org.openscience.cdk.pharmacophore
Class PharmacophoreUtils

java.lang.Object
  org.openscience.cdk.pharmacophore.PharmacophoreUtils

@TestClass(value="org.openscience.cdk.pharmacophore.PharmacophoreUtilityTest")
public class PharmacophoreUtils
extends Object

Provides some utility methods for pharmacophore handling.

Author:

Rajarshi Guha

Keywords:

pharmacophore, 3D isomorphism

Required library to be able to run this class:

xom-1.1.jar

Required library to be able to compile this class:

xom-1.1.jar

Belongs to CDK module:

pcore

Source code:

cdk-1.4.x

Constructor Summary

PharmacophoreUtils()

Method Summary

static List<PharmacophoreQuery>	readPharmacophoreDefinitions(InputStream ins) Read in a set of pharmacophore definitions to create pharmacophore queries.
static List<PharmacophoreQuery>	readPharmacophoreDefinitions(String filename) Read in a set of pharmacophore definitions to create pharmacophore queries.
static void	writePharmacophoreDefinition(List<PharmacophoreQuery> queries, OutputStream out) Write out one or more pharmacophore queries in the CDK XML format.
static void	writePharmacophoreDefinition(PharmacophoreQuery[] queries, OutputStream out) Write out one or more pharmacophore queries in the CDK XML format.
static void	writePharmacophoreDefinition(PharmacophoreQuery query, OutputStream out) Write out one or more pharmacophore queries in the CDK XML format.

Methods inherited from class java.lang.Object

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

Constructor Detail

PharmacophoreUtils

public PharmacophoreUtils()

Method Detail

readPharmacophoreDefinitions

@TestMethod(value="testReadPcoreDef, testInvalidPcoreXML")
public static List<PharmacophoreQuery> readPharmacophoreDefinitions(String filename)
                                                             throws CDKException,
                                                                    IOException

Read in a set of pharmacophore definitions to create pharmacophore queries.

Pharmacophore queries can be saved in an XML format which is described XXX. The file can contain multiple definitions. This method will process all the definitions and return a list fo PharmacophoreQuery objects which can be used with the PharmacophoreMatcher class.

The current schema for the document allows one to specify angle and distance constraints. Currently the CDK does not support angle constraints, so they are ignored.

The schema also specifies a units attribute for a given constraint. The current reader ignores this and assumes that all distances are in Angstroms.

Finally, if there is a description associated with a pharmacophore definition, it is available as the "description" property of the PharmacophoreQuery object.

Example usage is

 List defs = readPharmacophoreDefinitions("mydefs.xml");
 System.out.println("Number of definitions = "+defs.size());
 for (int i = 0; i < defs.size(); i++) {
     System.out.println("Desc: "+defs.get(i).getProperty("description");
 }
 

Parameters:

filename - The file to read the definitions from

Returns:

A list of PharmacophoreQuery objects

Throws:

CDKException - if there is an error in the format

IOException - if there is an error in opening the file

See Also:

PharmacophoreQueryAtom, PharmacophoreQueryBond, PharmacophoreQuery, PharmacophoreMatcher

readPharmacophoreDefinitions

@TestMethod(value="testReadPcoreDef, testReadPcoreAngleDef, testInvalidPcoreXML")
public static List<PharmacophoreQuery> readPharmacophoreDefinitions(InputStream ins)
                                                             throws IOException,
                                                                    CDKException

Read in a set of pharmacophore definitions to create pharmacophore queries.

Pharmacophore queries can be saved in an XML format which is described XXX. The file can contain multiple definitions. This method will process all the definitions and return a list of PharmacophoreQuery objects which can be used with the PharmacophoreMatcher class.

The current schema for the document allows one to specify angle and distance constraints.

The schema also specifies a units attribute for a given constraint. The current reader ignores this and assumes that all distances are in Angstroms and angles are in degrees.

Finally, if there is a description associated with a pharmacophore definition, it is available as the "description" property of the PharmacophoreQuery object.

Example usage is

 List defs = readPharmacophoreDefinitions"mydefs.xml");
 System.out.println("Number of definitions = "+defs.size());
 for (int i = 0; i < defs.size(); i++) {
     System.out.println("Desc: "+defs.get(i).getProperty("description");
 }
 

Parameters:

ins - The stream to read the definitions from

Returns:

A list of PharmacophoreQuery objects

Throws:

CDKException - if there is an error in the format

IOException - if there is an error in opening the file

See Also:

PharmacophoreQueryAtom, PharmacophoreQueryBond, PharmacophoreMatcher, PharmacophoreQuery

writePharmacophoreDefinition

@TestMethod(value="testPCoreWrite")
public static void writePharmacophoreDefinition(PharmacophoreQuery query,
                                                                OutputStream out)
                                         throws IOException

Write out one or more pharmacophore queries in the CDK XML format.

Parameters:

query - The pharmacophore queries

out - The OutputStream to write to

Throws:

IOException - if there is a problem writing the XML document

writePharmacophoreDefinition

@TestMethod(value="testPCoreWrite")
public static void writePharmacophoreDefinition(List<PharmacophoreQuery> queries,
                                                                OutputStream out)
                                         throws IOException

Write out one or more pharmacophore queries in the CDK XML format.

Parameters:

queries - The pharmacophore queries

out - The OutputStream to write to

Throws:

IOException - if there is a problem writing the XML document

writePharmacophoreDefinition

@TestMethod(value="testPCoreWrite")
public static void writePharmacophoreDefinition(PharmacophoreQuery[] queries,
                                                                OutputStream out)
                                         throws IOException

Write out one or more pharmacophore queries in the CDK XML format.

Parameters:

queries - The pharmacophore queries

out - The OutputStream to write to

Throws:

IOException - if there is a problem writing the XML document