Class SubstructureIdentifier
- java.lang.Object
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- org.biojava.nbio.structure.SubstructureIdentifier
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- All Implemented Interfaces:
Serializable
,StructureIdentifier
public class SubstructureIdentifier extends Object implements StructureIdentifier
This is the canonical way to identify a part of a structure.The current syntax allows the specification of a set of residues from the first model of a structure. Future versions may be extended to represent additional properties.
Identifiers should adhere to the following specification, although some additional forms may be tolerated where unambiguous for backwards compatibility.
name := pdbID | pdbID '.' chainID | pdbID '.' range range := range (',' range)? | chainID | chainID '_' resNum '-' resNum pdbID := [0-9][a-zA-Z0-9]{3} chainID := [a-zA-Z0-9]+ resNum := [-+]?[0-9]+[A-Za-z]?
For example:1TIM #whole structure 1tim #same as above 4HHB.C #single chain 3AA0.A,B #two chains 4GCR.A_1-40 #substructure 3iek.A_17-28,A_56-294,A_320-377 #substructure of 3 disjoint parts
More options may be added to the specification at a future time.- Author:
- dmyersturnbull, Spencer Bliven
- See Also:
- Serialized Form
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Constructor Summary
Constructors Constructor Description SubstructureIdentifier(String id)
Create a new identifier from a string.SubstructureIdentifier(String pdbId, List<ResidueRange> ranges)
Create a new identifier based on a set of ranges.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description protected static void
copyLigandsByProximity(Structure full, Structure reduced)
Supplements the reduced structure with ligands from the full structure based on a distance cutoff.protected static void
copyLigandsByProximity(Structure full, Structure reduced, double cutoff, int fromModel, int toModel)
Supplements the reduced structure with ligands from the full structure based on a distance cutoff.String
getIdentifier()
Get the String form of this identifier.String
getPdbId()
List<ResidueRange>
getResidueRanges()
Structure
loadStructure(AtomCache cache)
Loads the complete structure based ongetPdbId()
.Structure
reduce(Structure s)
Takes a complete structure as input and reduces it to residues present in the specified rangesSubstructureIdentifier
toCanonical()
Return itself.String
toString()
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Constructor Detail
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SubstructureIdentifier
public SubstructureIdentifier(String id)
Create a new identifier from a string.- Parameters:
id
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SubstructureIdentifier
public SubstructureIdentifier(String pdbId, List<ResidueRange> ranges)
Create a new identifier based on a set of ranges. If ranges is empty, includes all residues.- Parameters:
pdbId
-ranges
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Method Detail
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getIdentifier
public String getIdentifier()
Get the String form of this identifier. This provides the canonical form for a StructureIdentifier and has all the information needed to recreate a particular substructure. Example: 3iek.A_17-28,A_56-294- Specified by:
getIdentifier
in interfaceStructureIdentifier
- Returns:
- The String form of this identifier
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getResidueRanges
public List<ResidueRange> getResidueRanges()
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toCanonical
public SubstructureIdentifier toCanonical()
Return itself. SubstructureIdentifiers are canonical!- Specified by:
toCanonical
in interfaceStructureIdentifier
- Returns:
- A SubstructureIdentifier equivalent to this
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reduce
public Structure reduce(Structure s) throws StructureException
Takes a complete structure as input and reduces it to residues present in the specified rangesThe returned structure will be a shallow copy of the input, with shared Chains, Residues, etc.
Ligands are handled in a special way. If a full chain is selected (e.g. '1ABC.A') then any waters and ligands with matching chain name are included. If a residue range is present ('1ABC.A:1-100') then any ligands (technically non-water non-polymer atoms) within
StructureTools.DEFAULT_LIGAND_PROXIMITY_CUTOFF
of the selected range are included, regardless of chain.- Specified by:
reduce
in interfaceStructureIdentifier
- Parameters:
input
- A full structure, e.g. as loaded from the PDB. The structure ID should match that returned by getPdbId().- Returns:
- Throws:
StructureException
- See Also:
StructureTools.getReducedStructure(Structure, String)
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loadStructure
public Structure loadStructure(AtomCache cache) throws IOException, StructureException
Loads the complete structure based ongetPdbId()
.- Specified by:
loadStructure
in interfaceStructureIdentifier
- Parameters:
AtomCache
- A source of structures- Returns:
- A Structure containing at least the atoms identified by this, or null if no PDB ID is set
- Throws:
StructureException
- For errors loading and parsing the structureIOException
- Errors reading the structure from disk
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copyLigandsByProximity
protected static void copyLigandsByProximity(Structure full, Structure reduced)
Supplements the reduced structure with ligands from the full structure based on a distance cutoff. Ligand groups are moved (destructively) from full to reduced if they fall within the cutoff of any atom in the reduced structure. Thedefault cutoff
is used.- Parameters:
full
- Structure containing all ligandsreduced
- Structure with a subset of the polymer groups from full- See Also:
StructureTools.getLigandsByProximity(java.util.Collection, Atom[], double)
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copyLigandsByProximity
protected static void copyLigandsByProximity(Structure full, Structure reduced, double cutoff, int fromModel, int toModel)
Supplements the reduced structure with ligands from the full structure based on a distance cutoff. Ligand groups are moved (destructively) from full to reduced if they fall within the cutoff of any atom in the reduced structure.- Parameters:
full
- Structure containing all ligandsreduced
- Structure with a subset of the polymer groups from fullcutoff
- Distance cutoff (Å)fromModel
- source model in fulltoModel
- destination model in reduced- See Also:
StructureTools.getLigandsByProximity(java.util.Collection, Atom[], double)
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