Package 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 Details

  • Method Details

    • 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