|
|||||||||
| Home >> All >> joelib >> [ util overview ] | PREV CLASS NEXT CLASS | ||||||||
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD |
DETAIL: FIELD | CONSTR | METHOD | ||||||||
joelib.util
Class JHM
java.lang.Objectjoelib.util.JHM
- public class JHM
- extends java.lang.Object
JOELib hepler methods.
| Field Summary | |
static double |
DEG_TO_RAD
Description of the Field |
static java.lang.String |
eol
|
private static JHM |
jhm
|
private static org.apache.log4j.Category |
logger
|
private static int |
OE_RTREE_CUTOFF
|
static double |
RAD_TO_DEG
Description of the Field |
| Constructor Summary | |
private |
JHM()
Constructor for the JHM object |
| Method Summary | |
static void |
buildOERTreeVector(joelib.molecule.JOEAtom atom,
joelib.molecule.JOERTree prv,
joelib.molecule.JOERTree[] vt,
JOEBitVec bv)
|
(package private) double |
calcRMS(double[] r,
double[] f,
int size)
|
(package private) void |
cartesianToInternal(java.util.Vector vic,
joelib.molecule.JOEMol mol)
|
(package private) joelib.math.XYZVector |
centerCoords(double[] c,
int size)
|
boolean |
compareBonds(joelib.molecule.JOEBond a,
joelib.molecule.JOEBond b)
Description of the Method |
static void |
correctBadResonanceForm(joelib.molecule.JOEMol mol)
Description of the Method |
static int |
determineFRJ(joelib.molecule.JOEMol mol)
Description of the Method |
static boolean |
expandKekule(joelib.molecule.JOEMol mol,
java.util.Vector va,
joelib.util.iterator.AtomIterator ii,
int[] maxv,
boolean secondpass)
|
static void |
findRings(joelib.molecule.JOEMol mol,
java.util.Vector path,
JOEBitVec avisit,
JOEBitVec bvisit,
int natom,
int depth)
|
static int |
getCurrentValence(joelib.molecule.JOEAtom atom)
Gets the currentValence attribute of the JHM class |
static boolean |
getDFFVector(joelib.molecule.JOEMol mol,
java.util.Vector dffv,
JOEBitVec bv)
|
static java.lang.String |
getTempFileBase()
|
static JHM |
instance()
Description of the Method |
(package private) void |
internalToCartesian(java.util.Vector vic,
joelib.molecule.JOEMol mol)
|
static boolean |
kekulePropagate(joelib.molecule.JOEAtom atom,
java.util.Vector visit,
java.util.Vector ival,
int depth)
|
static double |
minimumPairRMS(joelib.molecule.JOEMol mol,
double[] a,
double[] b,
boolean[] one2one)
Description of the Method |
static boolean |
moleculeToFile(java.lang.String filename,
joelib.molecule.JOEMol mol,
joelib.io.IOType type,
boolean writeDescriptors)
|
static void |
resetVisit(joelib.molecule.JOEMol mol,
java.util.Vector visit,
int depth)
|
(package private) void |
rotateCoords(double[] c,
double[][] m,
int size)
|
static void |
setIntVectorToValue(java.util.Vector v,
int value)
|
static void |
setRotorToAngle(double[] c,
joelib.molecule.JOEAtom[] ref,
double ang,
java.util.Vector atoms)
This methodName will rotate the coordinates of 'atoms' such that tor == ang - atoms in 'tor' should be ordered such that the 3rd atom is the pivot around which atoms rotate ang is in degrees. |
static double |
signedVolume(joelib.math.XYZVector a,
joelib.math.XYZVector b,
joelib.math.XYZVector c,
joelib.math.XYZVector d)
Calculate the signed volume for an atom. |
static boolean |
tokenize(java.util.Vector vcr,
java.lang.String buf)
|
static boolean |
tokenize(java.util.Vector vcr,
java.lang.String buf,
java.lang.String delimstr)
|
static boolean |
tokenize(java.util.Vector vcr,
java.lang.String s,
java.lang.String delimstr,
int limit)
|
static int |
valenceSum(joelib.molecule.JOEAtom atom)
Description of the Method |
boolean |
writeTitles(java.io.OutputStream ofs,
joelib.molecule.JOEMol mol)
Description of the Method |
| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
| Field Detail |
logger
private static org.apache.log4j.Category logger
RAD_TO_DEG
public static final double RAD_TO_DEG
- Description of the Field
- See Also:
- Constant Field Values
DEG_TO_RAD
public static final double DEG_TO_RAD
- Description of the Field
- See Also:
- Constant Field Values
eol
public static final java.lang.String eol
OE_RTREE_CUTOFF
private static final int OE_RTREE_CUTOFF
- See Also:
- Constant Field Values
jhm
private static JHM jhm
| Constructor Detail |
JHM
private JHM()
- Constructor for the JHM object
| Method Detail |
getCurrentValence
public static int getCurrentValence(joelib.molecule.JOEAtom atom)
- Gets the currentValence attribute of the JHM class
getDFFVector
public static boolean getDFFVector(joelib.molecule.JOEMol mol, java.util.Vector dffv, JOEBitVec bv)
setIntVectorToValue
public static void setIntVectorToValue(java.util.Vector v, int value)
setRotorToAngle
public static void setRotorToAngle(double[] c,
joelib.molecule.JOEAtom[] ref,
double ang,
java.util.Vector atoms)
- This methodName will rotate the coordinates of 'atoms' such that tor == ang
- atoms in 'tor' should be ordered such that the 3rd atom is the pivot
around which atoms rotate ang is in degrees.
getTempFileBase
public static java.lang.String getTempFileBase()
buildOERTreeVector
public static void buildOERTreeVector(joelib.molecule.JOEAtom atom, joelib.molecule.JOERTree prv, joelib.molecule.JOERTree[] vt, JOEBitVec bv)
correctBadResonanceForm
public static void correctBadResonanceForm(joelib.molecule.JOEMol mol)
- Description of the Method
expandKekule
public static boolean expandKekule(joelib.molecule.JOEMol mol, java.util.Vector va, joelib.util.iterator.AtomIterator ii, int[] maxv, boolean secondpass)
findRings
public static void findRings(joelib.molecule.JOEMol mol, java.util.Vector path, JOEBitVec avisit, JOEBitVec bvisit, int natom, int depth)
instance
public static JHM instance()
- Description of the Method
kekulePropagate
public static boolean kekulePropagate(joelib.molecule.JOEAtom atom, java.util.Vector visit, java.util.Vector ival, int depth)
minimumPairRMS
public static double minimumPairRMS(joelib.molecule.JOEMol mol, double[] a, double[] b, boolean[] one2one)
- Description of the Method
moleculeToFile
public static boolean moleculeToFile(java.lang.String filename, joelib.molecule.JOEMol mol, joelib.io.IOType type, boolean writeDescriptors)
resetVisit
public static void resetVisit(joelib.molecule.JOEMol mol, java.util.Vector visit, int depth)
signedVolume
public static double signedVolume(joelib.math.XYZVector a, joelib.math.XYZVector b, joelib.math.XYZVector c, joelib.math.XYZVector d)
- Calculate the signed volume for an atom. If the atom has a valence of 3
the coordinates of an attached hydrogen are calculated
Calculate a signed volume given a set of 4 coordinates.
valenceSum
public static int valenceSum(joelib.molecule.JOEAtom atom)
- Description of the Method
compareBonds
public boolean compareBonds(joelib.molecule.JOEBond a, joelib.molecule.JOEBond b)
- Description of the Method
determineFRJ
public static int determineFRJ(joelib.molecule.JOEMol mol)
- Description of the Method
tokenize
public static boolean tokenize(java.util.Vector vcr, java.lang.String buf)
tokenize
public static boolean tokenize(java.util.Vector vcr, java.lang.String buf, java.lang.String delimstr)
tokenize
public static boolean tokenize(java.util.Vector vcr, java.lang.String s, java.lang.String delimstr, int limit)
writeTitles
public boolean writeTitles(java.io.OutputStream ofs, joelib.molecule.JOEMol mol)
- Description of the Method
calcRMS
double calcRMS(double[] r,
double[] f,
int size)
cartesianToInternal
void cartesianToInternal(java.util.Vector vic, joelib.molecule.JOEMol mol)
centerCoords
joelib.math.XYZVector centerCoords(double[] c, int size)
internalToCartesian
void internalToCartesian(java.util.Vector vic, joelib.molecule.JOEMol mol)
rotateCoords
void rotateCoords(double[] c,
double[][] m,
int size)
|
|||||||||
| Home >> All >> joelib >> [ util overview ] | PREV CLASS NEXT CLASS | ||||||||
|
SUMMARY: JAVADOC | SOURCE | DOWNLOAD | NESTED | FIELD | CONSTR | METHOD |
DETAIL: FIELD | CONSTR | METHOD | ||||||||