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Commits on Dec 9, 2024

• Updated to make class names in properties compliant with standard Python conventions and fixed bug in sequence_optimization

  ryanemenecker

  committed
  91438aa

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Commits on Nov 27, 2024

• Added additional properties for optimization, modified optimization kmer selection

  ryanemenecker

  committed
  3d416bd

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Commits on Nov 22, 2024

• another update to shuffling feature

  ryanemenecker

  committed
  7590bcc

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• modified shuffling in sequence optimization

  ryanemenecker

  committed
  bd9af27

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• bug fix in sequence optimziation

  ryanemenecker

  committed
  125c030

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Commits on Nov 20, 2024

• Updated readme.md to reflect updates

  ryanemenecker

  committed
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• Finished sequence_optimzation.py update, added properties epsilon and epsilon_vectors to properties.py to enable easy optimzation towards epsilon values

  ryanemenecker

  committed
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Commits on Nov 19, 2024

• continued improvements to sequence_optimization functionality. Small bug fix. Update to README.md.

  ryanemenecker

  committed
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Commits on Oct 31, 2024

• some fixes to sequence optimization function

  ryanemenecker

  committed
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Commits on Aug 16, 2024

• Merge pull request #2 from idptools/arbitrary_optimization

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  ryanemenecker

  authored
  55ee1c5

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• fixed backend bug

  ryanemenecker

  committed
  ce559a9

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Commits on Aug 13, 2024

• fixed backend bug

  ryanemenecker

  committed
  89dbe07

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Commits on Aug 5, 2024

• fixed formatting in README.md

  ryanemenecker

  committed
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Commits on Jul 23, 2024

• add amino acid pkl

  jlotthammer

  committed
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Commits on Jul 22, 2024

• bugfix on load config

  jlotthammer

  committed
  f13a344

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• properties to get_properties

  jlotthammer

  committed
  44ef507

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• updates for printing props

  jlotthammer

  committed
  f58e6fc

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• expose optimization code via sequence optimizer class

  jlotthammer

  committed
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Commits on Jul 5, 2024

• Merge branch 'main' of github.com:idptools/goose into arbitrary_optimization

  jlotthammer

  committed
  8a5856c

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• add initial code for arbitrary optimization problems

  jlotthammer

  committed
  a026791

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Commits on May 22, 2024

• Fixed a few bugs, added code to test perforance of seq generation using goose

  ryanemenecker

  committed
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Commits on May 17, 2024

• Updated to add CALVADOS2. Added ways to modulate interaction values between pairs of sequences. Made more efficient by preloading FINCHES model when using instead of iteratively having to load

  ryanemenecker

  committed
  f1409b9

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• improved efficiency for generating sequences by specific dimensions. Added backend functionality for sequence design by epsilon or epsilon interaction vectors

  ryanemenecker

  committed
  4a42e63

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Commits on May 15, 2024

• add get_data to init

  jlotthammer

  committed
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Commits on Mar 18, 2024

• Updated sequence creation by specifying Rg or Re to allow reduction of the number of positively charged residues.

  ryanemenecker

  committed
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Commits on Feb 7, 2024

• Change to backend of constant_class variant to make sure aromatics and positively charged residues can be interchanged when optimizing hydrophobicity.

  ryanemenecker

  committed
  d992edd

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• Fixed bug where charged residue and aromatic residue positions would not change within class for the constant_class variant generation.

  ryanemenecker

  committed
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Commits on Dec 11, 2023

• another quick bug fix

  ryanemenecker

  committed
  b5c6f6c

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• quick bug fix

  ryanemenecker

  committed
  cdc3929

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• added extensive sequence generation testing, fixed more bugs, improved sequence generation efficiency

  ryanemenecker

  committed
  1efc0a9

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Commits on Dec 5, 2023

• small bug fix

  ryanemenecker

  committed
  5cab3e0

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• Added thorough tests. Fixed bugs. Increased range of hydropathy values possible to make. Made sequence generation more robust

  ryanemenecker

  committed
  e7b868f

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Commits on Nov 27, 2023

• Update to increase max hydropathy value that GOOSE can make. Improvement in tests and exception handling

  ryanemenecker

  committed
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Commits on Nov 13, 2023

• Added upper version limit to be 3.11 due to versioneer incompatibility with 3.12

  alexholehouse

  committed
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Commits on Nov 11, 2023

• Added upper version limit to be 3.11 due to versioneer incompatibility with 3.12

  alexholehouse

  committed
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