Package org.biojava.nbio.structure.xtal
Class CrystalBuilder
- java.lang.Object
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- org.biojava.nbio.structure.xtal.CrystalBuilder
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public class CrystalBuilder extends Object
A class containing methods to find interfaces in a given crystallographic Structure by reconstructing the crystal lattice through application of symmetry operators- Author:
- Jose Duarte
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Field Summary
Fields Modifier and Type Field Description static int
DEF_NUM_CELLS
static double
DEFAULT_INTERFACE_DISTANCE_CUTOFF
Default maximum distance between two chains to be considered an interface.static javax.vecmath.Matrix4d
IDENTITY
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Constructor Summary
Constructors Constructor Description CrystalBuilder(Structure structure)
CrystalBuilder(Structure structure, Map<String,String> chainOrigNames, Map<String,javax.vecmath.Matrix4d> chainNcsOps)
Special constructor for NCS-aware CrystalBuilder.
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description static void
expandNcsOps(Structure structure, Map<String,String> chainOrigNames, Map<String,javax.vecmath.Matrix4d> chainNcsOps)
Apply the NCS operators in the given Structure adding new chains as needed.StructureInterfaceList
getUniqueInterfaces()
Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.StructureInterfaceList
getUniqueInterfaces(double cutoff)
Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates.boolean
hasNcsOps()
void
setNumCells(int numCells)
Set the number of neighboring crystal cells that will be used in the search for contactsvoid
translate(javax.vecmath.Matrix4d m, javax.vecmath.Vector3d translation)
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Field Detail
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DEF_NUM_CELLS
public static final int DEF_NUM_CELLS
- See Also:
- Constant Field Values
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DEFAULT_INTERFACE_DISTANCE_CUTOFF
public static final double DEFAULT_INTERFACE_DISTANCE_CUTOFF
Default maximum distance between two chains to be considered an interface.- See Also:
getUniqueInterfaces(double)
, Constant Field Values
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IDENTITY
public static final javax.vecmath.Matrix4d IDENTITY
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Constructor Detail
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CrystalBuilder
public CrystalBuilder(Structure structure, Map<String,String> chainOrigNames, Map<String,javax.vecmath.Matrix4d> chainNcsOps)
Special constructor for NCS-aware CrystalBuilder. The output list of interfaces will be pre-clustered by NCS-equivalence. RunexpandNcsOps(Structure, Map, Map)
first to extend the AU and get the equivalence information.- Parameters:
structure
- NCS-extended structurechainOrigNames
- chain names mapped to the original chain names (pre-NCS extension)chainNcsOps
- chain names mapped to the ncs operators that was used to generate them- Since:
- 5.0.0
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CrystalBuilder
public CrystalBuilder(Structure structure)
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Method Detail
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hasNcsOps
public boolean hasNcsOps()
- Returns:
- true if this CrystalBuilder is NCS-aware.
- Since:
- 5.0.0
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setNumCells
public void setNumCells(int numCells)
Set the number of neighboring crystal cells that will be used in the search for contacts- Parameters:
numCells
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getUniqueInterfaces
public StructureInterfaceList getUniqueInterfaces()
Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates. An interface is defined as any pair of chains that contact, i.e. for which there is at least a pair of atoms (one from each chain) within the default cutoff distance.- Returns:
- See Also:
DEFAULT_INTERFACE_DISTANCE_CUTOFF
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getUniqueInterfaces
public StructureInterfaceList getUniqueInterfaces(double cutoff)
Returns the list of unique interfaces that the given Structure has upon generation of all crystal symmetry mates. An interface is defined as any pair of chains that contact, i.e. for which there is at least a pair of atoms (one from each chain) within the given cutoff distance.- Parameters:
cutoff
- the distance cutoff for 2 chains to be considered in contact- Returns:
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translate
public void translate(javax.vecmath.Matrix4d m, javax.vecmath.Vector3d translation)
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expandNcsOps
public static void expandNcsOps(Structure structure, Map<String,String> chainOrigNames, Map<String,javax.vecmath.Matrix4d> chainNcsOps)
Apply the NCS operators in the given Structure adding new chains as needed. All chains are (re)assigned ids of the form: original_chain_id+ncs_operator_index+"n".- Parameters:
structure
- the structure to expandchainOrigNames
- new chain names mapped to the original chain nameschainNcsOps
- new chain names mapped to the ncs operators that was used to generate them- Since:
- 5.0.0
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