SmilesMatcher

java.lang.Object
- org.jmol.smiles.SmilesMatcher

All Implemented Interfaces:: SmilesMatcherInterface

public class SmilesMatcher
extends Object
implements SmilesMatcherInterface

Originating author: Nicholas Vervelle A class to handle a variety of SMILES/SMARTS-related functions, including: -- determining if two SMILES strings are equivalent -- determining the molecular formula of a SMILES or SMARTS string -- searching for specific runs of atoms in a 3D model -- searching for specific runs of atoms in a SMILES description -- generating valid (though not canonical) SMILES and bioSMILES strings -- getting atom-atom correlation maps to be used with biomolecular alignment methods

The original SMILES description can been found at the SMILES Home Page. Specification for this implementation can be found in package.html.

 
 public methods:
 
 int areEqual  -- checks a SMILES string against a reference (-1 for error; 0 for no finds; >0 for number of finds)
 
 BitSet[] find  -- finds one or more occurances of a SMILES or SMARTS string within a SMILES string
 
 int[][] getCorrelationMaps  -- returns correlated arrays of atoms
 
 String getLastError  -- returns any error that was last encountered.
 
 String getMolecularFormula   -- returns the MF of a SMILES or SMARTS string
 
 String getRelationship -- returns isomeric relationship
 
 String getSmiles  -- returns a standard SMILES string or a
                  Jmol BIOSMILES string with comment header.
 
 BitSet getSubstructureSet  -- returns a single BitSet with all found atoms included
   
   
   in Jmol script:
   
   string2.find("SMILES", string1)
   string2.find("SMARTS", string1)
   
   e.g.
   
     print "CCCC".find("SMILES", "C[C]")
 
   select search("smartsString")
   
   All bioSMARTS strings begin with ~ (tilde).

Author:: Bob Hanson

Field Summary

Fields
Modifier and Type Field and Description

private static int MODE_ARRAY

private static int MODE_ATROP

private static int MODE_BITSET

private static int MODE_MAP

Fields
Modifier and Type	Field and Description
`private static int`	`MODE_ARRAY`
`private static int`	`MODE_ATROP`
`private static int`	`MODE_BITSET`
`private static int`	`MODE_MAP`

Constructor Summary

Constructors
Constructor and Description

SmilesMatcher()

Constructors
Constructor and Description
`SmilesMatcher()`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method and Description
`int`	`areEqual(String smiles1, String smiles2)`
`boolean`	`areEqualTest(String smiles, SmilesSearch search)` for JUnit test, mainly
`String`	`cleanSmiles(String smiles)`
`int[][]`	`find(String pattern, String target, int flags)` Searches for all matches of a pattern within a SMILES string.
`private Object`	`findPriv(String pattern, SmilesSearch search, int flags, int mode)`
`String`	`getAtropisomerKeys(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags)` called by SmilesParser to get nn in ^nn- base on match to actual structure
`int[][]`	`getCorrelationMaps(String pattern, Node[] atoms, int atomCount, BS bsSelected, int flags)` Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.
`String`	`getLastException()`
`void`	`getMMFF94AtomTypes(String[] smarts, Node[] atoms, int ac, BS bsSelected, javajs.util.Lst<BS> ret, javajs.util.Lst<BS>[] vRings)` called by ForceFieldMMFF.setAtomTypes only
`String`	`getMolecularFormula(String pattern, boolean isSmarts)`
`String`	`getRelationship(String smiles1, String smiles2)`
`String`	`getSmiles(Node[] atoms, int ac, BS bsSelected, String bioComment, int flags)` internal to Jmol -- called by org.jmol.Viewer.getSmiles
`BS`	`getSubstructureSet(String pattern, Node[] atoms, int ac, BS bsSelected, int flags)` Returns a bitset matching the pattern within a set of Jmol atoms.
`BS[]`	`getSubstructureSetArray(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags)` Returns a vector of bitsets indicating which atoms match the pattern.
`private Object`	`matchPriv(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, boolean doTestAromatic, int flags, int mode)`
`String`	`polyhedronToSmiles(Node center, int[][] faces, int atomCount, javajs.util.P3[] points, int flags, String details)` Generate a topological SMILES string from a set of faces
`String`	`reverseChirality(String smiles)` Note, this may be incompatible with [$(select(..))] THIS IS NOT DEPENDABLE.

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail
- MODE_BITSET
```
private static final int MODE_BITSET
```
  See Also:
  
  Constant Field Values
- MODE_ARRAY
```
private static final int MODE_ARRAY
```
  See Also:
  
  Constant Field Values
- MODE_MAP
```
private static final int MODE_MAP
```
  See Also:
  
  Constant Field Values
- MODE_ATROP
```
private static final int MODE_ATROP
```
  See Also:
  
  Constant Field Values

Constructor Detail
- SmilesMatcher
```
public SmilesMatcher()
```

Method Detail

getLastException
```
public String getLastException()
```
Specified by:

getLastException in interface SmilesMatcherInterface

getMolecularFormula

public String getMolecularFormula(String pattern,
                                  boolean isSmarts)
                           throws Exception

Specified by:: getMolecularFormula in interface SmilesMatcherInterface
Throws:: Exception

getSmiles

public String getSmiles(Node[] atoms,
                        int ac,
                        BS bsSelected,
                        String bioComment,
                        int flags)
                 throws Exception

internal to Jmol -- called by org.jmol.Viewer.getSmiles

Specified by:: getSmiles in interface SmilesMatcherInterface
Throws:: Exception

areEqual

public int areEqual(String smiles1,
                    String smiles2)
             throws Exception

Specified by:: areEqual in interface SmilesMatcherInterface
Throws:: Exception

areEqualTest

public boolean areEqualTest(String smiles,
                            SmilesSearch search)
                     throws Exception

for JUnit test, mainly

Parameters:: smiles -; search -
Returns:: true only if the SMILES strings match and there are no errors
Throws:: Exception

find
```
public int[][] find(String pattern,
                    String target,
                    int flags)
             throws Exception
```
Searches for all matches of a pattern within a SMILES string. If SMILES (not isSmarts), requires that all atoms be part of the match.

Specified by:

find in interface SmilesMatcherInterface

Parameters:

pattern - SMILES or SMARTS pattern.

target -

flags -

Returns:

array of correlations of occurances of pattern within smiles

Throws:

Exception

getRelationship

public String getRelationship(String smiles1,
                              String smiles2)
                       throws Exception

Specified by:: getRelationship in interface SmilesMatcherInterface
Throws:: Exception

reverseChirality
```
public String reverseChirality(String smiles)
```
Note, this may be incompatible with [$(select(..))] THIS IS NOT DEPENDABLE. USE /invertStereo/ INSTEAD

Specified by:

reverseChirality in interface SmilesMatcherInterface

getSubstructureSet

public BS getSubstructureSet(String pattern,
                             Node[] atoms,
                             int ac,
                             BS bsSelected,
                             int flags)
                      throws Exception

Returns a bitset matching the pattern within a set of Jmol atoms.

Specified by:: getSubstructureSet in interface SmilesMatcherInterface
Parameters:: pattern - SMILES or SMARTS pattern.; atoms -; ac -; bsSelected -
Returns:: BitSet indicating which atoms match the pattern.
Throws:: Exception

getMMFF94AtomTypes

public void getMMFF94AtomTypes(String[] smarts,
                               Node[] atoms,
                               int ac,
                               BS bsSelected,
                               javajs.util.Lst<BS> ret,
                               javajs.util.Lst<BS>[] vRings)
                        throws Exception

called by ForceFieldMMFF.setAtomTypes only

Specified by:: getMMFF94AtomTypes in interface SmilesMatcherInterface
Throws:: Exception

getSubstructureSetArray

public BS[] getSubstructureSetArray(String pattern,
                                    Node[] atoms,
                                    int ac,
                                    BS bsSelected,
                                    BS bsAromatic,
                                    int flags)
                             throws Exception

Returns a vector of bitsets indicating which atoms match the pattern.

Specified by:: getSubstructureSetArray in interface SmilesMatcherInterface
Parameters:: pattern - SMILES or SMARTS pattern.; atoms -; ac -; bsSelected -; bsAromatic -
Returns:: BitSet Array indicating which atoms match the pattern.
Throws:: Exception

getAtropisomerKeys

public String getAtropisomerKeys(String pattern,
                                 Node[] atoms,
                                 int ac,
                                 BS bsSelected,
                                 BS bsAromatic,
                                 int flags)
                          throws Exception

called by SmilesParser to get nn in ^nn- base on match to actual structure

Parameters:: pattern -; atoms -; ac -; bsSelected -; bsAromatic -; flags -
Returns:: string of nn,nn,nn,nn
Throws:: Exception

polyhedronToSmiles

public String polyhedronToSmiles(Node center,
                                 int[][] faces,
                                 int atomCount,
                                 javajs.util.P3[] points,
                                 int flags,
                                 String details)
                          throws Exception

Generate a topological SMILES string from a set of faces

Specified by:: polyhedronToSmiles in interface SmilesMatcherInterface
Parameters:: faces -; atomCount -
Returns:: topological SMILES string
Throws:: Exception

getCorrelationMaps

public int[][] getCorrelationMaps(String pattern,
                                  Node[] atoms,
                                  int atomCount,
                                  BS bsSelected,
                                  int flags)
                           throws Exception

Rather than returning bitsets, this method returns the sets of matching atoms in array form so that a direct atom-atom correlation can be made.

Specified by:: getCorrelationMaps in interface SmilesMatcherInterface
Parameters:: pattern - SMILES or SMARTS pattern.; atoms -; bsSelected -
Returns:: a set of atom correlations
Throws:: Exception

findPriv

private Object findPriv(String pattern,
                        SmilesSearch search,
                        int flags,
                        int mode)
                 throws Exception

Throws:: Exception

matchPriv

private Object matchPriv(String pattern,
                         Node[] atoms,
                         int ac,
                         BS bsSelected,
                         BS bsAromatic,
                         boolean doTestAromatic,
                         int flags,
                         int mode)
                  throws Exception

Throws:: Exception

cleanSmiles
```
public String cleanSmiles(String smiles)
```
Specified by:

cleanSmiles in interface SmilesMatcherInterface

Class SmilesMatcher

Field Summary

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

MODE_BITSET

MODE_ARRAY

MODE_MAP

MODE_ATROP

Constructor Detail