public class MMCIFFileTools
extends java.lang.Object
AbstractBean
.
By default, all fields from the bean are taken as the CIF labels. Fields
may be omitted by annotating them as @IgnoreField
.
The CIF label for a field may be changed (for instance, for fields that
are not valid Java identifiers) by defining a function
static MapModifier and Type | Field | Description |
---|---|---|
static java.lang.String |
MMCIF_DEFAULT_VALUE |
The character to be printed out as a default value in mmCIF files, e.g.
|
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 | Description |
---|---|
MMCIFFileTools() |
Modifier and Type | Method | 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[] |
getFieldNames(java.lang.reflect.Field[] fields) |
Gets the mmCIF record name for each field.
|
static java.lang.reflect.Field[] |
getFields(java.lang.Class<?> c) |
Gets all fields for a particular class, filtering fields annotated
with
@IgnoreField . |
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.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. |
static <T> java.lang.String |
toMMCIF(java.util.List<T> list) |
Deprecated.
The
toMMCIF(List, Class) provides compile-time type safety |
static <T> java.lang.String |
toMMCIF(java.util.List<T> list,
java.lang.Class<T> klass) |
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. |
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.reflect.Field[] getFields(java.lang.Class<?> c)
@IgnoreField
.
As a side effect, calls setAccessible(true)
on all fields.c
- public static java.lang.String[] getFieldNames(java.lang.reflect.Field[] fields)
@CIFLabel
annotation.
As a side effect, calls setAccessible(true)
on all fields.fields
- public static <T> java.lang.String toMMCIF(java.util.List<T> list, java.lang.Class<T> klass)
org.biojava.nbio.structure.io.mmcif.model
to
a String representing them in mmCIF loop format with one record per line.list
- @Deprecated public static <T> java.lang.String toMMCIF(java.util.List<T> list)
toMMCIF(List, Class)
provides compile-time type safetyorg.biojava.nbio.structure.io.mmcif.model
to
a String representing them in mmCIF loop format with one record per line.list
- java.lang.ClassCastException
- if not all list elements have the same typepublic 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
-