public class StructureIO
extends java.lang.Object
Constructor and Description |
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StructureIO() |
Modifier and Type | Method and Description |
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static Structure |
getBiologicalAssembly(java.lang.String pdbId)
Returns the first biologicalAssembly that is available for a protein structure.
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static Structure |
getBiologicalAssembly(java.lang.String pdbId,
int biolAssemblyNr)
By default the getStructure method loads asym units.
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static int |
getNrBiologicalAssemblies(java.lang.String pdbId) |
static Structure |
getStructure(java.lang.String name)
Loads a structure based on a name.
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static boolean |
hasBiologicalAssembly(java.lang.String pdbId)
Does the provider PDB ID have a biological assembly?
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static void |
setAtomCache(AtomCache c) |
static void |
setPdbPath(java.lang.String pathToPDBFiles)
Utility method to set the location where PDB files can be found
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public static Structure getStructure(java.lang.String name) throws java.io.IOException, StructureException
Formal specification for how to specify the name: name := pdbID | pdbID '.' chainID | pdbID '.' range | scopID | biol | pdp range := '('? range (',' range)? ')'? | chainID | chainID '_' resNum '-' resNum pdbID := [0-9][a-zA-Z0-9]{3} chainID := [a-zA-Z0-9] scopID := 'd' pdbID [a-z_][0-9_] biol := 'BIOL:' pdbID [:]? [0-9]+ pdp := 'PDP:' pdbID[A-Za-z0-9_]+ resNum := [-+]?[0-9]+[A-Za-z]? Example structures: 1TIM #whole structure - asym unit 4HHB.C #single chain 4GCR.A_1-83 #one domain, by residue number 3AA0.A,B #two chains treated as one structure d2bq6a1 #scop domain BIOL:1fah #biological assembly nr 1 for 1fah BIOL:1fah:0 #asym unit for 1fah BIOL:1fah:1 #biological assembly nr 1 for 1fah BIOL:1fah:2 #biological assembly nr 2 for 1fahWith the additional set of rules:
#setStrictSCOP(boolean)
name
- java.io.IOException
- The PDB file cannot be cached due to IO errorsStructureException
- The name appeared valid but did not correspond to a structure.
Also thrown by some submethods upon errors, eg for poorly formatted subranges.public static void setAtomCache(AtomCache c)
public static Structure getBiologicalAssembly(java.lang.String pdbId) throws java.io.IOException, StructureException
http://www.pdb.org/pdb/101/static101.do?p=education_discussion/Looking-at-Structures/bioassembly_tutorial.html
pdbId
- StructureException
java.io.IOException
public static Structure getBiologicalAssembly(java.lang.String pdbId, int biolAssemblyNr) throws java.io.IOException, StructureException
pdbId
- biolAssemblyNr
- - the ith biological assembly that is available for a PDB ID (we start counting at 1, 0 represents the asym unit).StructureException
java.io.IOException
public static boolean hasBiologicalAssembly(java.lang.String pdbId)
pdbId
- public static int getNrBiologicalAssemblies(java.lang.String pdbId)
public static void setPdbPath(java.lang.String pathToPDBFiles)
pathToPDBFiles
-