Revision: 20943
http://sourceforge.net/p/jmol/code/20943
Author: hansonr
Date: 2016-02-04 02:30:08 +0000 (Thu, 04 Feb 2016)
Log Message:
-----------
Added Paths:
-----------
trunk/Jmol/unused/MOCalculationInterface.java
trunk/Jmol/unused/MepCalculationInterface.java
trunk/Jmol/unused/MinimizerInterface.java
trunk/Jmol/unused/QuantumPlaneCalculationInterface.java
trunk/Jmol/unused/VolumeDataInterface.java
Copied: trunk/Jmol/unused/MOCalculationInterface.java (from rev 20941,
trunk/Jmol/src/org/jmol/api/MOCalculationInterface.java)
===================================================================
--- trunk/Jmol/unused/MOCalculationInterface.java
(rev 0)
+++ trunk/Jmol/unused/MOCalculationInterface.java 2016-02-04 02:30:08 UTC
(rev 20943)
@@ -0,0 +1,35 @@
+package org.jmol.api;
+
+
+
+
+
+import javajs.util.Lst;
+import javajs.util.T3;
+
+import org.jmol.java.BS;
+
+
+public interface MOCalculationInterface {
+
+ public abstract boolean setupCalculation(VolumeDataInterface volumeData,
+ BS bsSelected, BS bsExclude,
+ BS[] bsMolecules,
+ String calculationType,
+ T3[] atomCoordAngstroms,
+ T3[] atoms,
+ int firstAtomOffset,
+ Lst<int[]> shells,
+ float[][] gaussians,
+ int[][] dfCoefMaps, Object slaters,
+ float[] moCoefficients,
+ float[] linearCombination,
+ boolean isSquaredLinear,
+ float[][] coefs,
+ float[] partialCharges,
+ boolean doNormalize, T3[] points,
+ float[] parameters, int testFlags);
+
+ public abstract void createCube();
+ public abstract float processPt(T3 pt);
+}
Copied: trunk/Jmol/unused/MepCalculationInterface.java (from rev 20941,
trunk/Jmol/src/org/jmol/api/MepCalculationInterface.java)
===================================================================
--- trunk/Jmol/unused/MepCalculationInterface.java
(rev 0)
+++ trunk/Jmol/unused/MepCalculationInterface.java 2016-02-04 02:30:08 UTC
(rev 20943)
@@ -0,0 +1,23 @@
+package org.jmol.api;
+
+
+
+import org.jmol.java.BS;
+import org.jmol.modelset.Atom;
+import org.jmol.viewer.Viewer;
+
+import javajs.util.P3;
+
+
+public interface MepCalculationInterface {
+
+ public abstract void calculate(VolumeDataInterface volumeData, BS bsSelected,
+ P3[] atomCoordAngstroms, float[] charges, int
calcType);
+
+ public abstract void assignPotentials(Atom[] atoms, float[] potentials, BS
bsAromatic, BS bsCarbonyl, BS bsIgnore, String data);
+
+ public abstract float valueFor(float x, float d2, int distanceMode);
+
+ public abstract void set(Viewer vwr);
+
+}
Copied: trunk/Jmol/unused/MinimizerInterface.java (from rev 20941,
trunk/Jmol/src/org/jmol/api/MinimizerInterface.java)
===================================================================
--- trunk/Jmol/unused/MinimizerInterface.java (rev 0)
+++ trunk/Jmol/unused/MinimizerInterface.java 2016-02-04 02:30:08 UTC (rev
20943)
@@ -0,0 +1,25 @@
+package org.jmol.api;
+
+
+import org.jmol.java.BS;
+import org.jmol.modelset.Atom;
+import org.jmol.modelset.Bond;
+import org.jmol.thread.JmolThread;
+import org.jmol.viewer.JmolAsyncException;
+
+
+
+public interface MinimizerInterface {
+
+ public abstract boolean minimize(int steps, double crit, BS bsSelected,
+ BS bsFixed, boolean haveFixed,
+ boolean isSilent, String ff) throws
Exception;
+ public abstract MinimizerInterface setProperty(String propertyName, Object
propertyValue);
+ public abstract Object getProperty(String propertyName, int param);
+ public abstract void calculatePartialCharges(Bond[] bonds, int bondCount,
Atom[] atoms, BS bsAtoms) throws JmolAsyncException;
+ public abstract boolean startMinimization();
+ public abstract boolean stepMinimization();
+ public abstract void endMinimization();
+ public abstract boolean minimizationOn();
+ public abstract JmolThread getThread();
+}
Copied: trunk/Jmol/unused/QuantumPlaneCalculationInterface.java (from rev
20941, trunk/Jmol/src/org/jmol/api/QuantumPlaneCalculationInterface.java)
===================================================================
--- trunk/Jmol/unused/QuantumPlaneCalculationInterface.java
(rev 0)
+++ trunk/Jmol/unused/QuantumPlaneCalculationInterface.java 2016-02-04
02:30:08 UTC (rev 20943)
@@ -0,0 +1,55 @@
+package org.jmol.api;
+
+/**
+ * Allows modification of the planes prior to isosurface creation
+ * Used by Noncovalent Interaction Calculation for progressive readers
+ */
+
+public interface QuantumPlaneCalculationInterface extends
MOCalculationInterface {
+
+ /**
+ * Planes to use for holding raw file data. These will be managed by
+ * VolumeFileReader, but they will be needed by the calculation.
+ *
+ * @param planes a set of four planes that shifts as the progressive
+ * Marching Cubes process moves along
+ */
+ public abstract void setPlanes(float[][] planes);
+
+ /**
+ * Fill this plane with data based on the current set of raw data planes.
+ * Really there are just two planes that are managed by VolumeFileReader
+ * and are interchanged as the Marching Cubes process moves along.
+ * @param x
+ *
+ * @param plane
+ */
+
+ public abstract void calcPlane(int x, float[] plane);
+
+ /**
+ *
+ * Data mapping function to radically increase speed and reduce
+ * memory requirements of mapping data when the mapping comes from
+ * the same data set as the points, so isosurface creation and
+ * data mapping can be carried out both in the first (and only) pass.
+ *
+ *
+ * @param vA absolute pointer to vertex A on grid
+ * @param vB absolute pointer to vertex B on grid
+ * @param f fractional way from A to B
+ * @return computed value
+ */
+ public abstract float process(int vA, int vB, float f);
+
+ /**
+ * Get that value that represents "no value" so that it can be
+ * disregarded in terms of recording and reporting the min/max/mean.
+ *
+ * @return NO_VALUE
+ */
+ public abstract float getNoValue();
+
+ public abstract void getPlane(int x, float[] yzPlane);
+
+}
Copied: trunk/Jmol/unused/VolumeDataInterface.java (from rev 20941,
trunk/Jmol/src/org/jmol/api/VolumeDataInterface.java)
===================================================================
--- trunk/Jmol/unused/VolumeDataInterface.java (rev 0)
+++ trunk/Jmol/unused/VolumeDataInterface.java 2016-02-04 02:30:08 UTC (rev
20943)
@@ -0,0 +1,47 @@
+package org.jmol.api;
+
+
+import javajs.util.T3;
+import javajs.util.T3i;
+import javajs.util.P4;
+import javajs.util.V3;
+
+public interface VolumeDataInterface {
+
+ public abstract void setVoxelDataAsArray(float[][][] voxelData);
+
+ public abstract float[][][] getVoxelData();
+
+ public abstract int setVoxelCounts(int nPointsX, int nPointsY, int nPointsZ);
+
+ public abstract int[] getVoxelCounts();
+
+ public abstract void setVolumetricVector(int i, float x, float y, float z);
+
+ public abstract float[] getVolumetricVectorLengths();
+
+ public abstract void setVolumetricOrigin(float x, float y, float z);
+
+ public abstract float[] getOriginFloat();
+
+ public abstract void setDataDistanceToPlane(P4 plane);
+
+ public abstract void setPlaneParameters(P4 plane);
+
+ public abstract float calcVoxelPlaneDistance(int x, int y, int z);
+
+ public abstract float distancePointToPlane(T3 pt);
+
+ public abstract void transform(V3 v1, V3 v2);
+
+ public abstract void voxelPtToXYZ(int x, int y, int z, T3 pt);
+
+ public abstract void xyzToVoxelPt(float x, float y, float z, T3i pt3i);
+
+ public abstract float lookupInterpolatedVoxelValue(T3 point, boolean
getSource);
+
+ public abstract void filterData(boolean isSquared, float invertCutoff);
+
+ public abstract void capData(P4 plane, float cutoff);
+
+}
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