public class SmilesGenerator
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private int |
ac |
private Node[] |
atoms |
private BS |
bsAromatic |
private BS |
bsBondsDn |
private BS |
bsBondsUp |
private BS |
bsIncludingH |
private BS |
bsSelected |
private BS |
bsToDo |
private boolean |
explicitH |
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 Node |
prevAtom |
private Node[] |
prevSp2Atoms |
private javajs.util.SB |
ringSets |
private VTemp |
vTemp |
Constructor and Description |
---|
SmilesGenerator() |
Modifier and Type | Method and Description |
---|---|
private void |
addBracketedBioName(javajs.util.SB sb,
Node atom,
java.lang.String atomName) |
private java.lang.String |
addStereoCheck(int atomIndex,
Node[] 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(Node atom,
int atomIndex,
Node[] stereo,
int stereoFlag) |
private void |
dumpRingKeys(javajs.util.SB sb,
java.util.Map<java.lang.String,java.lang.Object[]> ht) |
(package private) java.lang.String |
getBioSmiles(BNode[] atoms,
int ac,
BS bsSelected,
boolean allowUnmatchedRings,
boolean addCrossLinks,
java.lang.String comment) |
private char |
getBondStereochemistry(Edge bond,
Node 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(Node[] atoms,
int ac,
BS bsSelected,
boolean explicitH) |
private Node |
getSmiles(javajs.util.SB sb,
Node atom,
boolean allowConnectionsToOutsideWorld,
boolean allowBranches,
boolean explicitH) |
private java.lang.String |
getSmilesComponent(Node atom,
BS bs,
boolean allowConnectionsToOutsideWorld)
creates a valid SMILES string from a model.
|
private static java.lang.String |
getStereoFlag(Node atom0,
Node[] atoms,
int nAtoms,
VTemp v) |
private void |
setBondDirections()
Creates global BitSets bsBondsUp and bsBondsDown.
|
private java.lang.String |
sortInorganic(Node atom,
javajs.util.Lst<Edge> v)
We must sort the bond vector such that a diaxial pair is
first and last.
|
private Node[] atoms
private int ac
private BS bsSelected
private BS bsAromatic
private boolean explicitH
private javajs.util.SB ringSets
private VTemp vTemp
private int nPairs
private BS bsBondsUp
private BS bsBondsDn
private BS bsToDo
private Node prevAtom
private Node[] 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(Node[] atoms, int ac, BS bsSelected, boolean explicitH) throws InvalidSmilesException
InvalidSmilesException
java.lang.String getBioSmiles(BNode[] atoms, int ac, BS bsSelected, boolean allowUnmatchedRings, boolean addCrossLinks, java.lang.String comment) throws InvalidSmilesException
InvalidSmilesException
private void addBracketedBioName(javajs.util.SB sb, Node atom, java.lang.String atomName)
private java.lang.String getSmilesComponent(Node atom, BS bs, boolean allowConnectionsToOutsideWorld) throws InvalidSmilesException
atom
- bs
- allowConnectionsToOutsideWorld
- InvalidSmilesException
private char getBondStereochemistry(Edge bond, Node atomFrom)
bond
- atomFrom
- private void setBondDirections()
private Node getSmiles(javajs.util.SB sb, Node atom, boolean allowConnectionsToOutsideWorld, boolean allowBranches, boolean explicitH)
private java.lang.String sortInorganic(Node atom, javajs.util.Lst<Edge> v)
atom
- v
- private java.lang.String checkStereoPairs(Node atom, int atomIndex, Node[] stereo, int stereoFlag)
private static java.lang.String getStereoFlag(Node atom0, Node[] atoms, int nAtoms, VTemp v)
atom0
- atoms
- nAtoms
- v
- private java.lang.String addStereoCheck(int atomIndex, Node[] 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(javajs.util.SB sb, java.util.Map<java.lang.String,java.lang.Object[]> ht)
protected static java.lang.String getRingKey(int i0, int i1)