org.rcsb.mmtf.api

Interface StructureAdapterInterface

public interface StructureAdapterInterface

Interface to inflate a given MMTF data source.

Author:

Anthony Bradley

Method Summary

Modifier and Type	Method and Description
void	finalizeStructure() A generic function to be used at the end of all data addition to do required cleanup on the structure
void	initStructure(int totalNumBonds, int totalNumAtoms, int totalNumGroups, int totalNumChains, int totalNumModels, java.lang.String structureId) Used before any additions to do any required pre-processing.
void	setAtomInfo(java.lang.String atomName, int serialNumber, char alternativeLocationId, float x, float y, float z, float occupancy, float temperatureFactor, java.lang.String element, int charge) Sets the atom level information for a given atom.
void	setBioAssemblyTrans(int bioAssemblyIndex, int[] inputChainIndices, double[] inputTransform, java.lang.String name) Sets a single Bioassembly transformation to a structure.
void	setChainInfo(java.lang.String chainId, java.lang.String chainName, int groupCount) Sets the information for a given chain.
void	setEntityInfo(int[] chainIndices, java.lang.String sequence, java.lang.String description, java.lang.String type) Sets the entity level annotation for a chain(s).
void	setGroupBond(int atomIndexOne, int atomIndexTwo, int bondOrder) Sets an intra-group bond.
void	setGroupInfo(java.lang.String groupName, int groupNumber, char insertionCode, java.lang.String groupType, int atomCount, int bondCount, char singleLetterCode, int sequenceIndex, int secondaryStructureType) Sets the information for a given group / residue with atomic data.
void	setHeaderInfo(float rFree, float rWork, float resolution, java.lang.String title, java.lang.String depositionDate, java.lang.String releaseDate, java.lang.String[] experimnetalMethods) Sets the header information.
void	setInterGroupBond(int atomIndexOne, int atomIndexTwo, int bondOrder) Sets an inter-group bond.
void	setModelInfo(int modelId, int chainCount) Sets the number of chains for a given model.
void	setXtalInfo(java.lang.String spaceGroup, float[] unitCell, double[][] ncsOperatorList) Sets the space group and unit cell information.

Method Detail

initStructure

void initStructure(int totalNumBonds,
                   int totalNumAtoms,
                   int totalNumGroups,
                   int totalNumChains,
                   int totalNumModels,
                   java.lang.String structureId)

Used before any additions to do any required pre-processing. For example the user could use this to specify the amount of memory to be allocated.

Parameters:

totalNumBonds - the total number of bonds in the structure

totalNumAtoms - the total number of atoms found in the data.

totalNumGroups - the total number of groups found in the data.

totalNumChains - the total number of chains found in the data.

totalNumModels - the total number of models found in the data.

structureId - an identifier for the structure (e.g. PDB id).

finalizeStructure

void finalizeStructure()

A generic function to be used at the end of all data addition to do required cleanup on the structure

setModelInfo

void setModelInfo(int modelId,
                  int chainCount)

Sets the number of chains for a given model.

Parameters:

modelId - identifier of the model within the structure

chainCount - total number of chains within this model

setChainInfo

void setChainInfo(java.lang.String chainId,
                  java.lang.String chainName,
                  int groupCount)

Sets the information for a given chain.

Parameters:

chainId - chain identifier - length of one to four

chainName - chain name - public chain id

groupCount - number of groups/residues in chain

setEntityInfo

void setEntityInfo(int[] chainIndices,
                   java.lang.String sequence,
                   java.lang.String description,
                   java.lang.String type)

Sets the entity level annotation for a chain(s). ChainIds is a list of integers that indicate the chains this information refers to. Sequence is the one letter amino acid sequence. Description and title are both free forms strings describing the entity and acting as a title for the entity.

Parameters:

chainIndices - the indices of the chain this refers to.

sequence - the full sequence of the entity

description - the text description of the entity

type - as a string (POLYMER/NON-POLYMER and WATER)

setGroupInfo

void setGroupInfo(java.lang.String groupName,
                  int groupNumber,
                  char insertionCode,
                  java.lang.String groupType,
                  int atomCount,
                  int bondCount,
                  char singleLetterCode,
                  int sequenceIndex,
                  int secondaryStructureType)

Sets the information for a given group / residue with atomic data.

Parameters:

groupName - 3 letter code name of this group/residue

groupNumber - sequence position of this group

insertionCode - the one letter insertion code

groupType - a string indicating the type of group (as found in the chemcomp dictionary. Empty string if none available.

atomCount - the number of atoms in the group

bondCount - the number of unique bonds in the group

singleLetterCode - the single letter code of the group

sequenceIndex - the index of this group in the sequence

secondaryStructureType - the type of secondary structure used (types are according to DSSP and number to type mappings are defined in the specification)

setAtomInfo

void setAtomInfo(java.lang.String atomName,
                 int serialNumber,
                 char alternativeLocationId,
                 float x,
                 float y,
                 float z,
                 float occupancy,
                 float temperatureFactor,
                 java.lang.String element,
                 int charge)

Sets the atom level information for a given atom.

Parameters:

atomName - 1-3 long string of the unique name of the atom

serialNumber - a number counting atoms in a structure

alternativeLocationId - a character indicating the alternate location of the atom

x - the x cartesian coordinate

y - the y cartesian coordinate

z - the z cartesian coordinate

occupancy - the atomic occupancy

temperatureFactor - the B factor (temperature factor)

element - a 1-3 long string indicating the chemical element of the atom

charge - the atomic charge

setBioAssemblyTrans

void setBioAssemblyTrans(int bioAssemblyIndex,
                         int[] inputChainIndices,
                         double[] inputTransform,
                         java.lang.String name)

Sets a single Bioassembly transformation to a structure. bioAssemblyId indicates the index of the bioassembly.

Parameters:

bioAssemblyIndex - an integer index of this bioassembly.

inputChainIndices - the integer indices of the chains involved in this bioassembly.

inputTransform - a list of doubles indicating the transform for this bioassembly.

name - the name of the bioassembly

setXtalInfo

void setXtalInfo(java.lang.String spaceGroup,
                 float[] unitCell,
                 double[][] ncsOperatorList)

Sets the space group and unit cell information.

Parameters:

spaceGroup - the space group name, e.g. "P 21 21 21"

unitCell - an array of length 6 with the unit cell parameters in order: a, b, c, alpha, beta, gamma

ncsOperatorList - the list of NCS operation matrices

setGroupBond

void setGroupBond(int atomIndexOne,
                  int atomIndexTwo,
                  int bondOrder)

Sets an intra-group bond.

Parameters:

atomIndexOne - the atom index of the first partner in the bond

atomIndexTwo - the atom index of the second partner in the bond

bondOrder - the bond order

setInterGroupBond

void setInterGroupBond(int atomIndexOne,
                       int atomIndexTwo,
                       int bondOrder)

Sets an inter-group bond.

Parameters:

atomIndexOne - the atom index of the first partner in the bond

atomIndexTwo - the atom index of the second partner in the bond

bondOrder - the bond order

setHeaderInfo

void setHeaderInfo(float rFree,
                   float rWork,
                   float resolution,
                   java.lang.String title,
                   java.lang.String depositionDate,
                   java.lang.String releaseDate,
                   java.lang.String[] experimnetalMethods)

Sets the header information.

Parameters:

rFree - the measured R-Free for the structure

rWork - the measure R-Work for the structure

resolution - the resolution of the structure

title - the title of the structure

depositionDate - the deposition date of the structure

releaseDate - the release date of the structure

experimnetalMethods - the list of experimental methods in the structure