public class MMCIFFileTools
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
static java.lang.String |
MMCIF_DEFAULT_VALUE
The character to be printed out as a default value in mmCIF files, e.g. for the default alt_locs
|
static java.lang.String |
MMCIF_MISSING_VALUE
The character to be printed out in cases where a value is not assigned in mmCIF files
|
Constructor and Description |
---|
MMCIFFileTools() |
Modifier and Type | Method and Description |
---|---|
static AtomSite |
convertAtomToAtomSite(Atom a,
int model,
java.lang.String chainId,
java.lang.String internalChainId)
Converts an Atom object to an
AtomSite object. |
static AtomSite |
convertAtomToAtomSite(Atom a,
int model,
java.lang.String chainId,
java.lang.String internalChainId,
int atomId)
Converts an Atom object to an
AtomSite object. |
static java.util.List<AtomSite> |
convertChainToAtomSites(Chain c,
int model,
java.lang.String chainId,
java.lang.String internalChainId)
Converts a Chain into a List of
AtomSite objects |
static Cell |
convertCrystalCellToCell(CrystalCell c)
Converts a CrystalCell object to a
Cell object. |
static Symmetry |
convertSpaceGroupToSymmetry(SpaceGroup sg)
Converts a SpaceGroup object to a
Symmetry object. |
static java.util.List<AtomSite> |
convertStructureToAtomSites(Structure s)
Converts a Structure into a List of
AtomSite objects |
static java.lang.String |
toLoopMmCifHeaderString(java.lang.String categoryName,
java.lang.String className)
Produces a mmCIF loop header string for the given categoryName and className.
|
static java.lang.String |
toMMCIF(java.util.List<java.lang.Object> list)
Converts a list of mmCIF beans (see
org.biojava.nbio.structure.io.mmcif.model to
a String representing them in mmCIF loop format with one record per line. |
static java.lang.String |
toMMCIF(java.lang.String categoryName,
java.lang.Object o)
Converts a mmCIF bean (see
org.biojava.nbio.structure.io.mmcif.model to
a String representing it in mmCIF (single-record) format. |
public static final java.lang.String MMCIF_MISSING_VALUE
public static final java.lang.String MMCIF_DEFAULT_VALUE
public static java.lang.String toLoopMmCifHeaderString(java.lang.String categoryName, java.lang.String className) throws java.lang.ClassNotFoundException
org.biojava.nbio.structure.io.mmcif.model
packagecategoryName
- className
- java.lang.ClassNotFoundException
- if the given className can not be foundpublic static java.lang.String toMMCIF(java.lang.String categoryName, java.lang.Object o)
org.biojava.nbio.structure.io.mmcif.model
to
a String representing it in mmCIF (single-record) format.categoryName
- o
- public static java.lang.String toMMCIF(java.util.List<java.lang.Object> list)
org.biojava.nbio.structure.io.mmcif.model
to
a String representing them in mmCIF loop format with one record per line.list
- public static Symmetry convertSpaceGroupToSymmetry(SpaceGroup sg)
Symmetry
object.sg
- public static Cell convertCrystalCellToCell(CrystalCell c)
Cell
object.c
- public static AtomSite convertAtomToAtomSite(Atom a, int model, java.lang.String chainId, java.lang.String internalChainId)
AtomSite
object.a
- model
- chainId
- internalChainId
- public static AtomSite convertAtomToAtomSite(Atom a, int model, java.lang.String chainId, java.lang.String internalChainId, int atomId)
AtomSite
object.a
- model
- chainId
- internalChainId
- atomId
- the atom id to be written to AtomSitepublic static java.util.List<AtomSite> convertChainToAtomSites(Chain c, int model, java.lang.String chainId, java.lang.String internalChainId)
AtomSite
objectsc
- model
- chainId
- internalChainId
-