hPDB 1.2.0 → 1.2.0.1
raw patch · 3 files changed
+30/−3 lines, 3 filesdep ~basePVP: major bump suggested
API removals or changes: PVP suggests a major version bump
Dependency ranges changed: base
API changes (from Hackage documentation)
- Bio.PDB: covalentRadius :: (Eq a1, Fractional a, Show a1, IsString a1) => a1 -> a
+ Bio.PDB: covalentRadius :: (IsString a1, Show a1, Fractional a, Eq a1) => a1 -> a
- Bio.PDB.EventParser.HelixTypes: code2helix :: (Eq a, Num a) => a -> HelixT
+ Bio.PDB.EventParser.HelixTypes: code2helix :: (Num a, Eq a) => a -> HelixT
- Bio.PDB.EventParser.PDBEvents: Vector3 :: !Scalar -> !Scalar -> !Scalar -> Vector3
+ Bio.PDB.EventParser.PDBEvents: Vector3 :: UnpkScalar -> UnpkScalar -> UnpkScalar -> Vector3
- Bio.PDB.EventParser.PDBEvents: v3x :: Vector3 -> !Scalar
+ Bio.PDB.EventParser.PDBEvents: v3x :: Vector3 -> UnpkScalar
- Bio.PDB.EventParser.PDBEvents: v3y :: Vector3 -> !Scalar
+ Bio.PDB.EventParser.PDBEvents: v3y :: Vector3 -> UnpkScalar
- Bio.PDB.EventParser.PDBEvents: v3z :: Vector3 -> !Scalar
+ Bio.PDB.EventParser.PDBEvents: v3z :: Vector3 -> UnpkScalar
- Bio.PDB.Structure.Elements: covalentRadius :: (Eq a1, Fractional a, Show a1, IsString a1) => a1 -> a
+ Bio.PDB.Structure.Elements: covalentRadius :: (IsString a1, Show a1, Fractional a, Eq a1) => a1 -> a
- Bio.PDB.Structure.Vector: Vector3 :: !Scalar -> !Scalar -> !Scalar -> Vector3
+ Bio.PDB.Structure.Vector: Vector3 :: UnpkScalar -> UnpkScalar -> UnpkScalar -> Vector3
- Bio.PDB.Structure.Vector: v3x :: Vector3 -> !Scalar
+ Bio.PDB.Structure.Vector: v3x :: Vector3 -> UnpkScalar
- Bio.PDB.Structure.Vector: v3y :: Vector3 -> !Scalar
+ Bio.PDB.Structure.Vector: v3y :: Vector3 -> UnpkScalar
- Bio.PDB.Structure.Vector: v3z :: Vector3 -> !Scalar
+ Bio.PDB.Structure.Vector: v3z :: Vector3 -> UnpkScalar
- Bio.PDB.StructureBuilder: parseParallel :: [Char] -> ByteString -> (Structure, List PDBEvent)
+ Bio.PDB.StructureBuilder: parseParallel :: FilePath -> ByteString -> (Structure, List PDBEvent)
- Bio.PDB.StructureBuilder: parseWithNParallel :: Integral a => a -> [Char] -> ByteString -> (Structure, List PDBEvent)
+ Bio.PDB.StructureBuilder: parseWithNParallel :: Integral a => a -> FilePath -> ByteString -> (Structure, List PDBEvent)
Files
- README.md +24/−0
- changelog +3/−0
- hPDB.cabal +3/−3
README.md view
@@ -19,3 +19,27 @@ Details on official releases are on [Hackage](https://hackage.haskell.org/package/hPDB) This package is also a part of [Stackage](http://daniel-diaz.github.io/stackagelist/) - a stable subset of Hackage.++Projects for the future:+------------------------++Please let me know if you would be willing to push the project further.++In particular one may considering these features:++* Migrate out of `text-format`, since it gives portability trouble, and slows things down when printing.+* Migrate from `AC-Vector` to another vector library:+ - `vector-space`+ - or `linear`+* Use `lens` to facilitate access to the data structures.+ - torsion angles within protein/RNA chain.+* Add Octree to the default data structure (with automatic update.)+* Write a combinator library for generic fast parsing.+* Checking whether GHC 7.8 improved efficiency of fixed point arithmetic,+since PDB coordinates have dynamic range of just ~2^20 bits, with smallest+step of 0.001.+* Implement basic spatial operations of RMS superposition (with SVD),+affine transform on a substructure.+* Class-based wrappers showing Structure-Model-Chain-Residue-Atom interface+with possible wrapping of Repa/Accelerate arrays for fast computation.+
changelog view
@@ -1,5 +1,8 @@ -*-Changelog-*- +1.2.0.1 Dec 2014+ * Relaxed upper bounds+ 1.2.0 May 2014 * Iterable 3.0
hPDB.cabal view
@@ -1,5 +1,5 @@ name: hPDB-version: 1.2.0+version: 1.2.0.1 synopsis: Protein Databank file format library homepage: https://github.com/BioHaskell/hPDB stability: stable@@ -53,11 +53,11 @@ due to GHC bug #5289: . http://ghc.haskell.org/trac/ghc/ticket/5289- default: True+ default: False Library ghc-options: -fspec-constr-count=4 -O3 - build-depends: base>=4.0, base <4.8, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, QuickCheck >= 2.5.0.0, text>=0.11.1.13, iterable >= 3.0, tagged >= 0.7, parallel >= 3.0.0.0, bytestring, zlib, Octree>= 0.5+ build-depends: base>=4.0, base <4.9, ghc-prim, directory, mtl, template-haskell, vector, AC-Vector, containers, deepseq, QuickCheck >= 2.5.0.0, text>=0.11.1.13, iterable >= 3.0, tagged >= 0.7, parallel >= 3.0.0.0, bytestring, zlib, Octree>= 0.5 if flag(have-sse2) ghc-options: -msse2 if flag(have-mmap)