Code

Release #76

Code

Merged

prtos merged 160 commits intodevelopvalence-labs/OpenQDC:developfrom releasevalence-labs/OpenQDC:releaseCopy head branch name to clipboardJun 8, 2024

+6,567-4,763

Commits

Commits on Mar 22, 2024

• WIP

  

  FNTwin

  committed
  9a11358

• WIP

  

  FNTwin

  committed
  9745b4c

• Moved function to utils.io

  

  FNTwin

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  8835b8f

• Additional dependencies

  

  FNTwin

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  9a2e1d8

• Removed Mixin

  

  FNTwin

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  6dd9be6

• WIP Preprocess + property

  

  FNTwin

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  78c9f15

• Refactored Descriptor class

  

  FNTwin

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  55a6692

• Removed not used funcs

  

  FNTwin

  committed
  5b6ec7e

Commits on Mar 24, 2024

• Added support to get torch or jax tensors

  

  Nikhil Shenoy

  committed
  cbb494c

• Added support to get torch or jax tensors

  

  Nikhil Shenoy

  committed
  e22651f

• undo change

  

  Nikhil Shenoy

  committed
  0f59a04

• Added transform functionality test

  

  Nikhil Shenoy

  committed
  29929cf

Commits on Mar 25, 2024

• Added ACSF

  

  FNTwin

  committed
  736c12a

• Conversion dataset to extxyz

  

  FNTwin

  committed
  73a3443

• Updated code based on comments

  

  Nikhil Shenoy

  committed
  1c77666

• Added list check from convert dict keys

  

  Nikhil Shenoy

  committed
  327e363

• First implementation XYZ reader

  

  FNTwin

  committed
  5c16f79

• Import fix

  

  FNTwin

  committed
  8503b98

• test skipping if package noot present

  

  Nikhil Shenoy

  committed
  5139a57

• XYZDataset, FromFileDataset, Write interaction xyz

  

  FNTwin

  committed
  3fb274c

• Fixes

  

  FNTwin

  committed
  3b4823e

• Many-body Tensor Representation

  

  FNTwin

  committed
  356adb1

• Included dscribe in main deps, removed torch and jax

  

  FNTwin

  committed
  20caa4f

Commits on Mar 26, 2024

• wip

  

  FNTwin

  committed
  38675f3

• MTBR incorrect signature Fix (Thanks Danny)

  

  FNTwin

  committed
  4dd2af8

• Added jax/tensor support to interaction datasets

  

  Nikhil Shenoy

  committed
  fa141f5

• refactor interaction and initial testing

  

  Nikhil Shenoy

  committed
  31beb71

• minor changes

  

  Nikhil Shenoy

  committed
  dccf676

• dummy modification

  

  Nikhil Shenoy

  committed
  2ab64aa

• removed redundant line

  

  Nikhil Shenoy

  committed
  5197e32

• minor change

  

  Nikhil Shenoy

  committed
  d10b15b

Commits on Mar 27, 2024

• State Manager and Chain of Management

  

  FNTwin

  committed
  cb30c16

• Adressed comments + xyz file tests

  

  FNTwin

  committed
  ce8e2b5

Commits on Mar 28, 2024

• create method enums and refactor the rest accordingly

  prtos

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  dc74dd6

• adding new files

  prtos

  committed
  c34e53f

• fix import issues and update API doc files

  prtos

  committed
  ef4581d

• WIP

  

  FNTwin

  committed
  571b706

• Separated Statistics and Atom Energies

  

  FNTwin

  committed
  e6d51b7

• ATOM_TABLE import fix

  prtos

  committed
  05d39c9

Commits on Mar 29, 2024

• undo changes in interaction dataset, and minor change in shape

  

  Nikhil Shenoy

  committed
  189ab90

• QmInteractionMethod added

  prtos

  committed
  5ee18c2

• rename QmMethod classes

  prtos

  committed
  69c081f

Commits on Mar 30, 2024

• WIP

  

  FNTwin

  committed
  7a20193

Commits on Apr 1, 2024

• adding a missing file

  prtos

  committed
  b97cf25

• pre-commit

  

  Nikhil Shenoy

  committed
  4eff5f4

Commits on Apr 2, 2024

• changed super class to BaseInteractionDataset

  

  Nikhil Shenoy

  committed
  282dc91

• Parallelized function, better calculate specs, docstrings

  

  FNTwin

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  cef2b35

• descriptor tests

  

  FNTwin

  committed
  dbdd985

• Regression + Statistics abstraction

  

  FNTwin

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  c7ab437

• Docs+names

  

  FNTwin

  committed
  5cebb80

• added correction method

  prtos

  committed
  e3c4fcf

• Regressor tests

  

  FNTwin

  committed
  fe4b86a

• Fixed test

  

  FNTwin

  committed
  b968257

• :/

  

  FNTwin

  committed
  096b1a0

• Except linalgerror

  

  FNTwin

  committed
  c0b6131

• Merge branch 'refactoring_by_P' of https://github.com/OpenDrugDiscovery/openQDC into refactoring_by_P

  prtos

  committed
  a0ad3ab

• added correction method

  prtos

  committed
  fe2d9bd

• fixed pre-commits

  

  Nikhil Shenoy

  committed
  496267f

• missing import

  

  Nikhil Shenoy

  committed
  b4bb0f3

• str fix in cli

  

  Nikhil Shenoy

  committed
  085b933

• updated python version since strenum from py>3.11

  

  Nikhil Shenoy

  committed
  5fe28ce

Commits on Apr 3, 2024

• py3.8 compatibility, manual fixes to atom energies

  

  FNTwin

  committed
  05a6dbf

• pkgutils

  

  FNTwin

  committed
  65a8a12

• some debugging

  

  FNTwin

  committed
  3b4199f

• Merge pull request #75 from OpenDrugDiscovery/corrections

  Show description for 2513695
  FNTwin

  authored
  2513695

• Merge branch 'refactor' into pattern

  

  FNTwin

  committed
  6eabc0d

• Solved merged issues, added NONE PotentialMethod

  

  FNTwin

  committed
  2f6eddb

• Merge pull request #72 from OpenDrugDiscovery/refactoring_by_P

  Show description for 9574974
  FNTwin

  authored
  9574974

• Merge branch 'release' into testing

  

  Nikhil Shenoy

  committed
  701ef1e

• further simplified and rebase

  

  Nikhil Shenoy

  committed
  afea053

Commits on Apr 4, 2024

• Adressed comments, fixed NullEnergy e0s_matrix

  

  FNTwin

  committed
  34922c3

• Updated stats vector shape to atleast_2d

  

  FNTwin

  committed
  71113c0

• Solved merge issues, added some fixes

  

  FNTwin

  committed
  955e787

• fixes to xyz

  

  FNTwin

  committed
  1f9bb94

• Added log message

  

  FNTwin

  committed
  41a52d6

• Merge pull request #74 from OpenDrugDiscovery/pattern

  Show description for 247b0e1
  FNTwin

  authored
  247b0e1

• Merge branch 'release' into dataloader

  

  Nikhil Shenoy

  committed
  e331cc6

• Updated array stuff for xyz dataset

  

  Nikhil Shenoy

  committed
  1c10566

• Merge branch 'release' into dataloader

  

  Nikhil Shenoy

  committed
  f1769b3

• fix bug during rebase and tests

  

  Nikhil Shenoy

  committed
  ba22ee1

• array test debug

  

  Nikhil Shenoy

  committed
  ac593e3

• undo test change and reset state

  

  Nikhil Shenoy

  committed
  6f0d46f

• cleaner variant

  

  Nikhil Shenoy

  committed
  a8d0016

Commits on Apr 5, 2024

• Merge pull request #55 from OpenDrugDiscovery/dataloader

  Show description for ac299a5
  shenoynikhil

  authored
  ac299a5

• simplified component-wise-force stats calculation and bug-fix

  

  Nikhil Shenoy

  committed
  40d900d

• Loading stats with the right format

  

  Nikhil Shenoy

  committed
  a21cb18

• Bug fix in convert_array for interaction

  

  Nikhil Shenoy

  committed
  23f8a8b

• Better stats conversion, fixed a reference leak

  FNTwin

  committed
  d5a139b

• Test dataset

  FNTwin

  committed
  908ec35

• Merge branch 'simplify' of https://github.com/OpenDrugDiscovery/openQDC into simplify

  FNTwin

  committed
  55d9e68

• fixes

  

  Nikhil Shenoy

  committed
  ebc2adf

• Merge remote-tracking branch 'origin/release' into testing

  

  Nikhil Shenoy

  committed
  7ffd0b1

• removed ravel

  FNTwin

  committed
  a9c8f66

• Merge pull request #78 from OpenDrugDiscovery/simplify

  Show description for a71f4d7
  FNTwin

  authored
  a71f4d7

• Merge remote-tracking branch 'origin/release' into testing

  

  Nikhil Shenoy

  committed
  d15e9cf

• Updated metcalf

  

  Nikhil Shenoy

  committed
  ed8e264

Commits on Apr 6, 2024

• bug fix and simplifying interaction dataset

  

  Nikhil Shenoy

  committed
  18bc79c

• Updated tests for interaction datasets

  

  Nikhil Shenoy

  committed
  2a6e3ef

• removed stale stats in dummy interaction

  

  Nikhil Shenoy

  committed
  7493273

• changes based on comments

  

  Nikhil Shenoy

  committed
  ed73e7d

• Clean metcalf

  FNTwin

  committed
  0359022

• Simplification

  FNTwin

  committed
  33fa342

• cleaned des

  FNTwin

  committed
  cd486a8

• Simplified des dataset

  FNTwin

  committed
  80d7371

• removed redundant dataset files

  FNTwin

  committed
  f3d205c

• DES inerithance

  FNTwin

  committed
  da4fece

• Removed des and improved des naming

  FNTwin

  committed
  71ff741

• DES fixes

  FNTwin

  committed
  f6e12e1

• Removed comments

  FNTwin

  committed
  3328a65

• X40 and L70

  FNTwin

  committed
  8b28d59

• Safe opening

  FNTwin

  committed
  8595fd8

• Moved X40 in L7 and removed x40.py

  FNTwin

  committed
  ca1b4af

Commits on Apr 7, 2024

• Moved Yaml utils to _utils.py, L7 + X40 interface

  FNTwin

  committed
  4bec82d

Commits on Apr 8, 2024

• Merge testing + Add imports

  FNTwin

  committed
  a5ced0a

• Merge pull request #79 from OpenDrugDiscovery/interaction_impr

  Show description for a21963e
  shenoynikhil

  authored
  a21963e

Commits on Apr 12, 2024

• better convert function and n_body_first to ptr

  

  Nikhil Shenoy

  committed
  3303f95

Commits on Apr 13, 2024

• Preprocess cli + optional upload to preprocess

  FNTwin

  committed
  c8d245f

Commits on Apr 15, 2024

• Updated splinter reading from -1 to nan

  

  Nikhil Shenoy

  committed
  6f033cf

Commits on Apr 16, 2024

• Merge branch 'testing' into local_fetch

  

  FNTwin

  committed
  3d81df2

• Cli exception

  

  FNTwin

  committed
  6027ab0

• Fixes to x40,l7 preproc

  

  FNTwin

  committed
  970082d

• atom.txt packaging

  

  FNTwin

  committed
  486a59f

• Added init exc F405, F401 to toml

  

  FNTwin

  committed
  77e5e26

Commits on Apr 17, 2024

• Datasets from data generation

  

  FNTwin

  committed
  69df015

Commits on Apr 18, 2024

• Fixes for uploading

  

  FNTwin

  committed
  b0d8e0c

• Append to extend, metcalf

  

  FNTwin

  committed
  798f861

• Dummy fix

  

  FNTwin

  committed
  565dc26

• SpiceVL2

  

  FNTwin

  committed
  dcc1b6b

• Merge pull request #81 from OpenDrugDiscovery/spicevl2

  Show description for c88e18e
  FNTwin

  authored
  c88e18e

Commits on Apr 22, 2024

• WIP float64 conv

  

  FNTwin

  committed
  7f7b651

• fix small bug with DES subsets

  mcneela

  committed
  828e765

• Updated to float64

  

  FNTwin

  committed
  0b9404e

• Interaction float32

  

  FNTwin

  committed
  95f926d

Commits on Apr 23, 2024

• updated DES dataset subset handling

  mcneela

  committed
  d2cd5be

• Updated spiceV2 subsets

  

  FNTwin

  committed
  7a82b59

• Merge pull request #82 from OpenDrugDiscovery/subset-fix

  Show description for 82de349
  mcneela

  authored
  82de349

• Updated ani read_raw_energies

  

  FNTwin

  committed
  603496b

Commits on Apr 24, 2024

• Fixes + MD22

  

  FNTwin

  committed
  7eb6a1e

• Remove DataConfig WIP

  

  FNTwin

  committed
  2a292ab

• Fixed gdml read_raw_entries

  

  FNTwin

  committed
  be82226

• Fixed comp6 read_raw_entries

  

  FNTwin

  committed
  6a65923

• Added links

  

  FNTwin

  committed
  50823d0

• Logging, fixes to qmugs

  

  FNTwin

  committed
  22d0bf5

Commits on Apr 26, 2024

• Removed wip files

  

  FNTwin

  committed
  051c084

• Removed dataloader, converted mmap test files

  

  FNTwin

  committed
  703cca3

• Merge pull request #83 from OpenDrugDiscovery/float64

  Show description for 0c3f54a
  FNTwin

  authored
  0c3f54a

Commits on May 1, 2024

• Conversion of en fixes + datastructure for e0s_dict and retriaval of covs

  FNTwin

  committed
  cb6dbaf

• Tests

  FNTwin

  committed
  da767ef

• Added _original_unit to xyz

  FNTwin

  committed
  b8791d6

• Disable mkdocs

  

  FNTwin

  committed
  6abe893

• I hate mkdocs errors

  

  FNTwin

  committed
  8d21e15

• mkdocs action

  

  FNTwin

  committed
  46bc652

Commits on May 2, 2024

• Docstrings + naming

  FNTwin

  committed
  2f4b692

• Merge pull request #85 from OpenDrugDiscovery/atom_ener_structure

  Show description for dcd1bea
  FNTwin

  authored
  dcd1bea

• docstring

  FNTwin

  committed
  2669d21

Commits on May 6, 2024

• Issue fix

  

  FNTwin

  committed
  fcaed00

Commits on May 30, 2024

• fix metcalf dataset energies and reupload

  mcneela

  committed
  34f36b0

Commits on Jun 1, 2024

• Merge pull request #91 from OpenDrugDiscovery/fix-metcalf

  Show description for e85839a
  mcneela

  authored
  e85839a

Commits on Jun 8, 2024

• Merge pull request #84 from OpenDrugDiscovery/downloader

  Show description for 318e9c5
  prtos

  authored
  318e9c5

• Merge pull request #88 from OpenDrugDiscovery/forcemaskfix

  Show description for 10dc009
  prtos

  authored
  10dc009