mmtf decode module.
Methods
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<static> decodeMmtf(inputDict, params)
-
Decode MMTF fields
Parameters:
Name Type Argument Description inputDict
Object encoded MMTF data params
Object <optional>
decoding parameters Properties
Name Type Description ignoreFields
Array.<String> names of optional fields not to decode Returns:
mmtfData -
<inner> performDecoding(bytes, size, param)
-
[performDecoding description]
Parameters:
Name Type Description bytes
Integer [description] size
Integer [description] param
Uint8Array [description] Returns:
[description]- Type
- TypedArray
Type Definitions
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EncodedMmtfData
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Encoded mmtf data object. Also includes the fields from module:MmtfDecode.SharedMmtfData. See MMTF specification on how they are encoded.
Type:
- Object
- Mixes In:
Properties:
Name Type Argument Description bondAtomList
Uint8Array <optional>
Encoded bonded atom indices bondOrderList
Uint8Array <optional>
Encoded bond orders xCoordBig
Uint8Array Encoded x coordinates in Å, part 1 xCoordSmall
Uint8Array Encoded x coordinates in Å, part 2 yCoordBig
Uint8Array Encoded y coordinates in Å, part 1 yCoordSmall
Uint8Array Encoded y coordinates in Å, part 2 yCoordBig
Uint8Array Encoded y coordinates in Å, part 1 yCoordSmall
Uint8Array Encoded y coordinates in Å, part 2 bFactorBig
Uint8Array <optional>
Encoded B-factors in Å^2, part 1 bFactorSmall
Uint8Array <optional>
Encoded B-factors in Å^2, part 2 atomIdList
Uint8Array <optional>
Encoded atom ids altLocList
Uint8Array <optional>
Encoded alternate location labels occupancyList
Uint8Array <optional>
Encoded occupancies groupIdList
Uint8Array Encoded group ids groupTypeList
Uint8Array Encoded group types secStructList
Uint8Array <optional>
Encoded secondary structure codes insCodeList
Uint8Array <optional>
Encoded insertion codes seuenceIdList
Uint8Array <optional>
Encoded sequence ids chainIdList
Uint8Array Encoded chain ids chainNameList
Uint8Array <optional>
Encoded chain names -
MmtfData
-
Decoded mmtf data object. Also includes fields the from module:MmtfDecode.SharedMmtfData.
Type:
- Object
- Mixes In:
Properties:
Name Type Argument Description bondAtomList
Int32Array <optional>
List of bonded atom indices bondOrderList
Uint8Array <optional>
List of bond orders xCoordList
Float32Array List of x coordinates in Å yCoordList
Float32Array List of y coordinates in Å zCoordList
Float32Array List of z coordinates in Å bFactorList
Float32Array <optional>
List of B-factors in Å^2 atomIdList
Int32Array <optional>
List of atom ids altLocList
Uint8Array <optional>
List of alternate location labels occupancyList
Float32Array <optional>
List of occupancies groupIdList
Int32Array List of group ids groupTypeList
Int32Array List of group types secStructList
Int8Array <optional>
List of secondary structure codes, encoding 0: pi helix, 1: bend, 2: alpha helix, 3: extended, 4: 3-10 helix, 5: bridge, 6: turn, 7: coil, -1: undefined insCodeList
Uint8Array <optional>
List of insertion codes seuenceIdList
Int32Array <optional>
List of sequence ids chainIdList
Uint8Array List of chain ids chainNameList
Uint8Array <optional>
List of chain names -
Fields shared in encoded and decoded mmtf data objects.
Type:
- Object
Properties:
Name Type Argument Description mmtfVersion
String MMTF specification version mmtfProducer
String Program that created the file unitCell
Array.<Float> <optional>
Crystallographic unit cell Properties
Name Type Description 0
Float x length 1
Float y length 2
Float z length 3
Float alpha angle 4
Float beta angle 5
Float gamma angle spaceGroup
String <optional>
Hermann-Mauguin symbol structureId
String <optional>
Some reference, e.g. a PDB ID title
String <optional>
Short description depositionDate
String <optional>
Deposition date in YYYY-MM-DD format releaseDate
String <optional>
Release date in YYYY-MM-DD format experimentalMethods
Array.<String> <optional>
Structure determination methods resolution
Float <optional>
Resolution in Å rFree
Float <optional>
R-free value rWork
Float <optional>
R-work value numBonds
Integer Number of bonds numAtoms
Integer Number of atoms numGroups
Integer Number of groups (residues) numChains
Integer Number of chains numModels
Integer Number of models chainsPerModel
Array.<Integer> List of number of chains in each model groupsPerChain
Array.<Integer> List of number of groups in each chain entityList
Array.<Entity> <optional>
List of entity objects Properties
Name Type Description chainIndexList
Array.<Integer> Pointers into chain data fields description
String Description of the entity type
String Name of the entity type sequence
String One letter code sequence bioAssemblyList
Array.<Assembly> <optional>
List of assembly objects Properties
Name Type Description transformList
Array.<Transform> List of transform objects Properties
Name Type Description chainIndexList
Array.<Integer> Pointers into chain data fields matrix
Array.<Float> 4x4 transformation matrix ncsOperatorList
Array.<Array> <optional>
List of ncs operator matrices Properties
Type Description Array.<Float> 4x4 transformation matrix groupList
Array.<GroupType> List of groupType objects Properties
Name Type Description formalChargeList
Array.<Integer> List of atom formal charges elementList
Array.<String> List of elements atomNameList
Array.<String> List of atom names bondAtomList
Array.<Integer> List of bonded atom indices bondOrderList
Array.<Integer> List of bond orders groupName
String The name of the group singleLetterCode
String The single letter code chemCompType
String The chemical component type