org.biojava.nbio.structure.io.mmtf

Class MmtfUtils

java.lang.Object

org.biojava.nbio.structure.io.mmtf.MmtfUtils

public class MmtfUtils
extends Object

A utils class of functions needed for Biojava to read and write to mmtf.

Author:

Anthony Bradley

Constructor Summary

Constructors

Constructor and Description
MmtfUtils()

Method Summary

Modifier and Type	Method and Description
static void	addSeqRes(Chain modelChain, String sequence) Add the missing groups to the SeqResGroups.
static void	calculateDsspSecondaryStructure(Structure bioJavaStruct) Generate the secondary structure for a Biojava structure object.
static double[]	convertToDoubleArray(javax.vecmath.Matrix4d transformationMatrix) Convert a four-d matrix to a double array.
static String	dateToIsoString(Date inputDate) Covert a Date object to ISO time format.
static void	fixMicroheterogenity(Structure bioJavaStruct) This sets all microheterogeneous groups (previously alternate location groups) as separate groups.
static List<Atom>	getAtomsForGroup(Group inputGroup) Get a list of atoms for a group.
static double[][]	getNcsAsArray(javax.vecmath.Matrix4d[] ncsOperators) Get a list of length N*16 of a list of Matrix4d*N.
static javax.vecmath.Matrix4d[]	getNcsAsMatrix4d(double[][] ncsOperMatrixList) Get a list of N 4*4 matrices from a single list of doubles of length 16*N.
static int	getNumBondsInGroup(List<Atom> atomsInGroup) Find the number of bonds in a group
static int	getNumGroups(Structure structure) Count the total number of groups in the structure
static int	getSecStructType(Group group) Get the secondary structure as defined by DSSP.
static SecStrucType	getSecStructTypeFromDsspIndex(int dsspIndex) Set the DSSP type based on a numerical index.
static String	getSpaceGroupAsString(SpaceGroup spaceGroup) Get the string representation of a space group.
static MmtfSummaryDataBean	getStructureInfo(Structure structure) Get summary information for the structure.
static Map<double[],int[]>	getTransformMap(BioAssemblyInfo bioassemblyInfo, Map<String,Integer> chainIdToIndexMap) Convert a bioassembly information into a map of transform, chainindices it relates to.
static float[]	getUnitCellAsArray(PDBCrystallographicInfo xtalInfo) Get the length six array of the unit cell information.
static void	insertSeqResGroup(Chain chain, Group group, int sequenceIndexId) Insert the group in the given position in the sequence.
static void	setSecStructType(Group group, int dsspIndex) Get the secondary structure as defined by DSSP.
static AtomCache	setUpBioJava() Set up the configuration parameters for BioJava.
static AtomCache	setUpBioJava(String extraUrl) Set up the configuration parameters for BioJava.
static String[]	techniquesToStringArray(Set<ExperimentalTechnique> experimentalTechniques) Converts the set of experimental techniques to an array of strings.

Methods inherited from class java.lang.Object

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

Constructor Detail

MmtfUtils

public MmtfUtils()

Method Detail

setUpBioJava

public static AtomCache setUpBioJava()

Set up the configuration parameters for BioJava.

setUpBioJava

public static AtomCache setUpBioJava(String extraUrl)

Set up the configuration parameters for BioJava.

Parameters:

extraUrl - the string describing the URL (or file path) from which to get missing CCD entries.

fixMicroheterogenity

public static void fixMicroheterogenity(Structure bioJavaStruct)

This sets all microheterogeneous groups (previously alternate location groups) as separate groups. This is required because mmtf groups cannot have multiple HET codes.

Parameters:

bioJavaStruct -

calculateDsspSecondaryStructure

public static void calculateDsspSecondaryStructure(Structure bioJavaStruct)

Generate the secondary structure for a Biojava structure object.

Parameters:

bioJavaStruct - the Biojava structure for which it is to be calculate.

getSpaceGroupAsString

public static String getSpaceGroupAsString(SpaceGroup spaceGroup)

Get the string representation of a space group.

Parameters:

spaceGroup - the input SpaceGroup object

Returns:

the space group as a string.

getUnitCellAsArray

public static float[] getUnitCellAsArray(PDBCrystallographicInfo xtalInfo)

Get the length six array of the unit cell information.

Parameters:

xtalInfo - the input PDBCrystallographicInfo object

Returns:

the length six float array

techniquesToStringArray

public static String[] techniquesToStringArray(Set<ExperimentalTechnique> experimentalTechniques)

Converts the set of experimental techniques to an array of strings.

Parameters:

experimentalTechniques - the input set of experimental techniques

Returns:

the array of strings describing the methods used.

dateToIsoString

public static String dateToIsoString(Date inputDate)

Covert a Date object to ISO time format.

Parameters:

inputDate - The input date object

Returns:

the time in ISO time format

getTransformMap

public static Map<double[],int[]> getTransformMap(BioAssemblyInfo bioassemblyInfo,
                                                  Map<String,Integer> chainIdToIndexMap)

Convert a bioassembly information into a map of transform, chainindices it relates to.

Parameters:

bioassemblyInfo - the bioassembly info object for this structure

chainIdToIndexMap - the map of chain ids to the index that chain corresponds to.

Returns:

the bioassembly information (as primitive types).

convertToDoubleArray

public static double[] convertToDoubleArray(javax.vecmath.Matrix4d transformationMatrix)

Convert a four-d matrix to a double array. Row-packed.

Parameters:

transformationMatrix - the input matrix4d object

Returns:

the double array (16 long).

getNumGroups

public static int getNumGroups(Structure structure)

Count the total number of groups in the structure

Parameters:

structure - the input structure

Returns:

the total number of groups

getAtomsForGroup

public static List<Atom> getAtomsForGroup(Group inputGroup)

Get a list of atoms for a group. Only add each atom once.

Parameters:

inputGroup - the Biojava Group to consider

Returns:

the atoms for the input Biojava Group

getNumBondsInGroup

public static int getNumBondsInGroup(List<Atom> atomsInGroup)

Find the number of bonds in a group

Parameters:

atomsInGroup - the list of atoms in the group

Returns:

the number of atoms in the group

getSecStructType

public static int getSecStructType(Group group)

Get the secondary structure as defined by DSSP.

Parameters:

group - the input group to be calculated

Returns:

the integer index of the group type.

setSecStructType

public static void setSecStructType(Group group,
                                    int dsspIndex)

Get the secondary structure as defined by DSSP.

Parameters:

group - the input group to be calculated

dsspIndex - integer index of the group type.

getSecStructTypeFromDsspIndex

public static SecStrucType getSecStructTypeFromDsspIndex(int dsspIndex)

Set the DSSP type based on a numerical index.

Parameters:

dsspIndex - the integer index of the type to set

Returns:

the instance of the SecStrucType object holding this secondary structure type.

getStructureInfo

public static MmtfSummaryDataBean getStructureInfo(Structure structure)

Get summary information for the structure.

Parameters:

structure - the structure for which to get the information.

getNcsAsMatrix4d

public static javax.vecmath.Matrix4d[] getNcsAsMatrix4d(double[][] ncsOperMatrixList)

Get a list of N 4*4 matrices from a single list of doubles of length 16*N.

Parameters:

ncsOperMatrixList - the input list of doubles

Returns:

the list of 4*4 matrics

getNcsAsArray

public static double[][] getNcsAsArray(javax.vecmath.Matrix4d[] ncsOperators)

Get a list of length N*16 of a list of Matrix4d*N.

Parameters:

ncsOperators - the Matrix4d list

Returns:

the list of length N*16 of the list of matrices

insertSeqResGroup

public static void insertSeqResGroup(Chain chain,
                                     Group group,
                                     int sequenceIndexId)

Insert the group in the given position in the sequence.

Parameters:

chain - the chain to add the seq res group to

group - the group to add

sequenceIndexId - the index to add it in

addSeqRes

public static void addSeqRes(Chain modelChain,
                             String sequence)

Add the missing groups to the SeqResGroups.

Parameters:

modelChain - the chain to add the information for

sequence - the sequence of the construct