Ecosyste.ms: Issues

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GitHub / junioreif/OpenMiChroM issues and pull requests

#105 - Compute RDP error in CnbdTools.py

Issue - State: open - Opened by kevin-rice24 23 days ago

#104 - Enhanced backwards compatibility with previous function

Pull Request - State: closed - Opened by mellofariam about 1 month ago
Labels: bug, enhancement

#103 - Fix various bugs and improve code readability

Pull Request - State: closed - Opened by junioreif 2 months ago

#101 - The library is in violation of Polychrom's licencing terms

Issue - State: closed - Opened by mimakaev 5 months ago - 3 comments
Labels: help wanted

#100 - Compute RDP error

Issue - State: closed - Opened by laurendipaola 5 months ago

#99 - Optimization.py changes

Pull Request - State: closed - Opened by sudoneoox 5 months ago

#98 - normalize_matrix not defined fix

Pull Request - State: closed - Opened by sudoneoox 5 months ago

#97 - Main patch

Pull Request - State: closed - Opened by ronaldojunio 11 months ago

#96 - RDP definition needs to be updated

Pull Request - State: closed - Opened by ronaldojunio over 1 year ago

#91 - Dev tutorials updated and template scripts for Aries added

Pull Request - State: closed - Opened by ronaldojunio over 1 year ago

#90 - Ideal chromosome and methods name modified

Pull Request - State: closed - Opened by ronaldojunio over 1 year ago

#89 - fix: reinitialize system after force group assignment

Pull Request - State: closed - Opened by s-brahmachari over 1 year ago

#88 - fixed addAddtionalForce 2

Pull Request - State: closed - Opened by s-brahmachari over 1 year ago

#87 - added activity and fixed msd in cndbtools

Pull Request - State: closed - Opened by s-brahmachari over 1 year ago

#86 - Changes in Optimization

Pull Request - State: closed - Opened by ronaldojunio over 1 year ago - 1 comment

#85 - Updated Pulling Tutorial

Pull Request - State: closed - Opened by benruben87 over 1 year ago

#84 - Pulling Tutirial

Pull Request - State: closed - Opened by benruben87 over 1 year ago

#83 - Pulling tutorial

Pull Request - State: closed - Opened by benruben87 over 1 year ago - 1 comment

#82 - Chromosome Pulling Tutorial Addition

Pull Request - State: closed - Opened by benruben87 over 1 year ago

#81 - Updated Docs optimization tutorial

Pull Request - State: closed - Opened by ronaldojunio almost 2 years ago

#80 - Inconsistence during training Types vs IC

Issue - State: closed - Opened by contessoto almost 2 years ago - 1 comment
Labels: enhancement, invalid

#79 - Changed the lambda treatment in the end of the tutorial

Pull Request - State: closed - Opened by ronaldojunio almost 2 years ago

#78 - Update ChromDynamics.py

Pull Request - State: closed - Opened by ronaldojunio almost 2 years ago

#77 - Update Tutorial_Full_Inversion_Optimization.ipynb

Pull Request - State: closed - Opened by ronaldojunio almost 2 years ago

#76 - Update Tutorial_Single_Chromosome.ipynb

Pull Request - State: closed - Opened by ronaldojunio almost 2 years ago

#75 - Update Tutorial_Full_Inversion_Optimization.ipynb

Pull Request - State: closed - Opened by ronaldojunio almost 2 years ago

#74 - Update Tutorial_MiChroM_Optimization.ipynb

Pull Request - State: closed - Opened by ronaldojunio almost 2 years ago

#73 - Update Tutorial_Multiple_Chromosomes.ipynb

Pull Request - State: closed - Opened by ronaldojunio almost 2 years ago

#72 - Update Tutorial_Multiple_Chromosomes.ipynb

Pull Request - State: closed - Opened by ronaldojunio almost 2 years ago

#71 - Update README.rst

Pull Request - State: closed - Opened by ronaldojunio almost 2 years ago

#70 - Link is broken

Issue - State: closed - Opened by ronaldojunio almost 2 years ago - 1 comment

#69 - Optimization function get wrong number of parameters

Issue - State: closed - Opened by contessoto almost 2 years ago - 1 comment
Labels: bug

#68 - Correct distance factor in pdb vs gro

Issue - State: closed - Opened by contessoto almost 2 years ago
Labels: invalid

#67 - Add the optimization protocol as a new function

Issue - State: closed - Opened by contessoto about 2 years ago
Labels: documentation, enhancement

#66 - Add Tutorial for Quenching simulations

Issue - State: closed - Opened by contessoto about 2 years ago
Labels: documentation

#65 - Add Tutorial for analysis tools

Issue - State: closed - Opened by contessoto about 2 years ago
Labels: documentation

#64 - Add function to split or merge .cndb files

Issue - State: closed - Opened by contessoto about 2 years ago
Labels: bug, documentation, enhancement

#63 - Add Tutorials of the optimization protocol - 1st and 2nd order algorithms

Issue - State: closed - Opened by contessoto about 2 years ago
Labels: documentation

#62 - Update on tutorials for single and multiple chromosome simulation

Pull Request - State: closed - Opened by mellofariam about 2 years ago

#61 - Incorrect documentation for xyz() function in CndbTools

Issue - State: closed - Opened by mellofariam about 2 years ago
Labels: bug, documentation

#60 - setFibPosition input changes

Issue - State: closed - Opened by ChristianKKelley about 2 years ago - 3 comments
Labels: documentation, question

#59 - Changes on adding and removing forces from the system

Pull Request - State: closed - Opened by mellofariam about 2 years ago

#58 - Feature adam beta

Pull Request - State: closed - Opened by junioreif about 2 years ago

#56 - Revert "fixed bug in cndb load"

Pull Request - State: closed - Opened by junioreif about 2 years ago

#55 - Check

Pull Request - State: closed - Opened by s-brahmachari over 2 years ago

#54 - set initial velocities

Issue - State: closed - Opened by s-brahmachari over 2 years ago

#53 - add converters to cndbTools

Issue - State: closed - Opened by s-brahmachari over 2 years ago - 1 comment
Labels: bug, documentation, enhancement

#52 - set force group

Issue - State: closed - Opened by s-brahmachari over 2 years ago - 3 comments

#50 - fixed bug in cndb load

Pull Request - State: closed - Opened by s-brahmachari over 2 years ago

#49 - Added the documentation for initStructure(),loadPDB(), and loadGRO().

Pull Request - State: closed - Opened by mellofariam over 2 years ago

#48 - Fix load/save coordinate files.

Pull Request - State: closed - Opened by mellofariam over 2 years ago

#47 - Split trajs when computing in silico Hi-C

Issue - State: closed - Opened by contessoto over 2 years ago - 1 comment
Labels: enhancement

#46 - FENE calling for multichains

Issue - State: closed - Opened by contessoto over 2 years ago
Labels: enhancement

#45 - added methods to cndbtools

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

#44 - Issue in saveStructure for modes 'pdb' and 'gro'

Issue - State: closed - Opened by mellofariam almost 3 years ago - 2 comments
Labels: bug

#43 - Issue when loading initial structure from pdb files

Issue - State: closed - Opened by mellofariam almost 3 years ago - 2 comments
Labels: bug

#42 - Optimize probability calculation process

Pull Request - State: closed - Opened by ellenfidele almost 3 years ago

#41 - Include option to set the cutoff distance by user

Issue - State: closed - Opened by junioreif almost 3 years ago - 2 comments
Labels: enhancement

#40 - Wrong MODEL writing PDB file

Issue - State: closed - Opened by contessoto about 3 years ago - 1 comment
Labels: bug

#39 - Wrong path calling when using Windows

Issue - State: closed - Opened by contessoto about 3 years ago - 1 comment
Labels: bug

#38 - Typo in CustomIC energy function

Issue - State: closed - Opened by contessoto about 3 years ago - 1 comment
Labels: bug

#37 - updates to 1.0.0

Pull Request - State: closed - Opened by junioreif about 3 years ago

#36 - update to run in parallel

Pull Request - State: closed - Opened by junioreif over 3 years ago

#35 - add a function to remove harmonic restrictions

Pull Request - State: closed - Opened by junioreif over 3 years ago

#34 - Updates to 1.0.0

Pull Request - State: closed - Opened by junioreif over 3 years ago

#33 - mudei tal coisa

Pull Request - State: closed - Opened by junioreif over 3 years ago

#32 - Adding docs for Chirality analysis

Pull Request - State: closed - Opened by contessoto over 3 years ago

#31 - Adding docs for Chirality analysis

Pull Request - State: closed - Opened by contessoto over 3 years ago

#30 - Adding docs for Chirality analysis

Pull Request - State: closed - Opened by contessoto over 3 years ago

#29 - Vini

Pull Request - State: closed - Opened by contessoto over 3 years ago

#28 - Custom types training - A and B only

Issue - State: closed - Opened by contessoto over 3 years ago
Labels: enhancement

#27 - HIP support + Used platform info logged in file + Multiple GPU support

Pull Request - State: closed - Opened by ed29rice over 3 years ago

#26 - Default platform precision

Issue - State: closed - Opened by ed29rice over 3 years ago - 1 comment

#25 - Custom Types scrambled energy interactions

Issue - State: closed - Opened by contessoto over 3 years ago - 1 comment
Labels: bug

#24 - Print cndbTools.load

Issue - State: closed - Opened by contessoto over 3 years ago
Labels: enhancement

#23 - Filename issue when saving a structure

Issue - State: closed - Opened by contessoto over 3 years ago - 3 comments
Labels: bug

#22 - Looplist filename wrong call

Issue - State: closed - Opened by contessoto over 3 years ago - 1 comment
Labels: bug

#21 - Add Requirements for docs

Pull Request - State: closed - Opened by contessoto over 3 years ago

#19 - add feature to create hic

Pull Request - State: closed - Opened by junioreif over 3 years ago

#18 - 'Finishing' the first major version of the documentation

Pull Request - State: closed - Opened by contessoto over 3 years ago

#17 - Writing more details on the documentation and renaming some functions

Pull Request - State: closed - Opened by contessoto over 3 years ago

#15 - Chromosome Initial Collapse

Issue - State: closed - Opened by contessoto over 3 years ago
Labels: enhancement

#14 - Double Check the chr_beads - typelist function

Issue - State: closed - Opened by contessoto over 3 years ago - 1 comment
Labels: invalid

#13 - Multi-chain Custom Ideal Chromosome

Issue - State: closed - Opened by contessoto over 3 years ago - 1 comment
Labels: enhancement

#12 - Increasing documentation

Pull Request - State: closed - Opened by contessoto over 3 years ago

#11 - Remove some unused functions and add more text in the documentation

Pull Request - State: closed - Opened by contessoto over 3 years ago

#10 - Improving documentation of ChromDynamics

Pull Request - State: closed - Opened by contessoto over 3 years ago

#9 - Vini branch

Pull Request - State: closed - Opened by contessoto over 3 years ago

#8 - fixing .bib

Pull Request - State: closed - Opened by contessoto over 3 years ago

#7 - Add flat harmonic restraint and small correction in Translate types

Pull Request - State: closed - Opened by junioreif over 3 years ago

#6 - Vini branch

Pull Request - State: closed - Opened by contessoto over 3 years ago