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