rcsb/mmtf-java

The java implementation of the MMTF API, decoder and encoder.

mmtf-java's Issues

AdapterToStructureData must be serializable for Spark

Cannot use AdapterToStructureData in Spark jobs unless it is searializable.

use https instead of http

Use https://mmtf.rcsb.org ... in all URLs

Support loading of reduced structures

Currently the base URL is hard coded to use the full version of the MMTF files. We should add methods or a flag to be able to load reduced structures.

GenericEncoder: remove invalid constructor

The following constructor used the same precision for coordinates, B-factors, and occupancy. Usually, different precision is used for these quantities. This constructor should be removed.

/**
* The constructor for the encoder.
* @param structureDataInterface the interface of data to be encoded
* @param precision the precision for the storing of coordinate, B-factor and occupancy data
*/
public GenericEncoder(StructureDataInterface structureDataInterface, int precision) {
coordDivider = precision;
bfactorOccDivider = precision;
encode(structureDataInterface);
}

Unit test for: testReadFromReducedUrl() fails

This unit test fails for PDB ID 4CUP because the expected number of atoms should be:
115 CA's + 24 heterogen atoms = 139 atoms.

CA at alternative locations are not included in the reduced files, and therefore should not be counted.

API function mapping Chain Index to Entitity info

Currently requires some code to find this.

Extra residue bonds present in MMTF data from v1.0.9.

I recently updated to v1.0.9 from v1.0.5 to gain access to the HTTPS ReaderUtils function. I noticed one particular file is now producing extra bonds: 3N4B. There are now a total of 4135 residue bonds produced, instead of the correct 4131. In the rendering, these bonds are incorrect. Everything else in the file appears correct. Any ideas on what the problem may be?

I do not know if the data has changed or if the issue is in a version of the Java MMTF libs >1.0.5 as I cannot test from v1.0.5 anymore with HTTP.

How can the version number of the mmtf-java library be accessed programmatically?

A user, who used the .jar files directly, wants to get the version number of the mmtf-java library.

Support https

We need either methods to load structures using https or a flag to switch from http to https.

Encoder utils setUpBiojava should return the atom cache

This will help with flexibility downstream.

Need method to set mmtfProducer

Need method to set AdapterToStructureData.mmtfProducer

`ncsOperatorList` read as doubles - mmtf spec says should be floats.

When unpacking an mmtf file, this implementation expects doubles for the transformation matrices.
The specification outlines the float type as 32bit, and says this field is populated with floats.
Not sure if this should be changed - I suspect it might break parsing existing mmtf files, so maybe it needs to accept both types?

ReducedEncoder: DOD not handled as solvent

Make sure DOD is handled the same way as HOH. There is a logic error in the code.

simple alternative needed

I'm not seeing how one would integrate this mmtf-java package into a working Java program such as Jmol. It has a very large set of dependencies, including

org.msgpack.jackson.dataformat
fasterxml.jackson.annotation
fasterxml.jackson.core
fasterxml.jackson.databind

This amounts to over 5 MB of code and over 500 classes.

The decoding task, at least, is not at all that difficult. I have implemented it in Jmol using a very simple class that has only three generic dependencies (a byte array converter, a binary document reader, and an efficient JavaScript-compatible StringBuffer equivalent). See Jmol's MessagePackReader

I offer this code as a possible very lightweight alternative to what is presently on this site (4 files total; under 20K total for either .class or .js files).

So perhaps just suggesting development of a similar "mmtf-java-decode-lite"

Bob Hanson

Reuse ObjectMapper objectMapper = new ObjectMapper(new MessagePackFactory());

The MessagePack deserialization is slow.

https://github.com/FasterXML/jackson-databind suggest to instantiate ObjectMapper once and then reuse it.

Try to instantiate:
ObjectMapper objectMapper = new ObjectMapper(new MessagePackFactory());

once in the constructor and reuse it.

Release version 1.0.8

Please create a new version with all the latest fixes. We'll use the new version of mmtf-java to create an updated set of mmtf files.

Also, if you could send me instructions how to update a version, I'd be happy to do it myself in the future.

needs a readme.md

Dead code in DecoderUtils.addEntityInfo

This seems to be dead code:

String[] chainIdList = new String[dataApi.getEntityChainIndexList(i).length];
int counter = 0;
for (int chainInd : dataApi.getEntityChainIndexList(i)) {
chainIdList[counter] = dataApi.getChainIds()[chainInd];
counter++;
}