org.openscience.cdk.pharmacophore

Class PharmacophoreUtils

java.lang.Object

org.openscience.cdk.pharmacophore.PharmacophoreUtils

public class PharmacophoreUtils
extends Object

Provides some utility methods for pharmacophore handling.

Author:

Rajarshi Guha

Source code:

master

Belongs to CDK module:

pcore

Keywords:

pharmacophore, 3D isomorphism

Constructor Summary

Constructors

Constructor and Description
PharmacophoreUtils()

Method Summary

Methods

Modifier and Type	Method and Description
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

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

Constructor Detail

PharmacophoreUtils

public PharmacophoreUtils()

Method Detail

readPharmacophoreDefinitions

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<PharmacophoreQuery> 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

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<PharmacophoreQuery> 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

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

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

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