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Bond-Angle-Torsions coordinate module (#2668)
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* new MDAnalysis.analysis.bat module: convert between internal bond-angle-torsion and
   Cartesian coordinates (based on published research)
   * standard analysis class
   * can load and save results (numpy format)
   * references with duecredit
* tests
* docs with example
* update CHANGELOG and AUTHORS
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daveminh authored Jul 1, 2020
1 parent 3d95282 commit 8314f7d
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18 changes: 10 additions & 8 deletions package/CHANGELOG
Original file line number Diff line number Diff line change
Expand Up @@ -13,7 +13,8 @@ The rules for this file:
* release numbers follow "Semantic Versioning" http://semver.org

------------------------------------------------------------------------------
??/??/?? richardjgowers, IAlibay, hmacdope, orbeckst, cbouy, lilyminium
??/??/?? richardjgowers, IAlibay, hmacdope, orbeckst, cbouy, lilyminium,
daveminh

* 2.0.0

Expand All @@ -25,13 +26,14 @@ Fixes
* Testsuite does not any more matplotlib.use('agg') (#2191)

Enhancements
* Added the RDKitParser which creates a `core.topology.Topology` object from
an `rdkit.Chem.rdchem.Mol` object, and the RDKitReader to read coordinates
* Added the RDKitParser which creates a `core.topology.Topology` object from
an `rdkit.Chem.rdchem.Mol` object, and the RDKitReader to read coordinates
from RDKit conformers (Issue #2468, PR #2707)
* Added the `Aromaticities` topology attribute, and the `aromatic` selection
* Added the `Aromaticities` topology attribute, and the `aromatic` selection
token (Issue #2468, PR #2707)
* Added the `from_smiles` classmethod to the Universe (Issue #2468, PR #2707)
* Added computation of Mean Squared Displacements (#2438, PR #2619)
* Added converter between Cartesian and Bond-Angle-Torsion coordinates (PR #2668)

Changes
* Changes development status from Beta to Mature (Issue #2773)
Expand Down Expand Up @@ -67,7 +69,7 @@ Fixes
(Issue #2565)
* Made NoDataError a subclass of ValueError *and* AttributeError
(Issue #2635)
* Fixed select_atoms("around 0.0 ...") selections and capped_distance
* Fixed select_atoms("around 0.0 ...") selections and capped_distance
causing a segfault (Issue #2656 PR #2665)
* `PDBWriter` writes unitary `CRYST1` record (cubic box with sides of 1 Å)
when `u.dimensions` is `None` or `np.zeros(6)` (Issue #2679, PR #2685)
Expand All @@ -77,7 +79,7 @@ Fixes
* n_components correctly selects PCA components (Issue #2623)
* Use internal residue indices instead of resids for similarity and connectivity
selections (Issues #2669 and #2672, PR #2673)
* Checks for cryo-em 1 A^3 default CRYST1 record,
* Checks for cryo-em 1 A^3 default CRYST1 record,
disabling setting of box dimensions if found (Issue #2599)
* mdamath.angles now returns np.pi instead of -np.pi in cases of
lower bound roundoff errors. (Issue #2632, PR #2634)
Expand Down Expand Up @@ -138,7 +140,7 @@ Fixes
Enhancements
* Added support for FHI-AIMS input files (PR #2705)
* vastly improved support for 32-bit Windows (PR #2696)
* Added methods to compute the root-mean-square-inner-product of subspaces
* Added methods to compute the root-mean-square-inner-product of subspaces
and the cumulative overlap of a vector in a subspace for PCA (PR #2613)
* Added .frames and .times arrays to AnalysisBase (Issue #2661)
* Added elements attribute to PDBParser (Issue #2553, #2647)
Expand Down Expand Up @@ -185,7 +187,7 @@ Enhancements

Changes
* Unused `MDAnalysis.lib.mdamath._angle` has been removed (Issue #2650)
* Refactored dihedral selections and Ramachandran.__init__ to speed up
* Refactored dihedral selections and Ramachandran.__init__ to speed up
dihedral selections for faster tests (Issue #2671, PR #2706)
* Removes the deprecated `t0`, `tf`, and `dtmax` from
:class:Waterdynamics.SurvivalProbability. Instead the `start`, `stop` and
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