org.biojava.nbio.structure.io.mmcif

Class MMCIFFileTools

java.lang.Object

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

public class MMCIFFileTools
extends java.lang.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 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 Summary

Constructors

Constructor and Description
MMCIFFileTools()

Method Summary

Modifier and Type	Method and Description
static AtomSite	convertAtomToAtomSite(Atom a, int model, java.lang.String chainName, java.lang.String chainId) Converts an Atom object to an AtomSite object.
static AtomSite	convertAtomToAtomSite(Atom a, int model, java.lang.String chainName, java.lang.String chainId, int atomId) Converts an Atom object to an AtomSite object.
static java.util.List<AtomSite>	convertChainToAtomSites(Chain c, int model, java.lang.String chainName, java.lang.String chainId) Converts a Chain into a List of AtomSite objects
static Cell	convertCrystalCellToCell(CrystalCell c) Converts a CrystalCell object to a Cell object.
static java.util.List<AtomSite>	convertGroupToAtomSites(Group g, int model, java.lang.String chainName, java.lang.String chainId) Converts a Group into a List of AtomSite objects.
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 <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.
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.

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 java.lang.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 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

See Also:

Constant Field Values

Constructor Detail

MMCIFFileTools

public MMCIFFileTools()

Method Detail

toLoopMmCifHeaderString

public static java.lang.String toLoopMmCifHeaderString(java.lang.String categoryName,
                                                       java.lang.String className)
                                                throws java.lang.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:

java.lang.ClassNotFoundException - if the given className can not be found

toMMCIF

public 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.

Parameters:

categoryName -

o -

Returns:

getFields

public static java.lang.reflect.Field[] getFields(java.lang.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 java.lang.String[] getFieldNames(java.lang.reflect.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> 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.

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,
                                             java.lang.String chainName,
                                             java.lang.String chainId)

Converts an Atom object to an AtomSite object.

Parameters:

a -

model - the model number for the output AtomSites

chainName - the chain identifier (author id) for the output AtomSites

chainId - the internal chain identifier (asym id) for the output AtomSites

Returns:

convertAtomToAtomSite

public static AtomSite convertAtomToAtomSite(Atom a,
                                             int model,
                                             java.lang.String chainName,
                                             java.lang.String chainId,
                                             int atomId)

Converts an Atom object to an AtomSite object.

Parameters:

a - the atom

model - the model number for the output AtomSites

chainName - the chain identifier (author id) for the output AtomSites

chainId - the internal chain identifier (asym id) for the output AtomSites

atomId - the atom id to be written to AtomSite

Returns:

convertGroupToAtomSites

public static java.util.List<AtomSite> convertGroupToAtomSites(Group g,
                                                               int model,
                                                               java.lang.String chainName,
                                                               java.lang.String chainId)

Converts a Group into a List of AtomSite objects. Atoms in other altloc groups (different from the main group) are also included, removing possible duplicates via using the atom identifier to assess uniqueness.

Parameters:

g - the group

model - the model number for the output AtomSites

chainName - the chain identifier (author id) for the output AtomSites

chainId - the internal chain identifier (asym id) for the output AtomSites

Returns:

convertChainToAtomSites

public static java.util.List<AtomSite> convertChainToAtomSites(Chain c,
                                                               int model,
                                                               java.lang.String chainName,
                                                               java.lang.String chainId)

Converts a Chain into a List of AtomSite objects

Parameters:

c - the chain

model - the model number for the output AtomSites

chainName - the chain identifier (author id) for the output AtomSites

chainId - the internal chain identifier (asym id) for the output AtomSites

Returns:

convertStructureToAtomSites

public static java.util.List<AtomSite> convertStructureToAtomSites(Structure s)

Converts a Structure into a List of AtomSite objects

Parameters:

s -

Returns: