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johnmayjohnmay
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Cleanup code using generics
1 parent 1bf61af commit 05dd6e1

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‎descriptor/qsarmolecular/src/main/java/org/openscience/cdk/geometry/surface/NumericalSurface.java‎

Lines changed: 44 additions & 58 deletions
Original file line numberDiff line numberDiff line change
@@ -30,8 +30,7 @@
3030

3131
import javax.vecmath.Point3d;
3232
import java.util.ArrayList;
33-
import java.util.Iterator;
34-
import org.openscience.cdk.geometry.surface.Point_Type;
33+
import java.util.List;
3534

3635
/**
3736
* A class representing the solvent accessible surface area surface of a molecule.
@@ -59,12 +58,12 @@
5958
public class NumericalSurface {
6059

6160
private static ILoggingTool logger = LoggingToolFactory.createLoggingTool(NumericalSurface.class);
62-
double solventRadius = 1.4;
63-
int tesslevel = 4;
64-
IAtom[] atoms;
65-
ArrayList[] surfPoints;
66-
double[] areas;
67-
double[] volumes;
61+
double solventRadius = 1.4;
62+
int tesslevel = 4;
63+
IAtom[] atoms;
64+
List<Point3d>[] surfPoints;
65+
double[] areas;
66+
double[] volumes;
6867

6968
/**
7069
* Constructor to initialize the surface calculation with default values.
@@ -125,14 +124,14 @@ private void init() {
125124
// get r_f and geometric center
126125
Point3d cp = new Point3d(0, 0, 0);
127126
double maxRadius = 0;
128-
for (int i = 0; i < atoms.length; i++) {
129-
double vdwr = PeriodicTable.getVdwRadius(atoms[i].getSymbol());
127+
for (IAtom atom : atoms) {
128+
double vdwr = PeriodicTable.getVdwRadius(atom.getSymbol());
130129
if (vdwr + solventRadius > maxRadius)
131-
maxRadius = PeriodicTable.getVdwRadius(atoms[i].getSymbol()) + solventRadius;
130+
maxRadius = PeriodicTable.getVdwRadius(atom.getSymbol()) + solventRadius;
132131

133-
cp.x = cp.x + atoms[i].getPoint3d().x;
134-
cp.y = cp.y + atoms[i].getPoint3d().y;
135-
cp.z = cp.z + atoms[i].getPoint3d().z;
132+
cp.x = cp.x + atom.getPoint3d().x;
133+
cp.y = cp.y + atom.getPoint3d().y;
134+
cp.z = cp.z + atom.getPoint3d().z;
136135
}
137136
cp.x = cp.x / atoms.length;
138137
cp.y = cp.y / atoms.length;
@@ -154,7 +153,7 @@ private void init() {
154153
*/
155154

156155
// loop over atoms and get surface points
157-
this.surfPoints = new ArrayList[atoms.length];
156+
this.surfPoints = (List<Point3d>[]) new List[atoms.length];
158157
this.areas = new double[atoms.length];
159158
this.volumes = new double[atoms.length];
160159

@@ -177,36 +176,30 @@ private void init() {
177176
*/
178177
public Point3d[] getAllSurfacePoints() {
179178
int npt = 0;
180-
for (int i = 0; i < this.surfPoints.length; i++)
181-
npt += this.surfPoints[i].size();
179+
for (List<Point3d> surfPoint : this.surfPoints)
180+
npt += surfPoint.size();
182181
Point3d[] ret = new Point3d[npt];
183182
int j = 0;
184-
for (int i = 0; i < this.surfPoints.length; i++) {
185-
ArrayList arl = this.surfPoints[i];
186-
for (Iterator it = arl.iterator(); it.hasNext();) {
187-
ret[j] = (Point3d) it.next();
188-
j++;
183+
for (List<Point3d> points : this.surfPoints) {
184+
for (Point3d p : points) {
185+
ret[j++] = p;
189186
}
190187
}
191188
return (ret);
192189
}
193190

194191
public ArrayList<Point_Type> getAllPointswithAtomType() {
195192
int npt = 0;
196-
for (int i = 0; i < this.surfPoints.length; i++)
197-
npt += this.surfPoints[i].size();
198-
//Point3d[] ret = new Point3d[npt];
193+
for (List<Point3d> surfPoint : this.surfPoints)
194+
npt += surfPoint.size();
199195
ArrayList<Point_Type> point_types = new ArrayList<Point_Type>(npt);
200-
//ArrayList<Integer> atomtype = new ArrayList<Integer>(npt);
201196
int j = 0;
202197
for (int i = 0; i < this.surfPoints.length; i++) {
203-
ArrayList arl = this.surfPoints[i];
204-
//atomtype.add(this.atoms[i].getAtomicNumber());
205-
for (Iterator it = arl.iterator(); it.hasNext();) {
206-
//ret[j] = (Point3d) it.next();
198+
List<Point3d> arl = this.surfPoints[i];
199+
for (Point3d p : arl) {
207200
Point_Type point_type = new Point_Type();
208201
point_type.setAtom(this.atoms[i].getAtomicNumber());
209-
point_type.setCoord((Point3d) it.next());
202+
point_type.setCoord(p);
210203
point_types.add(point_type);
211204
j++;
212205
}
@@ -223,14 +216,9 @@ public ArrayList<Point_Type> getAllPointswithAtomType() {
223216
* @throws CDKException if the atom index is outside the range of allowable indices
224217
*/
225218
public Point3d[] getSurfacePoints(int atomIdx) throws CDKException {
226-
if (atomIdx >= this.surfPoints.length) {
219+
if (atomIdx >= this.surfPoints.length)
227220
throw new CDKException("Atom index was out of bounds");
228-
}
229-
ArrayList arl = this.surfPoints[atomIdx];
230-
Point3d[] ret = new Point3d[arl.size()];
231-
for (int i = 0; i < arl.size(); i++)
232-
ret[i] = (Point3d) arl.get(i);
233-
return (ret);
221+
return this.surfPoints[atomIdx].toArray(new Point3d[0]);
234222
}
235223

236224
/**
@@ -242,10 +230,9 @@ public Point3d[] getSurfacePoints(int atomIdx) throws CDKException {
242230
* @throws CDKException if the atom index is outside the range of allowable indices
243231
*/
244232
public double getSurfaceArea(int atomIdx) throws CDKException {
245-
if (atomIdx >= this.surfPoints.length) {
233+
if (atomIdx >= this.surfPoints.length)
246234
throw new CDKException("Atom index was out of bounds");
247-
}
248-
return (this.areas[atomIdx]);
235+
return this.areas[atomIdx];
249236
}
250237

251238
/**
@@ -254,7 +241,7 @@ public double getSurfaceArea(int atomIdx) throws CDKException {
254241
* @return An array of double giving the surface areas of all the atoms
255242
*/
256243
public double[] getAllSurfaceAreas() {
257-
return (this.areas);
244+
return this.areas;
258245
}
259246

260247
/**
@@ -265,9 +252,9 @@ public double[] getAllSurfaceAreas() {
265252
*/
266253
public double getTotalSurfaceArea() {
267254
double ta = 0.0;
268-
for (int i = 0; i < this.areas.length; i++)
269-
ta += this.areas[i];
270-
return (ta);
255+
for (double area : this.areas)
256+
ta += area;
257+
return ta;
271258
}
272259

273260
private void translatePoints(int atmIdx, Point3d[][] points, int pointDensity, IAtom atom, Point3d cp) {
@@ -278,8 +265,8 @@ private void translatePoints(int atmIdx, Point3d[][] points, int pointDensity, I
278265
double sumx = 0.0;
279266
double sumy = 0.0;
280267
double sumz = 0.0;
281-
for (int i = 0; i < points.length; i++) {
282-
Point3d p = points[i][1];
268+
for (Point3d[] point : points) {
269+
Point3d p = point[1];
283270
sumx += p.x;
284271
sumy += p.y;
285272
sumz += p.z;
@@ -293,9 +280,9 @@ private void translatePoints(int atmIdx, Point3d[][] points, int pointDensity, I
293280
this.areas[atmIdx] = area;
294281
this.volumes[atmIdx] = volume;
295282

296-
ArrayList tmp = new ArrayList();
297-
for (int i = 0; i < points.length; i++)
298-
tmp.add(points[i][0]);
283+
List<Point3d> tmp = new ArrayList<>();
284+
for (Point3d[] point : points)
285+
tmp.add(point[0]);
299286
this.surfPoints[atmIdx] = tmp;
300287
}
301288

@@ -324,20 +311,19 @@ private Point3d[][] atomicSurfacePoints(NeighborList nbrlist, int currAtomIdx, I
324311
}
325312

326313
Point3d[] tessPoints = tess.getTessAsPoint3ds();
327-
ArrayList points = new ArrayList();
328-
for (int i = 0; i < tessPoints.length; i++) {
329-
Point3d pt = tessPoints[i];
314+
List<Point3d[]> points = new ArrayList<>();
315+
for (Point3d pt : tessPoints) {
330316
boolean buried = false;
331-
for (int j = 0; j < data.length; j++) {
332-
if (data[j][0] * pt.x + data[j][1] * pt.y + data[j][2] * pt.z > data[j][3]) {
317+
for (double[] datum : data) {
318+
if (datum[0] * pt.x + datum[1] * pt.y + datum[2] * pt.z > datum[3]) {
333319
buried = true;
334320
break;
335321
}
336322
}
337-
if (buried == false) {
323+
if (!buried) {
338324
Point3d[] tmp = new Point3d[2];
339325
tmp[0] = new Point3d(totalRadius * pt.x + atom.getPoint3d().x, totalRadius * pt.y
340-
+ atom.getPoint3d().y, totalRadius * pt.z + atom.getPoint3d().z);
326+
+ atom.getPoint3d().y, totalRadius * pt.z + atom.getPoint3d().z);
341327
tmp[1] = pt;
342328
points.add(tmp);
343329
}
@@ -348,7 +334,7 @@ private Point3d[][] atomicSurfacePoints(NeighborList nbrlist, int currAtomIdx, I
348334
// original unit tesselation
349335
Point3d[][] ret = new Point3d[points.size()][2];
350336
for (int i = 0; i < points.size(); i++) {
351-
Point3d[] tmp = (Point3d[]) points.get(i);
337+
Point3d[] tmp = points.get(i);
352338
ret[i][0] = tmp[0];
353339
ret[i][1] = tmp[1];
354340
}

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