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johnmayjohnmay
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Remove unnecessary qualification.
1 parent a59d790 commit 3bcfe0d

1 file changed

Lines changed: 27 additions & 28 deletions

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

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

Lines changed: 27 additions & 28 deletions
Original file line numberDiff line numberDiff line change
@@ -524,7 +524,7 @@ private void calcGroup003_008_009_010(int i) {
524524

525525
if (fragment[i].equals("SsssCH")) {
526526

527-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
527+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
528528
int htype = getHAtomType(atomContainer.getAtom(i), ca);
529529
int carbonCount = 0;
530530
int heteroCount = 0;
@@ -562,7 +562,7 @@ else if (carbonCount == 0 && heteroCount == 3) {
562562
private void calcGroup004_011_to_014(int i) {
563563
// C in CR4, CR3X, CX4
564564
if (fragment[i].equals("SssssC")) {
565-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
565+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
566566
int carbonCount = 0;
567567
int heteroCount = 0;
568568
// logger.debug("here");
@@ -675,7 +675,7 @@ private void calcGroup017_019_020_038_to_041(int i) {
675675

676676
if (!fragment[i].equals("SdssC")) return;
677677

678-
java.util.List ca = atomContainer.getConnectedAtomsList(ai);
678+
List ca = atomContainer.getConnectedAtomsList(ai);
679679

680680
int rCount = 0;
681681
int xCount = 0;
@@ -848,7 +848,7 @@ private void calcGroup024_027_030_033_042(int i) {
848848
}
849849

850850
// check if both hetero atoms have at least one double bond
851-
java.util.List bonds = atomContainer.getConnectedBondsList(ca0);
851+
List bonds = atomContainer.getConnectedBondsList(ca0);
852852
boolean haveDouble1 = false;
853853
for (int k = 0; k <= bonds.size() - 1; k++) {
854854
if (((IBond) bonds.get(k)).getOrder() == IBond.Order.DOUBLE) {
@@ -904,7 +904,7 @@ private void calcGroup025_026_028_029_031_032_034_035_043_044(int i) {
904904
if (!fragment[i].equals("SsaaC") && !fragment[i].equals("SaaaC")) return;
905905

906906
IAtom ai = atomContainer.getAtom(i);
907-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
907+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
908908

909909
IAtom[] sameringatoms = new IAtom[2];
910910
IAtom nonringatom = atomContainer.getBuilder().newInstance(IAtom.class);
@@ -936,7 +936,7 @@ private void calcGroup025_026_028_029_031_032_034_035_043_044(int i) {
936936
}
937937

938938
// check if both hetero atoms have at least one double bond
939-
java.util.List bonds = atomContainer.getConnectedBondsList(sameringatoms[0]);
939+
List bonds = atomContainer.getConnectedBondsList(sameringatoms[0]);
940940

941941
boolean haveDouble1 = false;
942942

@@ -1151,7 +1151,7 @@ private void calcGroup056_57(int i) {
11511151
return;
11521152
}
11531153

1154-
java.util.List ca2 = atomContainer.getConnectedAtomsList(ca0);
1154+
List ca2 = atomContainer.getConnectedAtomsList(ca0);
11551155
for (int j = 0; j <= ca2.size() - 1; j++) {
11561156
if (atomContainer.getBond((IAtom) ca2.get(j), ca0).getOrder() == IBond.Order.DOUBLE) {
11571157
frags[57]++;
@@ -1164,7 +1164,7 @@ private void calcGroup056_57(int i) {
11641164
}
11651165

11661166
private void calcGroup058_61(int i) {
1167-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
1167+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
11681168

11691169
// 58: O in =O
11701170
// 61: --O in nitro, N-oxides
@@ -1199,7 +1199,7 @@ private void calcGroup059_060_063(int i) {
11991199
if (!fragment[i].equals("SssO") && !fragment[i].equals("SaaO")) return;
12001200

12011201
// Al-O-Ar, Ar2O
1202-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
1202+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
12031203
IAtom ca0 = (IAtom) ca.get(0);
12041204
IAtom ca1 = (IAtom) ca.get(1);
12051205

@@ -1215,7 +1215,7 @@ private void calcGroup059_060_063(int i) {
12151215
// O-P(=S)
12161216
// was considered to count as group 60
12171217

1218-
java.util.List ca2 = atomContainer.getConnectedAtomsList(((IAtom) ca.get(j)));
1218+
List ca2 = atomContainer.getConnectedAtomsList(((IAtom) ca.get(j)));
12191219
for (int k = 0; k <= ca2.size() - 1; k++) {
12201220
if (atomContainer.getBond(((IAtom) ca.get(j)), (IAtom) ca2.get(k)).getOrder() == IBond.Order.DOUBLE) {
12211221
if (!((IAtom) ca2.get(k)).getSymbol().equals("C")) {
@@ -1271,7 +1271,7 @@ private void calcGroup066_to_079(int i) {
12711271
for (int j = 0; j <= nbors.size() - 1; j++) {
12721272
if (nbors.get(j).getAtomicNumber() == 1)
12731273
continue;
1274-
java.util.List ca2 = atomContainer.getConnectedAtomsList((IAtom) nbors.get(j));
1274+
List ca2 = atomContainer.getConnectedAtomsList((IAtom) nbors.get(j));
12751275
for (int k = 0; k <= ca2.size() - 1; k++) {
12761276
IAtom ca2k = (IAtom) ca2.get(k);
12771277
if (atomContainer.indexOf(ca2k) != i) {
@@ -1426,10 +1426,10 @@ private void calcGroup081_to_085(int i) {
14261426

14271427
if (!fragment[i].equals("SsF")) return;
14281428

1429-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
1429+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
14301430
IAtom ca0 = (IAtom) ca.get(0);
14311431

1432-
java.util.List bonds = atomContainer.getConnectedBondsList(ca0);
1432+
List bonds = atomContainer.getConnectedBondsList(ca0);
14331433

14341434
int doublebondcount = 0;
14351435
int triplebondcount = 0;
@@ -1456,10 +1456,9 @@ else if (bj.getOrder() == IBond.Order.TRIPLE) {
14561456
hybrid = "sp";
14571457
}
14581458

1459-
java.util.List ca2 = atomContainer.getConnectedAtomsList(ca0);
1459+
List ca2 = atomContainer.getConnectedAtomsList(ca0);
14601460

14611461
int oxNum = 0;
1462-
14631462
for (int j = 0; j <= ca2.size() - 1; j++) {
14641463
IAtom ca2j = (IAtom) ca2.get(j);
14651464
if (isHetero(ca2j))
@@ -1490,10 +1489,10 @@ private void calcGroup086_to_090(int i) {
14901489

14911490
if (!fragment[i].equals("SsCl")) return;
14921491

1493-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
1492+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
14941493
IAtom ca0 = (IAtom) ca.get(0);
14951494

1496-
java.util.List bonds = atomContainer.getConnectedBondsList(ca0);
1495+
List bonds = atomContainer.getConnectedBondsList(ca0);
14971496

14981497
int doublebondcount = 0;
14991498
int triplebondcount = 0;
@@ -1520,7 +1519,7 @@ else if (bj.getOrder() == IBond.Order.TRIPLE) {
15201519
hybrid = "sp";
15211520
}
15221521

1523-
java.util.List ca2 = atomContainer.getConnectedAtomsList(ca0);
1522+
List ca2 = atomContainer.getConnectedAtomsList(ca0);
15241523

15251524
int oxNum = 0;
15261525

@@ -1561,10 +1560,10 @@ private void calcGroup091_to_095(int i) {
15611560

15621561
if (!fragment[i].equals("SsBr")) return;
15631562

1564-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
1563+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
15651564
IAtom ca0 = (IAtom) ca.get(0);
15661565

1567-
java.util.List bonds = atomContainer.getConnectedBondsList(ca0);
1566+
List bonds = atomContainer.getConnectedBondsList(ca0);
15681567

15691568
int doublebondcount = 0;
15701569
int triplebondcount = 0;
@@ -1591,7 +1590,7 @@ private void calcGroup091_to_095(int i) {
15911590
hybrid = "sp";
15921591
}
15931592

1594-
java.util.List ca2 = atomContainer.getConnectedAtomsList(ca0);
1593+
List ca2 = atomContainer.getConnectedAtomsList(ca0);
15951594

15961595
int oxNum = 0;
15971596

@@ -1633,10 +1632,10 @@ private void calcGroup096_to_100(int i) {
16331632

16341633
if (!fragment[i].equals("SsI")) return;
16351634

1636-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
1635+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
16371636
IAtom ca0 = (IAtom) ca.get(0);
16381637

1639-
java.util.List bonds = atomContainer.getConnectedBondsList(ca0);
1638+
List bonds = atomContainer.getConnectedBondsList(ca0);
16401639

16411640
int doublebondcount = 0;
16421641
int triplebondcount = 0;
@@ -1663,7 +1662,7 @@ else if (bj.getOrder() == IBond.Order.TRIPLE) {
16631662
hybrid = "sp";
16641663
}
16651664

1666-
java.util.List ca2 = atomContainer.getConnectedAtomsList(ca0);
1665+
List ca2 = atomContainer.getConnectedAtomsList(ca0);
16671666

16681667
int oxNum = 0;
16691668

@@ -1780,7 +1779,7 @@ private void calcGroup109(int i) {
17801779
// (it doesn't check which atoms are singly bonded to S
17811780
if (!fragment[i].equals("SdssS")) return;
17821781

1783-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
1782+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
17841783
IAtom ai = atomContainer.getAtom(i);
17851784
int sdOCount = 0;
17861785
int ssCCount = 0;
@@ -1805,7 +1804,7 @@ private void calcGroup109(int i) {
18051804
private void calcGroup110(int i) {
18061805
if (!fragment[i].equals("SddssS")) return;
18071806

1808-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
1807+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
18091808
IAtom ai = atomContainer.getAtom(i);
18101809
int sdOCount = 0;
18111810
int ssCCount = 0;
@@ -1839,7 +1838,7 @@ private void calcGroup116_117_120(int i) {
18391838

18401839
// S in R=S
18411840

1842-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
1841+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
18431842
IAtom ai = atomContainer.getAtom(i);
18441843

18451844
int xCount = 0;
@@ -1880,7 +1879,7 @@ private void calcGroup116_117_120(int i) {
18801879
private void calcGroup118_119(int i) {
18811880
if (!fragment[i].equals("SsssP")) return;
18821881

1883-
java.util.List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
1882+
List ca = atomContainer.getConnectedAtomsList(atomContainer.getAtom(i));
18841883
IAtom ai = atomContainer.getAtom(i);
18851884
int xCount = 0;
18861885
int rCount = 0;

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