Ecosyste.ms: Issues

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

GitHub / salilab/imp issues and pull requests

#1081 - Add "sparse" Keys

Issue - State: closed - Opened by benmwebb over 1 year ago - 1 comment
Labels: feature request

#1080 - Add Python pickle buffer support

Issue - State: open - Opened by benmwebb almost 2 years ago
Labels: performance

#1079 - build binaries for docker container?

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

#1078 - Allow list-like access to restraints in RestraintsScoringFunction

Issue - State: closed - Opened by benmwebb about 2 years ago
Labels: feature request, IMP.core

#1077 - Handle teardown of rigid body that is a member of another body

Issue - State: closed - Opened by benmwebb about 2 years ago
Labels: feature request, IMP.core

#1076 - Make IMP.atom.destroy() aware of rigid bodies

Issue - State: closed - Opened by benmwebb about 2 years ago
Labels: feature request, IMP.core

#1075 - Allow removing members from rigid bodies

Issue - State: closed - Opened by benmwebb about 2 years ago
Labels: feature request, IMP.core

#1074 - IMP/pmi returns type error during RB construction

Issue - State: open - Opened by Pellarin about 2 years ago - 1 comment

#1073 - Provide Python list-like object for IMP_LIST

Issue - State: closed - Opened by benmwebb about 2 years ago
Labels: feature request

#1072 - Improve CHARMMTopology.add_sequence() to accept full residue names

Issue - State: closed - Opened by benmwebb about 2 years ago
Labels: feature request, IMP.atom

#1071 - Improve CHARMMTopology.create_hierarchy() to assign multi-char chain IDs

Issue - State: closed - Opened by benmwebb about 2 years ago
Labels: feature request, IMP.atom

#1070 - CUDA-enabled random number functions ignore random seed

Issue - State: closed - Opened by benmwebb over 2 years ago
Labels: bug

#1069 - Can't connect IMP package to pycharm on mac

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

#1068 - Issue with pmi connectivity restraint at resolutions >1

Issue - State: closed - Opened by mphancock over 2 years ago - 4 comments

#1067 - submodules not installed

Issue - State: closed - Opened by Pellarin over 2 years ago - 5 comments

#1066 - compilation error

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

#1065 - Remove the workaround for llvm.43266?

Issue - State: closed - Opened by Chandlerooo over 2 years ago - 1 comment

#1064 - - Added the Residue-Protein Proximity restraint. This restraint is de…

Pull Request - State: closed - Opened by iecheverria over 2 years ago - 1 comment

#1063 - Move-aware MC acceptance does not match regular scoring in some cases

Issue - State: closed - Opened by benmwebb over 2 years ago
Labels: bug, IMP.core

#1062 - Segfaults trying to print Hierarchy objects with conda package on Mac

Issue - State: closed - Opened by benmwebb over 2 years ago - 2 comments
Labels: bug, IMP.atom

#1061 - Consider requiring Python `pathlib` module

Issue - State: closed - Opened by benmwebb over 2 years ago

#1060 - Improve interaction between `MovedParticlesRestraintCache` and RMF output

Issue - State: closed - Opened by benmwebb over 2 years ago - 1 comment

#1059 - Transform Cryo EM map

Issue - State: closed - Opened by YumengYan almost 3 years ago - 1 comment

#1057 - Principal inertia axes calculation for rigid bodies is buggy

Issue - State: closed - Opened by tanmoy7989 over 3 years ago - 4 comments
Labels: bug, IMP.core

#1056 - Speed up close pairs update for atomic simulations

Issue - State: closed - Opened by benmwebb almost 4 years ago - 1 comment
Labels: performance

#1055 - Handle MRC files with non-standard indexing

Pull Request - State: closed - Opened by benmwebb almost 4 years ago - 1 comment
Labels: IMP.em

#1054 - Error when accessing data array for certain EM maps.

Issue - State: closed - Opened by ichem001 almost 4 years ago - 4 comments
Labels: bug, IMP.em

#1053 - Error opening certain MRC files

Issue - State: closed - Opened by saltzberg almost 4 years ago - 9 comments
Labels: bug, IMP.em

#1052 - Installation problem

Issue - State: closed - Opened by celinasjose almost 4 years ago - 3 comments

#1051 - Minor changes to make out of tree builds painless

Pull Request - State: closed - Opened by tanmoy7989 almost 4 years ago

#1050 - Merge pull request #1 from salilab/develop

Pull Request - State: closed - Opened by tanmoy7989 almost 4 years ago - 2 comments

#1049 - Fixes pmi shuffle issue

Pull Request - State: closed - Opened by Stochastic13 almost 4 years ago - 3 comments

#1048 - PMI shuffle with bounding box setup not working with Gaussian-decorated beads

Issue - State: closed - Opened by Stochastic13 almost 4 years ago - 1 comment

#1047 - Package 'imp-python3' has no installation candidate

Issue - State: closed - Opened by ultimategamer309 about 4 years ago - 1 comment

#1046 - Merging the `fast_grid_based_em` branch onto the develop branch.

Pull Request - State: closed - Opened by ichem001 about 4 years ago - 5 comments

#1045 - Question about chi free in foxs

Issue - State: closed - Opened by itaneja2 about 4 years ago - 2 comments

#1044 - Cross correlation evaluates to > 1.0

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

#1043 - install error

Issue - State: closed - Opened by shiyi-pan about 4 years ago - 8 comments

#1042 - Crop a DensityMap using a particle set

Pull Request - State: closed - Opened by saltzberg about 4 years ago - 6 comments

#1041 - Drop support for Python 2.6

Issue - State: closed - Opened by benmwebb about 4 years ago - 1 comment

#1040 - Update minimum CMake version to 2.8.12

Issue - State: closed - Opened by benmwebb about 4 years ago
Labels: build system

#1039 - ImportError with Mac OS 10.15.5

Issue - State: closed - Opened by Pellarin about 4 years ago - 1 comment

#1038 - Installation error

Issue - State: closed - Opened by es15326 about 4 years ago - 1 comment

#1037 - Installation error

Issue - State: closed - Opened by es15326 about 4 years ago

#1036 - SampledDensityMap - Which constructor is chosen affects results.

Issue - State: open - Opened by ichem001 about 4 years ago - 3 comments
Labels: bug, IMP.em

#1035 - SAXS restraint error

Issue - State: closed - Opened by CRA-Murray over 4 years ago - 4 comments
Labels: bug, IMP.saxs

#1034 - Add CI github actions workflow

Pull Request - State: open - Opened by sethaxen over 4 years ago - 5 comments

#1033 - SteepestDescent.cpp

Issue - State: closed - Opened by mahdi65 over 4 years ago - 1 comment

#1032 - TransformationSymmetry not applied correctly

Issue - State: closed - Opened by benmwebb over 4 years ago - 1 comment
Labels: invalid

#1031 - Add support for OptimizerState in IMP.pmi

Issue - State: closed - Opened by tpeulen over 4 years ago - 2 comments
Labels: feature request

#1030 - Kinematics with rebased develop

Pull Request - State: closed - Opened by barakr over 4 years ago - 3 comments

#1028 - empty bayesianem module

Issue - State: closed - Opened by Pellarin almost 5 years ago - 2 comments

#1027 - Missing volume estimates for nucleic acids

Issue - State: open - Opened by benmwebb about 5 years ago
Labels: feature request, IMP.atom

#1026 - Add bayesianem as a submodule

Issue - State: closed - Opened by benmwebb over 5 years ago
Labels: build system

#1025 - Ubuntu packages don't include CMake config for out of tree builds

Issue - State: closed - Opened by benmwebb over 5 years ago
Labels: bug

#1022 - Improvements to Weight

Pull Request - State: closed - Opened by sethaxen over 5 years ago

#1021 - Introduce families of distributions and a `DistributionRestraint`

Issue - State: open - Opened by sethaxen over 5 years ago
Labels: feature request

#1019 - Enable `algebra::VectorKD` to be converted to list

Issue - State: closed - Opened by sethaxen over 5 years ago - 2 comments

#1018 - Improvements to `IMP::isd::Weight`

Issue - State: closed - Opened by sethaxen over 5 years ago - 1 comment
Labels: feature request

#1017 - Improvements to rigid body derivatives

Pull Request - State: closed - Opened by sethaxen over 5 years ago - 2 comments
Labels: bug, feature request, IMP.core

#1016 - Loss of precision with IMP::Vector in Python

Issue - State: closed - Opened by sethaxen over 5 years ago - 1 comment
Labels: bug

#1015 - Rename IMP::saxs 'rg' binary to avoid conflict with ripgrep

Issue - State: closed - Opened by benmwebb over 5 years ago
Labels: bug

#1014 - GSL simplex error when using high pixel size in EM2D

Issue - State: open - Opened by ichem001 over 5 years ago

#1013 - No module named 'imp'

Issue - State: closed - Opened by janekbii almost 6 years ago - 13 comments

#997 - Transition plan from PMI1 to PMI2

Issue - State: closed - Opened by benmwebb about 7 years ago - 1 comment

#982 - Proposal: put IMP tutorials in their own GitHub repositories

Issue - State: closed - Opened by benmwebb over 7 years ago - 1 comment
Labels: feature request, doc

#959 - Speed up scoring function when used with Monte Carlo

Issue - State: closed - Opened by benmwebb over 8 years ago - 10 comments
Labels: feature request, in progress, performance

#957 - (sovled) undesired Foxs program after compilation

Issue - State: closed - Opened by huge200890 over 8 years ago - 1 comment

#944 - Link ipython notebook examples on the examples page

Issue - State: closed - Opened by cgreenberg over 8 years ago - 3 comments
Labels: doc, build system

#934 - Add IMP::atom::mutate_residue

Issue - State: closed - Opened by sethaxen almost 9 years ago - 2 comments

#933 - Allow IMP::atom::get_next_residue and IMP::atom::get_previous_residue to consider PMI hierarchy structures

Issue - State: closed - Opened by sethaxen almost 9 years ago - 5 comments
Labels: bug, IMP.atom

#928 - Incorrect polymorphic behaviour in the LogWrapper(IMP::isd::ISDRestraintsTemp)

Issue - State: closed - Opened by Pellarin about 9 years ago - 3 comments

#885 - IMP.em.SampledDensityMap

Issue - State: closed - Opened by petercim almost 10 years ago - 2 comments

#824 - Invalid RMF files produced (rigid body members marked as rigid, not nonrigid)

Issue - State: closed - Opened by benmwebb over 10 years ago - 2 comments

#810 - VectorD checks don't appear to work

Issue - State: closed - Opened by benmwebb over 10 years ago
Labels: bug

#800 - Documentation about PairScores vs Restraints etc

Issue - State: closed - Opened by cgreenberg over 10 years ago - 6 comments
Labels: doc

#773 - reference frame orientations

Issue - State: closed - Opened by yannickspill almost 11 years ago - 11 comments
Labels: bug, question, IMP.core

#763 - Add function to compute the center of mass of a selection

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

#762 - Building occasionally leaves long-running swig processes

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

#760 - Investigate use of RMF as base data structure later for IMP

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

#759 - setup_environment.sh does not propagate mpirun path in $PATH

Issue - State: closed - Opened by yannickspill almost 11 years ago - 4 comments
Labels: bug, build system

#730 - Improve usage of Travis CI

Issue - State: closed - Opened by drussel almost 11 years ago - 2 comments
Labels: feature request

#702 - Check out Tao for optimization

Issue - State: closed - Opened by drussel about 11 years ago
Labels: question, performance

#698 - Don't have make_all_headers.py be used in targets in cmake

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

#695 - Remove uses of TNT

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

#655 - Improve named tuple

Issue - State: closed - Opened by drussel about 11 years ago
Labels: feature request, swig

#582 - Investigate getting good interrupt support in native code

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

#567 - Do quick mock up of multires domino

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

#555 - Make test_standards.py be a build target

Issue - State: closed - Opened by drussel over 11 years ago - 2 comments
Labels: feature request, build system

#501 - Consistently search in path relative to IMP executable/.pylib to find data

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

#340 - turn kinematics::DOFVector to standard IMP class

Issue - State: closed - Opened by barakr over 11 years ago - 1 comment
Labels: IMP.kinematics

#333 - kinematics cpp tests

Issue - State: closed - Opened by barakr over 11 years ago
Labels: bug, IMP.kinematics

#248 - Various IMP.em tests are pointlessly expensive

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

#186 - Add dependencies for tests

Issue - State: closed - Opened by drussel almost 12 years ago - 2 comments
Labels: feature request, build system

#174 - Clean code for clang shadow warning

Issue - State: closed - Opened by drussel almost 12 years ago - 1 comment
Labels: feature request, build system

#116 - Kinematic TODOs

Issue - State: closed - Opened by barakr about 12 years ago - 4 comments
Labels: feature request, IMP.kinematics