public class StructureTools
extends java.lang.Object
Modifier and Type | Field and Description |
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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 |
Constructor and Description |
---|
StructureTools() |
Modifier and Type | Method and 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) |
public static final java.lang.String caAtomName
public static final java.lang.String[] backboneAtomNames
public static final java.lang.Character UNKNOWN_GROUP_LABEL
public static java.util.logging.Logger logger
public static int getNrAtoms(Structure s)
s
- the structure objectpublic static int getNrGroups(Structure s)
s
- the structure objectpublic static Atom[] getAtomArray(Structure s, java.lang.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 objectpublic static Atom[] getBackboneAtomArray(Structure s)
s
- the structure objectpublic static java.lang.Character convert_3code_1code(java.lang.String code3) throws IllegalSymbolException
code3
- a three character amino acid representation StringIllegalSymbolException
public static java.lang.Character get1LetterCode(java.lang.String groupCode3)
groupCode3
- three letter representationpublic static boolean isNucleotide(java.lang.String groupCode3)