net.sf.ciccgrid.pws
Class Struct3D

java.lang.Object
  net.sf.ciccgrid.pws.Struct3D

public class Struct3D
extends java.lang.Object

Obtain 3D structures for Pubchem compounds.

The structures have been optimized using MMFF94.

Author:

rguha

Constructor Summary

Struct3D()

Method Summary

java.lang.String	getStructureByCID(java.lang.String cid) Get a 3D structure in SDF format by CID.
java.lang.String	getStructureByInChI(java.lang.String inchi) Get a 3D structure in SDF format by InChI.
java.lang.String	getStructureByInChIKey(java.lang.String inchikey) Get a 3D structure in SDF format by InChI key
java.lang.String[]	getStructureBySmarts(java.lang.String smarts, int howMany) Get 3D structures based on SMARTS patterns.

Methods inherited from class java.lang.Object

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

Constructor Detail

Struct3D

public Struct3D()
         throws java.sql.SQLException,
                java.lang.ClassNotFoundException

Throws:

java.sql.SQLException

java.lang.ClassNotFoundException

Method Detail

getStructureByCID

public java.lang.String getStructureByCID(java.lang.String cid)
                                   throws java.lang.Exception

Get a 3D structure in SDF format by CID.

Parameters:

cid - The CID of interest

Returns:

A string containing the structure in SDF format

Throws:

java.lang.Exception

getStructureByInChI

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

Get a 3D structure in SDF format by InChI.

Parameters:

inchi - The InChI of interest

Returns:

A string containing the structure in SDF format. If no matching structure was found returns and empty string

Throws:

java.lang.Exception

getStructureByInChIKey

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

Get a 3D structure in SDF format by InChI key

Parameters:

inchikey - The InChI key of interest

Returns:

A string containing the structure in SDF format. If no matching structure was found returns and empty string

Throws:

java.lang.Exception

getStructureBySmarts

public java.lang.String[] getStructureBySmarts(java.lang.String smarts,
                                               int howMany)
                                        throws java.lang.Exception

Get 3D structures based on SMARTS patterns.

Parameters:

smarts - The SMARTS pattern to look for

howMany - How many structures should be returned? If set to 0 then all the hits will be returned. For simple SMARTS (which match everything) this can result in a very large number of results and will probably crash the application container

Returns:

An array of strings, each string is the SDF formatted structure

Throws:

java.lang.Exception