Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / salilab/rmf issues and pull requests

#127 - Add a close() method to file handles

Issue - State: closed - Opened by benmwebb about 2 years ago - 1 comment
Labels: enhancement

#126 - RMF-medium_test_backwards.py fails with Timeout

Issue - State: closed - Opened by yurivict almost 4 years ago - 1 comment

#125 - Please make a release

Issue - State: closed - Opened by yurivict over 6 years ago - 3 comments

#123 - Help reading rmf data

Issue - State: closed - Opened by Pellarin almost 9 years ago - 2 comments
Labels: question

#122 - Handle non-atom nodes more completely in rmf_pdb

Issue - State: open - Opened by benmwebb almost 10 years ago

#121 - Nested rigid bodies not read correctly from rmf

Issue - State: closed - Opened by Pellarin over 10 years ago - 10 comments

#120 - Molecule names aren't stored properly (or at all?)

Issue - State: closed - Opened by cgreenberg over 10 years ago - 4 comments

#119 - Add an ExplicitResolution decorator to RMF

Issue - State: closed - Opened by cgreenberg over 10 years ago - 2 comments
Labels: enhancement

#118 - Investigate use of coverity scanning with rmf

Issue - State: closed - Opened by drussel almost 11 years ago

#116 - Provide more detail in benchmark table

Issue - State: closed - Opened by drussel almost 11 years ago

#115 - Early return in multistate example

Issue - State: closed - Opened by drussel almost 11 years ago

#114 - Multires example is not listed in docs

Issue - State: closed - Opened by drussel almost 11 years ago - 1 comment
Labels: bug

#113 - Add python pickle support for RMF::BufferConstHandle

Issue - State: closed - Opened by drussel almost 11 years ago - 1 comment
Labels: enhancement

#112 - Javascript RMF library

Issue - State: open - Opened by drussel almost 11 years ago - 1 comment
Labels: enhancement

#111 - Clean up branches in rmf repo

Issue - State: closed - Opened by drussel almost 11 years ago

#110 - Remove duplicate RMF::decorator doc block

Issue - State: closed - Opened by drussel almost 11 years ago

#109 - Expand description of get/set static/frame

Issue - State: closed - Opened by drussel almost 11 years ago

#108 - Simplify new RMF backend files

Issue - State: closed - Opened by drussel almost 11 years ago

#107 - Make decorator get static/frame return Nullable

Issue - State: closed - Opened by drussel almost 11 years ago

#106 - Explain factory in decorators page

Issue - State: closed - Opened by drussel almost 11 years ago
Labels: enhancement

#105 - License file missing

Issue - State: closed - Opened by drussel almost 11 years ago

#104 - SWIG on RHEL 6 doesn't match the Vector3(x,y,z) constructor

Issue - State: closed - Opened by drussel almost 11 years ago - 3 comments

#103 - Crash with hdf5 based files on ubuntu

Issue - State: closed - Opened by drussel about 11 years ago - 2 comments
Labels: bug

#102 - readme.md

Issue - State: closed - Opened by yannickspill about 11 years ago - 2 comments

#101 - rmf compile error

Issue - State: closed - Opened by yannickspill about 11 years ago - 2 comments
Labels: bug

#100 - Rename standard_deviations to variances

Issue - State: closed - Opened by drussel about 11 years ago

#99 - Make it clearer in docs which values each Enum can take

Issue - State: closed - Opened by drussel about 11 years ago

#98 - Add support for ellispoid-based alternatives

Issue - State: closed - Opened by drussel about 11 years ago

#97 - Add support for ellipsoids

Issue - State: closed - Opened by drussel about 11 years ago

#96 - VMD plugin crashes when concatenating files

Issue - State: closed - Opened by drussel about 11 years ago - 1 comment

#95 - Use cleanup_code.py in the decorator generation code

Issue - State: closed - Opened by drussel about 11 years ago

#94 - warnings

Issue - State: closed - Opened by yannickspill about 11 years ago - 4 comments

#93 - missing stuff

Issue - State: closed - Opened by yannickspill about 11 years ago - 1 comment

#92 - Include whole RMF lib in VMD plugjn

Issue - State: closed - Opened by drussel about 11 years ago - 1 comment
Labels: enhancement

#91 - Improve validation

Issue - State: open - Opened by drussel about 11 years ago
Labels: enhancement

#90 - Validator code is broken

Issue - State: closed - Opened by drussel about 11 years ago

#89 - broken

Issue - State: closed - Opened by yannickspill about 11 years ago - 6 comments

#87 - using conflicts

Issue - State: closed - Opened by yannickspill about 11 years ago
Labels: bug

#86 - Print attributes in alphabetical order

Issue - State: closed - Opened by drussel about 11 years ago

#85 - Add concept of resolution node (following IMP)

Issue - State: closed - Opened by drussel about 11 years ago

#84 - Add methods to get keys from factories

Issue - State: open - Opened by drussel about 11 years ago
Labels: enhancement

#83 - Make Vector class easily replaceable (e.g. with IMP VectorD)

Issue - State: closed - Opened by drussel about 11 years ago

#82 - Add Vector4s to file format

Issue - State: closed - Opened by drussel about 11 years ago

#81 - deprecation warnings

Issue - State: closed - Opened by yannickspill about 11 years ago - 2 comments

#80 - Explain _frame_ and _static_ versions of get functions

Issue - State: closed - Opened by drussel about 11 years ago

#79 - Remove type from geometry

Issue - State: closed - Opened by drussel about 11 years ago

#78 - Split off geometry coordinates

Issue - State: closed - Opened by drussel about 11 years ago

#77 - Store a single index for residues

Issue - State: closed - Opened by drussel about 11 years ago

#76 - fast build warnings

Issue - State: closed - Opened by duhovka about 11 years ago

#75 - in VMD plugin create a molecule per restraint

Issue - State: closed - Opened by drussel about 11 years ago

#74 - Add support for gzip streams using boost streams

Issue - State: closed - Opened by drussel about 11 years ago

#73 - Add support for ellipsoids

Issue - State: closed - Opened by drussel over 11 years ago
Labels: enhancement

#72 - Add a set_if_changed method

Issue - State: closed - Opened by drussel over 11 years ago

#71 - Add a post-load pass to implement backwards compatibility

Issue - State: closed - Opened by drussel over 11 years ago - 1 comment
Labels: enhancement

#70 - Move Chain to string rather than int

Issue - State: closed - Opened by drussel over 11 years ago
Labels: enhancement

#69 - Maybe add fixed vector storage type

Issue - State: closed - Opened by drussel over 11 years ago - 1 comment
Labels: enhancement

#68 - Add mmCIF backend

Issue - State: open - Opened by drussel over 11 years ago - 2 comments
Labels: enhancement

#67 - Move to salilab google analytics

Issue - State: closed - Opened by drussel over 11 years ago
Labels: enhancement

#66 - Use NodeID attributes for bonds rather than children

Issue - State: closed - Opened by drussel over 11 years ago

#65 - RMF3

Issue - State: closed - Opened by drussel over 11 years ago

#64 - problem with rmf_cat

Issue - State: closed - Opened by barakr over 11 years ago - 1 comment
Labels: bug

#63 - Make sure attempts to create frame ID with RMF.STATIC fails

Issue - State: closed - Opened by drussel over 11 years ago

#62 - Add python-specific get_key method

Issue - State: closed - Opened by drussel over 11 years ago
Labels: enhancement

#61 - Bug in Chimera plugin

Issue - State: closed - Opened by jkosinski over 11 years ago - 2 comments

#60 - is that possible to get (not link) the entire hierarchy stored in the rmf?

Issue - State: closed - Opened by Pellarin over 11 years ago - 2 comments
Labels: question

#59 - Check out having avro store int, value pairs rather than map

Issue - State: closed - Opened by drussel over 11 years ago

#58 - Reduce number of virtual function calls in reading

Issue - State: closed - Opened by drussel over 11 years ago - 2 comments
Labels: enhancement

#57 - Add a Vector3D class to speed up loading of coordinates

Issue - State: closed - Opened by drussel over 11 years ago
Labels: enhancement

#56 - Make VMD plugin not suppress REPRESENTATION nodes if there are just GEOMETRY nodes underneath

Issue - State: closed - Opened by drussel over 11 years ago
Labels: enhancement

#55 - Investigate instability when opening rmf2 files that are being written in Chimera

Issue - State: closed - Opened by drussel almost 12 years ago - 1 comment
Labels: bug, enhancement

#54 - Add warning when opening an already open rmf file

Issue - State: closed - Opened by drussel almost 12 years ago - 1 comment
Labels: enhancement

#53 - Make cmake more robust to changes in the file lists

Issue - State: closed - Opened by drussel almost 12 years ago
Labels: bug

#52 - Fix use of tmp on .cpp rmf test.

Issue - State: closed - Opened by drussel almost 12 years ago
Labels: bug

#51 - Provide a RMF.cmake that allows other cmake projects to find RMF

Issue - State: closed - Opened by drussel almost 12 years ago - 1 comment
Labels: enhancement

#50 - Add program to translate avro based rmfs to and from text files

Issue - State: closed - Opened by drussel almost 12 years ago - 1 comment
Labels: enhancement

#49 - Add support for saving derivatives of coordinates

Issue - State: closed - Opened by drussel almost 12 years ago

#48 - Make sure that boost::fileystem is used to get paths everywhere and to extract the right name

Issue - State: closed - Opened by drussel almost 12 years ago - 1 comment
Labels: bug

#47 - Clean up windows build warnings

Issue - State: closed - Opened by drussel almost 12 years ago

#46 - Warnings produced on miguelito

Issue - State: closed - Opened by drussel almost 12 years ago

#45 - Add complicated RMF files in all three types and tests that they can be read

Issue - State: closed - Opened by drussel almost 12 years ago - 1 comment
Labels: enhancement

#44 - Take advantage of patch to Avro to perform seeks in rmf2 files.

Issue - State: closed - Opened by drussel almost 12 years ago - 1 comment
Labels: enhancement

#43 - Add Bond decorator

Issue - State: closed - Opened by drussel almost 12 years ago
Labels: enhancement

#42 - write PyMol plugin for RMF

Issue - State: closed - Opened by barakr almost 12 years ago - 2 comments

#41 - Write VMD plugin to read rmf files

Issue - State: closed - Opened by drussel almost 12 years ago
Labels: enhancement

#40 - lots of unused parameters in hdf5 backend

Issue - State: closed - Opened by drussel almost 12 years ago
Labels: enhancement

#39 - .rmf files don't support frame types

Issue - State: closed - Opened by drussel almost 12 years ago
Labels: bug, wontfix

#38 - Slowness opening large rmf file

Issue - State: closed - Opened by drussel about 12 years ago - 1 comment

#37 - fix the make all header script to take the paths or glob strings

Issue - State: closed - Opened by drussel about 12 years ago
Labels: bug

#36 - Handling of exceptions on Windows doesn't work well

Issue - State: closed - Opened by drussel about 12 years ago - 1 comment
Labels: bug

#35 - Revisit rewriting of frames data file in rmf2

Issue - State: closed - Opened by drussel about 12 years ago
Labels: enhancement

#34 - Embed json files in library

Issue - State: closed - Opened by drussel about 12 years ago
Labels: enhancement

#33 - Put each backend in own namespace

Issue - State: closed - Opened by drussel about 12 years ago
Labels: enhancement

#32 - RMF build fails on RHEL5

Issue - State: closed - Opened by drussel about 12 years ago - 1 comment
Labels: bug

#31 - Add overview of how different types of data would be mapped to RMF

Issue - State: open - Opened by drussel about 12 years ago - 1 comment
Labels: enhancement

#30 - Generate an RMF.h

Issue - State: closed - Opened by drussel about 12 years ago
Labels: enhancement

#29 - Building on windows requires disabling the avro tests.

Issue - State: closed - Opened by drussel about 12 years ago - 1 comment
Labels: bug

#28 - The swig wrapper files are not updated when a header changes

Issue - State: closed - Opened by drussel about 12 years ago
Labels: bug