diff --git a/ChangeLog.md b/ChangeLog.md --- a/ChangeLog.md +++ b/ChangeLog.md @@ -2,6 +2,11 @@ ## Unreleased changes +## [0.1.1.2] - 2020-04-15 +### Changed +- Resolver version up. +- Move from `less-wrong` to `biocad`. + ## [0.1.1.1] - 2020-03-24 ### Fixed - Affine alignment matrix construction and traceback. diff --git a/README.md b/README.md --- a/README.md +++ b/README.md @@ -1,4 +1,4 @@ # cobot -[![Travis](https://img.shields.io/travis/less-wrong/cobot.svg)](https://travis-ci.org/less-wrong/cobot) -[![license](https://img.shields.io/github/license/less-wrong/cobot.svg)]() +[![Travis](https://img.shields.io/travis/biocad/cobot.svg)](https://travis-ci.org/less-wrong/cobot) +[![license](https://img.shields.io/github/license/biocad/cobot.svg)]() diff --git a/cobot.cabal b/cobot.cabal --- a/cobot.cabal +++ b/cobot.cabal @@ -1,130 +1,138 @@ cabal-version: 1.12 - --- This file has been generated from package.yaml by hpack version 0.31.2. --- --- see: https://github.com/sol/hpack --- --- hash: 19558d31d73118631f947a34b8de243404cf58e8942adbd414bf445b21381b86 - -name: cobot -version: 0.1.1.1 -synopsis: Computational biology toolkit to collaborate with researchers in constructive protein engineering -description: Please see the README on GitHub at -category: Bio -homepage: https://github.com/less-wrong/cobot#readme -bug-reports: https://github.com/less-wrong/cobot/issues -author: Pavel Yakovlev, Bogdan Neterebskii, Alexander Sadovnikov -maintainer: pavel@yakovlev.me -copyright: 2018—2019, Less Wrong Bio -license: BSD3 -license-file: LICENSE -build-type: Simple +name: cobot +version: 0.1.1.2 +license: BSD3 +license-file: LICENSE +copyright: 2018—2019, Less Wrong Bio +maintainer: pavel@yakovlev.me +author: Pavel Yakovlev, Bogdan Neterebskii, Alexander Sadovnikov +homepage: https://github.com/biocad/cobot#readme +bug-reports: https://github.com/biocad/cobot/issues +synopsis: Computational biology toolkit to collaborate with researchers in constructive protein engineering +description: + Please see the README on GitHub at +category: Bio +build-type: Simple extra-source-files: README.md ChangeLog.md source-repository head - type: git - location: https://github.com/less-wrong/cobot + type: git + location: https://github.com/biocad/cobot library - exposed-modules: - Bio.Chain - Bio.Chain.Alignment - Bio.Chain.Alignment.Algorithms - Bio.Chain.Alignment.Scoring - Bio.Chain.Alignment.Scoring.Loader - Bio.Chain.Alignment.Scoring.TH - Bio.Chain.Alignment.Type - Bio.Molecule - Bio.NucleicAcid.Chain - Bio.NucleicAcid.Nucleotide - Bio.NucleicAcid.Nucleotide.Instances - Bio.NucleicAcid.Nucleotide.Type - Bio.Protein.Algebra - Bio.Protein.AminoAcid - Bio.Protein.AminoAcid.Instances - Bio.Protein.AminoAcid.Type - Bio.Protein.Chain - Bio.Protein.Chain.Builder - Bio.Protein.Metric - Bio.Utils.Geometry - Bio.Utils.IUPAC - Bio.Utils.Matrix - Bio.Utils.Monomer - other-modules: - Paths_cobot - hs-source-dirs: - src - default-extensions: AllowAmbiguousTypes ConstraintKinds DeriveFoldable DeriveFunctor DeriveGeneric DeriveTraversable FlexibleContexts FlexibleInstances GeneralizedNewtypeDeriving MultiWayIf RankNTypes RecordWildCards ScopedTypeVariables TypeApplications TypeFamilies TypeSynonymInstances UndecidableInstances - build-depends: - array - , base >=4.7 && <5 - , bytestring - , containers - , deepseq - , lens - , linear - , megaparsec - , mtl - , split - , template-haskell - , text - default-language: Haskell2010 + exposed-modules: + Bio.Chain + Bio.Chain.Alignment + Bio.Chain.Alignment.Algorithms + Bio.Chain.Alignment.Scoring + Bio.Chain.Alignment.Scoring.Loader + Bio.Chain.Alignment.Scoring.TH + Bio.Chain.Alignment.Type + Bio.Molecule + Bio.NucleicAcid.Chain + Bio.NucleicAcid.Nucleotide + Bio.NucleicAcid.Nucleotide.Instances + Bio.NucleicAcid.Nucleotide.Type + Bio.Protein.Algebra + Bio.Protein.AminoAcid + Bio.Protein.AminoAcid.Instances + Bio.Protein.AminoAcid.Type + Bio.Protein.Chain + Bio.Protein.Chain.Builder + Bio.Protein.Metric + Bio.Utils.Geometry + Bio.Utils.IUPAC + Bio.Utils.Matrix + Bio.Utils.Monomer + hs-source-dirs: src + other-modules: + Paths_cobot + default-language: Haskell2010 + default-extensions: AllowAmbiguousTypes ConstraintKinds + DeriveFoldable DeriveFunctor DeriveGeneric DeriveTraversable + FlexibleContexts FlexibleInstances GeneralizedNewtypeDeriving + MultiWayIf RankNTypes RecordWildCards ScopedTypeVariables + TypeApplications TypeFamilies TypeSynonymInstances + UndecidableInstances + build-depends: + array >=0.5.4.0 && <0.6, + base >=4.7 && <5, + bytestring >=0.10.10.0 && <0.11, + containers >=0.6.2.1 && <0.7, + deepseq >=1.4.4.0 && <1.5, + lens >=4.18.1 && <4.19, + linear >=1.20.9 && <1.21, + megaparsec >=8.0.0 && <8.1, + mtl >=2.2.2 && <2.3, + split >=0.2.3.4 && <0.3, + template-haskell >=2.15.0.0 && <2.16, + text >=1.2.4.0 && <1.3 test-suite cobot-test - type: exitcode-stdio-1.0 - main-is: Spec.hs - other-modules: - HandcraftedSpec - JuliaSpec - Paths_cobot - hs-source-dirs: - test - default-extensions: AllowAmbiguousTypes ConstraintKinds DeriveFoldable DeriveFunctor DeriveGeneric DeriveTraversable FlexibleContexts FlexibleInstances GeneralizedNewtypeDeriving MultiWayIf RankNTypes RecordWildCards ScopedTypeVariables TypeApplications TypeFamilies TypeSynonymInstances UndecidableInstances - ghc-options: -threaded -rtsopts "-with-rtsopts=-A64m -qb0 -I0 -N -qn4" - build-depends: - array - , base >=4.7 && <5 - , bytestring - , cobot - , containers - , deepseq - , hspec - , lens - , linear - , megaparsec - , mtl - , split - , template-haskell - , text - default-language: Haskell2010 + type: exitcode-stdio-1.0 + main-is: Spec.hs + hs-source-dirs: test + other-modules: + HandcraftedSpec + JuliaSpec + Paths_cobot + default-language: Haskell2010 + default-extensions: AllowAmbiguousTypes ConstraintKinds + DeriveFoldable DeriveFunctor DeriveGeneric DeriveTraversable + FlexibleContexts FlexibleInstances GeneralizedNewtypeDeriving + MultiWayIf RankNTypes RecordWildCards ScopedTypeVariables + TypeApplications TypeFamilies TypeSynonymInstances + UndecidableInstances + ghc-options: -threaded -rtsopts + "-with-rtsopts=-A64m -qb0 -I0 -N -qn4" + build-depends: + array >=0.5.4.0 && <0.6, + base >=4.7 && <5, + bytestring >=0.10.10.0 && <0.11, + cobot -any, + containers >=0.6.2.1 && <0.7, + deepseq >=1.4.4.0 && <1.5, + hspec >=2.7.1 && <2.8, + lens >=4.18.1 && <4.19, + linear >=1.20.9 && <1.21, + megaparsec >=8.0.0 && <8.1, + mtl >=2.2.2 && <2.3, + split >=0.2.3.4 && <0.3, + template-haskell >=2.15.0.0 && <2.16, + text >=1.2.4.0 && <1.3 benchmark cobot-bench - type: exitcode-stdio-1.0 - main-is: Main.hs - other-modules: - Paths_cobot - hs-source-dirs: - bench - default-extensions: AllowAmbiguousTypes ConstraintKinds DeriveFoldable DeriveFunctor DeriveGeneric DeriveTraversable FlexibleContexts FlexibleInstances GeneralizedNewtypeDeriving MultiWayIf RankNTypes RecordWildCards ScopedTypeVariables TypeApplications TypeFamilies TypeSynonymInstances UndecidableInstances OverloadedStrings - ghc-options: -threaded -rtsopts "-with-rtsopts=-A64m -qb0 -I0 -N -qn4" - build-depends: - array - , base >=4.7 && <5 - , bytestring - , clock - , cobot - , containers - , criterion - , deepseq - , lens - , linear - , megaparsec - , mtl - , parallel - , random - , split - , template-haskell - , text - default-language: Haskell2010 + type: exitcode-stdio-1.0 + main-is: Main.hs + hs-source-dirs: bench + other-modules: + Paths_cobot + default-language: Haskell2010 + default-extensions: AllowAmbiguousTypes ConstraintKinds + DeriveFoldable DeriveFunctor DeriveGeneric DeriveTraversable + FlexibleContexts FlexibleInstances GeneralizedNewtypeDeriving + MultiWayIf RankNTypes RecordWildCards ScopedTypeVariables + TypeApplications TypeFamilies TypeSynonymInstances + UndecidableInstances OverloadedStrings + ghc-options: -threaded -rtsopts + "-with-rtsopts=-A64m -qb0 -I0 -N -qn4" + build-depends: + array >=0.5.4.0 && <0.6, + base >=4.7 && <5, + bytestring >=0.10.10.0 && <0.11, + clock ==0.8.*, + cobot -any, + containers >=0.6.2.1 && <0.7, + criterion >=1.5.6.2 && <1.6, + deepseq >=1.4.4.0 && <1.5, + lens >=4.18.1 && <4.19, + linear >=1.20.9 && <1.21, + megaparsec >=8.0.0 && <8.1, + mtl >=2.2.2 && <2.3, + parallel >=3.2.2.0 && <3.3, + random ==1.1.*, + split >=0.2.3.4 && <0.3, + template-haskell >=2.15.0.0 && <2.16, + text >=1.2.4.0 && <1.3 diff --git a/src/Bio/Protein/AminoAcid/Type.hs b/src/Bio/Protein/AminoAcid/Type.hs --- a/src/Bio/Protein/AminoAcid/Type.hs +++ b/src/Bio/Protein/AminoAcid/Type.hs @@ -1,13 +1,12 @@ +{-# LANGUAGE DeriveAnyClass #-} {-# LANGUAGE DeriveFunctor #-} {-# LANGUAGE TemplateHaskell #-} -{-# LANGUAGE DeriveAnyClass #-} module Bio.Protein.AminoAcid.Type where -import Control.DeepSeq (NFData (..)) +import Control.DeepSeq (NFData (..)) import Control.Lens -import Control.Monad.Identity (Identity) -import GHC.Generics (Generic (..)) +import GHC.Generics (Generic (..)) -- | Proteinogenic amino acids -- diff --git a/src/Bio/Protein/Chain/Builder.hs b/src/Bio/Protein/Chain/Builder.hs --- a/src/Bio/Protein/Chain/Builder.hs +++ b/src/Bio/Protein/Chain/Builder.hs @@ -5,20 +5,14 @@ , build ) where -import Data.Ix ( Ix ) import Control.Lens -import Linear.V3 ( V3 (..) - , cross - , _z - ) -import Linear.Vector ( negated - , unit - , (*^) - ) +import Data.Ix (Ix) +import Linear.V3 (V3 (..), _z) +import Linear.Vector (negated, unit, (*^)) -import Bio.Utils.Geometry hiding ( angle ) import Bio.Protein.AminoAcid import Bio.Protein.Chain +import Bio.Utils.Geometry hiding (angle) class Buildable a where type Monomer a :: * @@ -62,7 +56,7 @@ -- First: -- Ca_i N_i+1 C_i+1 -- * * * - -- + -- -- * * * -- N_i C_i Ca_i+1 -- Second: @@ -74,7 +68,7 @@ -- -- Let us enumerate atoms: 1 for N_i, 2 for Ca_i, 3 for C_i, 4 for N_i+1, 5 for Ca_i+1, 6 for C_i+1. -- We have to find points 4, 5, 6 using 1, 2, 3. To find this points let us introduce vectors named - -- like 'vij' from i to j, e.g. v12 is a vector from N_i to Ca_i. Our main idea will be to get a + -- like 'vij' from i to j, e.g. v12 is a vector from N_i to Ca_i. Our main idea will be to get a -- direction vector from i+1 to i, rotate it and then upscale by specified bond length. One thing to -- look at is the direction of rotations. If we have the first case, then the first rotation should be -- conterclock-wise, otherwise — clock-wise. To detect it we have to understand whether 3 is on the left