Package org.openscience.cdk.depict

Class 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 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

      • with

        public Abbreviations with​(Abbreviations.Option option)
        Convenience method to enable an option.
        Parameters:
        option - the option to enable.
        Returns:
        self, for chaining

      • without

        public Abbreviations without​(Abbreviations.Option option)
        Convenience method to disable an option.
        Parameters:
        option - the option to enable.
        Returns:
        self, for chaining

      • 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

      • setContractToSingleLabel

        public void setContractToSingleLabel​(boolean val)

      • 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

      • generate

        public List<Sgroup> generate​(IAtomContainer mol,
                             Map<IAtom,​Integer> atomSets)
        Find all enabled abbreviations in the provided molecule. They are not added to the existing Sgroups and may need filtering.
        Parameters:
        mol - molecule
        atomSets - mark atoms are belong to a set, sets can not be split in an abbreviation
        Returns:
        list of new abbreviation Sgroups

      • apply

        public int apply​(IAtomContainer mol)
        Generates and assigns abbreviations to a molecule. Abbreviations are first generated with generate(org.openscience.cdk.interfaces.IAtomContainer) and then applied to the molecule if it is reasonable to do so. Currently, we count the number of ring/chain atoms in/out of the contraction. If there are more atoms contracted than not it is not applied.
        Parameters:
        mol - molecule
        Returns:
        number of new abbreviations
        See Also:
        generate(IAtomContainer, Map)

      • apply

        public int apply​(IAtomContainer mol,
                 Map<IAtom,​Integer> atomSets)
        Generates and assigns abbreviations to a molecule. Abbreviations are first generated with generate(org.openscience.cdk.interfaces.IAtomContainer) and then applied to the molecule if it is reasonable to do so. Currently, we count the number of ring/chain atoms in/out of the contraction. If there are more atoms contracted than not it is not applied.
        Parameters:
        mol - molecule
        atomSets - atoms, keep these atoms together
        Returns:
        number of new abbreviations
        See Also:
        generate(IAtomContainer, Map)

      • 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