoElements()
830 upSecond = followingBond.getFromAtom() == atom3; in addBondStereoElements()
|
| H A D | SSSRFinder.java | 68 Atom atomFrom = bond.getFromAtom() ; in getRing()
|
| H A D | FusedRingBuilder.java | 337 b.getFromAtom().setSpareValency(true); in processPartiallyUnsaturatedHWSystems()
902 Atom from = bond.getFromAtom(); in fuseRings()
916 Atom from = bond.getFromAtom(); in fuseRings()
|
| H A D | Fragment.java | 465 if(b.getFromAtom() == atom) { in getIntraFragmentIncomingValency()
|
| H A D | StereochemistryHandler.java | 374 List<Atom> neighbours1 = potentialBond.getFromAtom().getAtomNeighbours(); in cisTransUnambiguousOnBond()
402 if (bond.getFromAtom().getFrag() ==preferredOriginatingFragment){ in sortInterFragmentBonds()
|
| H A D | FunctionalReplacement.java | 754 …m atomToAttachTo = bondToRemove.getFromAtom() == oxygenToReplace ? bondToRemove.getToAtom() : bo… in performPeroxyFunctionalReplacement()
|
| H A D | StructureBuilder.java | 596 …if (bond.getOrder()==2 && bond.getFromAtom().getElement() == ChemEl.C && bond.getToAtom().getEleme… in buildOxide()
598 state.fragManager.createBond(bond.getFromAtom(), oxideAtom, 1); in buildOxide()
606 Atom fromAtom =bond.getFromAtom(); in buildOxide()
2284 if (bond.getFromAtom() == atom){ in checkForConnectedOxo()
2288 connectedAtom = bond.getFromAtom(); in checkForConnectedOxo()
|
| H A D | FusedRingNumberer.java | 353 buildRingConnectionTables(tRing, null, 0, b1, b1.getFromAtom(), startingCT, cts); in determinePossiblePeripheryAtomOrders()
1641 List<Bond> neighbouringBonds = fusedBond.getFromAtom().getBonds(); in getStartingNonFusedBond()
|
| H A D | FragmentTools.java | 996 Atom fromAtom =bond.getFromAtom(); in notIn6MemberOrSmallerRing()
|
| H A D | StructureBuildingMethods.java | 1014 Atom a1 = b.getFromAtom(); in isCycloAlkaneSpecialCase()
|
| H A D | ComponentProcessor.java | 531 b.getFromAtom().getAtomIsInACycle() && in processXyleneLikeNomenclature()
535 b.getFromAtom().setSpareValency(true); in processXyleneLikeNomenclature()
|
| /dports/science/opsin/dan2097-opsin-9b25f7546b67/opsin-core/src/test/java/uk/ac/cam/ch/wwmm/opsin/ |
| H A D | BondTest.java | 25 assertEquals(a1, bond.getFromAtom()); in testBond()
|
| H A D | StereochemistryTest.java | 93 Atom stereoAtom1 = stereoBond.getFromAtom(); in findStereoCentresBut2ene()
|
| /dports/science/molsketch/Molsketch-0.7.2/libmolsketch/ |
| H A D | atompopup.cpp | 48 void getFromAtom() { in getFromAtom() function
193 if (itemValid(d->atom)) d->getFromAtom(); in propertiesChanged()
|