public interface StructureAdapterInterface
Modifier and Type | Method and Description |
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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,
String structureId)
Used before any additions to do any required pre-processing.
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void |
setAtomInfo(String atomName,
int serialNumber,
char alternativeLocationId,
float x,
float y,
float z,
float occupancy,
float temperatureFactor,
String element,
int charge)
Sets the atom level information for a given atom.
|
void |
setBioAssemblyTrans(int bioAssemblyIndex,
int[] inputChainIndices,
double[] inputTransform,
String name)
Sets a single Bioassembly transformation to a structure.
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void |
setChainInfo(String chainId,
String chainName,
int groupCount)
Sets the information for a given chain.
|
void |
setEntityInfo(int[] chainIndices,
String sequence,
String description,
String type)
Sets the entity level annotation for a chain(s).
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void |
setGroupBond(int atomIndexOne,
int atomIndexTwo,
int bondOrder)
Sets an intra-group bond.
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void |
setGroupInfo(String groupName,
int groupNumber,
char insertionCode,
String groupType,
int atomCount,
int bondCount,
char singleLetterCode,
int sequenceIndex,
int secondaryStructureType)
Sets the information for a given group / residue with atomic data.
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void |
setHeaderInfo(float rFree,
float rWork,
float resolution,
String title,
String depositionDate,
String releaseDate,
String[] experimnetalMethods)
Sets the header information.
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void |
setInterGroupBond(int atomIndexOne,
int atomIndexTwo,
int bondOrder)
Sets an inter-group bond.
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void |
setModelInfo(int modelId,
int chainCount)
Sets the number of chains for a given model.
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void |
setXtalInfo(String spaceGroup,
float[] unitCell,
double[][] ncsOperatorList)
Sets the space group and unit cell information.
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void initStructure(int totalNumBonds, int totalNumAtoms, int totalNumGroups, int totalNumChains, int totalNumModels, String structureId)
totalNumBonds
- the total number of bonds in the structuretotalNumAtoms
- 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).void finalizeStructure()
void setModelInfo(int modelId, int chainCount)
modelId
- identifier of the model within the structurechainCount
- total number of chains within this modelvoid setChainInfo(String chainId, String chainName, int groupCount)
chainId
- chain identifier - length of one to fourchainName
- chain name - public chain idgroupCount
- number of groups/residues in chainvoid setEntityInfo(int[] chainIndices, String sequence, String description, String type)
chainIndices
- the indices of the chain this refers to.sequence
- the full sequence of the entitydescription
- the text description of the entitytype
- as a string (POLYMER/NON-POLYMER and WATER)void setGroupInfo(String groupName, int groupNumber, char insertionCode, String groupType, int atomCount, int bondCount, char singleLetterCode, int sequenceIndex, int secondaryStructureType)
groupName
- 3 letter code name of this group/residuegroupNumber
- sequence position of this groupinsertionCode
- the one letter insertion codegroupType
- 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 groupbondCount
- the number of unique bonds in the groupsingleLetterCode
- the single letter code of the groupsequenceIndex
- the index of this group in the sequencesecondaryStructureType
- the type of secondary structure used (types are according to DSSP and number to
type mappings are defined in the specification)void setAtomInfo(String atomName, int serialNumber, char alternativeLocationId, float x, float y, float z, float occupancy, float temperatureFactor, String element, int charge)
atomName
- 1-3 long string of the unique name of the atomserialNumber
- a number counting atoms in a structurealternativeLocationId
- a character indicating the alternate
location of the atomx
- the x cartesian coordinatey
- the y cartesian coordinatez
- the z cartesian coordinateoccupancy
- the atomic occupancytemperatureFactor
- the B factor (temperature factor)element
- a 1-3 long string indicating the chemical element of the atomcharge
- the atomic chargevoid setBioAssemblyTrans(int bioAssemblyIndex, int[] inputChainIndices, double[] inputTransform, String name)
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 bioassemblyvoid setXtalInfo(String spaceGroup, float[] unitCell, double[][] ncsOperatorList)
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, gammancsOperatorList
- the list of NCS operation matricesvoid setGroupBond(int atomIndexOne, int atomIndexTwo, int bondOrder)
atomIndexOne
- the atom index of the first partner in the bondatomIndexTwo
- the atom index of the second partner in the bondbondOrder
- the bond ordervoid setInterGroupBond(int atomIndexOne, int atomIndexTwo, int bondOrder)
atomIndexOne
- the atom index of the first partner in the bondatomIndexTwo
- the atom index of the second partner in the bondbondOrder
- the bond ordervoid setHeaderInfo(float rFree, float rWork, float resolution, String title, String depositionDate, String releaseDate, String[] experimnetalMethods)
rFree
- the measured R-Free for the structurerWork
- the measure R-Work for the structureresolution
- the resolution of the structuretitle
- the title of the structuredepositionDate
- the deposition date of the structurereleaseDate
- the release date of the structureexperimnetalMethods
- the list of experimental methods in the structureCopyright © 2015–2016 RCSB PDB. All rights reserved.