Package org.biojava.bio.structure
Class StructureTools
- java.lang.Object
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- org.biojava.bio.structure.StructureTools
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public class StructureTools extends java.lang.Object
A class that provides some tool methods.- Since:
- 1.0
- Version:
- %I% %G%
- Author:
- Andreas Prlic
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Field Summary
Fields Modifier and Type Field Description static java.lang.String[]
backboneAtomNames
The names of the Atoms that form the backbone.static java.lang.String
caAtomName
The Atom name of C-alpha atoms.static java.util.logging.Logger
logger
static java.lang.Character
UNKNOWN_GROUP_LABEL
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Constructor Summary
Constructors Constructor Description StructureTools()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static java.lang.Character
convert_3code_1code(java.lang.String code3)
convert three character amino acid codes into single character e.g.static java.lang.Character
get1LetterCode(java.lang.String groupCode3)
convert a three letter code into single character.static Atom[]
getAtomArray(Structure s, java.lang.String[] atomNames)
Returns an array of the requested Atoms from the Structure object.static Atom[]
getAtomCAArray(Structure s)
Returns an Atom array of the CA atoms.static Atom[]
getBackboneAtomArray(Structure s)
Returns an Atom array of the MainChain atoms.static int
getNrAtoms(Structure s)
Count how many number of Atoms are contained within a Structure object.static int
getNrGroups(Structure s)
Count how many groups are contained within a structure object.static boolean
isNucleotide(java.lang.String groupCode3)
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Field Detail
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caAtomName
public static final java.lang.String caAtomName
The Atom name of C-alpha atoms.- See Also:
- Constant Field Values
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backboneAtomNames
public static final java.lang.String[] backboneAtomNames
The names of the Atoms that form the backbone.
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UNKNOWN_GROUP_LABEL
public static final java.lang.Character UNKNOWN_GROUP_LABEL
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logger
public static java.util.logging.Logger logger
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Method Detail
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getNrAtoms
public static int getNrAtoms(Structure s)
Count how many number of Atoms are contained within a Structure object.- Parameters:
s
- the structure object- Returns:
- the number of Atoms in this Structure
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getNrGroups
public static int getNrGroups(Structure s)
Count how many groups are contained within a structure object.- Parameters:
s
- the structure object- Returns:
- the number of groups in the structure
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getAtomArray
public static Atom[] getAtomArray(Structure s, java.lang.String[] atomNames)
Returns an array of the requested Atoms from the Structure object. Iterates over all groups and checks if the requested atoms are in this group, no matter if this is a AminoAcid or Hetatom group.- Parameters:
s
- the structure to get the atoms fromatomNames
- contains the atom names to be used.- Returns:
- an Atom[] array
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getAtomCAArray
public static Atom[] getAtomCAArray(Structure s)
Returns an Atom array of the CA atoms.- Parameters:
s
- the structure object- Returns:
- an Atom[] array
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getBackboneAtomArray
public static Atom[] getBackboneAtomArray(Structure s)
Returns an Atom array of the MainChain atoms.- Parameters:
s
- the structure object- Returns:
- an Atom[] array
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convert_3code_1code
public static java.lang.Character convert_3code_1code(java.lang.String code3) throws IllegalSymbolException
convert three character amino acid codes into single character e.g. convert CYS to C- Parameters:
code3
- a three character amino acid representation String- Returns:
- a character
- Throws:
IllegalSymbolException
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get1LetterCode
public static java.lang.Character get1LetterCode(java.lang.String groupCode3)
convert a three letter code into single character. catches for unusual characters- Parameters:
groupCode3
- three letter representation- Returns:
- null if group is a nucleotide code
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isNucleotide
public static boolean isNucleotide(java.lang.String groupCode3)
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