org.openscience.cdk.depict

Class Abbreviations

java.lang.Object

org.openscience.cdk.depict.Abbreviations

All Implemented Interfaces:

Iterable<String>

public class Abbreviations
extends Object
implements Iterable<String>

Utility class for abbreviating (sub)structures. Using either self assigned structural motifs or pre-loading a common set a structure depiction can be made more concise with the use of abbreviations (sometimes called superatoms).

Basic usage:

 Abbreviations abrv = new Abbreviations();

 // add some abbreviations, when overlapping (e.g. Me,Et,tBu) first one wins
 abrv.add("[Na+].[H-] NaH");
 abrv.add("*c1ccccc1 Ph");
 abrv.add("*C(C)(C)C tBu");
 abrv.add("*CC Et");
 abrv.add("*C Me");

 // maybe we don't want 'Me' in the depiction
 abrv.setEnabled("Me", false);

 // assign abbreviations with some filters
 int numAdded = abrv.apply(mol);

 // generate all but don't assign, need to be added manually
 // set/update the CDKConstants.CTAB_SGROUPS property of mol
 List<Sgroup> sgroups = abrv.generate(mol);
 

Predefined sets of abbreviations can be loaded, the following are on the classpath.

 // https://www.github.com/openbabel/superatoms
 abrv.loadFromFile("obabel_superatoms.smi");
 

See Also:

CDKConstants.CTAB_SGROUPS, Sgroup

Keywords:

abbreviate, depict, superatom

Constructor Summary

Constructors

Constructor and Description
Abbreviations()

Method Summary

Modifier and Type	Method and Description
boolean	add(IAtomContainer mol, String label) Add an abbreviation to the factory.
boolean	add(String line) Convenience method to add an abbreviation from a SMILES string.
int	apply(IAtomContainer mol) Generates and assigns abbreviations to a molecule.
List<Sgroup>	generate(IAtomContainer mol) Find all enabled abbreviations in the provided molecule.
boolean	isEnabled(String label) Check whether an abbreviation is enabled.
Iterator<String>	iterator() Iterate over loaded abbreviations.
int	loadFromFile(String path) Load a set of abbreviations from a classpath resource or file in SMILES format.
void	setContractOnHetero(boolean val) Set whether abbreviations should be further contracted when they are connected to a heteroatom, for example -NH-Boc becomes -NHBoc.
boolean	setEnabled(String label, boolean enabled) Set whether an abbreviation is enabled or disabled.

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.lang.Iterable

forEach, spliterator

Constructor Detail

Abbreviations

public Abbreviations()

Method Detail

iterator

public Iterator<String> iterator()

Iterate over loaded abbreviations. Both enabled and disabled abbreviations are listed.

Specified by:

iterator in interface Iterable<String>

Returns:

the abbreviations labels (e.g. Ph, Et, Me, OAc, etc.)

isEnabled

public boolean isEnabled(String label)

Check whether an abbreviation is enabled.

Parameters:

label - is enabled

Returns:

the label is enabled

setEnabled

public boolean setEnabled(String label,
                          boolean enabled)

Set whether an abbreviation is enabled or disabled.

Parameters:

label - the label (e.g. Ph, Et, Me, OAc, etc.)

enabled - flag the label as enabled or disabled

Returns:

the label state was modified

setContractOnHetero

public void setContractOnHetero(boolean val)

Set whether abbreviations should be further contracted when they are connected to a heteroatom, for example -NH-Boc becomes -NHBoc. By default this option is enabled.

Parameters:

val - on/off

generate

public List<Sgroup> generate(IAtomContainer mol)

Find all enabled abbreviations in the provided molecule. They are not added to the existing Sgroups and may need filtering.

Parameters:

mol - molecule

Returns:

list of new abbreviation Sgroups

apply

public int apply(IAtomContainer mol)

Generates and assigns abbreviations to a molecule. Abbrevations are first generated with generate(org.openscience.cdk.interfaces.IAtomContainer) and the filtered based on the coverage. Currently only abbreviations that cover 100%, or < 40% of the atoms are assigned.

Parameters:

mol - molecule

Returns:

number of new abbreviations

See Also:

generate(IAtomContainer)

add

public boolean add(String line)
            throws InvalidSmilesException

Convenience method to add an abbreviation from a SMILES string.

Parameters:

line - the smiles to add with a title (the label)

Returns:

the abbreviation was added, will be false if no title supplied

Throws:

InvalidSmilesException - the SMILES was not valid

add

public boolean add(IAtomContainer mol,
                   String label)

Add an abbreviation to the factory. Abbreviations can be of various flavour based on the number of attachments:

Detached - zero attachments, the abbreviation covers the whole structure (e.g. THF) Terminal - one attachment, covers substituents (e.g. Ph for Phenyl) Linker - [NOT SUPPORTED YET] two attachments, covers long repeated chains (e.g. PEG4)

Attachment points (if present) must be specified with zero element atoms.

 *c1ccccc1 Ph
 *OC(=O)C OAc
 

Parameters:

mol - the fragment to abbreviate

label - the label of the fragment

Returns:

the abbreviation was added

loadFromFile

public int loadFromFile(String path)
                 throws IOException

Load a set of abbreviations from a classpath resource or file in SMILES format. The title is seperated by a space.

 *c1ccccc1 Ph
 *c1ccccc1 OAc
 

Available:

obabel_superatoms.smi

https://www.github.com/openbabel/superatoms

Parameters:

path - classpath or filesystem path to a SMILES file

Returns:

the number of loaded abbreviation

Throws:

IOException