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arose committed Apr 26, 2016
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4 changes: 2 additions & 2 deletions CHANGELOG.md
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All notable changes to this project will be documented in this file, following the suggestions of [Keep a CHANGELOG](http://keepachangelog.com/). This project adheres to [Semantic Versioning](http://semver.org/).


## [Unreleased]
## [v0.2.2] - 2016-04-26
### Added
- jsdoc api documentation

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- Initial release


[Unreleased]: https://github.com/rcsb/mmtf-javascript/compare/v0.2.1...HEAD
[v0.2.2]: https://github.com/rcsb/mmtf-javascript/compare/v0.2.1...v0.2.2
[v0.2.1]: https://github.com/rcsb/mmtf-javascript/compare/v0.2.0...v0.2.1
[v0.2.0]: https://github.com/rcsb/mmtf-javascript/compare/v0.1.0...v0.2.0
205 changes: 7 additions & 198 deletions README.md
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[![Build Status](https://travis-ci.org/rcsb/mmtf-javascript.svg?branch=master)](https://travis-ci.org/rcsb/mmtf-javascript)
[![License](http://img.shields.io/badge/license-MIT-blue.svg?style=flat)](https://github.com/rcsb/mmtf-javascript/blob/master/LICENSE)
[![Version](http://img.shields.io/badge/version-0.2.1-blue.svg?style=flat)](https://github.com/rcsb/mmtf-javascript/releases/tag/v0.2.1)
[![Version](http://img.shields.io/badge/version-0.2.2-blue.svg?style=flat)](https://github.com/rcsb/mmtf-javascript/releases/tag/v0.2.2)
[![Changelog](https://img.shields.io/badge/changelog--lightgrey.svg?style=flat)](https://github.com/rcsb/mmtf-javascript/blob/master/CHANGELOG.md)


JavaScript decoder for MMTF files. For a description of the format see the [MMTF specification](https://github.com/rcsb/mmtf/blob/master/spec.md). The minified library is available for [download](dist/mmtf.js).
JavaScript decoder for MMTF files. For a description of the format see the [MMTF specification](https://github.com/rcsb/mmtf/blob/master/spec.md). See the full changelog is [here](https://github.com/rcsb/mmtf-javascript/blob/master/CHANGELOG.md).

## Table of contents

* [Decoding](#decoding)
* [Traversal](#traversal)
## Version 0.2.2


## Decoding

The decoder is exposed as `MMTF.decode` in the library file ([mmtf.js](dist/mmtf.js)) which accepts an `Uint8Array` containing the `mmtf` `msgpack` and returns the decoded `mmtf` data as an object with the following properties.


### Example

```JavaScript
// bin is Uint8Array containing the mmtf msgpack
var mmtfData = MMTF.decode( bin );
console.log( mmtfData.numAtoms );
```


### Properties

| Name | Type | Description | Optional |
|----------------------------|----------------|--------------------------------------------|:--------:|
| mmtfVersion | `String` | MMTF specification version | |
| mmtfProducer | `String` | Program that created the file | |
| unitCell | `Array` | Crystallographic unit cell | Y |
| spaceGroup | `String` | Hermann-Mauguin symbol | Y |
| structureId | `String` | Some reference, e.g. a PDB ID | Y |
| title | `String` | Short description | Y |
| depositionDate | `String` | Deposition date in YYYY-MM-DD format | Y |
| releaseDate | `String` | Release date in YYYY-MM-DD format | Y |
| experimentalMethods | `Array` | Structure determination methods | Y |
| resolution | `Number` | Resolution in Å | Y |
| rFree | `Number` | R-free value | Y |
| rWork | `Number` | R-work value | Y |
| numBonds | `Number` | Number of bonds | |
| numAtoms | `Number` | Number of atoms | |
| numGroups | `Number` | Number of groups (residues) | |
| numChains | `Number` | Number of chains | |
| numModels | `Number` | Number of models | |
| chainsPerModel | `Array` | List of number of chains in each model | |
| groupsPerChain | `Array` | List of number of groups in each chain | |
| entityList | `Array` | List of [`entity`](#entity) objects | Y |
| bioAssemblyList | `Array` | List of [`assembly`](#assembly) objects | Y |
| groupList | `Array` | List of [`groupType`](#groupType) objects | Y |
| bondAtomList | `Int32Array` | List of bonded atom indices | Y |
| bondOrderList | `Uint8Array` | List of bond orders | Y |
| 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` | List of B-factors in Å^2 | Y |
| atomIdList | `Int32Array` | List of atom ids | Y |
| altLocList | `Uint8Array` | List of alternate location labels | Y |
| occupancyList | `Float32Array` | List of occupancies | Y |
| groupIdList | `Int32Array` | List of group ids | |
| groupTypeList | `Int32Array` | List of group types | |
| secStructList | `Int8Array` | List of secondary structure codes | Y |
| insCodeList | `Uint8Array` | List of insertion codes | Y |
| seuenceIdList | `Int32Array` | List of sequence ids | Y |
| chainIdList | `Uint8Array` | List of chain ids | |
| chainNameList | `Uint8Array` | List of chain names | Y |


### Objects

#### entity

Fields in an `entity` object:

| Name | Type | Description |
|---------------------------|--------------|-----------------------------------|
| chainIndexList | `Array` | Pointers into chain data fields |
| description | `String` | Description of the entity |
| type | `String` | Name of the entity type |
| sequence | `String` | One letter code sequence |


#### assembly

Fields in an `assembly` object:

| Name | Type | Description |
|---------------------------|--------------|-----------------------------------|
| transformList | `Array` | List of `transform` objects |


Fields in a `transform` object:

| Name | Type | Description |
|---------------------------|--------------|-----------------------------------|
| chainIndexList | `Array` | Pointers into chain data fields |
| matrix | `Array` | 4x4 transformation matrix |


#### groupType

Fields of a `groupType` object:

| Name | Type | Description |
|---------------------------|--------------|-----------------------------------|
| atomChargeList | `Array` | List of atom formal charges |
| elementList | `Array` | List of elements |
| atomNameList | `Array` | List of atom names |
| bondAtomList | `Array` | List of bonded atom indices |
| bondOrderList | `Array` | List of bond orders |
| groupName | `String` | The name of the group |
| singleLetterCode | `String` | The single letter code |
| chemCompType | `String` | The chemical component type |


## Traversal

Helper function to loop over the structural data in the decoded `mmtf` data. Available as `MMTF.traverse` from [mmtf.js](dist/mmtf.js). Runnable example in [mmtf-traversal.html](examples/mmtf-traversal.html).


### Example

```JavaScript
// bin is an Uint8Array containing the mmtf msgpack
var mmtfData = MMTF.decode( bin );
var callbackDict = {
onModel: function( modelData ){ console.log( modelData ) },
onChain: function( chainData ){ console.log( chainData ) },
onGroup: function( groupData ){ console.log( groupData ) },
onAtom: function( atomData ){ console.log( atomData ) },
onBond: function( bondData ){ console.log( bondData ) }
};
MMTF.traverse( mmtfData, callbackDict );
```


### Objects

#### bondData

| Name | Type | Description |
|---------------------------|----------------|------------------------------------------------|
| atomIndex1 | `Integer` | First atom index of the bond |
| atomIndex2 | `Integer` | Second atom index of the bond |
| bondOrder | `Integer|null` | Order of the bond |


#### atomData

| Name | Type | Description |
|---------------------------|----------------|------------------------------------------------|
| element | `String` | Element |
| atomName | `String` | Atom name |
| atomCharge | `Integer` | Formal charge |
| xCoord | `Float` | X coordinate |
| yCoord | `Float` | Y coordinate |
| zCoord | `Float` | Z coordinate |
| bFactor | `Float|null` | B-factor |
| atomId | `Integer|null` | Atom ID |
| altLoc | `Char|null` | Alternate location label |
| occupancy | `Float|null` | Occupancy |
| atomIndex | `Integer` | Index of the atom |
| groupIndex | `Integer` | Index of the group |
| chainIndex | `Integer` | Index of the chain |
| modelIndex | `Integer` | Index of the model |


#### groupData

| Name | Type | Description |
|---------------------------|----------------|------------------------------------------------|
| groupName | `String` | Group name |
| singleLetterCode | `Char` | Group single letter code |
| checmCompType | `Integer` | Chemical component type |
| groupId | `Integer` | Group ID |
| groupType | `Integer` | Group type |
| secStruct | `Integer|null` | Secondary structure code |
| insCode | `Char|null` | Insertion code |
| sequenceIndex | `Integer|null` | Sequence index |
| atomCount | `Integer` | Number of atoms in the group |
| groupIndex | `Integer` | Index of the group |
| chainIndex | `Integer` | Index of the chain |
| modelIndex | `Integer` | Index of the model |


#### chainData

| Name | Type | Description |
|---------------------------|----------------|------------------------------------------------|
| chainId | `String` | Chain ID |
| chainName | `String|null` | Chain name |
| groupCount | `Integer` | Number of groups in the chain |
| chainIndex | `Integer` | Index of the chain |
| modelIndex | `Integer` | Index of the model |


#### modelData

| Name | Type | Description |
|---------------------------|----------------|------------------------------------------------|
| modelIndex | `Integer` | Index of the model |
| chainCount | `Integer` | Number of chains in the model |
* [See changelog](https://github.com/rcsb/mmtf-javascript/releases/tag/v0.2.2)
* [Download release](https://github.com/rcsb/mmtf-javascript/archive/v0.2.2.zip)
* [Minified MMTF module](https://github.com/rcsb/mmtf-javascript/blob/v0.2.2/dist/mmtf.js)
* [API documentation](https://rcsb.github.io/mmtf-javascript/docs/api/v0.2.2/index.html)

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