public class SmilesGenerator
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private int |
atomCount |
private JmolNode[] |
atoms |
private BS |
bsAromatic |
private BS |
bsBondsDn |
private BS |
bsBondsUp |
private BS |
bsIncludingH |
private BS |
bsSelected |
private BS |
bsToDo |
private java.util.Map<java.lang.String,java.lang.Object[]> |
htRings |
private java.util.Map<java.lang.String,java.lang.Object[]> |
htRingsSequence |
private int |
nPairs |
private JmolNode |
prevAtom |
private JmolNode[] |
prevSp2Atoms |
private SB |
ringSets |
private SmilesSearch.VTemp |
vTemp |
Constructor and Description |
---|
SmilesGenerator() |
Modifier and Type | Method and Description |
---|---|
private void |
addBracketedBioName(SB sb,
JmolNode a,
java.lang.String atomName) |
private java.lang.String |
addStereoCheck(int atomIndex,
JmolNode[] stereo,
int i,
java.lang.String s)
checks a group and either adds a new group to the growing
check string or returns null
|
private java.lang.String |
checkStereoPairs(JmolNode atom,
int atomIndex,
JmolNode[] stereo,
int stereoFlag) |
private void |
dumpRingKeys(SB sb,
java.util.Map<java.lang.String,java.lang.Object[]> ht) |
(package private) java.lang.String |
getBioSmiles(JmolNode[] atoms,
int atomCount,
BS bsSelected,
boolean allowUnmatchedRings,
boolean addCrossLinks,
java.lang.String comment) |
private char |
getBondStereochemistry(JmolEdge bond,
JmolNode atomFrom)
Retrieves the saved character based on the index of the bond.
|
private java.lang.String |
getRingCache(int i0,
int i1,
java.util.Map<java.lang.String,java.lang.Object[]> ht) |
protected static java.lang.String |
getRingKey(int i0,
int i1) |
(package private) java.lang.String |
getSmiles(JmolNode[] atoms,
int atomCount,
BS bsSelected) |
private JmolNode |
getSmiles(SB sb,
JmolNode atom,
boolean allowConnectionsToOutsideWorld,
boolean allowBranches) |
private java.lang.String |
getSmilesComponent(JmolNode atom,
BS bs,
boolean allowConnectionsToOutsideWorld)
creates a valid SMILES string from a model.
|
private static java.lang.String |
getStereoFlag(JmolNode atom0,
JmolNode[] atoms,
int nAtoms,
SmilesSearch.VTemp v) |
private void |
setBondDirections()
Creates global BitSets bsBondsUp and bsBondsDown.
|
private java.lang.String |
sortInorganic(JmolNode atom,
JmolList<JmolEdge> v)
We must sort the bond vector such that a diaxial pair is
first and last.
|
private JmolNode[] atoms
private int atomCount
private BS bsSelected
private BS bsAromatic
private SB ringSets
private SmilesSearch.VTemp vTemp
private int nPairs
private BS bsBondsUp
private BS bsBondsDn
private BS bsToDo
private JmolNode prevAtom
private JmolNode[] prevSp2Atoms
private java.util.Map<java.lang.String,java.lang.Object[]> htRingsSequence
private java.util.Map<java.lang.String,java.lang.Object[]> htRings
private BS bsIncludingH
java.lang.String getSmiles(JmolNode[] atoms, int atomCount, BS bsSelected) throws InvalidSmilesException
InvalidSmilesException
java.lang.String getBioSmiles(JmolNode[] atoms, int atomCount, BS bsSelected, boolean allowUnmatchedRings, boolean addCrossLinks, java.lang.String comment) throws InvalidSmilesException
InvalidSmilesException
private java.lang.String getSmilesComponent(JmolNode atom, BS bs, boolean allowConnectionsToOutsideWorld) throws InvalidSmilesException
atom
- bs
- allowConnectionsToOutsideWorld
- InvalidSmilesException
private char getBondStereochemistry(JmolEdge bond, JmolNode atomFrom)
bond
- atomFrom
- private void setBondDirections()
private JmolNode getSmiles(SB sb, JmolNode atom, boolean allowConnectionsToOutsideWorld, boolean allowBranches)
private java.lang.String sortInorganic(JmolNode atom, JmolList<JmolEdge> v)
atom
- v
- private java.lang.String checkStereoPairs(JmolNode atom, int atomIndex, JmolNode[] stereo, int stereoFlag)
private static java.lang.String getStereoFlag(JmolNode atom0, JmolNode[] atoms, int nAtoms, SmilesSearch.VTemp v)
atom0
- atoms
- nAtoms
- v
- private java.lang.String addStereoCheck(int atomIndex, JmolNode[] stereo, int i, java.lang.String s)
atomIndex
- stereo
- i
- s
- private java.lang.String getRingCache(int i0, int i1, java.util.Map<java.lang.String,java.lang.Object[]> ht)
private void dumpRingKeys(SB sb, java.util.Map<java.lang.String,java.lang.Object[]> ht)
protected static java.lang.String getRingKey(int i0, int i1)