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Added element enum to IAtom. Replaced getSymbol usage in HBondDonorCountDescriptor
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2 files changed

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‎base/interfaces/src/main/java/org/openscience/cdk/interfaces/IAtom.java‎

Lines changed: 123 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -32,6 +32,129 @@
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*/
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public interface IAtom extends IAtomType {
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35+
/**
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* Byte enum constants for element atomic numbers
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*/
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public static final byte Wildcard = 0;
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public static final byte H = 1;
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public static final byte He = 2;
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public static final byte Li = 3;
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public static final byte Be = 4;
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public static final byte B = 5;
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public static final byte C = 6;
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public static final byte N = 7;
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public static final byte O = 8;
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public static final byte F = 9;
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public static final byte Ne = 10;
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public static final byte Na = 11;
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public static final byte Mg = 12;
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public static final byte Al = 13;
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public static final byte Si = 14;
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public static final byte P = 15;
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public static final byte S = 16;
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public static final byte Cl = 17;
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public static final byte Ar = 18;
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public static final byte K = 19;
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public static final byte Ca = 20;
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public static final byte Sc = 21;
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public static final byte Ti = 22;
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public static final byte V = 23;
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public static final byte Cr = 24;
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public static final byte Mn = 25;
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public static final byte Fe = 26;
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public static final byte Co = 27;
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public static final byte Ni = 28;
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public static final byte Cu = 29;
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public static final byte Zn = 30;
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public static final byte Ga = 31;
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public static final byte Ge = 32;
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public static final byte As = 33;
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public static final byte Se = 34;
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public static final byte Br = 35;
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public static final byte Kr = 36;
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public static final byte Rb = 37;
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public static final byte Sr = 38;
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public static final byte Y = 39;
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public static final byte Zr = 40;
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public static final byte Nb = 41;
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public static final byte Mo = 42;
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public static final byte Tc = 43;
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public static final byte Ru = 44;
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public static final byte Rh = 45;
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public static final byte Pd = 46;
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public static final byte Ag = 47;
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public static final byte Cd = 48;
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public static final byte In = 49;
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public static final byte Sn = 50;
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public static final byte Sb = 51;
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public static final byte Te = 52;
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public static final byte I = 53;
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public static final byte Xe = 54;
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public static final byte Cs = 55;
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public static final byte Ba = 56;
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public static final byte La = 57;
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public static final byte Ce = 58;
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public static final byte Pr = 59;
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public static final byte Nd = 60;
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public static final byte Pm = 61;
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public static final byte Sm = 62;
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public static final byte Eu = 63;
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public static final byte Gd = 64;
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public static final byte Tb = 65;
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public static final byte Dy = 66;
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public static final byte Ho = 67;
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public static final byte Er = 68;
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public static final byte Tm = 69;
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public static final byte Yb = 70;
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public static final byte Lu = 71;
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public static final byte Hf = 72;
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public static final byte Ta = 73;
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public static final byte W = 74;
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public static final byte Re = 75;
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public static final byte Os = 76;
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public static final byte Ir = 77;
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public static final byte Pt = 78;
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public static final byte Au = 79;
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public static final byte Hg = 80;
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public static final byte Tl = 81;
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public static final byte Pb = 82;
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public static final byte Bi = 83;
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public static final byte Po = 84;
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public static final byte At = 85;
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public static final byte Rn = 86;
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public static final byte Fr = 87;
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public static final byte Ra = 88;
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public static final byte Ac = 89;
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public static final byte Th = 90;
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public static final byte Pa = 91;
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public static final byte U = 92;
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public static final byte Np = 93;
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public static final byte Pu = 94;
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public static final byte Am = 95;
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public static final byte Cm = 96;
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public static final byte Bk = 97;
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public static final byte Cf = 98;
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public static final byte Es = 99;
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public static final byte Fm = 100;
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public static final byte Md = 101;
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public static final byte No = 102;
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public static final byte Lr = 103;
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public static final byte Rf = 104;
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public static final byte Db = 105;
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public static final byte Sg = 106;
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public static final byte Bh = 107;
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public static final byte Hs = 108;
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public static final byte Mt = 109;
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public static final byte Ds = 110;
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public static final byte Rg = 111;
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public static final byte Cn = 112;
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public static final byte Nh = 113;
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public static final byte Fl = 114;
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public static final byte Mc = 115;
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public static final byte Lv = 116;
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public static final byte Ts = 117;
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public static final byte Og = 118;
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/**
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* Sets the partial charge of this atom.
37160
*

‎descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/HBondDonorCountDescriptor.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -140,7 +140,7 @@ public DescriptorValue calculate(IAtomContainer atomContainer) {
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atomloop: for (int atomIndex = 0; atomIndex < ac.getAtomCount(); atomIndex++) {
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IAtom atom = (IAtom) ac.getAtom(atomIndex);
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// checking for O and N atoms where the formal charge is >= 0
143-
if ((atom.getSymbol().equals("O") || atom.getSymbol().equals("N")) && atom.getFormalCharge() >= 0) {
143+
if ((atom.getAtomicNumber() == IAtom.O || atom.getAtomicNumber() == IAtom.N) && atom.getFormalCharge() >= 0) {
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// implicit hydrogens
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Integer implicitH = atom.getImplicitHydrogenCount();
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if (implicitH == CDKConstants.UNSET) implicitH = 0;
@@ -151,7 +151,7 @@ public DescriptorValue calculate(IAtomContainer atomContainer) {
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// explicit hydrogens
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java.util.List neighbours = ac.getConnectedAtomsList(atom);
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for (Object neighbour : neighbours) {
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if (((IAtom) neighbour).getSymbol().equals("H")) {
154+
if (((IAtom) neighbour).getAtomicNumber() == IAtom.H) {
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hBondDonors++;
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continue atomloop;
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}

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