META-INF/MANIFEST.MF
META-INF/SELFSIGN.SF
META-INF/SELFSIGN.RSA
META-INF/
org/
org/jmol/
org/jmol/smiles/
org/jmol/smiles/InvalidSmilesException.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.InvalidSmilesException extends java.lang.Exception {
public void <init> ()
public void <init> (java.lang.String)
public void <init> (java.lang.Throwable)
public void <init> (java.lang.String, java.lang.Throwable)
}
org/jmol/smiles/PatternMatcher.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.PatternMatcher extends java.lang.Object implements org.jmol.api.SmilesMatcherInterface {
private int atomCount
private org.jmol.modelset.ModelSet modelSet
public void <init> ()
public void setModelSet (org.jmol.modelset.ModelSet)
public java.util.BitSet getSubstructureSet (java.lang.String) throws java.lang.Exception
public java.util.BitSet getSubstructureSet (org.jmol.smiles.SmilesMolecule)
private void searchMatch (java.util.BitSet, org.jmol.smiles.SmilesMolecule, int)
private void searchMatch (java.util.BitSet, org.jmol.smiles.SmilesMolecule, org.jmol.smiles.SmilesAtom, int, int)
}
org/jmol/smiles/SmilesAtom.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.SmilesAtom extends java.lang.Object {
private int number
private String symbol
private int atomicMass
private int charge
private int hydrogenCount
private int matchingAtom
private String chiralClass
private int chiralOrder
private org.jmol.smiles.SmilesBond[] bonds
private int bondsCount
private static final int INITIAL_BONDS
public static final String DEFAULT_CHIRALITY
public static final String CHIRALITY_ALLENE
public static final String CHIRALITY_OCTAHEDRAL
public static final String CHIRALITY_SQUARE_PLANAR
public static final String CHIRALITY_TETRAHEDRAL
public static final String CHIRALITY_TRIGONAL_BIPYRAMIDAL
public void <init> (int)
public void createMissingHydrogen (org.jmol.smiles.SmilesMolecule)
public int getNumber ()
public java.lang.String getSymbol ()
public void setSymbol (java.lang.String)
public int getAtomicMass ()
public void setAtomicMass (int)
public int getCharge ()
public void setCharge (int)
public int getMatchingAtom ()
public void setMatchingAtom (int)
public java.lang.String getChiralClass ()
public void setChiralClass (java.lang.String)
public int getChiralOrder ()
public void setChiralOrder (int)
public int getHydrogenCount ()
public void setHydrogenCount (int)
public int getBondsCount ()
public org.jmol.smiles.SmilesBond getBond (int)
public void addBond (org.jmol.smiles.SmilesBond)
}
org/jmol/smiles/SmilesBond.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.SmilesBond extends java.lang.Object {
public static final int TYPE_UNKOWN
public static final int TYPE_NONE
public static final int TYPE_SINGLE
public static final int TYPE_DOUBLE
public static final int TYPE_TRIPLE
public static final int TYPE_AROMATIC
public static final int TYPE_DIRECTIONAL_1
public static final int TYPE_DIRECTIONAL_2
public static final char CODE_NONE
public static final char CODE_SINGLE
public static final char CODE_DOUBLE
public static final char CODE_TRIPLE
public static final char CODE_AROMATIC
public static final char CODE_DIRECTIONAL_1
public static final char CODE_DIRECTIONAL_2
private org.jmol.smiles.SmilesAtom atom1
private org.jmol.smiles.SmilesAtom atom2
private int bondType
public void <init> (org.jmol.smiles.SmilesAtom, org.jmol.smiles.SmilesAtom, int)
public static int getBondTypeFromCode (char)
public org.jmol.smiles.SmilesAtom getAtom1 ()
public void setAtom1 (org.jmol.smiles.SmilesAtom)
public org.jmol.smiles.SmilesAtom getAtom2 ()
public void setAtom2 (org.jmol.smiles.SmilesAtom)
public int getBondType ()
public void setBondType (int)
}
org/jmol/smiles/SmilesMolecule.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.SmilesMolecule extends java.lang.Object {
private org.jmol.smiles.SmilesAtom[] atoms
private int atomsCount
private org.jmol.smiles.SmilesBond[] bonds
private int bondsCount
private static final int INITIAL_ATOMS
private static final int INITIAL_BONDS
public void <init> ()
public org.jmol.smiles.SmilesAtom createAtom ()
public int getAtomsCount ()
public org.jmol.smiles.SmilesAtom getAtom (int)
public org.jmol.smiles.SmilesBond createBond (org.jmol.smiles.SmilesAtom, org.jmol.smiles.SmilesAtom, int)
public int getBondsCount ()
public org.jmol.smiles.SmilesBond getBond (int)
}
org/jmol/smiles/SmilesParser.class
<Unknown>
package org.jmol.smiles
public org.jmol.smiles.SmilesParser extends java.lang.Object {
private org.jmol.smiles.SmilesBond[] ringBonds
public void <init> ()
public org.jmol.smiles.SmilesMolecule parseSmiles (java.lang.String) throws org.jmol.smiles.InvalidSmilesException
private void parseSmiles (org.jmol.smiles.SmilesMolecule, java.lang.String, org.jmol.smiles.SmilesAtom) throws org.jmol.smiles.InvalidSmilesException
private org.jmol.smiles.SmilesAtom parseAtom (org.jmol.smiles.SmilesMolecule, java.lang.String, org.jmol.smiles.SmilesAtom, int, boolean) throws org.jmol.smiles.InvalidSmilesException
private void parseRing (org.jmol.smiles.SmilesMolecule, java.lang.String, org.jmol.smiles.SmilesAtom, int) throws org.jmol.smiles.InvalidSmilesException
}