net.sf.ciccgrid.pws
Class Structure

java.lang.Object
  net.sf.ciccgrid.pws.Structure

public class Structure
extends java.lang.Object

Methods to get various aspects of PubChem structures.

Author:

rguha

Constructor Summary

Structure()

Method Summary

java.lang.String	getCIDByInChI(java.lang.String inchi) Get CID by InChI.
java.lang.String	getCIDByInChIKey(java.lang.String inchikey) Get CID by InChI key.
java.lang.String[]	getCIDBySimilarity(java.lang.String smiles, double sim, int howMany, int speedup) Find compounds that are similar to the supplied molecule.
java.lang.String[]	getSmilesByCID(java.lang.String[] cids) Get the SMILES corresponding to a compound ID.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Structure

public Structure()
          throws java.sql.SQLException,
                 java.lang.ClassNotFoundException

Throws:

java.sql.SQLException

java.lang.ClassNotFoundException

Method Detail

getSmilesByCID

public java.lang.String[] getSmilesByCID(java.lang.String[] cids)
                                  throws java.lang.Exception

Get the SMILES corresponding to a compound ID.

Parameters:

cids - An array of strings representing the compound ID's for which the SMILES are desired

Returns:

A String array containing the corresponding SMILES

Throws:

java.lang.Exception

getCIDByInChI

public java.lang.String getCIDByInChI(java.lang.String inchi)
                               throws java.lang.Exception

Get CID by InChI.

Parameters:

inchi - The InChI string

Returns:

The CID if found or an empty string if not found

Throws:

java.lang.Exception

getCIDByInChIKey

public java.lang.String getCIDByInChIKey(java.lang.String inchikey)
                                  throws java.lang.Exception

Get CID by InChI key.

Parameters:

inchikey - The InChI key string

Returns:

The CID if found or an empty string if not found

Throws:

java.lang.Exception

getCIDBySimilarity

public java.lang.String[] getCIDBySimilarity(java.lang.String smiles,
                                             double sim,
                                             int howMany,
                                             int speedup)
                                      throws java.lang.Exception

Find compounds that are similar to the supplied molecule.

The similarity is obtained by calculating the Tanimoto coefficient between the 166 bit MACCS keys. Note however that this method is extremely slow since it has to do an exhaustiv comparison

Parameters:

smiles - The target SMILES

sim - The Tanimoto similarity cutoff (between 0 and 1)

howMany - How many should be returned? A negative number will return everything (which may be a huge number and will take a very long time)

speedup - If set to 0 then the speedup described by Swamidass & Baldi will not be employed. If any other value it will be employed. Note that the speedup is only relevant for relatively high similarity values and ends up being equivalent to linear search for low similarity values. For now this is ignored

Returns:

The CID's of the similar molecules. If there are no hits returned then it will return a String array with the single element equal to 'None'

Throws:

java.lang.Exception