Cont replacing getSymbol in ALOGPDescriptor using regex

xperrylinn · xperrylinn · commit cc814c32f561 · 2020-06-17T11:42:26.000-07:00
diff --git a/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.java b/descriptor/qsarmolecular/src/main/java/org/openscience/cdk/qsar/descriptors/molecular/ALOGPDescriptor.java
@@ -646,7 +646,7 @@ private void calcGroup016_018_036_037(int i) {
             }
 
             if (atomContainer.getBond(ai, ((IAtom) ca.get(j))).getOrder() == IBond.Order.SINGLE) {
-                if (!((IAtom) ca.get(j)).getSymbol().equals("C")) {
+                if (((IAtom) ca.get(j)).getAtomicNumber() != IElement.C) {
                     haveCsX = true;
                 }
 
@@ -656,7 +656,7 @@ private void calcGroup016_018_036_037(int i) {
 
             }
             else if (atomContainer.getBond(ai, ((IAtom) ca.get(j))).getOrder() == IBond.Order.DOUBLE) {
-                if (!((IAtom) ca.get(j)).getSymbol().equals("C")) {
+                if (((IAtom) ca.get(j)).getAtomicNumber() != IElement.C) {
                     haveCdX = true;
                 }
             }
@@ -782,7 +782,7 @@ else if (fragment[i].equals("SddC")) {
                 frags[22]++;
                 alogpfrag[i] = 22;
             }
-            else if (!((IAtom) nbors.get(0)).getSymbol().equals("C") && !((IAtom) nbors.get(1)).getSymbol().equals("C")) {// X==C==X
+            else if (((IAtom) nbors.get(0)).getAtomicNumber() != IElement.C && ((IAtom) nbors.get(1)).getAtomicNumber() != IElement.C) {// X==C==X
                 frags[40]++;
                 alogpfrag[i] = 40;
             }
@@ -794,11 +794,11 @@ else if (fragment[i].equals("StsC")) {
 
             for (int j = 0; j <= nbors.size() - 1; j++) {
                 if (atomContainer.getBond(ai, ((IAtom) nbors.get(j))).getOrder() == IBond.Order.SINGLE) {
-                    if (!((IAtom) nbors.get(j)).getSymbol().equals("C")) {
+                    if (((IAtom) nbors.get(j)).getAtomicNumber() != IElement.C) {
                         haveCsX = true;
                     }
                 } else if (atomContainer.getBond(ai, ((IAtom) nbors.get(j))).getOrder() == IBond.Order.TRIPLE) {
-                    if (!((IAtom) nbors.get(j)).getSymbol().equals("C")) {
+                    if (((IAtom) nbors.get(j)).getAtomicNumber() != IElement.C) {
                         haveCtX = true;
                     }
                 }
@@ -876,7 +876,7 @@ private void calcGroup024_027_030_033_042(int i) {
             }
         }
 
-        if (!(ca0).getSymbol().equals("C") && !((IAtom) nbors.get(1)).getSymbol().equals("C")) {
+        if ((ca0).getAtomicNumber() != IElement.C && ((IAtom) nbors.get(1)).getAtomicNumber() != IElement.C) {
             if (haveDouble1 && haveDouble2) { // X--CH--X
                 frags[30]++;
                 alogpfrag[i] = 30;
@@ -977,7 +977,7 @@ public int compare(IAtom a, IAtom b) {
 
         }
 
-        if (!sameringatoms[0].getSymbol().equals("C") && !sameringatoms[1].getSymbol().equals("C")) {
+        if (sameringatoms[0].getAtomicNumber() != IElement.C && sameringatoms[1].getAtomicNumber() != IElement.C) {
             if (haveDouble1 && haveDouble2) { // X--CR--X
                 if (nonringatom.getAtomicNumber() == IElement.C) {
                     frags[31]++;
@@ -1009,8 +1009,8 @@ public int compare(IAtom a, IAtom b) {
                 alogpfrag[i] = 26;
             }
 
-        } else if ((sameringatoms[0].getSymbol().equals("C") && !sameringatoms[1].getSymbol().equals("C"))
-                || (!sameringatoms[0].getSymbol().equals("C") && sameringatoms[1].getSymbol().equals("C"))) {
+        } else if ((sameringatoms[0].getSymbol().equals("C") && sameringatoms[1].getAtomicNumber() != IElement.C)
+                || (sameringatoms[0].getAtomicNumber() != IElement.C && sameringatoms[1].getSymbol().equals("C"))) {
 
             if (haveDouble1 && haveDouble2) { // R--CR--X
                 if (nonringatom.getAtomicNumber() == IElement.C) {
@@ -1294,7 +1294,7 @@ private void calcGroup059_060_063(int i) {
                          List ca2 = atomContainer.getConnectedAtomsList(((IAtom) ca.get(j)));
                          for (int k = 0; k <= ca2.size() - 1; k++) {
                              if (atomContainer.getBond(((IAtom) ca.get(j)), (IAtom) ca2.get(k)).getOrder() == IBond.Order.DOUBLE) {
-                                 if (!((IAtom) ca2.get(k)).getSymbol().equals("C")) {
+                                 if (((IAtom) ca2.get(k)).getAtomicNumber() != IElement.C) {
                                      frags[60]++;
                                      alogpfrag[i] = 60;
                                      return;
@@ -1483,7 +1483,7 @@ private void calcGroup066_to_079(int i) {
                         flag1 = true;
                     }
                 } else {
-                    if (!((IAtom) nbors.get(j)).getSymbol().equals("C")
+                    if (((IAtom) nbors.get(j)).getAtomicNumber() != IElement.C
                             || ((IAtom) nbors.get(j)).getFlag(CDKConstants.ISAROMATIC)) {
                         flag2 = true;
                     }
@@ -1982,7 +1982,7 @@ private void calcGroup116_117_120(int i) {
                     xCount++;
                 }
             } else if (atomContainer.getBond(ai, ((IAtom) ca.get(j))).getOrder() == IBond.Order.DOUBLE) {
-                if (!((IAtom) ca.get(j)).getSymbol().equals("C")) {
+                if (((IAtom) ca.get(j)).getAtomicNumber() != IElement.C) {
                     pdX = true;
                 }
             }

Original file line number	Diff line number	Diff line change
`@@ -646,7 +646,7 @@ private void calcGroup016_018_036_037(int i) {`
`646`	`646`	`}`
`647`	`647`
`648`	`648`	`if (atomContainer.getBond(ai, ((IAtom) ca.get(j))).getOrder() == IBond.Order.SINGLE) {`
`649`		`- if (!((IAtom) ca.get(j)).getSymbol().equals("C")) {`
	`649`	`+ if (((IAtom) ca.get(j)).getAtomicNumber() != IElement.C) {`
`650`	`650`	`haveCsX = true;`
`651`	`651`	`}`
`652`	`652`
`@@ -656,7 +656,7 @@ private void calcGroup016_018_036_037(int i) {`
`656`	`656`
`657`	`657`	`}`
`658`	`658`	`else if (atomContainer.getBond(ai, ((IAtom) ca.get(j))).getOrder() == IBond.Order.DOUBLE) {`
`659`		`- if (!((IAtom) ca.get(j)).getSymbol().equals("C")) {`
	`659`	`+ if (((IAtom) ca.get(j)).getAtomicNumber() != IElement.C) {`
`660`	`660`	`haveCdX = true;`
`661`	`661`	`}`
`662`	`662`	`}`
`@@ -782,7 +782,7 @@ else if (fragment[i].equals("SddC")) {`
`782`	`782`	`frags[22]++;`
`783`	`783`	`alogpfrag[i] = 22;`
`784`	`784`	`}`
`785`		`- else if (!((IAtom) nbors.get(0)).getSymbol().equals("C") && !((IAtom) nbors.get(1)).getSymbol().equals("C")) {// X==C==X`
	`785`	`+ else if (((IAtom) nbors.get(0)).getAtomicNumber() != IElement.C && ((IAtom) nbors.get(1)).getAtomicNumber() != IElement.C) {// X==C==X`
`786`	`786`	`frags[40]++;`
`787`	`787`	`alogpfrag[i] = 40;`
`788`	`788`	`}`
`@@ -794,11 +794,11 @@ else if (fragment[i].equals("StsC")) {`
`794`	`794`
`795`	`795`	`for (int j = 0; j <= nbors.size() - 1; j++) {`
`796`	`796`	`if (atomContainer.getBond(ai, ((IAtom) nbors.get(j))).getOrder() == IBond.Order.SINGLE) {`
`797`		`- if (!((IAtom) nbors.get(j)).getSymbol().equals("C")) {`
	`797`	`+ if (((IAtom) nbors.get(j)).getAtomicNumber() != IElement.C) {`
`798`	`798`	`haveCsX = true;`
`799`	`799`	`}`
`800`	`800`	`} else if (atomContainer.getBond(ai, ((IAtom) nbors.get(j))).getOrder() == IBond.Order.TRIPLE) {`
`801`		`- if (!((IAtom) nbors.get(j)).getSymbol().equals("C")) {`
	`801`	`+ if (((IAtom) nbors.get(j)).getAtomicNumber() != IElement.C) {`
`802`	`802`	`haveCtX = true;`
`803`	`803`	`}`
`804`	`804`	`}`
`@@ -876,7 +876,7 @@ private void calcGroup024_027_030_033_042(int i) {`
`876`	`876`	`}`
`877`	`877`	`}`
`878`	`878`
`879`		`- if (!(ca0).getSymbol().equals("C") && !((IAtom) nbors.get(1)).getSymbol().equals("C")) {`
	`879`	`+ if ((ca0).getAtomicNumber() != IElement.C && ((IAtom) nbors.get(1)).getAtomicNumber() != IElement.C) {`
`880`	`880`	`if (haveDouble1 && haveDouble2) { // X--CH--X`
`881`	`881`	`frags[30]++;`
`882`	`882`	`alogpfrag[i] = 30;`
`@@ -977,7 +977,7 @@ public int compare(IAtom a, IAtom b) {`
`977`	`977`
`978`	`978`	`}`
`979`	`979`
`980`		`- if (!sameringatoms[0].getSymbol().equals("C") && !sameringatoms[1].getSymbol().equals("C")) {`
	`980`	`+ if (sameringatoms[0].getAtomicNumber() != IElement.C && sameringatoms[1].getAtomicNumber() != IElement.C) {`
`981`	`981`	`if (haveDouble1 && haveDouble2) { // X--CR--X`
`982`	`982`	`if (nonringatom.getAtomicNumber() == IElement.C) {`
`983`	`983`	`frags[31]++;`
`@@ -1009,8 +1009,8 @@ public int compare(IAtom a, IAtom b) {`
`1009`	`1009`	`alogpfrag[i] = 26;`
`1010`	`1010`	`}`
`1011`	`1011`
`1012`		`- } else if ((sameringatoms[0].getSymbol().equals("C") && !sameringatoms[1].getSymbol().equals("C"))`
`1013`		`- \|\| (!sameringatoms[0].getSymbol().equals("C") && sameringatoms[1].getSymbol().equals("C"))) {`
	`1012`	`+ } else if ((sameringatoms[0].getSymbol().equals("C") && sameringatoms[1].getAtomicNumber() != IElement.C)`
	`1013`	`+ \|\| (sameringatoms[0].getAtomicNumber() != IElement.C && sameringatoms[1].getSymbol().equals("C"))) {`
`1014`	`1014`
`1015`	`1015`	`if (haveDouble1 && haveDouble2) { // R--CR--X`
`1016`	`1016`	`if (nonringatom.getAtomicNumber() == IElement.C) {`
`@@ -1294,7 +1294,7 @@ private void calcGroup059_060_063(int i) {`
`1294`	`1294`	`List ca2 = atomContainer.getConnectedAtomsList(((IAtom) ca.get(j)));`
`1295`	`1295`	`for (int k = 0; k <= ca2.size() - 1; k++) {`
`1296`	`1296`	`if (atomContainer.getBond(((IAtom) ca.get(j)), (IAtom) ca2.get(k)).getOrder() == IBond.Order.DOUBLE) {`
`1297`		`- if (!((IAtom) ca2.get(k)).getSymbol().equals("C")) {`
	`1297`	`+ if (((IAtom) ca2.get(k)).getAtomicNumber() != IElement.C) {`
`1298`	`1298`	`frags[60]++;`
`1299`	`1299`	`alogpfrag[i] = 60;`
`1300`	`1300`	`return;`
`@@ -1483,7 +1483,7 @@ private void calcGroup066_to_079(int i) {`
`1483`	`1483`	`flag1 = true;`
`1484`	`1484`	`}`
`1485`	`1485`	`} else {`
`1486`		`- if (!((IAtom) nbors.get(j)).getSymbol().equals("C")`
	`1486`	`+ if (((IAtom) nbors.get(j)).getAtomicNumber() != IElement.C`
`1487`	`1487`	`\|\| ((IAtom) nbors.get(j)).getFlag(CDKConstants.ISAROMATIC)) {`
`1488`	`1488`	`flag2 = true;`
`1489`	`1489`	`}`
`@@ -1982,7 +1982,7 @@ private void calcGroup116_117_120(int i) {`
`1982`	`1982`	`xCount++;`
`1983`	`1983`	`}`
`1984`	`1984`	`} else if (atomContainer.getBond(ai, ((IAtom) ca.get(j))).getOrder() == IBond.Order.DOUBLE) {`
`1985`		`- if (!((IAtom) ca.get(j)).getSymbol().equals("C")) {`
	`1985`	`+ if (((IAtom) ca.get(j)).getAtomicNumber() != IElement.C) {`
`1986`	`1986`	`pdX = true;`
`1987`	`1987`	`}`
`1988`	`1988`	`}`