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Renamed get/setHydrogenCount() to get/setImplicitHydrogenCount(), per…
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… report #3020065

Signed-off-by: Rajarshi  Guha <rajarshi.guha@gmail.com>
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@egonw @rajarshi
egonw authored and rajarshi committed Aug 29, 2010
1 parent 5a2bc65 commit 8ec9ad4
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Showing 79 changed files with 489 additions and 489 deletions.
10 changes: 5 additions & 5 deletions src/main/org/openscience/cdk/Atom.java
View file
Expand Up @@ -178,7 +178,7 @@ public Atom(IElement element) {
} else {
this.fractionalPoint3d = null;
}
this.hydrogenCount = ((IAtom)element).getHydrogenCount();
this.hydrogenCount = ((IAtom)element).getImplicitHydrogenCount();
this.charge = ((IAtom)element).getCharge();
this.stereoParity = ((IAtom)element).getStereoParity();
}
Expand Down Expand Up @@ -216,7 +216,7 @@ public Double getCharge() {
*
* @see #getHydrogenCount
*/
public void setHydrogenCount(Integer hydrogenCount) {
public void setImplicitHydrogenCount(Integer hydrogenCount) {
this.hydrogenCount = hydrogenCount;
notifyChanged();
}
Expand All @@ -228,7 +228,7 @@ public void setHydrogenCount(Integer hydrogenCount) {
*
* @see #setHydrogenCount
*/
public Integer getHydrogenCount() {
public Integer getImplicitHydrogenCount() {
return this.hydrogenCount;
}

Expand Down Expand Up @@ -370,8 +370,8 @@ public String toString() {
if (getSymbol() != null) {
stringContent.append(", S:").append(getSymbol());
}
if (getHydrogenCount() != null) {
stringContent.append(", H:").append(getHydrogenCount());
if (getImplicitHydrogenCount() != null) {
stringContent.append(", H:").append(getImplicitHydrogenCount());
}
if (getStereoParity() != null) {
stringContent.append(", SP:").append(getStereoParity());
Expand Down
8 changes: 4 additions & 4 deletions src/main/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
View file
Expand Up @@ -583,7 +583,7 @@ private IAtomType perceiveNitrogens(IAtomContainer atomContainer, IAtom atom) th
} else if (neighborCount == 2) {
IBond.Order maxOrder = atomContainer.getMaximumBondOrder(atom);
if (maxOrder == IBond.Order.SINGLE) {
if (atom.getHydrogenCount() != CDKConstants.UNSET && atom.getHydrogenCount() == 1) {
if (atom.getImplicitHydrogenCount() != CDKConstants.UNSET && atom.getImplicitHydrogenCount() == 1) {
IAtomType type = getAtomType("N.planar3");
if (isAcceptable(atom, atomContainer, type)) return type;
} else {
Expand Down Expand Up @@ -684,7 +684,7 @@ private IAtomType perceiveNitrogens(IAtomContainer atomContainer, IAtom atom) th
List<IBond> bonds = atomContainer.getConnectedBondsList(atom);
if (bonds.get(0).getFlag(CDKConstants.ISAROMATIC) &&
bonds.get(1).getFlag(CDKConstants.ISAROMATIC)) {
Integer hCount = atom.getHydrogenCount();
Integer hCount = atom.getImplicitHydrogenCount();
if (hCount == CDKConstants.UNSET || hCount == 0) {
IAtomType type = getAtomType("N.sp2");
if (isAcceptable(atom, atomContainer, type))
Expand Down Expand Up @@ -1545,10 +1545,10 @@ private boolean isAcceptable(IAtom atom, IAtomContainer container, IAtomType typ
int requiredContainerCount = type.getFormalNeighbourCount();
if (actualContainerCount != requiredContainerCount)
return false;
} else if (atom.getHydrogenCount() != CDKConstants.UNSET) {
} else if (atom.getImplicitHydrogenCount() != CDKConstants.UNSET) {
// confirm correct neighbour count
int connectedAtoms = container.getConnectedAtomsCount(atom);
int hCount = atom.getHydrogenCount();
int hCount = atom.getImplicitHydrogenCount();
int actualNeighbourCount = connectedAtoms + hCount;
int requiredNeighbourCount = type.getFormalNeighbourCount();
if (actualNeighbourCount > requiredNeighbourCount)
Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/atomtype/StructGenAtomTypeGuesser.java
View file
Expand Up @@ -83,7 +83,7 @@ public List<IAtomType> possibleAtomTypes(IAtomContainer atomContainer, IAtom ato
double bondOrderSum = atomContainer.getBondOrderSum(atom);
IBond.Order maxBondOrder = atomContainer.getMaximumBondOrder(atom);
int charge = atom.getFormalCharge();
int hcount = atom.getHydrogenCount();
int hcount = atom.getImplicitHydrogenCount();

List<IAtomType> matchingTypes = new ArrayList<IAtomType>();
IAtomType[] types = factory.getAtomTypes(atom.getSymbol());
Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/atomtype/StructGenMatcher.java
View file
Expand Up @@ -91,7 +91,7 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
double bondOrderSum = atomContainer.getBondOrderSum(atom);
IBond.Order maxBondOrder = atomContainer.getMaximumBondOrder(atom);
int charge = atom.getFormalCharge();
int hcount = atom.getHydrogenCount() == null ? 0 : atom.getHydrogenCount();
int hcount = atom.getImplicitHydrogenCount() == null ? 0 : atom.getImplicitHydrogenCount();

IAtomType[] types = factory.getAtomTypes(atom.getSymbol());
for (IAtomType type : types) {
Expand Down
10 changes: 5 additions & 5 deletions src/main/org/openscience/cdk/debug/DebugAtom.java
View file
Expand Up @@ -84,14 +84,14 @@ public Double getCharge() {
return super.getCharge();
}

public void setHydrogenCount(Integer hydrogenCount) {
public void setImplicitHydrogenCount(Integer hydrogenCount) {
logger.debug("Setting hydrogen count: ", hydrogenCount);
super.setHydrogenCount(hydrogenCount);
super.setImplicitHydrogenCount(hydrogenCount);
}

public Integer getHydrogenCount() {
logger.debug("Getting hydrogen count: ", super.getHydrogenCount());
return super.getHydrogenCount();
public Integer getImplicitHydrogenCount() {
logger.debug("Getting hydrogen count: ", super.getImplicitHydrogenCount());
return super.getImplicitHydrogenCount();
}

public void setPoint2d(Point2d point2d) {
Expand Down
10 changes: 5 additions & 5 deletions src/main/org/openscience/cdk/debug/DebugFragmentAtom.java
View file
Expand Up @@ -90,14 +90,14 @@ public Double getCharge() {
return super.getCharge();
}

public void setHydrogenCount(Integer hydrogenCount) {
public void setImplicitHydrogenCount(Integer hydrogenCount) {
logger.debug("Setting hydrogen count: ", hydrogenCount);
super.setHydrogenCount(hydrogenCount);
super.setImplicitHydrogenCount(hydrogenCount);
}

public Integer getHydrogenCount() {
logger.debug("Getting hydrogen count: ", super.getHydrogenCount());
return super.getHydrogenCount();
public Integer getImplicitHydrogenCount() {
logger.debug("Getting hydrogen count: ", super.getImplicitHydrogenCount());
return super.getImplicitHydrogenCount();
}

public void setPoint2d(Point2d point2d) {
Expand Down
10 changes: 5 additions & 5 deletions src/main/org/openscience/cdk/debug/DebugPseudoAtom.java
View file
Expand Up @@ -86,14 +86,14 @@ public Double getCharge() {
return super.getCharge();
}

public void setHydrogenCount(Integer hydrogenCount) {
public void setImplicitHydrogenCount(Integer hydrogenCount) {
logger.debug("Setting hydrogen count: ", hydrogenCount);
super.setHydrogenCount(hydrogenCount);
super.setImplicitHydrogenCount(hydrogenCount);
}

public Integer getHydrogenCount() {
logger.debug("Getting hydrogen count: ", super.getHydrogenCount());
return super.getHydrogenCount();
public Integer getImplicitHydrogenCount() {
logger.debug("Getting hydrogen count: ", super.getImplicitHydrogenCount());
return super.getImplicitHydrogenCount();
}

public void setPoint2d(Point2d point2d) {
Expand Down
12 changes: 6 additions & 6 deletions src/main/org/openscience/cdk/geometry/BondTools.java
View file
Expand Up @@ -209,13 +209,13 @@ private static boolean isEndOfDoubleBond(IAtomContainer container, IAtom atom, I
}

int hcount;
if (atom.getHydrogenCount() == CDKConstants.UNSET) hcount = 0;
else hcount = atom.getHydrogenCount();
if (atom.getImplicitHydrogenCount() == CDKConstants.UNSET) hcount = 0;
else hcount = atom.getImplicitHydrogenCount();

int lengthAtom = container.getConnectedAtomsList(atom).size() + hcount;

if (parent.getHydrogenCount() == CDKConstants.UNSET) hcount = 0;
else hcount = parent.getHydrogenCount();
if (parent.getImplicitHydrogenCount() == CDKConstants.UNSET) hcount = 0;
else hcount = parent.getImplicitHydrogenCount();

int lengthParent = container.getConnectedAtomsList(parent).size() + hcount;

Expand Down Expand Up @@ -256,8 +256,8 @@ private static boolean isEndOfDoubleBond(IAtomContainer container, IAtom atom, I
*/
private static boolean isStartOfDoubleBond(IAtomContainer container, IAtom a, IAtom parent, boolean[] doubleBondConfiguration) {
int hcount;
if (a.getHydrogenCount() == CDKConstants.UNSET) hcount = 0;
else hcount = a.getHydrogenCount();
if (a.getImplicitHydrogenCount() == CDKConstants.UNSET) hcount = 0;
else hcount = a.getImplicitHydrogenCount();

int lengthAtom = container.getConnectedAtomsList(a).size() + hcount;

Expand Down
4 changes: 2 additions & 2 deletions src/main/org/openscience/cdk/graph/invariant/CanonicalLabeler.java
View file
Expand Up @@ -130,7 +130,7 @@ private ArrayList createInvarLabel(IAtomContainer atomContainer) {
a = (IAtom)atoms.next();
inv = new StringBuffer();
inv.append(atomContainer.getConnectedAtomsList(a).size() +
(a.getHydrogenCount() == CDKConstants.UNSET ? 0 : a.getHydrogenCount())); //Num connections
(a.getImplicitHydrogenCount() == CDKConstants.UNSET ? 0 : a.getImplicitHydrogenCount())); //Num connections
inv.append(atomContainer.getConnectedAtomsList(a).size()); //Num of non H bonds
inv.append(PeriodicTable.getAtomicNumber(a.getSymbol()));

Expand All @@ -141,7 +141,7 @@ private ArrayList createInvarLabel(IAtomContainer atomContainer) {
else
inv.append(0); //Absolute charge
inv.append((int)Math.abs( (a.getFormalCharge() == CDKConstants.UNSET ? 0.0 : a.getFormalCharge()))); //Hydrogen count
inv.append((a.getHydrogenCount() == CDKConstants.UNSET ? 0 : a.getHydrogenCount()));
inv.append((a.getImplicitHydrogenCount() == CDKConstants.UNSET ? 0 : a.getImplicitHydrogenCount()));
vect.add(new InvPair(Long.parseLong(inv.toString()), a));
}
return vect;
Expand Down
8 changes: 4 additions & 4 deletions src/main/org/openscience/cdk/graph/invariant/HuLuIndexTool.java
View file
Expand Up @@ -165,18 +165,18 @@ public static double[] getAtomWeights(AtomContainer atomContainer) throws NoSuch

//weightArray[k] = atom.getValenceElectronsCount() - atom.getHydrogenCount(); // method unfinished
if(atom.getSymbol()=="O")
weightArray[i] = 6 - atom.getHydrogenCount();
weightArray[i] = 6 - atom.getImplicitHydrogenCount();
else
weightArray[i] = 4 - atom.getHydrogenCount();
weightArray[i] = 4 - atom.getImplicitHydrogenCount();



for (int j = 0; j < apspMatrix.length; j++)
{
if(atomContainer.getAtom(j).getSymbol()=="O")
valenceSum[apspMatrix[j][i]] += 6 - atomContainer.getAtom(j).getHydrogenCount();
valenceSum[apspMatrix[j][i]] += 6 - atomContainer.getAtom(j).getImplicitHydrogenCount();
else
valenceSum[apspMatrix[j][i]] += 4 - atomContainer.getAtom(j).getHydrogenCount();
valenceSum[apspMatrix[j][i]] += 4 - atomContainer.getAtom(j).getImplicitHydrogenCount();
}

Iterator bonds = atomContainer.bonds().iterator();
Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/inchi/InChIGenerator.java
View file
Expand Up @@ -257,7 +257,7 @@ private void generateInchiFromCDKAtomContainer(IAtomContainer atomContainer) thr
// atom.getHydrogenCount() returns number of implict hydrogens, not
// total number
// Ref: Posting to cdk-devel list by Egon Willighagen 2005-09-17
Integer implicitH = atom.getHydrogenCount();
Integer implicitH = atom.getImplicitHydrogenCount();
if (implicitH == CDKConstants.UNSET) implicitH = 0;

if (implicitH != 0) {
Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/inchi/InChIToStructure.java
View file
Expand Up @@ -169,7 +169,7 @@ protected void generateAtomContainerFromInchi(IChemObjectBuilder builder) throws
// Ref: Posting to cdk-devel list by Egon Willighagen 2005-09-17
int numH = iAt.getImplicitH();
if (numH != 0) {
cAt.setHydrogenCount(numH);
cAt.setImplicitHydrogenCount(numH);
}

molecule.addAtom(cAt);
Expand Down
4 changes: 2 additions & 2 deletions src/main/org/openscience/cdk/interfaces/IAtom.java
View file
Expand Up @@ -57,15 +57,15 @@ public interface IAtom extends IAtomType {
* @param hydrogenCount The number of hydrogen atoms bonded to this atom.
* @see #getHydrogenCount
*/
public void setHydrogenCount(Integer hydrogenCount);
public void setImplicitHydrogenCount(Integer hydrogenCount);

/**
* Returns the implicit hydrogen count of this atom.
*
* @return The hydrogen count of this atom.
* @see #setHydrogenCount
*/
public Integer getHydrogenCount();
public Integer getImplicitHydrogenCount();

/**
* Sets a point specifying the location of this
Expand Down
8 changes: 4 additions & 4 deletions src/main/org/openscience/cdk/io/cml/CMLCoreModule.java
View file
Expand Up @@ -1154,10 +1154,10 @@ protected void storeData() {

private void convertCMLToCDKHydrogenCounts() {
for (IAtom atom : currentMolecule.atoms()) {
if (atom.getHydrogenCount() != null) {
if (atom.getImplicitHydrogenCount() != null) {
int explicitHCount = AtomContainerManipulator.countExplicitHydrogens(currentMolecule, atom);
if (explicitHCount != 0) {
atom.setHydrogenCount(atom.getHydrogenCount() - explicitHCount);
atom.setImplicitHydrogenCount(atom.getImplicitHydrogenCount() - explicitHCount);
}
}
}
Expand Down Expand Up @@ -1401,9 +1401,9 @@ protected void storeAtomData() {
// FIXME: the hCount in CML is the total of implicit *and* explicit
String hCount = hCounts.get(i);
if (hCount != null) {
currentAtom.setHydrogenCount(Integer.parseInt(hCount));
currentAtom.setImplicitHydrogenCount(Integer.parseInt(hCount));
} else {
currentAtom.setHydrogenCount((Integer)CDKConstants.UNSET);
currentAtom.setImplicitHydrogenCount((Integer)CDKConstants.UNSET);
}
}

Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/io/cml/PDBConvention.java
View file
Expand Up @@ -530,7 +530,7 @@ protected void storeAtomData() {
if (hasHCounts) {
// cdo.setObjectProperty("Atom", "hydrogenCount", (String)hCounts.get(i));
// FIXME: the hCount in CML is the total of implicit *and* explicit
currentAtom.setHydrogenCount(Integer.parseInt((String)hCounts.get(i)));
currentAtom.setImplicitHydrogenCount(Integer.parseInt((String)hCounts.get(i)));
}

if (has2D) {
Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/io/iterator/event/EventCMLHandler.java
View file
Expand Up @@ -253,7 +253,7 @@ public void setObjectProperty(String objectType, String propertyType,
propertyType.equals("partialCharge")) {
currentAtom.setCharge(Double.parseDouble(propertyValue));
} else if (propertyType.equals("hydrogenCount")) {
currentAtom.setHydrogenCount(Integer.parseInt(propertyValue));
currentAtom.setImplicitHydrogenCount(Integer.parseInt(propertyValue));
} else if (propertyType.equals("dictRef")) {
currentAtom.setProperty("org.openscience.cdk.dict", propertyValue);
} else if (propertyType.equals("atomicNumber")) {
Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/isomorphism/IsomorphismTester.java
View file
Expand Up @@ -126,7 +126,7 @@ public boolean isIsomorphic(IMolecule mol2) {
atom1 = base.getAtom(f);
atom2 = compare.getAtom(g);
if (!(atom1.getSymbol().equals(atom2.getSymbol())) &&
atom1.getHydrogenCount() == atom2.getHydrogenCount())
atom1.getImplicitHydrogenCount() == atom2.getImplicitHydrogenCount())
{
return false;
}
Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/isomorphism/matchers/SymbolQueryAtom.java
View file
Expand Up @@ -47,7 +47,7 @@ public boolean matches(IAtom atom) {
if(ID!=null && HCount==0)
return this.getSymbol()!=(atom.getSymbol());
else if(ID==null && HCount!=0){
return (this.getHydrogenCount()==HCount);
return (this.getImplicitHydrogenCount()==HCount);
}
else
return this.getSymbol().equals(atom.getSymbol());
Expand Down
6 changes: 3 additions & 3 deletions src/main/org/openscience/cdk/isomorphism/matchers/smarts/ImplicitHCountAtom.java
View file
Expand Up @@ -43,7 +43,7 @@ public class ImplicitHCountAtom extends SMARTSAtom {
* @param hCount
*/
public ImplicitHCountAtom(int hCount) {
this.setHydrogenCount(hCount);
this.setImplicitHydrogenCount(hCount);
}

/**
Expand All @@ -53,8 +53,8 @@ public ImplicitHCountAtom(int hCount) {
* @return
*/
private int getIMPH(IAtom atom){
if (atom.getHydrogenCount() == CDKConstants.UNSET) return 0;
else return atom.getHydrogenCount();
if (atom.getImplicitHydrogenCount() == CDKConstants.UNSET) return 0;
else return atom.getImplicitHydrogenCount();
}
/* (non-Javadoc)
* @see org.openscience.cdk.isomorphism.matchers.smarts.SMARTSAtom#matches(org.openscience.cdk.interfaces.IAtom)
Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/iupac/parser/MoleculeBuilder.java
View file
Expand Up @@ -469,7 +469,7 @@ private void addAtom(String newAtomType, IAtom otherConnectingAtom, Order bondOr
{
//Create the new atom and bond.
Atom newAtom = new Atom(newAtomType);
newAtom.setHydrogenCount(hydrogenCount);
newAtom.setImplicitHydrogenCount(hydrogenCount);
Bond newBond = new Bond(newAtom, otherConnectingAtom, bondOrder);

//Add the new atom and bond to the molecule.
Expand Down
4 changes: 2 additions & 2 deletions src/main/org/openscience/cdk/layout/AtomPlacer.java
View file
Expand Up @@ -334,7 +334,7 @@ public void placeLinearChain(IAtomContainer atomContainer, Vector2d initialBondV
// the correct counts need saving and restoring
int[] numh = new int[atomContainer.getAtomCount()];
for (int i = 0, n = atomContainer.getAtomCount(); i < n; i ++) {
Integer tmp = atomContainer.getAtom(i).getHydrogenCount();
Integer tmp = atomContainer.getAtom(i).getImplicitHydrogenCount();
if (tmp == CDKConstants.UNSET) numh[i]= 0;
else numh[i] = tmp;
}
Expand Down Expand Up @@ -385,7 +385,7 @@ public void placeLinearChain(IAtomContainer atomContainer, Vector2d initialBondV

// BUGFIX part 2 - restore hydrogen counts
for (int i = 0, n = atomContainer.getAtomCount(); i < n; i ++) {
atomContainer.getAtom(i).setHydrogenCount(numh[i]);
atomContainer.getAtom(i).setImplicitHydrogenCount(numh[i]);
}
}

Expand Down
2 changes: 1 addition & 1 deletion src/main/org/openscience/cdk/libio/cml/Convertor.java
View file
Expand Up @@ -636,7 +636,7 @@ public CMLAtom cdkAtomToCMLAtom(IAtomContainer container, IAtom cdkAtom) {

// CML's hydrogen count consists of the sum of implicit and explicit
// hydrogens (see bug #1655045).
Integer totalHydrogen = cdkAtom.getHydrogenCount();
Integer totalHydrogen = cdkAtom.getImplicitHydrogenCount();
if (totalHydrogen != null) {
if (container != null) {
Iterator<IBond> bonds = container.getConnectedBondsList(cdkAtom).iterator();
Expand Down

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