gnina/libmolgrid issues and pull requests

#123 - add length and DDP support to MolIterDataset

Pull Request - State: closed - Opened by drewnutt 2 months ago - 1 comment

#122 - MolDataset -> MolMapDataset and MolIterDataset

Pull Request - State: open - Opened by drewnutt 3 months ago

#121 - Updated MolDataset

Pull Request - State: closed - Opened by drewnutt 3 months ago

#120 - Specifying grid centers for all Examples in a batch

Issue - State: closed - Opened by jacobdurrant 4 months ago - 2 comments

#119 - Saving in-memory cache to disk

Issue - State: closed - Opened by jacobdurrant 4 months ago - 8 comments

#118 - How can I visualize my voxel grid

Issue - State: closed - Opened by drorhunvural 9 months ago - 1 comment

#117 - Simple example of multi-atom molecule to density to molecule

Issue - State: closed - Opened by GregorySchwing 12 months ago - 4 comments

#116 - General Question about AtomTyping

Issue - State: closed - Opened by GregorySchwing 12 months ago - 2 comments

#115 - SystemError importing molgrid

Issue - State: closed - Opened by niccolo93 12 months ago - 3 comments

#114 - Issue when install libmolgrid from source

Issue - State: closed - Opened by JonasLi-19 about 1 year ago - 9 comments

#113 - example code in libmolgrid github

Issue - State: open - Opened by croshong over 1 year ago - 4 comments

#112 - Bump nokogiri from 1.13.7 to 1.14.3 in /docs

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago - 1 comment
Labels: dependencies

#111 - libmolgrid install error

Issue - State: open - Opened by croshong over 1 year ago - 1 comment

#110 - .

Issue - State: closed - Opened by ckami12138 over 1 year ago

#109 - Taking care of each region when creating a gninatype

Issue - State: open - Opened by drorhunvural over 1 year ago - 1 comment

#108 - libmolgrid install in python2

Issue - State: closed - Opened by croshong over 1 year ago - 1 comment

#107 - data_root error while defining ExampleProvider

Issue - State: open - Opened by drorhunvural over 1 year ago - 3 comments

#106 - Is there a relationship between dataset structure and ExampleProvider

Issue - State: closed - Opened by drorhunvural over 1 year ago - 5 comments

#105 - The ExampleProvider populate part is not working properly.

Issue - State: closed - Opened by drorhunvural over 1 year ago - 7 comments

#104 - Attempting compilation for unknown architectures

Issue - State: closed - Opened by chedatomasz over 1 year ago - 1 comment

#103 - Bump nokogiri from 1.13.7 to 1.14.1 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago - 2 comments
Labels: dependencies

#102 - Bump activesupport from 6.0.4 to 6.0.6.1 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#101 - libmolgrid issues about stratifying receptors

Issue - State: open - Opened by YanjingLiLi over 1 year ago - 1 comment

#100 - libmolgrid issue

Issue - State: open - Opened by amarye almost 2 years ago - 4 comments

#99 - Libmolgrid does not provide consistent batching

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

#98 - Conda forge package

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

#97 - Bump nokogiri from 1.13.7 to 1.13.9 in /docs

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 2 comments
Labels: dependencies

#96 - File Format Question

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

#95 - missing cuda know drivers to

Issue - State: open - Opened by EricDeveaud about 2 years ago

#94 - arm64 architecture support

Issue - State: closed - Opened by czabriskie about 2 years ago - 1 comment

#93 - Pip Installation Error

Issue - State: closed - Opened by drorhunvural about 2 years ago - 1 comment

#92 - Bump nokogiri from 1.13.4 to 1.13.7 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#91 - Bump tzinfo from 1.2.9 to 1.2.10 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#90 - Cannot pip install

Issue - State: closed - Opened by emarsh25 about 2 years ago - 3 comments

#89 - Bump nokogiri from 1.13.4 to 1.13.6 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#88 - Bump nokogiri from 1.12.5 to 1.13.4 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#87 - Error in pytest

Issue - State: open - Opened by lh12565 over 2 years ago - 5 comments

#86 - Bump nokogiri from 1.12.5 to 1.13.3 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 2 comments
Labels: dependencies

#85 - Installation

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

#84 - cannot install from source (make error)

Issue - State: open - Opened by sll513 over 2 years ago - 6 comments

#83 - CUDA error

Issue - State: open - Opened by JIBSN over 2 years ago - 2 comments

#82 - Is there any plan of making an OpenCL accelerated version for non-CUDA users?

Issue - State: open - Opened by CoryKornowicz over 2 years ago - 1 comment

#81 - make error

Issue - State: open - Opened by hanshangjin almost 3 years ago - 3 comments

#80 - can I get point clouds?

Issue - State: open - Opened by likun1212 almost 3 years ago - 1 comment

#79 - process froze when calling next_batch

Issue - State: open - Opened by yuanqidu almost 3 years ago - 7 comments

#78 - Consistency of Voxels from PDB format versus gninatypes

Issue - State: closed - Opened by JoshuaMeyers almost 3 years ago - 6 comments

#77 - Iterating over ExampleDataset

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

#76 - Protein only

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

#75 - Operating on pairs of inputs

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

#74 - cmake error

Issue - State: open - Opened by HBioquant almost 3 years ago - 1 comment

#73 - Memory leak using CoordinateSet init with OBMol

Issue - State: closed - Opened by bbaillif almost 3 years ago - 2 comments

#72 - how to make the grid density much sharper?

Issue - State: closed - Opened by yangxiufengsia about 3 years ago - 2 comments

#71 - Bump nokogiri from 1.12.3 to 1.12.5 in /docs

Pull Request - State: closed - Opened by dependabot[bot] about 3 years ago
Labels: dependencies

#70 - Imports fail in "Grid single molecule" tutorial

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

#69 - How to voxelize a single .pdb file?

Issue - State: closed - Opened by mangalp about 3 years ago - 2 comments

#68 - Is it possible to know the set of examples next_batch extracts?

Issue - State: closed - Opened by shikhar2333 about 3 years ago - 4 comments

#67 - atom type values higher than 1 when resolution is 1

Issue - State: closed - Opened by mgm-14392 about 3 years ago - 3 comments

#66 - "CUDA Error: invalid argument" when use molgrid.GridMaker in multi-GPU setting

Issue - State: closed - Opened by KuNyaa about 3 years ago - 4 comments

#65 - RDKit failures if molgrid is imported first

Issue - State: open - Opened by RMeli over 3 years ago - 5 comments

#64 - Behavior for only ligands in types file and ExampleProvider

Issue - State: closed - Opened by mgm-14392 over 3 years ago - 2 comments

#63 - MolDataset Test Fixes and Collate Function

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

#62 - Segmentation fault with CoordinateSet in Python

Issue - State: open - Opened by RMeli over 3 years ago - 7 comments

#61 - Missing attribute version

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

#60 - Does libmolgrid allows pytorch distribtued data parallel?

Issue - State: closed - Opened by yangxiufengsia over 3 years ago - 20 comments

#59 - Fail to import the MolDataset

Issue - State: closed - Opened by wenxianxian over 3 years ago - 4 comments

#58 - libmolgrid fails at make

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

#57 - Grids are not centered when dimension is not divisible by resolution

Issue - State: open - Opened by mattragoza over 3 years ago
Labels: bug

#56 - What is the input format?

Issue - State: closed - Opened by mgarort over 3 years ago - 4 comments

#55 - Question about atom_typer.cpp

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

#54 - MolDataset fixes

Pull Request - State: closed - Opened by drewnutt over 3 years ago - 1 comment

#53 - fixed keyword args errors with ExampleDataset

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

#52 - Cleaned up MolDataset

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

#51 - visualization of grid density of protein-ligand

Issue - State: closed - Opened by yangxiufengsia over 3 years ago - 13 comments

#50 - does libmolgrid automatically center the grid around ligand?

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

#49 - PyTest confitest file

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

#48 - what is the input format for ligand only

Issue - State: closed - Opened by yangxiufengsia almost 4 years ago - 2 comments

#47 - Question: access or enforce grid center in Gridmaker forward()

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

#46 - Memory leak using cache_structs

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

#45 - Memory leak when using cache_mols

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

#44 - Using GninaVectorTyper creates 'NaN' values

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

#43 - Forces CUDA Device 0

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

#42 - conda obabel and molgrid

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

#41 - duplicate_poses was never being updated according to the settings

Pull Request - State: closed - Opened by Jsunseri over 4 years ago

#40 - problem with type conversion?

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

#39 - backward_grad() to help with backprop from atomic gradient loss

Pull Request - State: closed - Opened by RishalAggarwal over 4 years ago

#38 - 1-cossim() loss on atom gradients

Pull Request - State: closed - Opened by RishalAggarwal over 4 years ago

#37 - Troubles compiling libmolgrid

Issue - State: closed - Opened by wquc over 4 years ago - 6 comments

#36 - backward_grad() for higher order grid gradients

Pull Request - State: closed - Opened by RishalAggarwal over 4 years ago

#35 - Bump nokogiri from 1.10.4 to 1.10.9 in /docs

Pull Request - State: closed - Opened by dependabot[bot] over 4 years ago - 1 comment
Labels: dependencies

#34 - cmake error

Issue - State: closed - Opened by hnljq over 4 years ago - 3 comments

#33 - Question about center of the grid

Issue - State: closed - Opened by koshkabb over 4 years ago - 3 comments

#32 - Segmentation fault

Issue - State: closed - Opened by koshkabb over 4 years ago - 17 comments

#31 - libmolgrid on OS X?

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

#30 - update docs

Pull Request - State: closed - Opened by Jsunseri over 4 years ago

#29 - Can't use ExempleProvider.populate()

Issue - State: closed - Opened by mpds over 4 years ago - 16 comments

#28 - update docs to refer to ExampleProviderSettings from ExampleProvider

Pull Request - State: closed - Opened by Jsunseri over 4 years ago

#27 - more python constructor info, emphasize that documentation of setting…

Pull Request - State: closed - Opened by Jsunseri over 4 years ago

#26 - remove unused initialized variable

Pull Request - State: closed - Opened by Jsunseri over 4 years ago

#25 - type_size -> num_types in README

Pull Request - State: closed - Opened by Jsunseri over 4 years ago

#24 - use num_types instead of type_size

Pull Request - State: closed - Opened by Jsunseri over 4 years ago

GitHub / gnina/libmolgrid issues and pull requests