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java.lang.Objectorg.biojava3.protmod.structure.StructureUtil
public final class StructureUtil
Method Summary | |
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static 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 List<Atom[]> |
findAtomLinkages(Group group1,
Group group2,
List<String> potentialNamesOfAtomOnGroup1,
List<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,
String nameOfAtomOnGroup1,
String nameOfAtomOnGroup2,
double bondLengthTolerance)
Find a linkage between two groups within tolerance of bond length. |
static Atom[] |
findNearestAtomLinkage(Group group1,
Group group2,
List<String> potentialNamesOfAtomOnGroup1,
List<String> potentialNamesOfAtomOnGroup2,
boolean ignoreNCLinkage,
double bondLengthTolerance)
Find a linkage between two groups within tolerance of bond length, from potential atoms. |
static List<Group> |
getAminoAcids(Chain chain)
Get all amino acids in a chain. |
static double |
getAtomDistance(Atom atom1,
Atom atom2)
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static List<String> |
getAtomNames(Group group)
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static StructureAtom |
getStructureAtom(Atom atom,
boolean isParentAminoAcid)
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static StructureAtomLinkage |
getStructureAtomLinkage(Atom atom1,
boolean isParentAminoAcid1,
Atom atom2,
boolean isParentAminoAcid2)
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static StructureGroup |
getStructureGroup(Group group,
boolean isAminoAcid)
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Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Method Detail |
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public static StructureGroup getStructureGroup(Group group, boolean isAminoAcid)
group
- a Group
in structure.isAminoAcid
- true if it is an amino acid.
StructureGroup
of the group.public static StructureAtom getStructureAtom(Atom atom, boolean isParentAminoAcid)
atom
- a Atom
in structure.isParentAminoAcid
- true if the containing group is an amino acid.
StructureAtom
of the atom.public static StructureAtomLinkage getStructureAtomLinkage(Atom atom1, boolean isParentAminoAcid1, Atom atom2, boolean isParentAminoAcid2)
atom1
- the first Atom
in structure.isParentAminoAcid1
- true if the first containing group is an amino acid..atom2
- the second Atom
in structure.isParentAminoAcid2
- true if the second containing group is an amino acid..
StructureAtomLinkage
of the two atoms.public static double getAtomDistance(Atom atom1, Atom atom2)
atom1
- the first Atom
in structure.atom2
- the second Atom
in structure.
public static Atom[] findNearestAtomLinkage(Group group1, Group group2, List<String> potentialNamesOfAtomOnGroup1, List<String> potentialNamesOfAtomOnGroup2, boolean ignoreNCLinkage, double bondLengthTolerance)
group1
- the first Group
.group2
- the second Group
.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.
public static List<Atom[]> findAtomLinkages(Group group1, Group group2, boolean ignoreNCLinkage, double bondLengthTolerance)
group1
- the first Group
.group2
- the second Group
.ignoreNCLinkage
- true to ignore all N-C linkagesbondLengthTolerance
- bond length error tolerance.
public static List<Atom[]> findAtomLinkages(Group group1, Group group2, List<String> potentialNamesOfAtomOnGroup1, List<String> potentialNamesOfAtomOnGroup2, boolean ignoreNCLinkage, double bondLengthTolerance)
group1
- the first Group
.group2
- the second Group
.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.
public static Atom[] findLinkage(Group group1, Group group2, String nameOfAtomOnGroup1, String nameOfAtomOnGroup2, double bondLengthTolerance)
group1
- the first Group
.group2
- the second Group
.nameOfAtomOnGroup1
- atom name of the first group.nameOfAtomOnGroup2
- atom name of the second group.bondLengthTolerance
- bond length error tolerance.
public static List<String> getAtomNames(Group group)
group
- a Group
.
public static List<Group> getAminoAcids(Chain chain)
chain
-
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