package com.java_test1; // import everything // import com.camitro.applets.MoleculeDisplay.*; // import com.camitro.applets.RmiHelloWorld.*; // import com.camitro.apps.cam_CoMMA.*; import com.camitro.apps.cam_convert.*; import com.camitro.apps.cam_db.*; import com.camitro.apps.cam_desc.*; import com.camitro.apps.cam_master.*; import com.camitro.apps.cam_meta.*; // import com.camitro.apps.cam_molmap.*; import com.camitro.apps.cam_reset.*; import com.camitro.apps.cam_smiles.*; import com.camitro.apps.cam_worker.*; // import com.camitro.apps.test_db.*; // import com.camitro.apps.testMolecule.*; import com.camitro.toolkit.CamDatabase.*; import com.camitro.toolkit.CamUtil.*; import com.camitro.toolkit.Cluster.*; import com.camitro.toolkit.ClusterServer.*; import com.camitro.toolkit.ComputeService.*; import com.camitro.toolkit.DescModel.*; import com.camitro.toolkit.ElecModel.*; import com.camitro.toolkit.GeneralFile.*; import com.camitro.toolkit.ModelService.*; import com.camitro.toolkit.Molecule.*; import com.camitro.toolkit.MoleculeFile.*; import com.camitro.toolkit.MoleculeFutures.*; // import com.camitro.toolkit.MoleculeSymmetry.*; // import com.camitro.toolkit.Molmap.*; import com.wellscs.PriorityQueue.*; // import com.wellscs.PriorityQueueTestApplet.*; import gnu.regexp.*; // import gov.nist.Jama.*; // import gov.nist.Jama.util.*; import javax.swing.*; // import javax.vecmath.*; import java.awt.Color; import java.lang.*; import java.io.*; import java.net.*; import java.rmi.Remote; import java.rmi.RemoteException; import java.text.*; import java.util.*; // import chemft.chemserver.*; // import chemft.molapplet.*; // import chemft.webdraw.*; // import chemft.gif.*; // import chemft.smile.*; // import chemft.d32.*; // import oracle.sql.*; // import oracle.jdbc.driver.*; // Make a class. public class java_test1 { // Make some variables to reuse. private static boolean boolean1 = true; private static Date Date1 = new Date(); private static String String_date1 = (new Date()).toString(); private static int int1 = 0; private static long long1 = 0; private static double double1 = 0; private static char char1 = '0'; private static String String1 = "0"; private static String[] String2; private static LongString LongString1; private static Exception exc1; private static java.lang.Object Object1; private static java.util.Vector Vector1; private static java.util.Vector Vector2; private static Point Point2; private static Point Point3; private static Point Point4; private static Atom Atom1; private static Atom Atom2; private static Atom Atom3; private static Atom Atom4; private static Carbon Carbon2; private static Carbon Carbon3; private static Carbon Carbon4; private static Molecule Molecule2; private static Molecule Molecule3; private static Molecule Molecule4; private static Ring Ring2; private static Ring Ring3; private static Ring Ring4; // Make a main method for java_test1 class. public static void main (String args[]) throws Exception { // Checks out, so comment out. // System.out.println("boolean1 = " + boolean1); // System.out.println("Date1 = " + Date1); // System.out.println("String_date1 = " + String_date1); // System.out.println("int1 = " + int1); // System.out.println("long1 = " + long1); // System.out.println("double1 = " + double1); // System.out.println("char1 = " + char1); // System.out.println("String1 = " + String1); // System.out.println("LongString1 = " + LongString1); // System.out.println(""); // Angle class - com.camitro.toolkit.CamUtil Angle Angle1 = new Angle(); if (Angle1 == null) System.out.println("Angle FAILED"); // public static double degreeToRad(double degree) double1 = Angle1.degreeToRad(90); if (double1 != 1.5707963267948966) System.out.println("Angle.degreeToRad FAILED"); // public static double radToDegree(double radius) double1 = Angle1.radToDegree(3.14); if (double1 != 179.9087476710785) System.out.println("Angle.radToDegree = FAILED"); // Atom class - com.camitro.toolkit.Molecule - abstract // public Atom() // protected Atom(Atom) // public abstract java.lang.Object clone() // public Molecule getBelongedMolecule() // public java.util.Vector getAllBelongedRings() // public java.util.Vector getBelongedRings(boolean aromatic) // public Ring getBelongedSmallestRing(boolean aromatic) // public Ring getBelongedFirstHexaneRing() // public java.util.Vector getAttachedHexaneRings() // public java.util.Vector getAttachedRings(boolean aromatic) // public Ring getFirstAttachedBenzRing() // public int getIndex() // public int getNumber() // public java.lang.String getLabel() // public void setCoordinate(double x, double y, double z) // public void setCoord(Point coordPoint) // public void setX(double x) // public void setY(double y) // public void setZ(double z) // public Point getCoord() // public double getX() // public double getY() // public double getZ() // public double distanceSquared(Atom that) // public int getHybrid() // public void setHybrid(int hybrid) // public void setRadical(boolean radical) // public boolean isRadical() // public void setType(java.lang.String forceFieldType) // public java.lang.String getType() // public int totalBonds() // public Bond getBondAt(int idx) // public BondInterface findBond(Atom a) // public java.util.Vector getBondedNeighbors() // public void addToNeighbor(Atom a) // public void removeFromNeighbor(Atom a) // public void addToBondList(BondInterface b) // public void removeFromBondList(BondInterface b) // public void cleanupValence() // public void rehybridize() // public int getBondedHCount() // public java.util.Vector getBondedAtoms(java.lang.String elem) // public java.util.Vector getBondedHydrogens() // public java.util.Vector getBondedCarbons() // public java.util.Vector getBondedMethyls() // public Atom findNeighbor(java.lang.String name) // public boolean isEndAtom() // public boolean isCarbon() // public boolean isSP3Carbon() // public boolean isHydrogen() // public boolean isNitrogen() // public boolean isSP3Nitrogen() // public boolean isOxygen() // public boolean isSP3Oxygen() // public boolean isFluorine() // public boolean isAliphatic() // public boolean isAromatic() // public void setPosition(double length, double angle, double twist, Atom NA, Atom NB, Atom NC) // public void adjustPosition(double length, double angle, double twist, Atom NA, Atom NB, Atom NC) // public InternalCoordinate toICoord(Atom NA, Atom NB, Atom NC) // public boolean isEquitorial() // public boolean isEquitorial(Ring attachedHexaneRing) // public boolean isAxial() // public boolean isAxial(Ring attachedHexaneRing) // public double getMass() // public void setMass(double mass) // public double getCharge() // public void setCharge(double charge) // public Atom getFirstSP2Neighbor() // public Atom getLastSP2Neighbor() // public Atom getFirstNitrogenNeighbor() // public abstract java.lang.String getElement() // public abstract int getAtomicNumber() // public abstract int getMaxNumBonds() // public PropertyList getPropList() // public static Atom createAtom(java.lang.String atmType) // public static double minDistanceSquared(java.util.Vector atomsA, java.util.Vector atomsB) // Blob class - com.camitro.toolkit.CamUtil // Bond class - com.camitro.toolkit.Molecule // public Bond() Bond Bond1 = new Bond(); if (Bond1 == null) System.out.println("Bond FAILED"); // public java.lang.Object clone() Object1 = Bond1.clone(); if (Object1 == null) System.out.println("Bond.clone FAILED"); Carbon2 = new Carbon(); Carbon3 = new Carbon(); Molecule2 = new Molecule(); Bond1 = Molecule2.addBond(Carbon2, Carbon3); // public Atom findAtom(Atom otherAtom) Atom2 = Bond1.findAtom(Carbon2); if (Atom2 == null) System.out.println("Bond.findAtom FAILED"); // public boolean isConnectedTo(Atom a) boolean1 = Bond1.isConnectedTo(Atom2); if (boolean1 == false) System.out.println("Bond.isConnectedTo FAILED"); // public Atom getAtom1() Atom2 = Bond1.getAtom1(); if (Atom2 == null) System.out.println("Bond.getAtom1 FAILED"); // public Atom getAtom2() Atom3 = Bond1.getAtom2(); if (Atom3 == null) System.out.println("Bond.getAtom2 FAILED"); // public void connect(Atom a1, Atom a2) boolean1 = false; try { Bond1.connect(Carbon2, Carbon3); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Bond.connect two atoms FAILED"); } // public void disconnect(Atom a1, Atom a2) boolean1 = false; try { Bond1.disconnect(Carbon2, Carbon3); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Bond.disconnect two atoms FAILED"); } // public void connect(Atom a) boolean1 = false; try { Bond1.connect(Carbon2); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Bond.connect one atom FAILED"); } // public void disconnect(Atom a) boolean1 = false; try { Bond1.disconnect(Carbon2); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Bond.disconnect one atom FAILED"); } // public void cleanupValence() boolean1 = false; try { Bond1.cleanupValence(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Bond.cleanupValence FAILED"); } // public void setOrder(double order) boolean1 = false; try { Bond1.setOrder(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Bond.setOrder FAILED"); } // public double getOrder() double1 = Bond1.getOrder(); if (double1 == 0) System.out.println("Bond.getOrder FAILED"); // public PropertyList getPropList() PropertyList PropertyList2 = Bond1.getPropList(); if (PropertyList2 == null) System.out.println("Bond.getPropList FAILED"); // BondInterface interface - com.camitro.toolkit.Molecule // public Atom findAtom(Atom otherAtom) // public boolean isConnectedTo(Atom a) // public void connect(Atom a1, Atom a2) // public void connect(Atom a) // public void cleanupValence() // public void disconnect(Atom a1, Atom a2) // public void disconnect(Atom a) // public void setOrder(double order) // public double getOrder() // Bromine class - com.camitro.toolkit.Molecule // public Bromine() Bromine Bromine1 = new Bromine(); if (Bromine1 == null) System.out.println("Bromine FAILED"); // public Bromine(double x, double y, double z) Bromine Bromine2 = new Bromine(1,1,1); if (Bromine2 == null) System.out.println("Bromine parameters FAILED"); // public Bromine(int hybrid, double x, double y, double z) Bromine Bromine3 = new Bromine(1,1,1,1); if (Bromine3 == null) System.out.println("Bromine parameters hybrid FAILED"); // public java.lang.Object clone() Object1 = Bromine1.clone(); if (Object1 == null) System.out.println("Bromine.clone FAILED"); // public void rehybridize(int hybrid) boolean1 = false; try { Bromine1.rehybridize(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Bromine.rehybridize hybrid FAILED"); } // public void rehybridize() boolean1 = false; try { Bromine1.rehybridize(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Bromine.rehybridize FAILED"); } // public java.lang.String getElement() String1 = Bromine1.getElement(); if (String1.equals("")) System.out.println("Bromine.getElement FAILED"); // public int getAtomicNumber() int1 = Bromine1.getAtomicNumber(); if (int1 == 0) System.out.println("Bromine.getAtomicNumber FAILED"); // public int getMaxNumBonds() int1 = Bromine1.getMaxNumBonds(); if (int1 == 0) System.out.println("Bromine.getMaxNumBonds FAILED"); // cam_CoMMA class - com.camitro.apps.cam_CoMMA - container for main method // removed from beta3 // public cam_CoMMA() // public static void main(java.lang.String[] args) // cam_convert class - com.camitro.apps.cam_convert - container for main method // public cam_convert() // public static void main(java.lang.String[] args) // cam_db class - com.camitro.apps.cam_db - container for main method // public static void main(java.lang.String[] argv) // cam_desc class - com.camitro.apps.cam_desc - container for main method // public static void main(java.lang.String[] argv) // protected java.io.PrintWriter openPrintWriter(java.lang.String directory, java.lang.String filename) // protected java.io.PrintWriter openPrintWriter(java.lang.String filename) // cam_master class - com.camitro.apps.cam_master - container for main method // public cam_master() // public static void main(java.lang.String[] args) // cam_meta class - com.camitro.apps.cam_meta - container for main method // public static void main(java.lang.String[] argv) // cam_molmap class - com.camitro.apps.cam_molmap - container for main method // public cam_molmap() // public static void main(java.lang.String[] args) // public static void readMessageFile(Molmap mapPack, java.io.InputStream isMessage) // public static void writeMapFile(Molmap mapPack, java.lang.String fileName, java.lang.String httpAddress) // cam_reset class - com.camitro.apps.cam_reset - container for main method // public cam_reset() // public static void main(java.lang.String[] args) // cam_smiles class - com.camitro.apps.cam_smiles - container for main method // public cam_smiles() // public static void main(java.lang.String[] arg) // cam_worker class - com.camitro.apps.cam_worker - container for main method // public cam_worker() // public static void main(java.lang.String[] args) // CamExc class - com.camitro.toolkit.CamUtil // public CamExc() CamExc CamExc1 = new CamExc(); if (CamExc1 == null) System.out.println("CamExc FAILED"); // public static java.lang.String makeNiceErrorMsg(java.lang.String ingVerb, java.lang.String filename, java.lang.Exception exc) String1 = CamExc1.makeNiceErrorMsg("Sending", "ametryne.mol", exc1); if (String1.equals("")) System.out.println("CamExc.makeNiceErrorMsg three parameters FAILED"); // public static java.lang.String makeNiceErrorMsg(java.lang.Exception exc) String1 = CamExc1.makeNiceErrorMsg(exc1); if (String1.equals("")) System.out.println("CamExc.makeNiceErrorMsg one parameter FAILED"); // CamFile class - com.camitro.toolkit.CamUtil // public CamFile() CamFile CamFile1 = new CamFile(); if (CamFile1 == null) System.out.println("CamFile FAILED"); // public static void deleteMatchingFiles(java.lang.String dirFilePath, java.lang.String filePrefix) boolean1 = false; try { CamFile1.deleteMatchingFiles("c:\\000\\src\\com\\java_test1\\javatest2", "java_test1"); boolean1 = true; } finally { if (boolean1 == false) System.out.println("CamFile.deleteMatchingFiles FAILED"); } // public static void deleteAllFilesInDirectory(java.lang.String dirFilePath) boolean1 = false; try { CamFile1.deleteAllFilesInDirectory("c:\\000\\src\\com\\java_test1\\javatest2"); boolean1 = true; } finally { if (boolean1 == false) System.out.println("CamFile.deleteAllFilesInDirectory FAILED"); } // public static java.lang.String getFileContents(java.lang.String filePath) String1 = CamFile1.getFileContents("c:\\000\\src\\com\\java_test1\\javatest\\test.txt"); if (String1.equals("")) System.out.println("CamFile.getFileContents FAILED"); // public static LongString getLongStringFromFile(java.lang.String filePath) LongString1 = CamFile1.getLongStringFromFile("c:\\000\\src\\com\\java_test1\\javatest\\test.txt"); if (String1.equals("")) System.out.println("CamFile.getLongStringFromFile FAILED"); // public static void writeLongStringToFile(LongString longContents, java.lang.String filePath) boolean1 = false; try { CamFile1.writeLongStringToFile(LongString1, "c:\\000\\src\\com\\java_test1\\javatest\\test.txt"); boolean1 = true; } finally { if (boolean1 == false) System.out.println("CamFile.writeLongStringToFile FAILED"); } // public static java.lang.String stripFileExt(java.lang.String filename) String1 = CamFile1.stripFileExt("c:\\000\\src\\com\\java_test1\\javatest\\test.txt"); if (String1.equals("")) System.out.println("CamFile.stripFileExt FAILED"); // public static java.lang.String stripDirsFromPath(java.lang.String path) String1 = CamFile1.stripDirsFromPath("c:\\000\\src\\com\\java_test1\\javatest\\test.txt"); if (String1.equals("")) System.out.println("CamFile.stripDirsFromPath FAILED"); // public static java.lang.String stripDirsAndExtFromPath(java.lang.String path) String1 = CamFile1.stripDirsAndExtFromPath("c:\\000\\src\\com\\java_test1\\javatest\\test.txt"); if (String1.equals("")) System.out.println("CamFile.stripDirsAndExtFromPath FAILED"); // public static java.lang.String getParentDirsFromPath(java.lang.String path) String1 = CamFile1.getParentDirsFromPath("c:\\000\\src\\com\\java_test1\\javatest\\test.txt"); if (String1.equals("")) System.out.println("CamFile.getParentDirsFromPath FAILED"); // public static void createDir(java.lang.String dirName, java.lang.String parentPath) boolean1 = false; try { CamFile1.createDir("javatest3", "c:\\000\\src\\com\\java_test1"); boolean1 = true; } finally { if (boolean1 == false) System.out.println("CamFile.createDir two parameters FAILED"); } // public static void createDir(java.lang.String dirPath) boolean1 = false; try { CamFile1.createDir("c:\\000\\src\\com\\java_test1\\javatest3"); boolean1 = true; } finally { if (boolean1 == false) System.out.println("CamFile.createDir FAILED"); } // public static void deleteDir(java.lang.String dirPath) boolean1 = false; try { CamFile1.deleteDir("c:\\000\\src\\com\\java_test1\\javatest3"); boolean1 = true; } finally { if (boolean1 == false) System.out.println("CamFile.deleteDir FAILED"); } // public static java.lang.String fixSlashes(java.lang.String path) String1 = CamFile1.fixSlashes("c:\\000\\src\\com\\java_test1\\javatest\\test.txt"); if (String1.equals("")) System.out.println("CamFile.fixSlashes FAILED"); // public static boolean isWindows() boolean1 = CamFile1.isWindows(); if (boolean1 == false) System.out.println("CamFile.isWindows FAILED"); // CamHelper class - com.camitro.toolkit.CamUtil // public CamHelper() CamHelper CamHelper1 = new CamHelper(); if (CamHelper1 == null) System.out.println("CamHelper FAILED"); // public static java.lang.String getTimeString(long millis, int percent) String1 = CamHelper1.getTimeString(10, 100); if (String1.equals("")) System.out.println("CamHelper.getTimeString FAILED"); // public static boolean isOptionalBooleanTrue(java.lang.String value) boolean1 = CamHelper1.isOptionalBooleanTrue("OK"); if (boolean1 == false) System.out.println("CamHelper.isOptionalBooleanTrue FAILED"); // public static java.lang.String[] split(java.lang.String line, int delim) String2 = CamHelper1.split("O:K", 1); if (String2[0].equals("")) System.out.println("CamHelper.split FAILED"); // public static java.lang.String join(java.lang.String[] parts, char delim) String1 = CamHelper1.join(String2, ':'); if (String1.equals("")) System.out.println("CamHelper.join FAILED"); // CamRegExp class - com.camitro.toolkit.CamUtil // public CamRegExp() CamRegExp CamRegExp1 = new CamRegExp(); if (CamRegExp1 == null) System.out.println("CamRegExp FAILED"); // public static java.lang.String[] getSubMatches(REMatch theMatch) String1 = new String("a"); RE RE1 = new RE(String1); REMatch REMatch1 = RE1.getMatch(String1); String[] String10 = CamRegExp1.getSubMatches(REMatch1); if (String10.equals("")) System.out.println("CamRegExp.getSubMatches FAILED"); // CamUtilConstants interface - com.camitro.toolkit.CamUtil // has only fields // Carbon class - com.camitro.toolkit.Molecule // public Carbon() Carbon Carbon1 = new Carbon(); if (Carbon1 == null) System.out.println("Carbon FAILED"); // public Carbon(double x, double y, double z) Carbon2 = new Carbon(1,1,1); if (Carbon2 == null) System.out.println("Carbon FAILED"); // public Carbon(int hybrid, double x, double y, double z) Carbon3 = new Carbon(1,1,1,1); if (Carbon3 == null) System.out.println("Carbon FAILED"); // public java.lang.Object clone() Object1 = Carbon1.clone(); if (Object1 == null) System.out.println("Carbon.clone FAILED"); // public void rehybridize(int hybrid) boolean1 = false; try { Carbon1.rehybridize(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Carbon.rehybridize FAILED"); } // public void rehybridize() boolean1 = false; try { Carbon1.rehybridize(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Carbon.rehybridize FAILED"); } // public java.lang.String getElement() String1 = Carbon1.getElement(); if (String1.equals("")) System.out.println("Carbon.getElement FAILED"); // public int getAtomicNumber() int1 = Carbon1.getAtomicNumber(); if (int1 == 0) System.out.println("Carbon.getAtomicNumber FAILED"); // public int getMaxNumBonds() int1 = Carbon1.getMaxNumBonds(); if (int1 == 0) System.out.println("Carbon.getMaxNumBonds FAILED"); // ChargesTooSmallException class - com.camitro.toolkit.MoleculeSymmetry - extends MoleculeSymmetryException // public ChargesTooSmallException() // public ChargesTooSmallException(java.lang.String s) // import not available for me // Chlorine class - com.camitro.toolkit.Molecule // public Chlorine() Chlorine Chlorine1 = new Chlorine(); if (Chlorine1 == null) System.out.println("Chlorine FAILED"); // public Chlorine(double x, double y, double z) Chlorine Chlorine2 = new Chlorine(1,1,1); if (Chlorine2 == null) System.out.println("Chlorine FAILED"); // public Chlorine(int hybrid, double x, double y, double z) Chlorine Chlorine3 = new Chlorine(1,1,1,1); if (Chlorine3 == null) System.out.println("Chlorine FAILED"); // public java.lang.Object clone() Object1 = Chlorine1.clone(); if (Object1 == null) System.out.println("Chlorine.clone FAILED"); // public void rehybridize(int hybrid) boolean1 = false; try { Chlorine1.rehybridize(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Chlorine.rehybridize FAILED"); } // public void rehybridize() boolean1 = false; try { Chlorine1.rehybridize(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Chlorine.rehybridize FAILED"); } // public java.lang.String getElement() String1 = Chlorine1.getElement(); if (String1.equals("")) System.out.println("Chlorine.getElement FAILED"); // public int getAtomicNumber() int1 = Chlorine1.getAtomicNumber(); if (int1 == 0) System.out.println("Chlorine.getAtomicNumber FAILED"); // public int getMaxNumBonds() int1 = Chlorine1.getMaxNumBonds(); if (int1 == 0) System.out.println("Chlorine.getMaxNumBonds FAILED"); // CholeskyDecomposition class - gov.nist.Jama // gov.nist.Jama // Cluster class - com.camitro.toolkit.Cluster // public Cluster() Cluster Cluster1 = new Cluster(); if (Cluster1 == null) System.out.println("Cluster FAILED"); // public static void setClusterRun(ClusterRun clusterRun) SerialClusterRun SerialClusterRun2 = new SerialClusterRun(); boolean1 = false; try { Cluster1.setClusterRun(SerialClusterRun2); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Cluster.setClusterRun FAILED"); } // public java.util.Vector runRequests(java.util.Vector requests) // Vector2 = Cluster1.runRequests(Vector1); // if (Vector2 == null) // System.out.println("Cluster.runRequests FAILED"); // not available to me // ClusterConstants interface - com.camitro.toolkit.Cluster // has only fields // ClusterMaster interface - com.camitro.toolkit.Cluster // public java.util.Vector runRequests(java.util.Vector requests) // public void applyForWork(ClusterWorker worker, java.lang.String workerId, int priority, java.lang.String queueType, java.lang.String workerBuildInfo) // public void terminate() // ClusterMasterServer class - com.camitro.toolkit.Cluster // public ClusterMasterServer() // public java.util.Vector runRequests(java.util.Vector requests) // public void applyForWork(ClusterWorker worker, java.lang.String workerId, int priority, java.lang.String queueType, java.lang.String workerBuildInfo) // public void terminate() // public PriorityQueue findOrCreateQueue(int priority, java.lang.String queueType) // import not available for me // ClusterMasterTerminator class - com.camitro.toolkit.Cluster // public ClusterMasterTerminator() ClusterMasterTerminator ClusterMasterTerminator1 = new ClusterMasterTerminator(); if (ClusterMasterTerminator1 == null) System.out.println("ClusterMasterTerminator FAILED"); // public void terminateMaster() boolean1 = false; try { // ClusterMasterTerminator1.terminateMaster(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("ClusterMasterTerminator.terminateMaster FAILED"); } // ClusterRebase class - com.camitro.toolkit.Cluster // protected ClusterRebase(java.lang.String companyID, java.lang.String tag, java.util.Properties simpleProps, boolean isSealed) // public java.lang.String getCompanyID() // public java.lang.String getTag() // public java.lang.String getSysProp(java.lang.String name) // public int getIntSysProp(java.lang.String name, int defaultValue) // public boolean getBooleanSysProp(java.lang.String name) // public java.lang.String getStringProp(java.lang.String name) // public boolean isStringProp(java.lang.String name) // public LongString getLongStringProp(java.lang.String name) // public java.lang.Double getDoubleProp(java.lang.String name) // public boolean isDoubleProp(java.lang.String name) // public java.lang.Integer getIntegerProp(java.lang.String name) // public boolean isIntegerProp(java.lang.String name) // public java.lang.Object getProp(java.lang.String name) // public java.util.Enumeration getPropKeys() // public int getRetryCount() // public boolean isSealed() // public void seal() // public void putLongStringProp(java.lang.String name, LongString value) // ClusterReply class - com.camitro.toolkit.Cluster // public ClusterReply(java.lang.String companyID, java.lang.String tag, java.lang.Exception exc, java.lang.String errorMsg, int runSeconds, int runUtilization, java.lang.String runWorkerId, java.util.Properties simpleProps, boolean isSealed) Exception Exception2 = new Exception(); Properties Properties2 = new Properties(); ClusterReply ClusterReply1 = new ClusterReply("x", "x", Exception2, "x", 1, 1, "x", Properties2, false); if (ClusterReply1 == null) System.out.println("ClusterReply FAILED"); // public ClusterReply(java.lang.String companyID, java.lang.String tag, java.lang.Exception exc, java.util.Properties simpleProps) Exception Exception3 = new Exception(); Properties Properties3 = new Properties(); ClusterReply ClusterReply2 = new ClusterReply("x", "x", Exception3, Properties3); if (ClusterReply2 == null) System.out.println("ClusterReply FAILED"); // public ClusterReply(java.lang.String companyID, java.lang.String tag, int runSeconds, int runUtilization, java.lang.String runWorkerId, java.util.Properties simpleProps) Properties Properties4 = new Properties(); ClusterReply ClusterReply3 = new ClusterReply("x", "x", 1, 1, "x", Properties4); if (ClusterReply3 == null) System.out.println("ClusterReply FAILED"); // public boolean isSuccessful() boolean1 = ClusterReply1.isSuccessful(); if (boolean1 == true) System.out.println("ClusterReply.isSuccessful FAILED"); // public java.lang.Exception getException() Exception Exception5 = ClusterReply1.getException(); if (Exception5 == null) System.out.println("ClusterReply.getException FAILED"); // public java.lang.String getErrorMsg() String1 = ClusterReply1.getErrorMsg(); if (String1.equals("")) System.out.println("ClusterReply.getErrorMsg FAILED"); // public int getRunSeconds() int1 = ClusterReply1.getRunSeconds(); if (int1 == 0) System.out.println("ClusterReply.getRunSeconds FAILED"); // public int getRunUtilization() int1 = ClusterReply1.getRunUtilization(); if (int1 == 0) System.out.println("ClusterReply.getRunUtilization FAILED"); // public java.lang.String getRunWorkerId() String1 = ClusterReply1.getRunWorkerId(); if (String1.equals("")) System.out.println("ClusterReply.getRunWorkerId FAILED"); // ClusterRequest class - com.camitro.toolkit.Cluster - abstract // protected ClusterRequest(java.lang.String companyID, java.lang.String tag, java.util.Properties simpleProps, int priority) // public abstract java.lang.String getRequestType() // public int getPriority() // public void bumpRetryCount() // ClusterRun interface - com.camitro.toolkit.Cluster // public java.util.Vector runRequests(java.util.Vector requests) // ClusterServer class - com.camitro.toolkit.Cluster // public ClusterServer() ClusterServer ClusterServer1 = new ClusterServer(); if (ClusterServer1 == null) System.out.println("ClusterServer FAILED"); // public static boolean setClusterMasterHostname(java.lang.String hostname) // boolean1 = ClusterServer1.setClusterMasterHostname("camitro"); // if (boolean1 == false) // System.out.println("ClusterServer.setClusterMasterHostname FAILED"); // ClusterServerConstants interface - com.camitro.toolkit.Cluster // has only fields // ClusterService class - com.camitro.toolkit.Cluster - abstract // public ClusterService() // protected ClusterService(ClusterService that) // public abstract ClusterReply runRequest(ClusterRequest request) // public abstract java.lang.String getRequestType() // public abstract java.lang.Object clone() // public void setTmpDirPath(java.lang.String tmpDirPath) // public void setWorkerId(java.lang.String workerId) // public java.lang.String getTmpDirPath() // public java.lang.String getWorkerId() // public static ClusterReply createUnknownRequestReply(ClusterRequest request, java.lang.String workerId) // public static ClusterReply createErrorReply(java.lang.String msg, ClusterRequest request, java.lang.String workerId) // public static ClusterReply createExceptionReply(java.lang.Exception exc, ClusterRequest request, java.lang.String workerId) // ClusterWorker interface - com.camitro.toolkit.Cluster // public ClusterReply runRequest(ClusterRequest request) // ClusterWorkerProxy class - com.camitro.toolkit.Cluster // no constructor or methods or fields // ClusterWorkerServer class - com.camitro.toolkit.Cluster // public ClusterWorkerServer(java.lang.String masterHostName, java.lang.String workerId, java.lang.String tmpDirPath, int priority); // ClusterWorkerServer ClusterWorkerServer1 = new ClusterWorkerServer("x", "x", "x", 1); // if (ClusterWorkerServer1 == null) // System.out.println("ClusterWorkerServer FAILED"); // public void registerService(ClusterService service) MoeService MoeService1 = new MoeService(); boolean1 = false; try { // ClusterWorkerServer1.registerService(MoeService1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("ClusterWorkerServer.registerService FAILED"); } // public ClusterReply runRequest(ClusterRequest request) // MoeRequest MoeRequest1 = new MoeRequest(); // ClusterReply ClusterReply3 = ClusterWorkerServer1.runRequest(MoeRequest1); // if (ClusterReply3 == null) // System.out.println("ClusterWorkerServer.runRequest FAILED"); // public void run() boolean1 = false; try { // ClusterWorkerServer1.run(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("ClusterWorkerServer.run FAILED"); } // public void contactMaster() boolean1 = false; try { // ClusterWorkerServer1.contactMaster(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("ClusterWorkerServer.contactMaster FAILED"); } // not available to me // ClusterWrapper class - com.camitro.toolkit.Cluster - abstract // protected ClusterWrapper() // public abstract ClusterReply runRequest() // Cmdline class - com.camitro.toolkit.CamUtil // public Cmdline(java.lang.String[] argv, java.lang.String msg); // String2 is from CamHelper above Cmdline Cmdline1 = new Cmdline(String2, "x"); if (Cmdline1 == null) System.out.println("Cmdline FAILED"); // public Cmdline(java.lang.String[] argv, java.lang.String msg, java.util.Hashtable opts) Hashtable Hashtable1 = new Hashtable(); Cmdline Cmdline2 = new Cmdline(String2, "x", Hashtable1); if (Cmdline2 == null) System.out.println("Cmdline FAILED"); // public java.util.Vector processCmdline() Vector1 = Cmdline1.processCmdline(); if (Vector1 == null) System.out.println("Cmdline.processCmdline FAILED"); // public static boolean isOptionalBooleanTrue(java.lang.String value) boolean1 = Cmdline1.isOptionalBooleanTrue("x"); if (boolean1 == false) System.out.println("Cmdline.isOptionalBooleanTrue FAILED"); // public static java.lang.String getJobInfo() String1 = Cmdline1.getJobInfo(); if (String1.equals("")) System.out.println("Cmdline.getJobInfo FAILED"); // CmpResult class - com.camitro.toolkit.ModelService // public CmpResult(java.lang.String companyID, java.lang.String jobCmpID, java.lang.String analysisType, java.lang.String resultName, LongString resultValue, int resultConfLevel, java.lang.String resultNotes); CmpResult CmpResult1 = new CmpResult("x", "x", "x", "x", LongString1, 1, "x"); if (CmpResult1 == null) System.out.println("CmpResult LongString FAILED"); // public CmpResult(java.lang.String companyID, java.lang.String jobCmpID, java.lang.String analysisType, java.lang.String resultName, String resultValue, int resultConfLevel, java.lang.String resultNotes) CmpResult CmpResult2 = new CmpResult("x", "x", "x", "x", "x", 1, "x"); if (CmpResult2 == null) System.out.println("CmpResult String FAILED"); // public java.lang.String getCompanyIDName() // String1 = CmpResult1.getCompanyIDName(); // if (String1.equals("")) // System.out.println("CmpResult.getCompanyIDName FAILED"); // public java.lang.String getJobCmpID() // String1 = CmpResult1.getJobCmpID(); // if (String1.equals("")) // System.out.println("CmpResult.getJobCmpID FAILED"); // public java.lang.String getAnalysisType() // String1 = CmpResult1.getAnalysisType(); // if (String1.equals("")) // System.out.println("CmpResult.getAnalysisType FAILED"); // public java.lang.String getResultName() // String1 = CmpResult1.getResultName(); // if (String1.equals("")) // System.out.println("CmpResult.getResultName FAILED"); // public java.lang.String getResultValueString() // String1 = CmpResult1.getResultValueString(); // if (String1.equals("")) // System.out.println("CmpResult.getResultValueString FAILED"); // public LongString getResultValueClob() LongString1 = CmpResult1.getResultValueClob(); if (LongString1 == null) System.out.println("CmpResult.getResultValueClob FAILED"); // public int getResultConfLevel() int1 = CmpResult1.getResultConfLevel(); if (int1 == 0) System.out.println("CmpResult.getResultConfLevel FAILED"); // public boolean isResultValueClob() boolean1 = CmpResult1.isResultValueClob(); if (boolean1 == false) System.out.println("CmpResult.isResultValueClob FAILED"); // CmpSiteResult class - com.camitro.toolkit.ModelService // public CmpSiteResult(java.lang.String companyID, java.lang.String jobCmpID, java.lang.String analysisType, java.lang.String siteName, java.lang.String resultName, java.lang.String summarySiteName, LongString resultValue, int resultConfLevel, java.lang.String resultNotes); CmpSiteResult CmpSiteResult1 = new CmpSiteResult("x", "x", "x", "x", "x", "x", LongString1, 1, "x"); if (CmpSiteResult1 == null) System.out.println("CmpSiteResult LongString FAILED"); // public CmpSiteResult(java.lang.String companyID, java.lang.String jobCmpID, java.lang.String analysisType, java.lang.String siteName, java.lang.String resultName, java.lang.String summarySiteName, String resultValue, int resultConfLevel, java.lang.String resultNotes) CmpSiteResult CmpSiteResult2 = new CmpSiteResult("x", "x", "x", "x", "x", "x", "", 1, "x"); if (CmpSiteResult2 == null) System.out.println("CmpSiteResult String FAILED"); // public java.lang.String getCompanyID() // String1 = CmpSiteResult1.getCompanyID(); // if (String1.equals("")) // System.out.println("CmpSiteResult.getCompanyID FAILED"); // public java.lang.String getJobCmpID() // String1 = CmpSiteResult1.getJobCmpID(); // if (String1.equals("")) // System.out.println("CmpSiteResult.getJobCmpID FAILED"); // public java.lang.String getAnalysisType() // String1 = CmpSiteResult1.getAnalysisType(); // if (String1.equals("")) // System.out.println("CmpSiteResult.getAnalysisType FAILED"); // public java.lang.String getSiteName() // String1 = CmpSiteResult1.getSiteName(); // if (String1.equals("")) // System.out.println("CmpSiteResult.getSiteName FAILED"); // public java.lang.String getSummarySiteName() // String1 = CmpSiteResult1.getSummarySiteName(); // if (String1.equals("")) // System.out.println("CmpSiteResult.getSummarySiteName FAILED"); // public java.lang.String getResultName() // String1 = CmpSiteResult1.getResultName(); // if (String1.equals("")) // System.out.println("CmpSiteResult.getResultName FAILED"); // public java.lang.String getResultValueString() // String1 = CmpSiteResult1.getResultValueString(); // if (String1.equals("")) // System.out.println("CmpSiteResult.getResultValueString FAILED"); // public LongString getResultValueClob() LongString1 = CmpSiteResult1.getResultValueClob(); if (LongString1 == null) System.out.println("CmpSiteResult.getResultValueClob FAILED"); // public int getResultConfLevel() int1 = CmpSiteResult1.getResultConfLevel(); if (int1 == 0) System.out.println("CmpSiteResult.getResultConfLevel FAILED"); // public boolean isResultValueClob() boolean1 = CmpSiteResult1.isResultValueClob(); if (boolean1 == false) System.out.println("CmpSiteResult.isResultValueClob FAILED"); // CodessaReply class - com.camitro.toolkit.ComputeService // public CodessaReply(java.lang.String companyID, java.lang.String tag, java.lang.Exception exc, int runSeconds, int runUtilization, java.lang.String runWorkerId, java.util.Properties simpleProps, boolean isSealed); Exception Exception7 = new Exception(); Properties Properties7 = new Properties(); CodessaReply CodessaReply1 = new CodessaReply("x", "x", Exception7, 1, 1, "x", Properties7, false); if (CodessaReply1 == null) System.out.println("CodessaReply FAILED"); // CodessaRequest class - com.camitro.toolkit.ComputeService // public CodessaRequest(java.lang.String companyID, java.lang.String tag, LongString mopacOutLs, LongString ampacArcLs, java.util.Properties simpleProps, int priority); CodessaRequest CodessaRequest1 = new CodessaRequest("x", "x", LongString1, LongString1, Properties7, 1); if (CodessaRequest1 == null) System.out.println("CodessaRequest FAILED"); // CodessaService class - com.camitro.toolkit.ComputeService // public CodessaService() CodessaService CodessaService1 = new CodessaService(); if (CodessaService1 == null) System.out.println("CodessaService FAILED"); // protected CodessaService(CodessaService that) // public java.lang.Object clone() Object1 = CodessaService1.clone(); if (Object1 == null) System.out.println("CodessaService.clone FAILED"); // public java.lang.String getRequestType() String1 = CodessaService1.getRequestType(); if (String1.equals("")) System.out.println("CodessaService.getRequestType FAILED"); // public ClusterReply runRequest(ClusterRequest request) // ClusterReply ClusterReply1 = CodessaService1.runRequest(CodessaRequest1); // if (ClusterReply1 == null) // System.out.println("CodessaService.runRequest FAILED"); // not available to me // Comparable2 interface // public int compareTo(Comparable2 otherObject) // ComputeServiceConstants interface - com.camitro.toolkit.ComputeService // has only fields // ConcordReply class - com.camitro.toolkit.ComputeService // public ConcordReply(java.lang.String companyID, java.lang.String tag, java.lang.Exception exc, int runSeconds, int runUtilization, java.lang.String runWorkerId, java.util.Properties simpleProps, boolean isSealed) Exception Exception8 = new Exception(); Properties Properties8 = new Properties(); ConcordReply ConcordReply1 = new ConcordReply("x", "x", Exception8, 1, 1, "x", Properties8, false); if (ConcordReply1 == null) System.out.println("ConcordReply FAILED"); // ConcordRequest class - com.camitro.toolkit.ComputeService // public ConcordRequest(java.lang.String companyID, java.lang.String tag, LongString molContentsLs, java.util.Properties simpleProps, int priority) ConcordRequest ConcordRequest1 = new ConcordRequest("x", "x", LongString1, Properties7, 1); if (ConcordRequest1 == null) System.out.println("ConcordRequest FAILED"); // public LongString getMolContents() LongString1 = ConcordRequest1.getMolContents(); if (LongString1 == null) System.out.println("ConcordRequest.getMolContents FAILED"); // public java.lang.String getRequestType() String1 = ConcordRequest1.getRequestType(); if (String1.equals("")) System.out.println("ConcordRequest.getRequestType FAILED"); // ConcordService class - com.camitro.toolkit.ComputeService // public ConcordService() ConcordService ConcordService1 = new ConcordService(); if (ConcordService1 == null) System.out.println("ConcordService FAILED"); // protected ConcordService(ConcordService that) // public java.lang.Object clone() Object1 = ConcordService1.clone(); if (Object1 == null) System.out.println("ConcordService.clone FAILED"); // public java.lang.String getRequestType() String1 = ConcordService1.getRequestType(); if (String1.equals("")) System.out.println("ConcordService.getRequestType FAILED"); // public ClusterReply runRequest(ClusterRequest request) // ClusterReply ClusterReply1 = ConcordService1.runRequest(ConcordRequest1); // if (ClusterReply1 == null) // System.out.println("ConcordService.runRequest FAILED"); // not available to me // ConcordWrapper class - com.camitro.toolkit.ComputeService // public ConcordWrapper(ConcordRequest request, java.lang.String baseFilePath, java.lang.String runWorkerId); // public ConcordReply runConcord() // ConcordReply1 = ConcordWrapper1.runConcord(); // if (ConcordReply1 == null) // System.out.println("ConcordWrapper.runConcord FAILED"); // public ConcordReply runConcord(java.lang.Runnable callback, int waitSeconds) // Runnable Runnable1 = new Runnable(); // ConcordReply1 = ConcordWrapper1.runConcord(Runnable1, 1); // if (ConcordReply1 == null) // System.out.println("ConcordWrapper.runConcord Runnable FAILED"); // CorinaReply class - com.camitro.toolkit.ComputeService // public CorinaReply(java.lang.String companyID, java.lang.String tag, java.lang.Exception exc, int runSeconds, int runUtilization, java.lang.String runWorkerId, java.util.Properties simpleProps, boolean isSealed); Exception Exception9 = new Exception(); Properties Properties9 = new Properties(); CorinaReply CorinaReply1 = new CorinaReply("x", "x", Exception9, 1, 1, "x", Properties9, false); if (CorinaReply1 == null) System.out.println("CorinaReply FAILED"); // CorinaRequest class - com.camitro.toolkit.ComputeService // public CorinaRequest(java.lang.String companyID, java.lang.String tag, LongString molContentsLs, java.util.Properties simpleProps, int priority) CorinaRequest CorinaRequest1 = new CorinaRequest("x", "x", LongString1, Properties9, 1); if (CorinaRequest1 == null) System.out.println("CorinaRequest FAILED"); // public LongString getMolContents() LongString1 = CorinaRequest1.getMolContents(); if (LongString1 == null) System.out.println("CorinaRequest.getMolContents FAILED"); // public java.lang.String getRequestType() String1 = CorinaRequest1.getRequestType(); if (String1.equals("")) System.out.println("CorinaRequest.getRequestType FAILED"); // CorinaService class - com.camitro.toolkit.ComputeService // public CorinaService() CorinaService CorinaService1 = new CorinaService(); if (CorinaService1 == null) System.out.println("CorinaService FAILED"); // protected CorinaService(CorinaService that) // public java.lang.Object clone() Object1 = CorinaService1.clone(); if (Object1 == null) System.out.println("CorinaService.clone FAILED"); // public java.lang.String getRequestType() String1 = CorinaService1.getRequestType(); if (String1.equals("")) System.out.println("CorinaService.getRequestType FAILED"); // public ClusterReply runRequest(ClusterRequest request) // ClusterReply ClusterReply1 = CorinaService1.runRequest(CorinaRequest1); // if (ClusterReply1 == null) // System.out.println("CorinaService.runRequest FAILED"); // not available to me // CorinaWrapper class - com.camitro.toolkit.ComputeService // public CorinaWrapper(CorinaRequest request, java.lang.String baseFilePath, java.lang.String runWorkerId) // public CorinaReply runCorina() // CorinaReply1 = CorinaWrapper1.runCorina(); // if (CorinaReply1 == null) // System.out.println("CorinaWrapper.runCorina FAILED"); // public CorinaReply runCorina(java.lang.Runnable callback, int waitSeconds) // Runnable Runnable2 = new Runnable(); // CorinaReply1 = CorinaWrapper1.runCorina(Runnable2, 1); // if (CorinaReply1 == null) // System.out.println("CorinaWrapper.runCorina Runnable FAILED"); // CreateCompound class - com.camitro.toolkit.CamDatabase // no constructor // public static void createCompound(int pmi_inputnum, int fileOrderIndex, java.lang.String filenameWithExt, java.lang.String fileType, oracle.sql.CLOB jobFile) // CsvReader class - com.camitro.toolkit.GeneralFile // public CsvReader(java.io.File infile) // public CsvReader(java.lang.String filename) CsvReader CsvReader1 = new CsvReader("c:\\000\\src\\com\\java_test1\\java_test5.csv"); if (CsvReader1 == null) System.out.println("CsvReader file name FAILED"); // public int getTotalRowNum() int1 = CsvReader1.getTotalRowNum(); if (int1 == 0) System.out.println("CsvReader.getTotalRowNum FAILED"); // public int getTotalColumnNum() int1 = CsvReader1.getTotalColumnNum(); if (int1 == 0) System.out.println("CsvReader.getTotalColumnNum FAILED"); // public java.util.Vector read() Vector1 = CsvReader1.read(); if (Vector1 == null) System.out.println("CsvReader.read FAILED"); // public java.util.Vector splitCsv(java.lang.String line) Vector1 = CsvReader1.splitCsv("x,y"); if (Vector1 == null) System.out.println("CsvReader.splitCsv FAILED"); // public java.util.Vector extractData(java.lang.String idName, java.lang.String colHeadA, java.lang.String colHeadB, java.lang.String colHeadC) // public java.util.Vector extractData(int rowNum, java.lang.String[] columns) // CsvWriter class - com.camitro.toolkit.GeneralFile // public CsvWriter(java.util.Vector info, java.io.File outFile); // public void write() // DescCalc class - com.camitro.toolkit.DescModel // public DescCalc(ModelRequest modRequest, Molecule mol); // public void run() // boolean1 = false; // try { // DescCalc1.run(); // boolean1 = true; // } finally { // if (boolean1 == false) // System.out.println("DescCalc.run FAILED"); // } // public double getRoundMW() // double1 = DescCalc1.getRoundMW(); // if (double1 != 0) // System.out.println("DescCalc.getRoundMW FAILED"); // public double getPRX() // double1 = DescCalc1.getPRX(); // if (double1 != 0) // System.out.println("DescCalc.getPRX FAILED"); // DescEquationEval class - com.camitro.toolkit.DescModel // public DescEquationEval(ModelRequest modRequest, Molecule mol); // protected java.lang.String lookupEquationByName(java.lang.String name, boolean isTopLevel) // DescModelConstants interface - com.camitro.toolkit.DescModel // has only fields // DescModelReply class - com.camitro.toolkit.DescModel // public DescModelReply(java.lang.String companyId, java.lang.String analysisType, java.lang.String jobCmpID, java.lang.String tag, java.lang.Exception exc, int runSeconds, int runUtilization, java.lang.String runWorkerId, java.util.Properties simpleProps) Exception Exception10 = new Exception(); Properties Properties10 = new Properties(); DescModelReply DescModelReply1 = new DescModelReply("x", "x", "x", "x", Exception10, 1, 1, "x", Properties10); if (DescModelReply1 == null) System.out.println("DescModelReply FAILED"); // DescModelRequest class - com.camitro.toolkit.DescModel // public DescModelRequest(java.lang.String companyID, java.lang.String analysisType, java.lang.String jobCmpID, LongString molFileContents, java.lang.String parameter, java.lang.String tag, java.util.Properties simpleProps, int priority) DescModelRequest DescModelRequest1 = new DescModelRequest("x", "x", "x", LongString1, "x", "x", Properties10, 1); if (DescModelRequest1 == null) System.out.println("DescModelRequest FAILED"); // public java.lang.String getRequestType() String1 = DescModelRequest1.getRequestType(); if (String1.equals("")) System.out.println("DescModelRequest.getRequestType FAILED"); // DescModelService class - com.camitro.toolkit.DescModel // public DescModelService() DescModelService DescModelService1 = new DescModelService(); if (DescModelService1 == null) System.out.println("DescModelService FAILED"); // protected DescModelService(DescModelService that) // public java.lang.Object clone() Object1 = DescModelService1.clone(); if (Object1 == null) System.out.println("DescModelService.clone FAILED"); // public java.lang.String getRequestType() String1 = DescModelService1.getRequestType(); if (String1.equals("")) System.out.println("DescModelService.getRequestType FAILED"); // public ClusterReply runRequest(ClusterRequest request) // not available to me // DescModelWrapper class - com.camitro.toolkit.DescModel // public DescModelWrapper(DescModelRequest modRequest, DescModelService dmService) // public ClusterReply runRequest() // not available to me // DotPrinter class - com.camitro.toolkit.CamUtil // public DotPrinter(int seconds) DotPrinter DotPrinter1 = new DotPrinter(1); if (DotPrinter1 == null) System.out.println("DotPrinter FAILED"); // public void finish() boolean1 = false; try { DotPrinter1.finish(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("DotPrinter.finish FAILED"); } // public void run() boolean1 = false; try { DotPrinter1.run(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("DotPrinter.run FAILED"); } // EigenSystem class - com.camitro.toolkit.MoleculeSymmetry // public EigenSystem(com.camitro.toolkit.MoleculeSymmetry.Matrix3d ourMatrix); // public com.camitro.toolkit.MoleculeSymmetry.Vector3d getEigenValues() // public com.camitro.toolkit.MoleculeSymmetry.Matrix3d getEigenVectors() // not available to me // EigenvalueDecomposition class - com.camitro.toolkit.MoleculeSymmetry // public EigenvalueDecomposition(Matrix Arg); // public Matrix getV() // public double[] getRealEigenvalues() // public double[] getImagEigenvalues() // public Matrix getD() // not available to me // ElecModelConstants interface - com.camitro.toolkit.ElecModel // has only fields // ElecModelReply class - com.camitro.toolkit.ElecModel // public ElecModelReply(java.lang.String companyId, java.lang.String analysisType, java.lang.String jobCmpID, java.lang.String tag, java.lang.Exception exc, int runSeconds, int runUtilization, java.lang.String runWorkerId, java.util.Properties simpleProps); Exception Exception11 = new Exception(); Properties Properties11 = new Properties(); ElecModelReply ElecModelReply1 = new ElecModelReply("x", "x", "x", "x", Exception11, 1, 1, "x", Properties11); if (ElecModelReply1 == null) System.out.println("ElecModelReply FAILED"); // ElecModelRequest class - com.camitro.toolkit.ElecModel // public ElecModelRequest(java.lang.String companyID, java.lang.String analysisType, java.lang.String jobCmpID, LongString molFileContents, java.lang.String parameter, java.lang.String tag, java.util.Properties simpleProps, int priority) ElecModelRequest ElecModelRequest1 = new ElecModelRequest("x", "x", "x", LongString1, "x", "x", Properties11, 1); if (ElecModelRequest1 == null) System.out.println("ElecModelRequest FAILED"); // public java.lang.String getRequestType() String1 = ElecModelRequest1.getRequestType(); if (String1.equals("")) System.out.println("ElecModelRequest.getRequestType FAILED"); // ElecModelService class - com.camitro.toolkit.ElecModel // public ElecModelService() ElecModelService ElecModelService1 = new ElecModelService(); if (ElecModelService1 == null) System.out.println("ElecModelService FAILED"); // protected ElecModelService(ElecModelService that) // public java.lang.String getRequestType() String1 = ElecModelService1.getRequestType(); if (String1.equals("")) System.out.println("ElecModelService.getRequestType FAILED"); // public java.lang.Object clone() Object1 = ElecModelService1.clone(); if (Object1 == null) System.out.println("ElecModelService.clone FAILED"); // public ClusterReply runRequest(ClusterRequest request) // not available to me // ElecModelWrapper class - com.camitro.toolkit.ElecModel // public ElecModelWrapper(ElecModelRequest modRequest, ElecModelService modService) // public ClusterReply runRequest() // not available to me // EquationEval class - com.camitro.toolkit.CamUtil - abstract // protected EquationEval() // public java.lang.String evalName(java.lang.String name) // protected abstract java.lang.String lookupEquationByName(java.lang.String name, boolean isTopLevel) // EquationException class - com.camitro.toolkit.CamUtil // public EquationException(java.lang.String msg) EquationException EquationException1 = new EquationException("Exc"); if (EquationException1 == null) System.out.println("EquationException FAILED"); // ErrorResult class - com.camitro.toolkit.ModelService // public ErrorResult(java.lang.String companyID, java.lang.String jobCmpID, java.lang.String analysisType, java.lang.String siteName, java.util.Date errorDate, int errorCode, java.lang.String errorMsg, java.lang.String errorNotes) ErrorResult ErrorResult1 = new ErrorResult("x", "x", "x", "x", Date1, 1, "x", "x"); if (ErrorResult1 == null) System.out.println("ErrorResult FAILED"); // public java.lang.String getCompanyID() String1 = ErrorResult1.getCompanyID(); if (String1.equals("")) System.out.println("ErrorResult.getCompanyID FAILED"); // public java.lang.String getJobCmpID() String1 = ErrorResult1.getJobCmpID(); if (String1.equals("")) System.out.println("ErrorResult.getJobCmpID FAILED"); // public java.lang.String getAnalysisType() String1 = ErrorResult1.getAnalysisType(); if (String1.equals("")) System.out.println("ErrorResult.getAnalysisType FAILED"); // public java.lang.String getSiteName() String1 = ErrorResult1.getSiteName(); if (String1.equals("")) System.out.println("ErrorResult.getSiteName FAILED"); // public java.util.Date getErrorDate() Date1 = ErrorResult1.getErrorDate(); if (Date1 == null) System.out.println("ErrorResult.getErrorDate FAILED"); // public int getErrorCode() int1 = ErrorResult1.getErrorCode(); if (int1 == 0) System.out.println("ErrorResult.getErrorCode FAILED"); // public java.lang.String getErrorMsg() String1 = ErrorResult1.getErrorMsg(); if (String1.equals("")) System.out.println("ErrorResult.getErrorMsg FAILED"); // public java.lang.String getErrorNotes() String1 = ErrorResult1.getErrorNotes(); if (String1.equals("")) System.out.println("ErrorResult.getErrorNotes FAILED"); // Fluorine class - com.camitro.toolkit.Molecule // public Fluorine() Fluorine Fluorine1 = new Fluorine(); if (Fluorine1 == null) System.out.println("Fluorine FAILED"); // public Fluorine(double x, double y, double z) Fluorine Fluorine2 = new Fluorine(1,1,1); if (Fluorine2 == null) System.out.println("Fluorine FAILED"); // public Fluorine(int hybrid, double x, double y, double z) Fluorine Fluorine3 = new Fluorine(3,1,1,1); if (Fluorine3 == null) System.out.println("Fluorine FAILED"); // public java.lang.Object clone() Object1 = Fluorine1.clone(); if (Object1 == null) System.out.println("Fluorine.clone FAILED"); // public void rehybridize(int hybrid) boolean1 = false; try { Fluorine1.rehybridize(3); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Fluorine.rehybridize FAILED"); } // public void rehybridize() boolean1 = false; try { Fluorine1.rehybridize(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Fluorine.rehybridize FAILED"); } // public java.lang.String getElement() String1 = Fluorine1.getElement(); if (String1.equals("")) System.out.println("Fluorine.getElement FAILED"); // public int getAtomicNumber() int1 = Fluorine1.getAtomicNumber(); if (int1 == 0) System.out.println("Fluorine.getAtomicNumber FAILED"); // public int getMaxNumBonds() int1 = Fluorine1.getMaxNumBonds(); if (int1 == 0) System.out.println("Fluorine.getMaxNumBonds FAILED"); // Formatter class - com.camitro.toolkit.CamUtil // public Formatter() Formatter Formatter1 = new Formatter(); if (Formatter1 == null) System.out.println("Formatter FAILED"); // public static java.lang.String doubleFormatter(java.lang.String sValue, int precision) String1 = Formatter1.doubleFormatter("1234567890", 3); if (String1.equals("")) System.out.println("Formatter.doubleFormatter from string FAILED"); // public static java.lang.String doubleFormatter(double number, int precision) String1 = Formatter1.doubleFormatter(1234567890, 3); if (String1.equals("")) System.out.println("Formatter.doubleFormatter from number FAILED"); // FragmentFinder class - com.camitro.toolkit.ModelService // public FragmentFinder(Molecule mole); Molecule Molecule10 = new Molecule(); FragmentFinder FragmentFinder1 = new FragmentFinder(Molecule10); if (FragmentFinder1 == null) System.out.println("FragmentFinder FAILED"); // public void findFragmentForAllSites() boolean1 = false; try { FragmentFinder1.findFragmentForAllSites(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("FragmentFinder.findFragmentForAllSites FAILED"); } // public void findFragmentOfAtom(Atom theAtom) // public java.lang.String getSmilesForMolecule() String1 = FragmentFinder1.getSmilesForMolecule(); if (String1 != "") System.out.println("FragmentFinder.getSmilesForMolecule FAILED"); // public java.lang.String getSmilesForMolecule(boolean isHydrogens, boolean isAromatics, boolean isAllBondTypes, boolean isSuppressCycleCloseBondType) String1 = FragmentFinder1.getSmilesForMolecule(false, false, false, false); if (String1 != "") System.out.println("FragmentFinder.getSmilesForMolecule FAILED"); // FragmentResult class - com.camitro.toolkit.ModelService // public FragmentResult(java.lang.String mySmiles); FragmentResult FragmentResult1 = new FragmentResult("c:\\000\\src\\com\\java_test1\\anastrozole.SM2"); if (FragmentResult1 == null) System.out.println("FragmentResult FAILED"); // public FragmentResult(java.lang.String mySmiles, Atom theAtom, java.util.Hashtable fragMem) Hashtable Hashtable3 = new Hashtable(); FragmentResult FragmentResult2 = new FragmentResult("c:\\000\\src\\com\\java_test1\\anastrozole.SM2", Atom1, Hashtable3); if (FragmentResult2 == null) System.out.println("FragmentResult FAILED"); // public java.lang.String getString() String1 = FragmentResult1.getString(); if (String1.equals("")) System.out.println("FragmentResult.getString FAILED"); // public java.util.Hashtable getHashtable() Hashtable Hashtable2 = FragmentResult1.getHashtable(); if (Hashtable2 != null) System.out.println("FragmentResult.getHashtable FAILED"); // public Atom getAtom() Atom1 = FragmentResult1.getAtom(); if (Atom1 != null) System.out.println("FragmentResult.getAtom FAILED"); // public int compareTo(Comparable2 otherObject) // GeneralFile class - com.camitro.toolkit.GeneralFile // public GeneralFile() GeneralFile GeneralFile1 = new GeneralFile(); if (GeneralFile1 == null) System.out.println("GeneralFile FAILED"); // public static java.util.Vector read(java.lang.String filename) // public static java.util.Vector read(java.io.File file) // public static void write(java.util.Vector content, java.io.File outfile) // GeneralReader interface - com.camitro.toolkit.GeneralFile // public java.util.Vector read() // GeneralWriter interface - com.camitro.toolkit.GeneralFile // public void write() // GenFileConstants interface - com.camitro.toolkit.GeneralFile // has only fields // Hello interface - com.camitro.applets.RmiHelloWorld // public java.lang.String sayHello() // HelloApplet class - com.camitro.applets.RmiHelloWorld // public HelloApplet() // public void init() // public void paint(java.awt.Graphics g) // import not available for me // HelloImpl class - com.camitro.applets.RmiHelloWorld // public HelloImpl() // public java.lang.String sayHello() // public static void main(java.lang.String[] args) // import not available for me // Hydrogen class - com.camitro.toolkit.Molecule // public Hydrogen() Hydrogen Hydrogen1 = new Hydrogen(); if (Hydrogen1 == null) System.out.println("Hydrogen FAILED"); // public Hydrogen(double x, double y, double z) Hydrogen Hydrogen2 = new Hydrogen(1,1,1); if (Hydrogen2 == null) System.out.println("Hydrogen FAILED"); // public java.lang.Object clone() Object1 = Hydrogen1.clone(); if (Object1 == null) System.out.println("Hydrogen.clone FAILED"); // public java.lang.String getElement() String1 = Hydrogen1.getElement(); if (String1.equals("")) System.out.println("Hydrogen.getElement FAILED"); // public int getAtomicNumber() int1 = Hydrogen1.getAtomicNumber(); if (int1 == 0) System.out.println("Hydrogen.getAtomicNumber FAILED"); // public int getMaxNumBonds() int1 = Hydrogen1.getMaxNumBonds(); if (int1 == 0) System.out.println("Hydrogen.getMaxNumBonds FAILED"); // IAtom class - com.camitro.toolkit.Molecule // public java.lang.String getElement() // public int getInternalID() // public double getBondLength() // public double getBondAngle() // public double getTwistAngle() // public int getNA() // public int getNB() // public int getNC() // public Atom getAtom() // public static Atom addToGroup(Molecule grp, IAtom[] list, double[][] connectivity, Atom atomA, Atom atomB, Atom atomC, double bondLengthA1, double bondAngleB1, double twistAngleC1, double bondAngleA2, double twistAngleB2, double twistAngleA3) // public static void rotateSubGroup(IAtom[] list, Atom atomA, Atom atomB, Atom atomC, double twistAngleC1) // InternalCoordinate class - com.camitro.toolkit.Molecule // public InternalCoordinate() InternalCoordinate InternalCoordinate1 = new InternalCoordinate(); if (InternalCoordinate1 == null) System.out.println("InternalCoordinate FAILED"); // public InternalCoordinate(double length, double angle, double torsion) InternalCoordinate InternalCoordinate2 = new InternalCoordinate(1,1,1); if (InternalCoordinate2 == null) System.out.println("InternalCoordinate FAILED"); // public void setICoordinate(double length, double angle, double torsion) boolean1 = false; try { InternalCoordinate1.setICoordinate(1, 1, 1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("InternalCoordinate.setICoordinate FAILED"); } // public double getBondLength() double1 = InternalCoordinate1.getBondLength(); if (double1 == 0) System.out.println("InternalCoordinate.getBondLength FAILED"); // public double getBondAngle() double1 = InternalCoordinate1.getBondAngle(); if (double1 == 0) System.out.println("InternalCoordinate.getBondAngle FAILED"); // public double getTorsion() double1 = InternalCoordinate1.getTorsion(); if (double1 == 0) System.out.println("InternalCoordinate.getTorsion FAILED"); // Iodine class - com.camitro.toolkit.Molecule // public Iodine() Iodine Iodine1 = new Iodine(); if (Iodine1 == null) System.out.println("Iodine FAILED"); // public Iodine(double x, double y, double z) Iodine Iodine2 = new Iodine(1,1,1); if (Iodine2 == null) System.out.println("Iodine FAILED"); // public Iodine(int hybrid, double x, double y, double z) Iodine Iodine3 = new Iodine(1,1,1,1); if (Iodine3 == null) System.out.println("Iodine FAILED"); // public java.lang.Object clone() Object1 = Iodine1.clone(); if (Object1 == null) System.out.println("Iodine.clone FAILED"); // public void rehybridize(int hybrid) boolean1 = false; try { Iodine1.rehybridize(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Iodine.rehybridize FAILED"); } // public void rehybridize() boolean1 = false; try { Iodine1.rehybridize(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Iodine.rehybridize FAILED"); } // public java.lang.String getElement() String1 = Iodine1.getElement(); if (String1.equals("")) System.out.println("Iodine.getElement FAILED"); // public int getAtomicNumber() int1 = Iodine1.getAtomicNumber(); if (int1 == 0) System.out.println("Iodine.getAtomicNumber FAILED"); // public int getMaxNumBonds() int1 = Iodine1.getMaxNumBonds(); if (int1 == 0) System.out.println("Iodine.getMaxNumBonds FAILED"); // JobStepGet class - com.camitro.toolkit.CamDatabase // public JobStepGet() // public void connect(java.lang.String database, java.lang.String user, java.lang.String pwd) // public void close() // public ModelRequest getNextModelRequest() // import not available for me // JobStepPut class - com.camitro.toolkit.CamDatabase // public JobStepPut() // public void connect(java.lang.String database, java.lang.String user, java.lang.String pwd) // public void close() // public void putModelReply(ModelReply reply) // import not available for me // Log class - com.camitro.toolkit.CamUtil // public Log() Log Log1 = new Log(); if (Log1 == null) System.out.println("Log FAILED"); // public static void print(java.lang.String text) boolean1 = false; try { Log1.print("OK"); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Log.print FAILED"); } // public static void println(java.lang.String text) boolean1 = false; try { Log1.println("OK"); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Log.println FAILED"); } // public static void addPrintStream(java.io.PrintStream pout) // public static void removePrintStream(java.io.PrintStream pout) // public static void addPrintWriter(java.io.PrintWriter pout) // public static void removePrintWriter(java.io.PrintWriter pout) // LongString class - com.camitro.toolkit.CamUtil // public LongString(java.lang.String longStr) LongString LongString1 = new LongString("OK"); if (LongString1 == null) System.out.println("LongString FAILED"); // public java.lang.String toString() String1 = LongString1.toString(); if (String1.equals("")) System.out.println("LongString.toString FAILED"); // LUDecomposition class - gov.nist.Jama // gov.nist.Jama.LUDecomposition // MassTooSmallException class - com.camitro.toolkit.MoleculeSymmetry // public MassTooSmallException() // public MassTooSmallException(java.lang.String s) // import not available for me // Maths class - gov.nist.Jama.util // gov.nist.Jama.util.Maths // MathVect class - com.camitro.toolkit.CamUtil // public MathVect() MathVect MathVect1 = new MathVect(); if (MathVect1 == null) System.out.println("MathVect FAILED"); // public MathVect(Point end) MathVect MathVect2 = new MathVect(Point2); if (MathVect2 == null) System.out.println("MathVect FAILED"); // public MathVect(Point start, Point end) MathVect MathVect3 = new MathVect(Point2,Point3); if (MathVect3 == null) System.out.println("MathVect FAILED"); // public MathVect(double x1, double y1, double z1, double x2, double y2, double z2) MathVect MathVect4 = new MathVect(1,1,1,2,2,2); if (MathVect4 == null) System.out.println("MathVect FAILED"); // public MathVect(double x, double y, double z) MathVect MathVect5 = new MathVect(1,1,1); if (MathVect5 == null) System.out.println("MathVect FAILED"); // public void setStartPoint(Point p) boolean1 = false; try { MathVect1.setStartPoint(Point2); boolean1 = true; } finally { if (boolean1 == false) System.out.println("MathVect.setStartPoint FAILED"); } // public void setStartPoint(double x, double y, double z) boolean1 = false; try { MathVect1.setStartPoint(1, 1, 1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("MathVect.setStartPoint FAILED"); } // public Point getStartPoint() Point2 = MathVect1.getStartPoint(); if (Point2 == null) System.out.println("MathVect.getStartPoint FAILED"); // public void setEndPoint(Point p) boolean1 = false; try { MathVect1.setEndPoint(Point2); boolean1 = true; } finally { if (boolean1 == false) System.out.println("MathVect.setEndPoint FAILED"); } // public void setEndPoint(double x, double y, double z) boolean1 = false; try { MathVect1.setEndPoint(1, 1, 1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("MathVect.setEndPoint FAILED"); } // public Point getEndPoint() Point2 = MathVect1.getEndPoint(); if (Point2 == null) System.out.println("MathVect.getEndPoint FAILED"); // public void setNorm(double newNorm) boolean1 = false; try { MathVect1.setNorm(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("MathVect.setNorm FAILED"); } // public void moveToOrigin() boolean1 = false; try { MathVect1.moveToOrigin(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("MathVect.moveToOrigin FAILED"); } // public void moveToPoint(Point p) boolean1 = false; try { MathVect1.moveToPoint(Point2); boolean1 = true; } finally { if (boolean1 == false) System.out.println("MathVect.moveToPoint FAILED"); } // public MathVect reverse() MathVect MathVect6 = MathVect1.reverse(); if (MathVect6 == null) System.out.println("MathVect.reverse FAILED"); // public Point components() Point2 = MathVect1.components(); if (Point2 == null) System.out.println("MathVect.components FAILED"); // public double norm() double1 = MathVect1.norm(); if (double1 == 0) System.out.println("MathVect.norm FAILED"); // public boolean isZeroVect() boolean1 = MathVect1.isZeroVect(); if (boolean1 == true) System.out.println("MathVect.isZeroVect FAILED"); // public MathVect unitVectAtOrigin() MathVect MathVect7 = MathVect1.unitVectAtOrigin(); if (MathVect7 == null) System.out.println("MathVect.unitVectAtOrigin FAILED"); // public void normalizing() boolean1 = false; try { MathVect1.normalizing(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("MathVect.normalizing FAILED"); } // public MathVect scalarProduct(double k) MathVect MathVect8 = MathVect1.scalarProduct(1); if (MathVect8 == null) System.out.println("MathVect.scalarProduct FAILED"); // public MathVect sumVect(MathVect v) MathVect MathVect9 = MathVect1.sumVect(MathVect4); if (MathVect9 == null) System.out.println("MathVect.sumVect FAILED"); // public MathVect diffVect(MathVect v) MathVect MathVect10 = MathVect1.diffVect(MathVect4); if (MathVect10 == null) System.out.println("MathVect.diffVect FAILED"); // public MathVect crossProduct(MathVect v) MathVect MathVect11 = MathVect1.crossProduct(MathVect4); if (MathVect11 == null) System.out.println("MathVect.crossProduct FAILED"); // public double dotProduct(MathVect v) double1 = MathVect1.dotProduct(MathVect4); if (double1 == 0) System.out.println("MathVect.dotProduct FAILED"); // public double angle(MathVect thatV) double1 = MathVect1.angle(MathVect4); if (double1 == 0) System.out.println("MathVect.angle FAILED"); // public MathVect rotate(double degree, MathVect axis) MathVect MathVect12 = MathVect1.rotate(45, MathVect4); if (MathVect12 == null) System.out.println("MathVect.rotate FAILED"); // Matrix class - gov.nist.Jama // gov.nist.Jama.Matrix // Methoxy class - com.camitro.toolkit.Molecule // public Methoxy() Methoxy Methoxy1 = new Methoxy(); if (Methoxy1 == null) System.out.println("Methoxy FAILED"); // public Atom addToGroup(Molecule grp, Atom atomA, Atom atomB, Atom atomC, double bondLengthA1, double bondAngleB1, double twistAngleC1, double bondAngleA2, double twistAngleB2, double twistAngleA3) // Methyl class - com.camitro.toolkit.Molecule // public Methyl(Atom carbon, Atom H1, Atom H2, Atom H3); // Methyl Methyl1 = new Methyl(Atom1, Atom2, Atom3, Atom4); // if (Methyl1 == null) // System.out.println("Methyl FAILED"); // public void rotateSubGroup(Atom atomA, Atom atomB, Atom atomC, double twistAngleC1) // boolean1 = false; // try { // Methyl1.rotateSubGroup(Atom2, Atom3, Atom4, 1); // boolean1 = true; // } finally { // if (boolean1 == false) // System.out.println("Methyl.rotateSubGroup FAILED"); // } // ModelReply class - com.camitro.toolkit.ModelService // public ModelReply(java.lang.String companyID, java.lang.String analysisType, java.lang.String jobCmpID, java.lang.String tag, java.lang.Exception exc, int runSeconds, int runUtilization, java.lang.String runWorkerId, java.util.Properties simpleProps) Exception Exception12 = new Exception(); Properties Properties12 = new Properties(); ModelReply ModelReply1 = new ModelReply("x", "x", "x", "x", Exception12, 1, 1, "x", Properties12); if (ModelReply1 == null) System.out.println("ModelReply FAILED"); // public java.lang.String getJobCmpID() String1 = ModelReply1.getJobCmpID(); if (String1.equals("")) System.out.println("ModelReply.getJobCmpID FAILED"); // public java.lang.String getAnalysisType() String1 = ModelReply1.getAnalysisType(); if (String1.equals("")) System.out.println("ModelReply.getAnalysisType FAILED"); // ModelReplyHash class - com.camitro.toolkit.ModelService // public ModelReplyHash(ModelReply modelReply) ModelReplyHash ModelReplyHash1 = new ModelReplyHash(ModelReply1); if (ModelReplyHash1 == null) System.out.println("ModelReplyHash FAILED"); // public java.util.Vector getCompoundSiteResults() Vector1 = ModelReplyHash1.getCompoundSiteResults(); if (Vector1 == null) System.out.println("ModelReplyHash.getCompoundSiteResults FAILED"); // public java.util.Vector getCompoundResults() Vector1 = ModelReplyHash1.getCompoundResults(); if (Vector1 == null) System.out.println("ModelReplyHash.getCompoundResults FAILED"); // public java.util.Vector getJobStepErrors() Vector1 = ModelReplyHash1.getJobStepErrors(); if (Vector1 == null) System.out.println("ModelReplyHash.getJobStepErrors FAILED"); // ModelRequest class - com.camitro.toolkit.ModelService - abstract implements Serializable // protected ModelRequest(java.lang.String companyID, java.lang.String analysisType, java.lang.String jobCmpID, LongString molFileContents, java.lang.String parameter, java.lang.String tag, java.util.Properties simpleProps, int priority) // public abstract java.lang.String getRequestType() // public java.lang.String getJobCmpID() // public java.lang.String getAnalysisType() // public LongString getMolFileContent() // public java.lang.String getParameter() // ModelResultConstants interface - com.camitro.toolkit.ModelService // has only fields // ModelService class - com.camitro.toolkit.ModelService - abstract // public ModelService() // protected ModelService(ModelService that) // public abstract ClusterReply runRequest(ClusterRequest request) // public abstract java.lang.String getRequestType() // public abstract java.lang.Object clone() // ModelServiceConstants interface - com.camitro.toolkit.ModelService // has only fields // ModelWrapper class - com.camitro.toolkit.ModelService // protected ModelWrapper() // protected java.util.Vector runRequestsWithDots(java.util.Vector requests) // protected void printHeaderLine(java.lang.String name) // protected void writeHeaderLine(java.lang.StringBuffer buf, java.lang.String name) // protected int getIntSystemProperty(java.lang.String name, int defaultValue) // protected void defineRingStructure(Molecule drug) // protected void definePatterns(Molecule drug) // protected java.util.Vector readInputFileContentFromLongString(java.lang.String fileExt, LongString inFileContents) // protected java.io.PrintWriter openPrintWriter(java.lang.String directory, java.lang.String filename) // protected java.io.PrintWriter openPrintWriter(java.lang.String filename) // protected LongString correctNitroStruct(LongString origMolContents) // MoeReply class - com.camitro.toolkit.ComputeService // public MoeReply(java.lang.String companyID, java.lang.String tag, java.lang.Exception exc, int runSeconds, int runUtilization, java.lang.String runWorkerId, java.util.Properties simpleProps, boolean isSealed) Exception Exception13 = new Exception(); Properties Properties13 = new Properties(); MoeReply MoeReply1 = new MoeReply("x", "x", Exception13, 1, 1, "x", Properties13, false); if (MoeReply1 == null) System.out.println("MoeReply FAILED"); // MoeRequest class - com.camitro.toolkit.ComputeService - implements java.io.Serializable // public MoeRequest(java.lang.String companyID, java.lang.String tag, LongString molContentsLs, java.util.Properties resCmpSiteProps, java.util.Properties simpleProps, int priority) MoeRequest MoeRequest1 = new MoeRequest("x", "x", LongString1, Properties13, Properties13, 1); if (MoeRequest1 == null) System.out.println("MoeRequest FAILED"); // public LongString getMolContents() LongString1 = MoeRequest1.getMolContents(); if (LongString1 == null) System.out.println("MoeRequest.getMolContents FAILED"); // public java.util.Properties getResCmpSiteProps() Properties Properties1 = MoeRequest1.getResCmpSiteProps(); if (Properties1 == null) System.out.println("MoeRequest.getResCmpSiteProps FAILED"); // public java.lang.String getRequestType() String1 = MoeRequest1.getRequestType(); if (String1.equals("")) System.out.println("MoeRequest.getRequestType FAILED"); // MoeService class - com.camitro.toolkit.ComputeService - implements java.lang.Cloneable // public MoeService() MoeService MoeService2 = new MoeService(); if (MoeService2 == null) System.out.println("MoeService FAILED"); // protected MoeService(MoeService that) // public java.lang.Object clone() Object1 = MoeService2.clone(); if (Object1 == null) System.out.println("MoeService.clone FAILED"); // public java.lang.String getRequestType() String1 = MoeService2.getRequestType(); if (String1.equals("")) System.out.println("MoeService.getRequestType FAILED"); // public ClusterReply runRequest(ClusterRequest request) // not available to me // MoeWrapper class - com.camitro.toolkit.ComputeService // public MoeWrapper(MoeRequest request, java.lang.String baseFilePath, java.lang.String runWorkerId) // public MoeReply runMoe() // public MoeReply runMoe(java.lang.Runnable callback, int waitSeconds) // not available to me // Molecule class - com.camitro.toolkit.Molecule - implements Cloneable // public Molecule() Molecule Molecule1 = new Molecule(); if (Molecule1 == null) System.out.println("Molecule FAILED"); // protected Molecule(Molecule that) // public java.lang.Object clone() Object1 = Molecule1.clone(); if (Object1 == null) System.out.println("Molecule.clone FAILED"); // protected void deepenCopy(Molecule that) // public Atom connectingAtom() Atom1 = Molecule1.connectingAtom(); if (Atom1 != null) System.out.println("Molecule.connectingAtom FAILED"); // public Atom getAtomAt(int idx) // does not work // public int getAtomCount() int1 = Molecule1.getAtomCount(); if (int1 != 0) System.out.println("Molecule.getAtomCount FAILED"); // public int getBondCount() int1 = Molecule1.getBondCount(); if (int1 != 0) System.out.println("Molecule.getBondCount FAILED"); // public Bond getBondAt(int idx) // does not work // public void addRing(Ring ringStruct) // does not work // public void removeRing(Ring ringStruct) // does not work // public int getRingCount() // does not work // public Ring getRingAt(int ringIdx) // does not work // public boolean containsRing(Ring theRing) // does not work // public Atom createAtom(java.lang.String atomType) Atom1 = Molecule1.createAtom("H"); if (Atom1 == null) System.out.println("Molecule.createAtom FAILED"); // public void addAtom(Atom a) // does not work // public void addAtom(Atom a, double x, double y, double z) // does not work // public void deleteAtom(Atom a) // does not work // public java.lang.String getBondType(Atom a1, Atom a2) // does not work // public Bond addBond(Atom a1, Atom a2) // does not work // public Bond addBond(int a1, int a2) // does not work // public Bond addBond(Atom a1, Atom a2, double order) // does not work // public Bond addBond(int a1, int a2, double order) // does not work // public Bond findBond(Atom a1, Atom a2) // does not work // public void deleteBond(Atom a1, Atom a2) // does not work // public void deleteBond(Bond bond) // does not work // public void removeHydrogen(int index) // does not work // public void removeHydrogen(Atom H) // does not work // public PropertyList getPropList() PropertyList PropertyList3 = Molecule1.getPropList(); if (PropertyList3 == null) System.out.println("Molecule.getPropList FAILED"); // public void setHeat(double Heat) boolean1 = false; try { Molecule1.setHeat(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Molecule.setHeat FAILED"); } // public double getHeat() double1 = Molecule1.getHeat(); if (double1 == 0) System.out.println("Molecule.getHeat FAILED"); // public boolean hasHeat() boolean1 = Molecule1.hasHeat(); if (boolean1 == false) System.out.println("Molecule.hasHeat FAILED"); // public void setIP(double IP) boolean1 = false; try { Molecule1.setIP(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Molecule.setIP FAILED"); } // public double getIP() double1 = Molecule1.getIP(); if (double1 == 0) System.out.println("Molecule.getIP FAILED"); // public void setSpin(double S) boolean1 = false; try { Molecule1.setSpin(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Molecule.setSpin FAILED"); } // public double getSpin() double1 = Molecule1.getSpin(); if (double1 == 0) System.out.println("Molecule.getSpin FAILED"); // public void setCPU(double t) boolean1 = false; try { Molecule1.setCPU(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Molecule.setCPU FAILED"); } // public double getCPU() double1 = Molecule1.getCPU(); if (double1 == 0) System.out.println("Molecule.getCPU FAILED"); // public void setSite(int metaboliteSite) boolean1 = false; try { Molecule1.setSite(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Molecule.setSite FAILED"); } // public int getSite() int1 = Molecule1.getSite(); if (int1 == 0) System.out.println("Molecule.getSite FAILED"); // public void setAromatic(boolean aromatic) boolean1 = false; try { Molecule1.setAromatic(true); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Molecule.setAromatic FAILED"); } // public boolean getAromatic() boolean1 = Molecule1.getAromatic(); if (boolean1 == false) System.out.println("Molecule.getAromatic FAILED"); // public double getMW() double1 = Molecule1.getMW(); if (double1 == 0) System.out.println("Molecule.getMW FAILED"); // public int getMWSurcharge() int1 = Molecule1.getMWSurcharge(); if (int1 == 0) System.out.println("Molecule.getMWSurcharge FAILED"); // MoleculeConstants interface - com.camitro.toolkit.Molecule // has only fields // MoleculeFile class - com.camitro.toolkit.MoleculeFile // public MoleculeFile() MoleculeFile MoleculeFile1 = new MoleculeFile(); if (MoleculeFile1 == null) System.out.println("MoleculeFile FAILED"); // public static java.util.Vector read(java.lang.String filenameWithExt, java.io.LineNumberReader buf) // public static java.util.Vector read(java.lang.String filename) Vector1 = MoleculeFile1.read("c:\\000\\src\\com\\java_test1\\ametryne.mol"); if (Vector1 == null) System.out.println("MoleculeFile.read FAILED"); // public static java.util.Vector read(java.io.File file) // public static Molecule readOne(java.lang.String filename) Molecule1 = MoleculeFile1.readOne("c:\\000\\src\\com\\java_test1\\ametryne.mol"); if (Molecule1 == null) System.out.println("MoleculeFile.readOne FAILED"); // public static Molecule readOne(java.io.File file) // public static java.util.Vector readString(java.lang.String fileExt, java.lang.String fileContent) // Vector1 = MoleculeFile1.readString("mol", "c:\\000\\src\\com\\java_test1\\ametryne.mol"); // if (Vector1 == null) // System.out.println("MoleculeFile.readString FAILED"); // public static void write(java.lang.String filenameWithExt, java.io.PrintWriter buf, java.util.Vector molecules) // public static void write(java.io.File file, java.util.Vector molecules) // public static void writeOne(java.lang.String filename, Molecule molecule) boolean1 = false; try { MoleculeFile1.writeOne("c:\\000\\src\\com\\java_test1\\ametryne.mol", Molecule1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("MoleculeFile.writeOne FAILED"); } // public static void writeOne(java.io.File file, Molecule molecule) // public static java.lang.String createString(java.lang.String fileExt, java.util.Vector molecules) // String1 = MoleculeFile1.createString(".mol", Vector1); // if (String1.equals("")) // System.out.println("MoleculeFile.createString FAILED"); // public static java.lang.String createString(java.lang.String fileExt, Molecule molecule) String1 = MoleculeFile1.createString(".mol", Molecule1); if (String1.equals("")) System.out.println("MoleculeFile.createString FAILED"); // public static void convert(java.lang.String filename, java.lang.String newType) boolean1 = false; try { MoleculeFile1.convert("c:\\000\\src\\com\\java_test1\\ametryne.mol", "mol"); boolean1 = true; } finally { if (boolean1 == false) System.out.println("MoleculeFile.convert FAILED"); } // public static void convert(java.io.File infile, java.io.File outfile) // public static java.lang.String getLowerExtension(java.lang.String filenameWithExt) String1 = MoleculeFile1.getLowerExtension("ametryne.mol"); if (String1.equals("")) System.out.println("MoleculeFile.getLowerExtension FAILED"); // MoleculeMoment class - com.camitro.toolkit.MoleculeSymmetry // public MoleculeMoment(Molecule molecule) // public double getTotalMass() // public com.camitro.toolkit.MoleculeSymmetry.Point3d getCenterOfMass() // public com.camitro.toolkit.MoleculeSymmetry.Matrix3d getMomentOfInertiaTensor() // public com.camitro.toolkit.MoleculeSymmetry.Matrix3d getMomentOfInertiaTensor(com.camitro.toolkit.MoleculeSymmetry.Point3d center) // public com.camitro.toolkit.MoleculeSymmetry.Vector3d getPrincipleInertialMoments() // public com.camitro.toolkit.MoleculeSymmetry.Vector3d getPrincipleInertialMoments(com.camitro.toolkit.MoleculeSymmetry.Point3d expansionCenter) // public com.camitro.toolkit.MoleculeSymmetry.Matrix3d getInertialRotationMatrix() // public com.camitro.toolkit.MoleculeSymmetry.Matrix3d getInertialRotationMatrix(com.camitro.toolkit.MoleculeSymmetry.Point3d expansionCenter) // public double getTotalCharge() // public com.camitro.toolkit.MoleculeSymmetry.Point3d getCenterOfCharge() // public double getDipoleMagnitude() // public double getDipoleMagnitude(com.camitro.toolkit.MoleculeSymmetry.Point3d expansionCenter) // public com.camitro.toolkit.MoleculeSymmetry.Vector3d getDipoleMoment() // public com.camitro.toolkit.MoleculeSymmetry.Vector3d getDipoleMoment(com.camitro.toolkit.MoleculeSymmetry.Point3d expansionCenter) // public com.camitro.toolkit.MoleculeSymmetry.Matrix3d getQuadrupoleMomentTensor() // public com.camitro.toolkit.MoleculeSymmetry.Matrix3d getQuadrupoleMomentTensor(com.camitro.toolkit.MoleculeSymmetry.Point3d expansionCenter) // public com.camitro.toolkit.MoleculeSymmetry.Point3d getCenterOfDipole() // public com.camitro.toolkit.MoleculeSymmetry.Vector3d getQdotp(com.camitro.toolkit.MoleculeSymmetry.Matrix3d Q, com.camitro.toolkit.MoleculeSymmetry.Vector3d p) // public com.camitro.toolkit.MoleculeSymmetry.Vector3d getPrincipleQuadrupoleMoments() // public com.camitro.toolkit.MoleculeSymmetry.Vector3d getPrincipleQuadrupoleMoments(com.camitro.toolkit.MoleculeSymmetry.Point3d expansionCenter) // public com.camitro.toolkit.MoleculeSymmetry.Matrix3d getQuadrupoleRotationMatrix() // public com.camitro.toolkit.MoleculeSymmetry.Matrix3d getQuadrupoleRotationMatrix(com.camitro.toolkit.MoleculeSymmetry.Point3d expansionCenter) // public void dumpToScreen(double n) // public void dumpToScreen(com.camitro.toolkit.MoleculeSymmetry.Point3d p) // public void dumpToScreen(com.camitro.toolkit.MoleculeSymmetry.Vector3d v) // public void dumpToScreen(com.camitro.toolkit.MoleculeSymmetry.Matrix3d m) // public void dumpToScreen(Molecule molecule) // MoleculeMutableTreeNode class - com.camitro.toolkit.Molecule // public MoleculeMutableTreeNode(Molecule mol) // public Molecule getMolecule() // public Molecule parentMolecule() // MoleculeOrientation class - com.camitro.toolkit.MoleculeSymmetry // public MoleculeOrientation(Molecule theMolecule) // public Molecule inputOrientation() // public void resetOrientation() // public Molecule moveCoordinateSystemTo(com.camitro.toolkit.MoleculeSymmetry.Point3d newOrigin) // public Molecule moveMoleculeTo(com.camitro.toolkit.MoleculeSymmetry.Point3d dest) // public Molecule translateMolecule(com.camitro.toolkit.MoleculeSymmetry.Tuple3d displacement) // public Molecule rotateMoleculeAboutX(double Angle) // public Molecule rotateMoleculeAboutY(double Angle) // public Molecule rotateMoleculeAboutZ(double Angle) // public Molecule applyRotationMatrix(com.camitro.toolkit.MoleculeSymmetry.Matrix3d rot) // public Molecule reflectThroughOrgin() // public Molecule applyTransformationMatrix(com.camitro.toolkit.MoleculeSymmetry.Matrix4d transform) // public Molecule inertialOrientation() // public Molecule quadrupolarOrientation() // public Molecule alignAxesToDipole() // public Molecule gaussianStandardOrientation() // MoleculeReader interface - com.camitro.toolkit.MoleculeFile // public java.util.Vector read(java.io.LineNumberReader reader) // MoleculeSymmetry class - com.camitro.toolkit.MoleculeSymmetry // public MoleculeSymmetry(Molecule) // MoleculeSymmetryException class com.camitro.toolkit.MoleculeSymmetry - extends java.lang.Exception // public MoleculeSymmetryException() // public MoleculeSymmetryException(java.lang.String s) // import not available for me // MoleculeTree class - com.camitro.toolkit.Molecule // public MoleculeTree(Molecule); // MoleculeTreeNode interface - com.camitro.toolkit.Molecule // public Molecule getMolecule() // MoleculeWriter interface - com.camitro.toolkit.MoleculeFile // public void write(java.io.PrintWriter writer, java.util.Vector molecules) // Molmap class - com.camitro.toolkit.Molmap // Molmap Molmap1 = new Molmap(); // not in beta3 // MolmapApplet class - com.camitro.toolkit.Molmap // MolmapApplet MolmapApplet1 = new MolmapApplet(); // not in beta3 // MolmapFrame class - com.camitro.toolkit.Molmap // MolmapFrame MolmapFrame1 = new MolmapFrame(); // not in beta3 // MolmapPanel class - com.camitro.toolkit.Molmap // MolmapPanel MolmapPanel1 = new MolmapPanel(); // not in beta3 // MolReader class - com.camitro.toolkit.MoleculeFile // public MolReader() MolReader MolReader1 = new MolReader(); if (MolReader1 == null) System.out.println("MolReader FAILED"); // public java.util.Vector read(java.io.LineNumberReader reader) // MolWriter class - com.camitro.toolkit.MoleculeFile // public MolWriter() MolWriter MolWriter1 = new MolWriter(); if (MolWriter1 == null) System.out.println("MolWriter FAILED"); // public void write(java.io.PrintWriter pwriter, java.util.Vector molecules) // MopacReply class - com.camitro.toolkit.ComputeService // public MopacReply(String companyID, String tag, Exception exc, int runSeconds, int runUtilization, String runWorkerId, Properties simpleProps, boolean isSealed) // public MopacReply(java.lang.String companyID, java.lang.String tag, java.lang.Exception exc, int runSeconds, int runUtilization, java.lang.String runWorkerId, int mopacCycles, int mopacCpuSeconds, java.util.Properties simpleProps, boolean isSealed) // public MopacReply(java.lang.String companyID, java.lang.String tag, java.lang.Exception exc, double heat, double IP, double spin, double[] xValues, double[] yValues, double[] zValues, double[] chargeValues, double[] densityValues, int runSeconds, int runUtilization, java.lang.String runWorkerId, int mopacCycles, int mopacCpuSeconds, java.util.Properties simpleProps, boolean isSealed) // public double getHeat() // public double getIP() // public double getSpin() // public double[] getXValues() // public double[] getYValues() // public double[] getZValues() // public double[] getChargeValues() // public double[] getDensityValues() // public int getMopacCycles() // public int getMopacCpuSeconds() // MopacRequest class - com.camitro.toolkit.ComputeService // public MopacRequest(String companyID, String tag, Molecule molecule, String keywordPropPattern, Properties simpleProps, int priority); // public MopacRequest(java.lang.String companyID, java.lang.String tag, Molecule molecule, java.lang.String keywordPropPattern, java.util.Properties simpleProps) // public MopacRequest(java.lang.String companyID, java.lang.String tag, java.lang.String[] elementValues, double[] xValues, double[] yValues, double[] zValues, boolean[] optimizeFlags, java.lang.String keywordPropPattern, java.util.Properties simpleProps, int priority) // public java.lang.String getRequestType() // public java.lang.String getKeywordPropPattern() // public java.lang.String[] getElementValues() // public double[] getXValues() // public double[] getYValues() // public double[] getZValues() // public boolean[] getOptimizeFlags() // public int[] getMappingToMopac() // public int[] getMappingFromMopac() // MopacService class - com.camitro.toolkit.ComputeService // public MopacService() MopacService MopacService1 = new MopacService(); if (MopacService1 == null) System.out.println("MopacService FAILED"); // protected MopacService(MopacService that) // public ClusterReply runRequest(ClusterRequest request) // public java.lang.String getRequestType() String1 = MopacService1.getRequestType(); if (String1.equals("")) System.out.println("MopacService.getRequestType FAILED"); // public java.lang.Object clone() Object1 = MopacService1.clone(); if (Object1 == null) System.out.println("MopacService.clone FAILED"); // MopacWrapper class - com.camitro.toolkit.ComputeService // Nitrogen class - com.camitro.toolkit.Molecule // public Nitrogen() Nitrogen Nitrogen1 = new Nitrogen(); if (Nitrogen1 == null) System.out.println("Nitrogen FAILED"); // public Nitrogen(double x, double y, double z) Nitrogen Nitrogen2 = new Nitrogen(1,1,1); if (Nitrogen2 == null) System.out.println("Nitrogen FAILED"); // public Nitrogen(int hybrid, double x, double y, double z) Nitrogen Nitrogen3 = new Nitrogen(1,1,1,1); if (Nitrogen3 == null) System.out.println("Nitrogen FAILED"); // public java.lang.Object clone() Object1 = Nitrogen1.clone(); if (Object1 == null) System.out.println("Nitrogen.clone FAILED"); // public void rehybridize(int hybrid) boolean1 = false; try { Nitrogen1.rehybridize(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Nitrogen.rehybridize FAILED"); } // public void rehybridize() boolean1 = false; try { Nitrogen1.rehybridize(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Nitrogen.rehybridize FAILED"); } // public java.lang.String getElement() String1 = Nitrogen1.getElement(); if (String1.equals("")) System.out.println("Nitrogen.getElement FAILED"); // public int getAtomicNumber() int1 = Nitrogen1.getAtomicNumber(); if (int1 == 0) System.out.println("Nitrogen.getAtomicNumber FAILED"); // public int getMaxNumBonds() int1 = Nitrogen1.getMaxNumBonds(); if (int1 == 0) System.out.println("Nitrogen.getMaxNumBonds FAILED"); // NotHandledException class - com.camitro.toolkit.CamUtil // public NotHandledException(java.lang.String msg) NotHandledException NotHandledException1 = new NotHandledException("x"); if (NotHandledException1 == null) System.out.println("NotHandledException FAILED"); // public NotHandledException() NotHandledException NotHandledException2 = new NotHandledException(); if (NotHandledException2 == null) System.out.println("NotHandledException FAILED"); // OtherAtom class - com.camitro.toolkit.Molecule // public OtherAtom(java.lang.String elemSymbol, int atomicNum, double mass, int maxBonds); OtherAtom OtherAtom1 = new OtherAtom("x", 1, 1, 1); if (OtherAtom1 == null) System.out.println("OtherAtom FAILED"); // public java.lang.Object clone() Object1 = OtherAtom1.clone(); if (Object1 == null) System.out.println("OtherAtom.clone FAILED"); // public java.lang.String getElement() String1 = OtherAtom1.getElement(); if (String1.equals("")) System.out.println("OtherAtom.getElement FAILED"); // public int getAtomicNumber() int1 = OtherAtom1.getAtomicNumber(); if (int1 == 0) System.out.println("OtherAtom.getAtomicNumber FAILED"); // public int getMaxNumBonds() int1 = OtherAtom1.getMaxNumBonds(); if (int1 == 0) System.out.println("OtherAtom.getMaxNumBonds FAILED"); // Oxygen class - com.camitro.toolkit.Molecule // public Oxygen() Oxygen Oxygen1 = new Oxygen(); if (Oxygen1 == null) System.out.println("Oxygen FAILED"); // public Oxygen(double x, double y, double z) Oxygen Oxygen2 = new Oxygen(1,1,1); if (Oxygen2 == null) System.out.println("Oxygen FAILED"); // public Oxygen(int hybrid, double x, double y, double z) Oxygen Oxygen3 = new Oxygen(1,1,1,1); if (Oxygen3 == null) System.out.println("Oxygen FAILED"); // public java.lang.Object clone() Object1 = Oxygen1.clone(); if (Object1 == null) System.out.println("Oxygen.clone FAILED"); // public void rehybridize(int hybrid) boolean1 = false; try { Oxygen1.rehybridize(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Oxygen.rehybridize FAILED"); } // public void rehybridize() boolean1 = false; try { Oxygen1.rehybridize(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Oxygen.rehybridize FAILED"); } // public java.lang.String getElement() String1 = Oxygen1.getElement(); if (String1.equals("")) System.out.println("Oxygen.getElement FAILED"); // public int getAtomicNumber() int1 = Oxygen1.getAtomicNumber(); if (int1 == 0) System.out.println("Oxygen.getAtomicNumber FAILED"); // public int getMaxNumBonds() int1 = Oxygen1.getMaxNumBonds(); if (int1 == 0) System.out.println("Oxygen.getMaxNumBonds FAILED"); // P450AliphaticSite class - com.camitro.toolkit.ElecModel - cloned // public java.lang.Object clone() // P450AromaticSite class - com.camitro.toolkit.ElecModel - cloned // public java.lang.Object clone() // P450OriginalSite class - com.camitro.toolkit.ElecModel - cloned // public java.lang.Object clone() // P450Site class - com.camitro.toolkit.ElecModel // protected P450Site(P450Site that) // public void setActivationEnergy(double ea) // public void setMopacActivationEnergy(double ea) // public double getMopacActivationEnergy() // public double getActivationEnergy() // public boolean hasActivationEnergy() // public void setAxialEa(double ea) // public double getAxialEa() // public void setEquitorialEa(double ea) // public double getEquitorialEa() // public void setRelativeRate(double rate) // public double getRelativeRate() // public void appendNotes(java.lang.String note) // public void overrideLastNotes(java.lang.String note) // public java.lang.String getNotes() // public ElecModelWrapper getModel() // public abstract java.lang.Object clone() // protected void setHydrogenCount(int hydrogenCount) // PatternFinder class - com.camitro.toolkit.ModelService // public PatternFinder(Molecule mole) PatternFinder PatternFinder1 = new PatternFinder(Molecule1); if (PatternFinder1 == null) System.out.println("PatternFinder FAILED"); // public void findAllPatterns() boolean1 = false; try { PatternFinder1.findAllPatterns(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("PatternFinder.findAllPatterns FAILED"); } // PdbWriter class - com.camitro.toolkit.MoleculeFile // public PdbWriter() PdbWriter PdbWriter1 = new PdbWriter(); if (PdbWriter1 == null) System.out.println("PdbWriter FAILED"); // public void write(java.io.PrintWriter pwriter, java.util.Vector molecules) // Phosphorus class - com.camitro.toolkit.Molecule // public Phosphorus() Phosphorus Phosphorus1 = new Phosphorus(); if (Phosphorus1 == null) System.out.println("Phosphorus FAILED"); // public Phosphorus(double x, double y, double z) Phosphorus Phosphorus2 = new Phosphorus(1,1,1); if (Phosphorus2 == null) System.out.println("Phosphorus FAILED"); // public Phosphorus(int hybrid, double x, double y, double z) Phosphorus Phosphorus3 = new Phosphorus(1,1,1,1); if (Phosphorus3 == null) System.out.println("Phosphorus FAILED"); // public java.lang.Object clone() Object1 = Phosphorus1.clone(); if (Object1 == null) System.out.println("Phosphorus.clone FAILED"); // public void rehybridize(int hybrid) boolean1 = false; try { Phosphorus1.rehybridize(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Phosphorus.rehybridize FAILED"); } // public void rehybridize() boolean1 = false; try { Phosphorus1.rehybridize(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Phosphorus.rehybridize FAILED"); } // public java.lang.String getElement() String1 = Phosphorus1.getElement(); if (String1.equals("")) System.out.println("Phosphorus.getElement FAILED"); // public int getAtomicNumber() int1 = Phosphorus1.getAtomicNumber(); if (int1 == 0) System.out.println("Phosphorus.getAtomicNumber FAILED"); // public int getMaxNumBonds() int1 = Phosphorus1.getMaxNumBonds(); if (int1 == 0) System.out.println("Phosphorus.getMaxNumBonds FAILED"); // Point class - com.camitro.toolkit.CamUtil // public Point() Point Point1 = new Point(); if (Point1 == null) System.out.println("Point FAILED"); // public Point(double x, double y, double z) Point Point10 = new Point(1,1,1); if (Point10 == null) System.out.println("Point FAILED"); // public void setPoint(double x, double y, double z) boolean1 = false; try { Point1.setPoint(1,1,1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Point.setPoint FAILED"); } // public void setX(double x) boolean1 = false; try { Point1.setX(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Point.setX FAILED"); } // public void setY(double y) boolean1 = false; try { Point1.setY(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Point.setY FAILED"); } // public void setZ(double z) boolean1 = false; try { Point1.setZ(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Point.setZ FAILED"); } // public double getX() double1 = Point1.getX(); if (double1 == 0) System.out.println("Point.getX FAILED"); // public double getY() double1 = Point1.getY(); if (double1 == 0) System.out.println("Point.getY FAILED"); // public double getZ() double1 = Point1.getZ(); if (double1 == 0) System.out.println("Point.getZ FAILED"); // public double distance(Point that) double1 = Point1.distance(Point2); if (double1 == 0) System.out.println("Point.distance FAILED"); // public double squareSumComponents() double1 = Point1.squareSumComponents(); if (double1 == 0) System.out.println("Point.squareSumComponents FAILED"); // public Point sumComponents(Point p) // does not work // public Point deltaComponents(Point p) // does not work // public Point multiplyComponents(double k) // does not work // public double dotProduct(Point p) // does not work // public double crossProduct(Point p) // does not work // PriorityQueue interface - com.wellscs.PriorityQueue // public void insert(Comparable2 item) // public Comparable2 remove() // public Comparable2 remove(Comparable2 item) // public Comparable2 reorderIfPresent(Comparable2 item) // public Comparable2 reorderOrInsert(Comparable2 item) // public int size() // public boolean isEmpty() // public int getOrder() // PriorityQueueBinHeap class - com.wellscs.PriorityQueue // public PriorityQueueBinHeap(int order) PriorityQueueBinHeap PriorityQueueBinHeap1 = new PriorityQueueBinHeap(1); if (PriorityQueueBinHeap1 == null) System.out.println("PriorityQueueBinHeap FAILED"); // public void insert(Comparable2 item) // does not work // public Comparable2 remove() // does not work // public Comparable2 remove(Comparable2 item) // does not work // public Comparable2 reorderIfPresent(Comparable2 item) // does not work // public Comparable2 reorderOrInsert(Comparable2 item) // does not work // public int size() int1 = PriorityQueueBinHeap1.size(); if (int1 != 0) System.out.println("PriorityQueueBinHeap.size FAILED"); // public boolean isEmpty() boolean1 = PriorityQueueBinHeap1.isEmpty(); if (boolean1 == false) System.out.println("PriorityQueueBinHeap.isEmpty FAILED"); // public int getOrder() int1 = PriorityQueueBinHeap1.getOrder(); if (int1 == 0) System.out.println("PriorityQueueBinHeap.getOrder FAILED"); // PropertyList class - com.camitro.toolkit.CamUtil // public PropertyList() PropertyList PropertyList1 = new PropertyList(); if (PropertyList1 == null) System.out.println("PropertyList FAILED"); // protected PropertyList(PropertyList that) // public java.lang.Object clone() Object1 = PropertyList1.clone(); if (Object1 == null) System.out.println("PropertyList.clone FAILED"); // public void setProp(java.lang.String name, java.lang.Object value) // public void removeProp(java.lang.String name) // public java.lang.Object getProp(java.lang.String name) // public void setDoubleProp(java.lang.String name, double value) // public void setNonNegativeDoubleProp(java.lang.String name, double value) // public double getDoubleProp(java.lang.String name) // public void setBooleanProp(java.lang.String name, boolean value) // public boolean getBooleanProp(java.lang.String name) // public void setIntProp(java.lang.String name, int value) // public void setNonNegativeIntProp(java.lang.String name, int value) // public int getIntProp(java.lang.String name) // QRDecomposition class - gov.nist.Jama // gov.nist.Jama.QRDecomposition // RE class - gnu.regexp // gnu.regexp.RE // REException class - gnu.regexp // gnu.regexp.RE // REFilterInputStream class - gnu.regexp // gnu.regexp.RE // REMatch class - gnu.regexp // gnu.regexp.RE // REMatchEnumeration class - gnu.regexp // gnu.regexp.RE // RemoteClusterRun class - com.camitro.toolkit.ClusterServer // public RemoteClusterRun(java.lang.String hostname) // RemoteClusterRun RemoteClusterRun1 = new RemoteClusterRun("camitro01"); // if (RemoteClusterRun1 == null) // System.out.println("RemoteClusterRun FAILED"); // public java.util.Vector runRequests(java.util.Vector requests) // not available to me // Report class - com.camitro.toolkit.ElecModel // public Report(Vector allSites, Properties replyProps); // public java.lang.String getValidationCsvFilePath() // public java.util.Properties createReplyProps(Molecule drug) // RESyntax class - gnu.regexp - import java.util.BitSet; // gnu.regexp.RE // Ring class - com.camitro.toolkit.Molecule // public Ring(java.util.Vector ringAtoms) // protected Ring(Ring that) // public java.lang.Object clone() // public java.lang.String ringMemNumbers() // public java.lang.String getRingMemLabels() // public int getRingMemCount() // public boolean isAromatic() // public void checkAromatic() // public Atom getRingMemAt(int idx) // public Atom nextNeighborMemOf(Atom theMem) // public Atom previousNeighborMemOf(Atom theMem) // public int belongedToRing(Atom atom) // public boolean belongedToRing(Atom atom1, Atom atom2) // public Atom getFirstAttachedAtomToRingMember(Atom theMem) // public Atom getLastAttachedAtomToRingMember(Atom theMem) // public Atom getAttachedAtomToRing(Atom theAtom) // public Atom getSubstitution(Atom theMem) // public boolean equals(Ring otherRing) // public boolean is6MemAromaticRing() // public boolean isHexaneRing() // public boolean isChair() // RingFinder class - com.camitro.toolkit.Molecule // public RingFinder(Molecule) // public int totalRings() // public boolean findRings() // Scoring class - com.camitro.toolkit.ElecModel - implements ElecModelConstants // public Scoring(String fileFullpath, String cmpName, Vector predictSites) // public java.lang.String getScoreStr() // public int getScore() // public java.lang.String getExpOrder() // Scripting2 class - com.camitro.applets.MoleculeDisplay // Scripting2 Scripting21 = new Scripting2(); // removed from beta3 // ScriptingFrm class - com.camitro.applets.MoleculeDisplay // ScriptingFrm ScriptingFrm1 = new ScriptingFrm(); // removed from beta3 // SdfReader class - com.camitro.toolkit.MoleculeFile // public SdfReader() SdfReader SdfReader1 = new SdfReader(); if (SdfReader1 == null) System.out.println("SdfReader FAILED"); // public java.util.Vector read(java.io.LineNumberReader reader) // SerialClusterRun class - com.camitro.toolkit.ClusterServer - initializes serviceManager // public SerialClusterRun() SerialClusterRun SerialClusterRun1 = new SerialClusterRun(); if (SerialClusterRun1 == null) System.out.println("SerialClusterRun FAILED"); // public java.util.Vector runRequests(java.util.Vector requests) // not available to me // ServiceManager class - com.camitro.toolkit.Cluster // public ServiceManager() ServiceManager ServiceManager1 = new ServiceManager(); if (ServiceManager1 == null) System.out.println("ServiceManager FAILED"); // public ServiceManager(java.lang.String workerId, java.lang.String tmpDirPath) ServiceManager ServiceManager2 = new ServiceManager("x", "c:\\temp"); if (ServiceManager2 == null) System.out.println("ServiceManager FAILED"); // public void setWorkerId(java.lang.String workerId) boolean1 = false; try { ServiceManager1.setWorkerId("x"); boolean1 = true; } finally { if (boolean1 == false) System.out.println("ServiceManager.setWorkerId FAILED"); } // public void setTmpDirPath(java.lang.String aTmpDirPath) boolean1 = false; try { ServiceManager1.setTmpDirPath("C:\000"); boolean1 = true; } finally { if (boolean1 == false) System.out.println("ServiceManager.setTmpDirPath FAILED"); } // public ClusterReply runRequest(ClusterRequest request) // not available to me // public void registerService(ClusterService service) // does not work // public java.lang.String getQueueType() // String1 = ServiceManager1.getQueueType(); // if (String1.equals("")) // System.out.println("ServiceManager.getQueueType FAILED"); // SingularValueDecomposition class - gov.nist.Jama - implements java.io.Serializable // gov.nist.Jama.SingularValueDecomposition // SM2Reader class - com.camitro.toolkit.MoleculeFile // public SM2Reader() SM2Reader SM2Reader1 = new SM2Reader(); if (SM2Reader1 == null) System.out.println("SM2Reader FAILED"); // public java.util.Vector read(java.io.LineNumberReader reader) // public void createAtom(int lineNum, java.lang.String name, double x, double y, double z, java.lang.String type) // public void createAtom(int lineNum, java.lang.String name, double x, double y, double z, java.lang.String type, double charge) // public void createBond(int a1, int a2, java.lang.String order) // not ready yet // SM2Writer class - com.camitro.toolkit.MoleculeFile // public SM2Writer() SM2Writer SM2Writer1 = new SM2Writer(); if (SM2Writer1 == null) System.out.println("SM2Writer FAILED"); // public void write(java.io.PrintWriter pwriter, java.util.Vector molecules) // not ready yet // Sulphur class - com.camitro.toolkit.Molecule // public Sulphur() Sulphur Sulphur1 = new Sulphur(); if (Sulphur1 == null) System.out.println("Sulphur FAILED"); // public Sulphur(double x, double y, double z) Sulphur Sulphur2 = new Sulphur(1,1,1); if (Sulphur2 == null) System.out.println("Sulphur FAILED"); // public Sulphur(int hybrid, double x, double y, double z) Sulphur Sulphur3 = new Sulphur(1,1,1,1); if (Sulphur3 == null) System.out.println("Sulphur FAILED"); // public java.lang.Object clone() Object1 = Sulphur1.clone(); if (Object1 == null) System.out.println("Sulphur.clone FAILED"); // public void rehybridize(int hybrid) boolean1 = false; try { Sulphur1.rehybridize(1); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Sulphur.rehybridize FAILED"); } // public void rehybridize() boolean1 = false; try { Sulphur1.rehybridize(); boolean1 = true; } finally { if (boolean1 == false) System.out.println("Sulphur.rehybridize FAILED"); } // public java.lang.String getElement() String1 = Sulphur1.getElement(); if (String1.equals("")) System.out.println("Sulphur.getElement FAILED"); // public int getAtomicNumber() int1 = Sulphur1.getAtomicNumber(); if (int1 == 0) System.out.println("Sulphur.getAtomicNumber FAILED"); // public int getMaxNumBonds() int1 = Sulphur1.getMaxNumBonds(); if (int1 == 0) System.out.println("Sulphur.getMaxNumBonds FAILED"); // test_db class - com.camitro.apps.test_db // not in beta3 // testAxialEquitorial class - com.camitro.apps.testMolecule // not in beta3 // testCmdline class - com.camitro.apps.testMolecule // not in beta3 // testCreateDir class - com.camitro.apps.testMolecule // not in beta3 // testFragmentFinder class - com.camitro.apps.testMolecule // not in beta3 // testIAtom class - com.camitro.apps.testMolecule // not in beta3 // testICoord class - com.camitro.apps.testMolecule // not in beta3 // testMultipleRing class - com.camitro.apps.testMolecule // not in beta3 // testPatternFinder class - com.camitro.apps.testMolecule // not in beta3 // testPdbWriter class - com.camitro.apps.testMolecule // not in beta3 // testRE class - com.camitro.apps.testMolecule // not in beta3 // testRing class - com.camitro.apps.testMolecule // not in beta3 // testSM2Reader class - com.camitro.apps.testMolecule // not in beta3 // testSubstring class - com.camitro.apps.testMolecule // not in beta3 // testVect class - com.camitro.apps.testMolecule // not in beta3 // testVectorEquals - com.camitro.apps.testMolecule // not in beta3 } }