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Replace atom Symbol with Integer constant comparison #827

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Merged
merged 15 commits into from
Feb 8, 2022
Merged

Replace atom Symbol with Integer constant comparison #827

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5438272
Interface constants are public static final by default. It is much mo…
johnmay Feb 7, 2022
b2b9475
First batch of converting symbol equality to int comparissions
johnmay Feb 7, 2022
07adbd2
Negation of {string}.equals({var}.getSymbol()).
johnmay Feb 7, 2022
1955e63
{string}.equals({var}.getSymbol())
johnmay Feb 7, 2022
ae5ebb5
Some missing imports
johnmay Feb 7, 2022
4d9715e
Mocked object needs updating
johnmay Feb 7, 2022
9affa18
Also now if atomic num is null
johnmay Feb 7, 2022
bacb2cc
Replace with switch
johnmay Feb 7, 2022
ae6f544
Additional null check
johnmay Feb 7, 2022
498bd3b
A few equalsIgnoreCases
johnmay Feb 7, 2022
3dc4015
Replace comparisson between atom ref with Integer rather than String
johnmay Feb 7, 2022
99ca0b4
Replace String comparission on chained symbol access.
johnmay Feb 7, 2022
1e2f936
Bug detected by SonarCloud - the if condition does nothing. Reading t…
johnmay Feb 8, 2022
430e809
Less code smell
johnmay Feb 8, 2022
eb4eee1
Swap ordering of test assertions
johnmay Feb 8, 2022
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3 changes: 2 additions & 1 deletion base/atomtype/src/main/java/org/openscience/cdk/atomtype/EStateAtomTypeMatcher.java
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Expand Up @@ -26,6 +26,7 @@
import org.openscience.cdk.interfaces.IAtomContainer;
import org.openscience.cdk.interfaces.IAtomType;
import org.openscience.cdk.interfaces.IBond;
import org.openscience.cdk.interfaces.IElement;
import org.openscience.cdk.interfaces.IRing;
import org.openscience.cdk.interfaces.IRingSet;

Expand Down Expand Up @@ -78,7 +79,7 @@ public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom)
for (int j = 0; j <= attachedAtoms.size() - 1; j++) {
IAtom attached = (IAtom) attachedAtoms.get(j);
IBond b = atomContainer.getBond(atom, attached);
if ("H".equals(attached.getSymbol())) NumHAtoms++;
if (attached.getAtomicNumber() == IElement.H) NumHAtoms++;

if (atom.getFlag(CDKConstants.ISAROMATIC) && attached.getFlag(CDKConstants.ISAROMATIC)) {

Expand Down
26 changes: 14 additions & 12 deletions base/atomtype/src/main/java/org/openscience/cdk/atomtype/SybylAtomTypeMatcher.java
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Expand Up @@ -112,16 +112,18 @@ public IAtomType[] findMatchingAtomTypes(IAtomContainer atomContainer) throws CD
@Override
public IAtomType findMatchingAtomType(IAtomContainer atomContainer, IAtom atom) throws CDKException {
IAtomType type = cdkMatcher.findMatchingAtomType(atomContainer, atom);
if ("Cr".equals(atom.getSymbol())) {
// if only I had good descriptions of the Sybyl atom types
int neighbors = atomContainer.getConnectedBondsCount(atom);
if (neighbors > 4 && neighbors <= 6)
return factory.getAtomType("Cr.oh");
else if (neighbors > 0) return factory.getAtomType("Cr.th");
} else if ("Co".equals(atom.getSymbol())) {
// if only I had good descriptions of the Sybyl atom types
int neibors = atomContainer.getConnectedBondsCount(atom);
if (neibors == 6) return factory.getAtomType("Co.oh");
if (atom.getAtomicNumber() != null) {
if (atom.getAtomicNumber() == IElement.Cr) {
// if only I had good descriptions of the Sybyl atom types
int neighbors = atomContainer.getConnectedBondsCount(atom);
if (neighbors > 4 && neighbors <= 6)
return factory.getAtomType("Cr.oh");
else if (neighbors > 0) return factory.getAtomType("Cr.th");
} else if (atom.getAtomicNumber() == IElement.Co) {
// if only I had good descriptions of the Sybyl atom types
int neibors = atomContainer.getConnectedBondsCount(atom);
if (neibors == 6) return factory.getAtomType("Co.oh");
}
}
if (type == null)
return null;
Expand All @@ -142,7 +144,7 @@ private boolean isCarbonyl(IAtomContainer atomContainer, IAtom atom) {
if (neighbors.size() != 1) return false;
IBond neighbor = neighbors.get(0);
IAtom neighborAtom = neighbor.getOther(atom);
if ("C".equals(neighborAtom.getSymbol())) {
if (neighborAtom.getAtomicNumber() == IElement.C) {
if (neighbor.getOrder() == IBond.Order.SINGLE) {
if (countAttachedBonds(atomContainer, neighborAtom, IBond.Order.DOUBLE, "O") == 1) return true;
} else if (neighbor.getOrder() == IBond.Order.DOUBLE) {
Expand All @@ -157,7 +159,7 @@ private boolean isNitro(IAtomContainer atomContainer, IAtom atom) {
if (neighbors.size() != 3) return false;
int oxygenCount = 0;
for (IAtom neighbor : neighbors)
if ("O".equals(neighbor.getSymbol())) oxygenCount++;
if (neighbor.getAtomicNumber() == IElement.O) oxygenCount++;
return (oxygenCount == 2);
}

Expand Down
323 changes: 189 additions & 134 deletions base/core/src/main/java/org/openscience/cdk/atomtype/CDKAtomTypeMatcher.java
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2 changes: 1 addition & 1 deletion base/data/src/main/java/org/openscience/cdk/formula/MolecularFormula.java
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Expand Up @@ -393,7 +393,7 @@ protected boolean isTheSame(IIsotope isotopeOne, IIsotope isotopeTwo) {
if (exactMass1 == null) exactMass1 = -1.0;
if (exactMass2 == null) exactMass2 = -1.0;

if (!isotopeOne.getSymbol().equals(isotopeTwo.getSymbol())) return false;
if (!isotopeOne.getAtomicNumber().equals(isotopeTwo.getAtomicNumber())) return false;
if (natAbund1.doubleValue() != natAbund2) return false;
return exactMass1.doubleValue() == exactMass2;
}
Expand Down
256 changes: 130 additions & 126 deletions base/interfaces/src/main/java/org/openscience/cdk/interfaces/IElement.java
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Expand Up @@ -29,128 +29,132 @@
*/
public interface IElement extends IChemObject {

/**
* Byte enum constants for element atomic numbers
*/
public static final byte Wildcard = 0;
public static final byte H = 1;
public static final byte He = 2;
public static final byte Li = 3;
public static final byte Be = 4;
public static final byte B = 5;
public static final byte C = 6;
public static final byte N = 7;
public static final byte O = 8;
public static final byte F = 9;
public static final byte Ne = 10;
public static final byte Na = 11;
public static final byte Mg = 12;
public static final byte Al = 13;
public static final byte Si = 14;
public static final byte P = 15;
public static final byte S = 16;
public static final byte Cl = 17;
public static final byte Ar = 18;
public static final byte K = 19;
public static final byte Ca = 20;
public static final byte Sc = 21;
public static final byte Ti = 22;
public static final byte V = 23;
public static final byte Cr = 24;
public static final byte Mn = 25;
public static final byte Fe = 26;
public static final byte Co = 27;
public static final byte Ni = 28;
public static final byte Cu = 29;
public static final byte Zn = 30;
public static final byte Ga = 31;
public static final byte Ge = 32;
public static final byte As = 33;
public static final byte Se = 34;
public static final byte Br = 35;
public static final byte Kr = 36;
public static final byte Rb = 37;
public static final byte Sr = 38;
public static final byte Y = 39;
public static final byte Zr = 40;
public static final byte Nb = 41;
public static final byte Mo = 42;
public static final byte Tc = 43;
public static final byte Ru = 44;
public static final byte Rh = 45;
public static final byte Pd = 46;
public static final byte Ag = 47;
public static final byte Cd = 48;
public static final byte In = 49;
public static final byte Sn = 50;
public static final byte Sb = 51;
public static final byte Te = 52;
public static final byte I = 53;
public static final byte Xe = 54;
public static final byte Cs = 55;
public static final byte Ba = 56;
public static final byte La = 57;
public static final byte Ce = 58;
public static final byte Pr = 59;
public static final byte Nd = 60;
public static final byte Pm = 61;
public static final byte Sm = 62;
public static final byte Eu = 63;
public static final byte Gd = 64;
public static final byte Tb = 65;
public static final byte Dy = 66;
public static final byte Ho = 67;
public static final byte Er = 68;
public static final byte Tm = 69;
public static final byte Yb = 70;
public static final byte Lu = 71;
public static final byte Hf = 72;
public static final byte Ta = 73;
public static final byte W = 74;
public static final byte Re = 75;
public static final byte Os = 76;
public static final byte Ir = 77;
public static final byte Pt = 78;
public static final byte Au = 79;
public static final byte Hg = 80;
public static final byte Tl = 81;
public static final byte Pb = 82;
public static final byte Bi = 83;
public static final byte Po = 84;
public static final byte At = 85;
public static final byte Rn = 86;
public static final byte Fr = 87;
public static final byte Ra = 88;
public static final byte Ac = 89;
public static final byte Th = 90;
public static final byte Pa = 91;
public static final byte U = 92;
public static final byte Np = 93;
public static final byte Pu = 94;
public static final byte Am = 95;
public static final byte Cm = 96;
public static final byte Bk = 97;
public static final byte Cf = 98;
public static final byte Es = 99;
public static final byte Fm = 100;
public static final byte Md = 101;
public static final byte No = 102;
public static final byte Lr = 103;
public static final byte Rf = 104;
public static final byte Db = 105;
public static final byte Sg = 106;
public static final byte Bh = 107;
public static final byte Hs = 108;
public static final byte Mt = 109;
public static final byte Ds = 110;
public static final byte Rg = 111;
public static final byte Cn = 112;
public static final byte Nh = 113;
public static final byte Fl = 114;
public static final byte Mc = 115;
public static final byte Lv = 116;
public static final byte Ts = 117;
public static final byte Og = 118;
// Integer enum constants for element atomic numbers

/** Wildcard atom is atomic number 0 */
int Wildcard = 0;
/** Hydrogen atomic number */
int H = 1;
int He = 2;
int Li = 3;
int Be = 4;
int B = 5;
/** Carbon atomic number */
int C = 6;
/** Nitrogen atomic number */
int N = 7;
/** Oxygen atomic number */
int O = 8;
int F = 9;
int Ne = 10;
int Na = 11;
int Mg = 12;
int Al = 13;
int Si = 14;
int P = 15;
int S = 16;
int Cl = 17;
int Ar = 18;
int K = 19;
int Ca = 20;
int Sc = 21;
int Ti = 22;
int V = 23;
int Cr = 24;
int Mn = 25;
int Fe = 26;
int Co = 27;
int Ni = 28;
int Cu = 29;
int Zn = 30;
int Ga = 31;
int Ge = 32;
int As = 33;
int Se = 34;
int Br = 35;
int Kr = 36;
int Rb = 37;
int Sr = 38;
int Y = 39;
int Zr = 40;
int Nb = 41;
int Mo = 42;
int Tc = 43;
int Ru = 44;
int Rh = 45;
int Pd = 46;
int Ag = 47;
int Cd = 48;
int In = 49;
int Sn = 50;
int Sb = 51;
int Te = 52;
int I = 53;
int Xe = 54;
int Cs = 55;
int Ba = 56;
int La = 57;
int Ce = 58;
int Pr = 59;
int Nd = 60;
int Pm = 61;
int Sm = 62;
int Eu = 63;
int Gd = 64;
int Tb = 65;
int Dy = 66;
int Ho = 67;
int Er = 68;
int Tm = 69;
int Yb = 70;
int Lu = 71;
int Hf = 72;
int Ta = 73;
int W = 74;
int Re = 75;
int Os = 76;
int Ir = 77;
int Pt = 78;
int Au = 79;
int Hg = 80;
int Tl = 81;
int Pb = 82;
int Bi = 83;
int Po = 84;
int At = 85;
int Rn = 86;
int Fr = 87;
int Ra = 88;
int Ac = 89;
int Th = 90;
int Pa = 91;
int U = 92;
int Np = 93;
int Pu = 94;
int Am = 95;
int Cm = 96;
int Bk = 97;
int Cf = 98;
int Es = 99;
int Fm = 100;
int Md = 101;
int No = 102;
int Lr = 103;
int Rf = 104;
int Db = 105;
int Sg = 106;
int Bh = 107;
int Hs = 108;
int Mt = 109;
int Ds = 110;
int Rg = 111;
int Cn = 112;
int Nh = 113;
int Fl = 114;
int Mc = 115;
int Lv = 116;
int Ts = 117;
int Og = 118;

/**
* Returns the atomic number of this element.
Expand All @@ -168,7 +172,7 @@ public interface IElement extends IChemObject {
*
* @see #setAtomicNumber
*/
public Integer getAtomicNumber();
Integer getAtomicNumber();

/**
* Sets the atomic number of this element.
Expand All @@ -177,7 +181,7 @@ public interface IElement extends IChemObject {
*
* @see #getAtomicNumber
*/
public void setAtomicNumber(Integer atomicNumber);
void setAtomicNumber(Integer atomicNumber);

/**
* Returns the element symbol of this element.
Expand All @@ -186,7 +190,7 @@ public interface IElement extends IChemObject {
*
* @see #setSymbol
*/
public String getSymbol();
String getSymbol();

/**
* Sets the element symbol of this element.
Expand All @@ -195,6 +199,6 @@ public interface IElement extends IChemObject {
*
* @see #getSymbol
*/
public void setSymbol(String symbol);
void setSymbol(String symbol);

}
2 changes: 1 addition & 1 deletion ...phism/src/main/java/org/openscience/cdk/isomorphism/matchers/SymbolChargeIDQueryAtom.java
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Expand Up @@ -45,7 +45,7 @@ public void setOperator(String str) {}

@Override
public boolean matches(IAtom atom) {
return this.getSymbol().equals(atom.getSymbol()) && Objects.equals(this.getFormalCharge(), atom.getFormalCharge())
return this.getAtomicNumber().equals(atom.getAtomicNumber()) && Objects.equals(this.getFormalCharge(), atom.getFormalCharge())
&& this.getID().equals(atom.getID());
};

Expand Down
2 changes: 1 addition & 1 deletion ...action/src/main/java/org/openscience/cdk/graph/invariant/ConjugatedPiSystemsDetector.java
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Expand Up @@ -158,7 +158,7 @@ private static int checkAtom(IAtomContainer ac, IAtom currentAtom) {
if (se == 1) {
check = 0; //// DETECTION of radicals
} else if (ac.getConnectedLonePairsCount(currentAtom) > 0
/* && (currentAtom.getSymbol().equals("N") */) {
/* && (currentAtom.getAtomicNumber() == IElement.N */) {
check = 0; //// DETECTION of lone pair
} else {
int highOrderBondCount = 0;
Expand Down
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