org.biojava.nbio.structure.io.mmcif

Class MMCIFFileTools

java.lang.Object

org.biojava.nbio.structure.io.mmcif.MMCIFFileTools

public class MMCIFFileTools
extends Object

Some tools for mmCIF file writing. See http://www.iucr.org/__data/assets/pdf_file/0019/22618/cifguide.pdf CIF categories are represented as a simple bean, typically extending 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 Map getCIFLabelMap() mapping from the field's name to the correct label.

Author:

Jose Duarte, Spencer Bliven

Field Summary

Fields

Modifier and Type	Field and Description
static 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 String	MMCIF_MISSING_VALUE The character to be printed out in cases where a value is not assigned in mmCIF files

Constructor Summary

Constructors

Constructor and Description
MMCIFFileTools()

Method Summary

Modifier and Type	Method and Description
static AtomSite	convertAtomToAtomSite(Atom a, int model, String chainId, String internalChainId) Converts an Atom object to an AtomSite object.
static AtomSite	convertAtomToAtomSite(Atom a, int model, String chainId, String internalChainId, int atomId) Converts an Atom object to an AtomSite object.
static List<AtomSite>	convertChainToAtomSites(Chain c, int model, String authorId, String asymId) 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 List<AtomSite>	convertStructureToAtomSites(Structure s) Converts a Structure into a List of AtomSite objects
static String[]	getFieldNames(Field[] fields) Gets the mmCIF record name for each field.
static Field[]	getFields(Class<?> c) Gets all fields for a particular class, filtering fields annotated with @IgnoreField.
static String	toLoopMmCifHeaderString(String categoryName, String className) Produces a mmCIF loop header string for the given categoryName and className.
static <T> String	toMMCIF(List<T> list, 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.
static String	toMMCIF(String categoryName, Object o) Converts a mmCIF bean (see org.biojava.nbio.structure.io.mmcif.model to a String representing it in mmCIF (single-record) format.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

MMCIF_MISSING_VALUE

public static final String MMCIF_MISSING_VALUE

The character to be printed out in cases where a value is not assigned in mmCIF files

See Also:

Constant Field Values

MMCIF_DEFAULT_VALUE

public static final String MMCIF_DEFAULT_VALUE

The character to be printed out as a default value in mmCIF files, e.g. for the default alt_locs

See Also:

Constant Field Values

Constructor Detail

MMCIFFileTools

public MMCIFFileTools()

Method Detail

toLoopMmCifHeaderString

public static String toLoopMmCifHeaderString(String categoryName,
                                             String className)
                                      throws ClassNotFoundException

Produces a mmCIF loop header string for the given categoryName and className. className must be one of the beans in the org.biojava.nbio.structure.io.mmcif.model package

Parameters:

categoryName -

className -

Returns:

Throws:

ClassNotFoundException - if the given className can not be found

toMMCIF

public static String toMMCIF(String categoryName,
                             Object o)

Converts a mmCIF bean (see org.biojava.nbio.structure.io.mmcif.model to a String representing it in mmCIF (single-record) format.

Parameters:

categoryName -

o -

Returns:

getFields

public static Field[] getFields(Class<?> c)

Gets all fields for a particular class, filtering fields annotated with @IgnoreField. As a side effect, calls setAccessible(true) on all fields.

Parameters:

c -

Returns:

getFieldNames

public static String[] getFieldNames(Field[] fields)

Gets the mmCIF record name for each field. This is generally just the name of the field or the value specified by the @CIFLabel annotation. As a side effect, calls setAccessible(true) on all fields.

Parameters:

fields -

Returns:

toMMCIF

public static <T> String toMMCIF(List<T> list,
                                 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.

Parameters:

list -

Returns:

convertSpaceGroupToSymmetry

public static Symmetry convertSpaceGroupToSymmetry(SpaceGroup sg)

Converts a SpaceGroup object to a Symmetry object.

Parameters:

sg -

Returns:

convertCrystalCellToCell

public static Cell convertCrystalCellToCell(CrystalCell c)

Converts a CrystalCell object to a Cell object.

Parameters:

c -

Returns:

convertAtomToAtomSite

public static AtomSite convertAtomToAtomSite(Atom a,
                                             int model,
                                             String chainId,
                                             String internalChainId)

Converts an Atom object to an AtomSite object.

Parameters:

a -

model -

chainId -

internalChainId -

Returns:

convertAtomToAtomSite

public static AtomSite convertAtomToAtomSite(Atom a,
                                             int model,
                                             String chainId,
                                             String internalChainId,
                                             int atomId)

Converts an Atom object to an AtomSite object.

Parameters:

a -

model -

chainId -

internalChainId -

atomId - the atom id to be written to AtomSite

Returns:

convertChainToAtomSites

public static List<AtomSite> convertChainToAtomSites(Chain c,
                                                     int model,
                                                     String authorId,
                                                     String asymId)

Converts a Chain into a List of AtomSite objects

Parameters:

c -

model -

authorId -

asymId -

Returns:

convertStructureToAtomSites

public static List<AtomSite> convertStructureToAtomSites(Structure s)

Converts a Structure into a List of AtomSite objects

Parameters:

s -

Returns: