Module: MmtfTraverse

Methods

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<static> traverseMmtf(mmtfData, eventCallbacks, params)

Traverse the MMTF structure data.

Parameters:

Name	Type	Argument	Description
mmtfData	module:MmtfDecode.MmtfData		decoded mmtf data
eventCallbacks	Object		Properties Name Type Argument Description onModel module:MmtfTraverse.onModel <optional> called for each model onChain module:MmtfTraverse.onChain <optional> called for each chain onGroup module:MmtfTraverse.onGroup <optional> called for each group onAtom module:MmtfTraverse.onAtom <optional> called for each atom onBond module:MmtfTraverse.onBond <optional> called for each bond
params	Object	<optional>	traversal parameters Properties Name Type Argument Description firstModelOnly Boolean <optional> traverse only the first model

Type Definitions

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onAtom(atomData)

Parameters:

Name	Type	Description
atomData	Object	Properties Name Type Argument Description atomIndex Integer index of the atom groupIndex Integer index of the parent group chainIndex Integer index of the parent chain modelIndex Integer index of the parent model atomId Integer <nullable> atom id element String IUPAC element name, 0 to 3 characters atomName String name of the atom, 0 to 5 characters formalCharge Integer formal charge of the atom xCoord Float x coordinate in Å yCoord Float y coordinate in Å zCoord Float z coordinate in Å bFactor Float <nullable> B-factor in in Å^2 altLoc Char <nullable> alternate location identifier occupancy Float <nullable> occupancy of the atom

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onBond(bondData)

Parameters:

Name	Type	Description
bondData	Object	Properties Name Type Description atomIndex1 Integer index of the first atom atomIndex2 Integer index of the secound atom bondOrder Integer bond order, allowed values are 1 to 3

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onChain(chainData)

Parameters:

Name	Type	Description
chainData	Object	Properties Name Type Argument Description groupCount Integer number of groups in the chain chainIndex Integer index of the chain modelIndex Integer index of the parent model chainId String chain id chainName String <nullable> additional chain name

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onGroup(groupData)

Parameters:

Name	Type	Description
groupData	Object	Properties Name Type Argument Description atomCount Integer number of atoms in the group groupIndex Integer index of the group chainIndex Integer index of the parent chain modelIndex Integer index of the parent model groupId Integer group id (residue number) groupType Integer index to an entry in module:MmtfDecode.MmtfData#groupList groupName String name of the group, 0 to 5 characters singleLetterCode Char IUPAC single letter code, otherwise 'X', 1 character chemCompType String chemical component type from the mmCIF dictionary secStruct Integer <nullable> sencoded secondary structure | 0: pi helix, 1: bend, 2: alpha helix, 3: extended, 4: 3-10 helix, 5: bridge, 6: turn, 7: coil, -1: undefined insCode Char <nullable> insertion code sequenceIndex Integer <nullable> index to the `sequence` property of the corresponding entity, -1 when the entity has no sequence

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onModel(modelData)

Parameters:

Name	Type	Description
modelData	Object	Properties Name Type Description chainCount Integer number of chains in the model modelIndex Integer index of the model