Owner

salilab

8 indexed repositories · View on GitHub

imp
The Integrative Modeling Platform

C++ · 81 stars
pmi
Python Modeling Interface

Python · 14 stars
rmf
The library to support reading and writing of RMF files.

C++ · 9 stars
saliweb
Simple framework for web services in the Sali lab

Python · 5 stars
npctransport
IMP module for simulating transport through the NPC.

C++ · 3 stars
optrep
IMP module for optimal coarse-grained bead representation

Python · 0 stars
actin_tutorial
IMP/PMI tutorial, modeling the complex of actin and tropomodulin-gelsolin chimera

Python · 0 stars
imp_analysis_tutorial

Python · 0 stars

Beginner friendly Everything

Open All

Add Python pickle buffer support Open

performance

salilab/imp#1080 · 1 assignee · Opened Mar 30, 2023
IMP/pmi returns type error during RB construction Open

salilab/imp#1074 · 4 comments · 1 assignee · Opened Nov 22, 2022
running modeling.py in a cluster environment Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

salilab/imp_analysis_tutorial#2 · 5 comments · Opened Jan 2, 2021
Add support for login via GitHub/Google etc. Open

enhancement

salilab/saliweb#1 · 1 assignee · Opened Dec 21, 2020
SampledDensityMap - Which constructor is chosen affects results. Open

bug IMP.em

salilab/imp#1036 · 3 comments · 1 assignee · Opened Nov 9, 2020
Missing volume estimates for nucleic acids Open

feature request IMP.atom

salilab/imp#1027 · 1 assignee · Opened Dec 9, 2019
Add tests for analysis Open

salilab/actin_tutorial#1 · 1 assignee · Opened Nov 19, 2019
RWMC fails for bounded Nuisances with defined score at the boundary Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

salilab/imp#1023 · Opened Sep 8, 2019
Introduce families of distributions and a `DistributionRestraint` Open

feature request

Difficulty 5/5 Over a week Newbie friendliness 20/100

salilab/imp#1021 · Opened Sep 7, 2019
Raise exception when derivatives are requested from non-differentiable restraint Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

salilab/imp#1020 · Opened Sep 7, 2019
GSL simplex error when using high pixel size in EM2D Open

salilab/imp#1014 · 1 assignee · Opened May 24, 2019
add test for spherical bounding box (box_is_on==2) vs rectangular bounding box (now only box_is_on==2) Open

unit test

salilab/npctransport#25 · 1 assignee · Opened Dec 15, 2018
Deleting fragment / beads from RMF in PMI 2.0 Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

salilab/pmi#246 · 1 comment · Opened Nov 19, 2018
Add option to calculate sampling precision not bead wise but domain wise Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

salilab/optrep#5 · Opened Oct 31, 2018
Add options to PMI's topology file to merge it with the topology file used by this module Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

salilab/optrep#4 · Opened Oct 31, 2018
Allow unambiguous inter-molecular crosslinks in restraints Open

enhancement

salilab/pmi#245 · 2 comments · 1 assignee · Opened Oct 24, 2018
Add SingletonDerivativeModifier complement to TransformationSymmetry Open

feature request

salilab/imp#1011 · 1 assignee · Opened Sep 26, 2018
Add interface to NAMD Open

feature request

salilab/imp#1010 · 4 comments · 1 assignee · Opened Sep 20, 2018
Reimplement Nuisance to sample in an unconstrained space Open

feature request IMP.isd

salilab/imp#1007 · 3 comments · 1 assignee · Opened Aug 9, 2018
Truncate IMP.isd.GaussianRestraint and IMP.isd.StudentTRestraint properly Open

IMP.isd

salilab/imp#1006 · 1 assignee · Opened Jul 30, 2018
Decide how to deal with ambiguity Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

salilab/optrep#3 · 1 comment · Opened Apr 11, 2018
Align the models before calculating bead-wise sampling precision Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

salilab/optrep#2 · Opened Apr 11, 2018
Add an option to add different set of CG bead sizes for different domains Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

salilab/optrep#1 · Opened Apr 11, 2018
SampledDensityMap - Model and map generated from model do not align. Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

salilab/imp#1002 · 1 comment · Opened Apr 3, 2018
Add crosslink restraint to specific state Open

enhancement question

Difficulty 4/5 3-5 days Newbie friendliness 25/100

salilab/pmi#238 · Opened Mar 12, 2018
XLs restraint: stat file reports only the likelihood as score Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

salilab/imp#1000 · 1 comment · Opened Feb 9, 2018
properly test chains with suffixes Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

salilab/npctransport#23 · Opened Feb 2, 2018
error in CloseBipartitePairContainer when including pairs on same rigid body Open

bug

Difficulty 3/5 1-2 days Newbie friendliness 55/100

salilab/imp#998 · Opened Nov 17, 2017
missing density band when using SampledDensityMaps Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

salilab/imp#987 · Opened Jul 31, 2017
Track provenance information for all modeling inputs Open

feature request

salilab/imp#976 · 1 comment · 1 assignee · Opened Apr 18, 2017
PMI2 RMF hierarchies of input and output RMFs different Open

Difficulty 4/5 3-5 days Newbie friendliness 42/100

salilab/pmi#224 · Opened Nov 15, 2016
Clustering function without stat file Open

Difficulty 4/5 3-5 days Newbie friendliness 28/100

salilab/pmi#222 · Opened Nov 15, 2016
MPI number of cores problem for Analysis macro Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

salilab/pmi#221 · Opened Nov 15, 2016
Clustering and MPI: multiple copy of same models Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

salilab/pmi#219 · 2 comments · Opened Nov 2, 2016
Set resolution in analysis replica exchange macro Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

salilab/pmi#218 · 2 comments · Opened Oct 25, 2016
Standardise crosslinking classes Open

salilab/pmi#214 · 4 comments · 1 assignee · Opened Oct 7, 2016
Separate IMP.Restraint and PMI restraint classes Open

salilab/pmi#211 · 2 comments · 1 assignee · Opened Oct 4, 2016
Consider using DCD or other formats for trajectories Open

feature request

salilab/imp#964 · 1 assignee · Opened Sep 30, 2016
Speed up release build Open

feature request performance

salilab/imp#963 · 1 comment · 1 assignee · Opened Sep 14, 2016
IMP.em.FitRestraint is much slower with use_rigid_bodies = True Open

performance

Difficulty 4/5 3-5 days Newbie friendliness 45/100

salilab/imp#954 · Opened Jun 29, 2016
Add connectivity restraint to BuildSystem macro Open

Difficulty 5/5 Over a week Newbie friendliness 20/100

salilab/pmi#203 · 1 comment · Opened May 12, 2016
Add an IMP.atom.get_leaves(hier) which is aware of representations Open

Difficulty 3/5 1-2 days Newbie friendliness 45/100

salilab/imp#947 · Opened May 8, 2016
Use atom::create_clone for faster copying and cloning Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

salilab/pmi#201 · Opened May 6, 2016
Analysis Violations class should take into account copy number (ambiguity) Open

Difficulty 4/5 3-5 days Newbie friendliness 45/100

salilab/pmi#197 · Opened Apr 22, 2016
Documentation for crosslink analysis Open

Difficulty 3/5 1-2 days Newbie friendliness 35/100

salilab/pmi#189 · Opened Mar 17, 2016
Overload RotamerCalculator.get_rotamer() to take ResidueType and necessary coordinate elements Open

feature request

salilab/imp#936 · 1 assignee · Opened Feb 17, 2016
Add support to clone a state Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

salilab/pmi#164 · Opened Jan 30, 2016
Standardization of terms Open

Difficulty 5/5 Over a week Newbie friendliness 25/100

salilab/pmi#163 · 4 comments · Opened Jan 28, 2016
Functions that could go in the PMI restraint base class Open

salilab/pmi#156 · 33 comments · 1 assignee · Opened Jan 27, 2016
Topology: Molecule.create_clone() should let you pass a structure to read Open

Difficulty 3/5 1-2 days Newbie friendliness 38/100

salilab/pmi#153 · Opened Jan 27, 2016

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