Module: MmtfDecode

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

Type

module:MmtfDecode.MmtfData

Type Definitions

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EncodedMmtfData

Encoded mmtf data object. Also includes the fields from module:MmtfDecode.SharedMmtfData. See MMTF specification on how they are encoded.

Type:

• Object

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

Mixes In:

• module:MmtfDecode.SharedMmtfData

---

MmtfData

Decoded mmtf data object. Also includes fields the from module:MmtfDecode.SharedMmtfData.

Type:

• Object

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

Mixes In:

• module:MmtfDecode.SharedMmtfData

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SharedMmtfData

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
groupList	Array.<GroupType>		List of groupType objects Properties Name Type Description atomChargeList 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