Building innovative

drug discovery alliances

Custom Calculators in ChemAxon Tools and Knime

Evotec AG, Custom Calculators in ChemAxon Tools and Knime, 23rd May 2012

PAGE

Agenda

1

ESMA – current Calculations and Models

Writing Custom Calculators

Integrating with Marvin

Integrating with InstantJChem

Combining Custom Calculators and ChemAxon/Infocom nodes

Demonstration

Conclusions

PAGE

Agenda

2

ESMA – current Calculations and Models

Writing Custom Calculators

Integrating with Marvin

Integrating with InstantJChem

Combining Custom Calculators and ChemAxon/Infocom nodes

Demonstration

Conclusions

PAGE

Custom Calculators

3

ESMA – Evoseek Searching and Modelling Application

Large integrated application

Java WebStart

Big code base

Complicated to change

Complicated to extend

Calculations and presentation

locked together

PAGE

Agenda

4

ESMA – current Calculations and Models

Writing Custom Calculators

Integrating with Marvin

Integrating with InstantJChem

Combining Custom Calculators and ChemAxon/Infocom nodes

Demonstration

Conclusions

PAGE

Custom Calculators

5

3 Interfaces to conform to

Object calculate (String mol)

throws CalculatorException

String getResult (String mol)

Public interface

CalculatorFacade

Public interface

ChargedCalculatorFacade

Object calculate (String mol,

double phValue) throws

CalculatorException

String getResult (String mol,

double phValue)

Public interface

ActivityCalculatorFacade

Object calculate (String mol,

double ic50, int

multiplicator) throws

CalculatorException

String getResult (String mol,

double ic50, int

multiplicator)

PAGE

Custom Calculators

6

3 Interfaces to conform to

Object calculate (String mol)

throws CalculatorException

Public interface

CalculatorAlgorithm

Public interface

ChargedCalculator

double getPhValue ()

void setPhValue (double

phValue)

Public interface

ActivityCalculator

int getMultiplicator ()

void setMultiplicator

(final int multiplicator)

double getIc50Value ()

void setIc50Value

(final double ic50Value)

PAGE

Custom Calculators

7

Implementation

@Override

public final Object calculate (final String mol) throws CalculatorException

final BBBAlgorithm calculator = new BBBAlgorithm ()

return calculator.calculate (mol)

@Override

public final String getResult (final String mol)

final Object result = calculate (mol)

…

return formattedResult

Public class BBB implements CalculatorFacade

PAGE

static final String REFERENCE = "Norinder Adv. Drug Del. Rev. 2002, 291"

private static final String ERROR_MESSAGE = "BBB prediction failed: "

protected BBBAlgorithm ()

…

@Override

public final Object calculate(final String mol) throws CalculatorException

final List<String> BBB = new ArrayList<String> ()

…

return BBB

Public class BBBAlgorithm implements CalculatorAlgorithm

Custom Calculators

8

Implementation

PAGE

Agenda

9

ESMA – current Calculations and Models

Writing Custom Calculators

Integrating with Marvin

Integrating with InstantJChem

Combining Custom Calculators and ChemAxon/Infocom nodes

Demonstration

Conclusions

PAGE

Custom Calculators

10

Adding new tools in Marvin

PAGE

Custom Calculators

11

Adding a new service

PAGE

Extending ChemAxon tools

12

Selecting the method

PAGE

Extending ChemAxon tools

13

Using the new services

PAGE

Custom Calculators

14

Saving/Loading the configuration

PAGE

Custom Calculators

15

Example calculations

PAGE

Agenda

16

ESMA – current Calculations and Models

Writing Custom Calculators

Integrating with Marvin

Integrating with InstantJChem

Combining Custom Calculators and ChemAxon/Infocom nodes

Demonstration

Conclusions

PAGE

Custom Calculators

17

Instant JChem

PAGE

Custom Calculators

18

cxcalc and Chemical Terms – command line

cxcalc can be used to access the Custom Calculators

Custom Calculators can be mixed with ChemAxon calculators

Results can be output to SDF files

Chemical Terms calculations can also access the Custom Calculators

Access from the command line

Access in Instant JChem

Combine with ChemAxon calculators

PAGE

Agenda

19

ESMA – current Calculations and Models

Writing Custom Calculators

Integrating with Marvin

Integrating with InstantJChem

Combining Custom Calculators and ChemAxon/Infocom nodes

Demonstration

Conclusions

PAGE

Custom Calculators

20

Adding custom Calculators to Knime

public class BBBCellFactory extends SingleCellFactory

public BBBCellFactory (DataColumnSpec newColSpec, final int columnIndex, final float pH)

...

@Override

public DataCell getCell (DataRow row)

...

BBB bbb = new BBB ();

• bbb.calculateFromSmiles(currentValue, m_Ph))

return new StringCell ((String)

Import com.evotec.calculators.bbb.BBB

PAGE

Custom Calculators

21

Using Evotec nodes with ChemAxon nodes

PAGE

Custom Calculators

22

Using Evotec nodes with ChemAxon nodes via Knime Web Portal

PAGE

Agenda

23

ESMA – current Calculations and Models

Writing Custom Calculators

Integrating with Marvin

Integrating with InstantJChem

Combining Custom Calculators and ChemAxon/Infocom nodes

Demonstration

Conclusions

PAGE

Custom Calculators

24

Adding a new Calculator to Marvin Sketch

Demonstration

PAGE

Agenda

25

ESMA – current Calculations and Models

Writing Custom Calculators

Integrating with Marvin

Integrating with InstantJChem

Combining Custom Calculators and ChemAxon/Infocom nodes

Demonstration

Conclusions

PAGE

Conclusions

26

Custom Calculators

We have created a library of custom calculations

The library can be quickly and easily updated

The library can be exposed to chemists through their desktop

ChemAxon tools

The library can also be exposed using Knime to work with

ChemAxon/Infocom nodes

Your contact:

Building innovative

drug discovery alliances

Dr Bob Marmon Senior Applications Developer, eScience

+44.(0).1235.44-1402 bob.marmon@evotec.com