Class QuatSymmetryDetector
- java.lang.Object
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- org.biojava.nbio.structure.symmetry.core.QuatSymmetryDetector
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public class QuatSymmetryDetector extends Object
Detects the symmetry (global, pseudo, internal and local) of protein structures.The
SubunitClustererParameters
determine the subunit definition and clustering, while theQuatSymmetryParameters
determine the calculated symmetry results (point group and axes).- Author:
- Peter Rose, Aleix Lafita
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static QuatSymmetryResults
calcGlobalSymmetry(List<Subunit> subunits, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)
Calculate GLOBAL symmetry results.static QuatSymmetryResults
calcGlobalSymmetry(Structure structure, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)
Calculate GLOBAL symmetry results.static QuatSymmetryResults
calcGlobalSymmetry(Stoichiometry composition, QuatSymmetryParameters symmParams)
Calculate GLOBAL symmetry results.static List<QuatSymmetryResults>
calcLocalSymmetries(List<Subunit> subunits, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)
Returns a List of LOCAL symmetry results.static List<QuatSymmetryResults>
calcLocalSymmetries(Structure structure, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)
Returns a List of LOCAL symmetry results.static List<QuatSymmetryResults>
calcLocalSymmetries(Stoichiometry globalComposition, QuatSymmetryParameters symmParams)
Returns a List of LOCAL symmetry results.
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Method Detail
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calcGlobalSymmetry
public static QuatSymmetryResults calcGlobalSymmetry(Structure structure, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)
Calculate GLOBAL symmetry results. This means that allSubunit
are included in the symmetry.- Parameters:
structure
- protein chains will be extracted asSubunit
symmParams
- quaternary symmetry parametersclusterParams
- subunit clustering parameters- Returns:
- GLOBAL quaternary structure symmetry results
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calcGlobalSymmetry
public static QuatSymmetryResults calcGlobalSymmetry(List<Subunit> subunits, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)
Calculate GLOBAL symmetry results. This means that allSubunit
are included in the symmetry.- Parameters:
subunits
- list ofSubunit
symmParams
- quaternary symmetry parametersclusterParams
- subunit clustering parameters- Returns:
- GLOBAL quaternary structure symmetry results
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calcGlobalSymmetry
public static QuatSymmetryResults calcGlobalSymmetry(Stoichiometry composition, QuatSymmetryParameters symmParams)
Calculate GLOBAL symmetry results. This means that allSubunit
are included in the symmetry.- Parameters:
composition
-Stoichiometry
object that contains clustering resultssymmParams
- quaternary symmetry parameters- Returns:
- GLOBAL quaternary structure symmetry results
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calcLocalSymmetries
public static List<QuatSymmetryResults> calcLocalSymmetries(Structure structure, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)
Returns a List of LOCAL symmetry results. This means that a subset of theSubunitCluster
is left out of the symmetry calculation. Each element of the List is one possible LOCAL symmetry result.Determine local symmetry if global structure is: (1) asymmetric, C1; (2) heteromeric (belongs to more than 1 subunit cluster); (3) more than 2 subunits (heteromers with just 2 chains cannot have local symmetry)
- Parameters:
structure
- protein chains will be extracted asSubunit
symmParams
- quaternary symmetry parametersclusterParams
- subunit clustering parameters- Returns:
- List of LOCAL quaternary structure symmetry results. Empty if none.
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calcLocalSymmetries
public static List<QuatSymmetryResults> calcLocalSymmetries(List<Subunit> subunits, QuatSymmetryParameters symmParams, SubunitClustererParameters clusterParams)
Returns a List of LOCAL symmetry results. This means that a subset of theSubunitCluster
is left out of the symmetry calculation. Each element of the List is one possible LOCAL symmetry result.Determine local symmetry if global structure is: (1) asymmetric, C1; (2) heteromeric (belongs to more than 1 subunit cluster); (3) more than 2 subunits (heteromers with just 2 chains cannot have local symmetry)
- Parameters:
subunits
- list ofSubunit
symmParams
- quaternary symmetry parametersclusterParams
- subunit clustering parameters- Returns:
- List of LOCAL quaternary structure symmetry results. Empty if none.
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calcLocalSymmetries
public static List<QuatSymmetryResults> calcLocalSymmetries(Stoichiometry globalComposition, QuatSymmetryParameters symmParams)
Returns a List of LOCAL symmetry results. This means that a subset of theSubunitCluster
is left out of the symmetry calculation. Each element of the List is one possible LOCAL symmetry result.Determine local symmetry if global structure is: (1) asymmetric, C1; (2) heteromeric (belongs to more than 1 subunit cluster); (3) more than 2 subunits (heteromers with just 2 chains cannot have local symmetry)
- Parameters:
globalComposition
-Stoichiometry
object that contains global clustering resultssymmParams
- quaternary symmetry parameters- Returns:
- List of LOCAL quaternary structure symmetry results. Empty if none.
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