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java.lang.Objectorg.biojava.bio.structure.StructureTools
public class StructureTools
A class that provides some tool methods.
Field Summary | |
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static String[] |
backboneAtomNames
The names of the Atoms that form the backbone. |
static String |
caAtomName
The Atom name of C-alpha atoms. |
static Logger |
logger
|
static Character |
UNKNOWN_GROUP_LABEL
|
Constructor Summary | |
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StructureTools()
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Method Summary | |
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static Character |
convert_3code_1code(String code3)
convert three character amino acid codes into single character e.g. |
static Character |
get1LetterCode(String groupCode3)
convert a three letter code into single character. |
static Atom[] |
getAtomArray(Structure s,
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(String groupCode3)
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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 |
Field Detail |
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public static final String caAtomName
public static final String[] backboneAtomNames
public static final Character UNKNOWN_GROUP_LABEL
public static Logger logger
Constructor Detail |
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public StructureTools()
Method Detail |
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public static int getNrAtoms(Structure s)
s
- the structure object
public static int getNrGroups(Structure s)
s
- the structure object
public static Atom[] getAtomArray(Structure s, String[] atomNames)
s
- the structure to get the atoms fromatomNames
- contains the atom names to be used.
public static Atom[] getAtomCAArray(Structure s)
s
- the structure object
public static Atom[] getBackboneAtomArray(Structure s)
s
- the structure object
public static Character convert_3code_1code(String code3) throws IllegalSymbolException
code3
- a three character amino acid representation String
IllegalSymbolException
public static Character get1LetterCode(String groupCode3)
groupCode3
- three letter representation
public static boolean isNucleotide(String groupCode3)
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