Package org.biojava.nbio.protmod.structure

Class StructureUtil

java.lang.Object

org.biojava.nbio.protmod.structure.StructureUtil

public final class StructureUtil
extends Object

Method Summary

Modifier and Type	Method	Description
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)
static List<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)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Detail

getStructureGroup

public static StructureGroup getStructureGroup(Group group,
                                               boolean isAminoAcid)

Parameters:

group - a Group in structure.

isAminoAcid - true if it is an amino acid.

Returns:

the StructureGroup of the group.

getStructureAtom

public static StructureAtom getStructureAtom(Atom atom,
                                             boolean isParentAminoAcid)

Parameters:

atom - a Atom in structure.

isParentAminoAcid - true if the containing group is an amino acid.

Returns:

the StructureAtom of the atom.

getStructureAtomLinkage

public static StructureAtomLinkage getStructureAtomLinkage(Atom atom1,
                                                           boolean isParentAminoAcid1,
                                                           Atom atom2,
                                                           boolean isParentAminoAcid2)

Parameters:

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..

Returns:

the StructureAtomLinkage of the two atoms.

getAtomDistance

public static double getAtomDistance(Atom atom1,
                                     Atom atom2)

Parameters:

atom1 - the first Atom in structure.

atom2 - the second Atom in structure.

Returns:

the distance between the two atoms in Angstrom.

findNearestAtomLinkage

public 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.

Parameters:

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 linkages

bondLengthTolerance - bond length error tolerance.

Returns:

an array of two Atoms that form bond between each other if found; null, otherwise.

findAtomLinkages

public 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.

Parameters:

group1 - the first Group.

group2 - the second Group.

ignoreNCLinkage - true to ignore all N-C linkages

bondLengthTolerance - bond length error tolerance.

Returns:

a list, each element of which is an array of two Atoms that form bond between each other.

findAtomLinkages

public 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.

Parameters:

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 linkages

bondLengthTolerance - bond length error tolerance.

Returns:

a list, each element of which is an array of two Atoms that form bond between each other.

findLinkage

public static Atom[] findLinkage(Group group1,
                                 Group group2,
                                 String nameOfAtomOnGroup1,
                                 String nameOfAtomOnGroup2,
                                 double bondLengthTolerance)

Find a linkage between two groups within tolerance of bond length.

Parameters:

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.

Returns:

an array of two Atoms that form bond between each other if found; null, otherwise.

getAtomNames

public static List<String> getAtomNames(Group group)

Parameters:

group - a Group.

Returns:

all atom names of the group.

getAminoAcids

public static List<Group> getAminoAcids(Chain chain)

Get all amino acids in a chain.

Parameters:

chain -

Returns: