Class StructureUtil
- java.lang.Object
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- org.biojava.nbio.protmod.structure.StructureUtil
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public final class StructureUtil extends java.lang.Object
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static java.util.List<Atom[]>
findAtomLinkages(Group group1, Group group2, boolean ignoreNCLinkage, double bondLengthTolerance)
Find linkages between two groups within tolerance of bond length, from potential atoms.static java.util.List<Atom[]>
findAtomLinkages(Group group1, Group group2, java.util.List<java.lang.String> potentialNamesOfAtomOnGroup1, java.util.List<java.lang.String> potentialNamesOfAtomOnGroup2, boolean ignoreNCLinkage, double bondLengthTolerance)
Find linkages between two groups within tolerance of bond length, from potential atoms.static Atom[]
findLinkage(Group group1, Group group2, java.lang.String nameOfAtomOnGroup1, java.lang.String nameOfAtomOnGroup2, double bondLengthTolerance)
Find a linkage between two groups within tolerance of bond length.static Atom[]
findNearestAtomLinkage(Group group1, Group group2, java.util.List<java.lang.String> potentialNamesOfAtomOnGroup1, java.util.List<java.lang.String> potentialNamesOfAtomOnGroup2, boolean ignoreNCLinkage, double bondLengthTolerance)
Find a linkage between two groups within tolerance of bond length, from potential atoms.static java.util.List<Group>
getAminoAcids(Chain chain)
Get all amino acids in a chain.static double
getAtomDistance(Atom atom1, Atom atom2)
static java.util.List<java.lang.String>
getAtomNames(Group group)
static StructureAtom
getStructureAtom(Atom atom, boolean isParentAminoAcid)
static StructureAtomLinkage
getStructureAtomLinkage(Atom atom1, boolean isParentAminoAcid1, Atom atom2, boolean isParentAminoAcid2)
static StructureGroup
getStructureGroup(Group group, boolean isAminoAcid)
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Method Detail
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getStructureGroup
public static StructureGroup getStructureGroup(Group group, boolean isAminoAcid)
- Parameters:
group
- aGroup
in structure.isAminoAcid
- true if it is an amino acid.- Returns:
- the
StructureGroup
of the group.
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getStructureAtom
public static StructureAtom getStructureAtom(Atom atom, boolean isParentAminoAcid)
- Parameters:
atom
- aAtom
in structure.isParentAminoAcid
- true if the containing group is an amino acid.- Returns:
- the
StructureAtom
of the atom.
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getStructureAtomLinkage
public static StructureAtomLinkage getStructureAtomLinkage(Atom atom1, boolean isParentAminoAcid1, Atom atom2, boolean isParentAminoAcid2)
- Parameters:
atom1
- the firstAtom
in structure.isParentAminoAcid1
- true if the first containing group is an amino acid..atom2
- the secondAtom
in structure.isParentAminoAcid2
- true if the second containing group is an amino acid..- Returns:
- the
StructureAtomLinkage
of the two atoms.
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findNearestAtomLinkage
public static Atom[] findNearestAtomLinkage(Group group1, Group group2, java.util.List<java.lang.String> potentialNamesOfAtomOnGroup1, java.util.List<java.lang.String> potentialNamesOfAtomOnGroup2, boolean ignoreNCLinkage, double bondLengthTolerance)
Find a linkage between two groups within tolerance of bond length, from potential atoms.- Parameters:
group1
- the firstGroup
.group2
- the secondGroup
.potentialNamesOfAtomOnGroup1
- potential names of the atom on the first group. If null, search all atoms on the first group.potentialNamesOfAtomOnGroup2
- potential names of the atom on the second group. If null, search all atoms on the second group.ignoreNCLinkage
- true to ignore all N-C linkagesbondLengthTolerance
- bond length error tolerance.- Returns:
- an array of two Atoms that form bond between each other if found; null, otherwise.
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findAtomLinkages
public static java.util.List<Atom[]> findAtomLinkages(Group group1, Group group2, boolean ignoreNCLinkage, double bondLengthTolerance)
Find linkages between two groups within tolerance of bond length, from potential atoms.
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findAtomLinkages
public static java.util.List<Atom[]> findAtomLinkages(Group group1, Group group2, java.util.List<java.lang.String> potentialNamesOfAtomOnGroup1, java.util.List<java.lang.String> potentialNamesOfAtomOnGroup2, boolean ignoreNCLinkage, double bondLengthTolerance)
Find linkages between two groups within tolerance of bond length, from potential atoms.- Parameters:
group1
- the firstGroup
.group2
- the secondGroup
.potentialNamesOfAtomOnGroup1
- potential names of the atom on the first group. If null, search all atoms on the first group.potentialNamesOfAtomOnGroup2
- potential names of the atom on the second group. If null, search all atoms on the second group.ignoreNCLinkage
- true to ignore all N-C linkagesbondLengthTolerance
- bond length error tolerance.- Returns:
- a list, each element of which is an array of two Atoms that form bond between each other.
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findLinkage
public static Atom[] findLinkage(Group group1, Group group2, java.lang.String nameOfAtomOnGroup1, java.lang.String nameOfAtomOnGroup2, double bondLengthTolerance)
Find a linkage between two groups within tolerance of bond length.- Parameters:
group1
- the firstGroup
.group2
- the secondGroup
.nameOfAtomOnGroup1
- atom name of the first group.nameOfAtomOnGroup2
- atom name of the second group.bondLengthTolerance
- bond length error tolerance.- Returns:
- an array of two Atoms that form bond between each other if found; null, otherwise.
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getAtomNames
public static java.util.List<java.lang.String> getAtomNames(Group group)
- Parameters:
group
- aGroup
.- Returns:
- all atom names of the group.
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