MDAnalysis 2.8.0__tar.gz → 2.10.0__tar.gz

{mdanalysis-2.8.0 → mdanalysis-2.10.0}/AUTHORS

@@ -82,7 +82,7 @@ Chronological list of authors
   - Shantanu Srivastava
   - Pedro Reis
   - Zhenbo Li
- 2017
+2017
   - Ruggero Cortini
   - Kashish Punjani
   - Utkarsh Bansal
@@ -233,7 +233,7 @@ Chronological list of authors
   - Lawson Woods
   - Johannes Stöckelmaier
   - Jenna M. Swarthout Goddard
-  2024
+2024
   - Aditya Keshari
   - Philipp Stärk
   - Kai Niklas Spauszus
@@ -244,7 +244,25 @@ Chronological list of authors
   - Fabian Zills
   - Laksh Krishna Sharma
   - Matthew Davies
-
+  - Jia-Xin Zhu
+  - Tanish Yelgoe
+2025
+  - Joshua Raphael Uy 
+  - Namir Oues
+  - Pavel Buslaev  
+  - Lexi Xu
+  - BHM-Bob G  
+  - Yu-Yuan (Stuart) Yang
+  - James Rowe
+  - Debasish Mohanty  
+  - Abdulrahman Elbanna
+  - Tulga-Erdene Sodjargal
+  - Gareth Elliott
+  - Marc Schuh
+  - Sirsha Ganguly
+  - Amruthesh Thirumalaiswamy
+  - Ch Zhang
+  - Raúl Lois-Cuns  
 
 External code
 -------------

{mdanalysis-2.8.0 → mdanalysis-2.10.0}/CHANGELOG

@@ -14,9 +14,142 @@ The rules for this file:
 
 
 -------------------------------------------------------------------------------
+10/18/25 IAlibay, orbeckst, BHM-Bob, TRY-ER, Abdulrahman-PROG, pbuslaev,
+         yuxuanzhuang, yuyuan871111, tanishy7777, tulga-rdn, Gareth-elliott,
+         hmacdope, tylerjereddy, cbouy, talagayev, DrDomenicoMarson, amruthesht,
+         p-j-smith, gitzhangch, raulloiscuns
+
+ * 2.10.0
+
+Fixes
+ * Fix incorrect conversion factors for speed units A/fs, A/us, A/ms
+   in MDAnalysis.units (Issue #5051, PR #5053)
+ * `analysis.polymer.sort_backbone` is now working for discontinuous polymers
+   and does not result in an infinite loop (Issue #5112, PR #5113)
+ * Fix atom selection parsing to allow escaping keywords with a backslash
+   (Issue #5111, PR #5119)
+ * Fix DCDWriter to correctly write unit cell angles as cosines following
+   NAMD/VMD convention (Issue #5069)
+ * Fixed an integer overflow in large DCD file seeks on Windows
+   (Issue #4879, PR #5086)
+ * Fix compile failure due to numpy issues in transformations.c (Issue #5061, PR #5068)
+ * Fix incorrect `self.atom` assignment in SingleFrameReaderBase (Issue #5052, PR #5055)
+ * Fixes bug in `analysis/hydrogenbonds.py`: `_donors` and `_hydrogens`
+   were not updated when the `acceptors_sel` and `hydrogens_sel` were provided
+   after initialization. (Issue #5010, PR #5018)
+ * Fixes bug in `analysis/gnm.py`: `closeContactGNMAnalysis`: correct the
+   `residue_index_map` generation when selection is not `protein`.
+   (Issue #4924, PR #4961)
+ * Reads `segids` column in `PDBParser` from 73-76 instead of 67-76 to
+   align the standard of a PDBReader (e.g., Chimera, CHARMM, Gemmi).
+   (Issue #4948, PR #5001)
+ * Fixes the benchmark `SimpleRmsBench` in `benchmarks/analysis/rms.py`
+   by changing the way weights for RMSD are calculated, instead of
+   directly passing them. (Issue #3520, PR #5006)
+
+Enhancements
+ * Add conversion factor for speed unit A/ns and additional representations (Å/fs, A/µs,
+   Å/μs, Å/ms) (PR #5053)
+ * Improved performance of `analysis.rdf.InterRDF_s` > 20-fold
+   by using vectorized NumPy calculations. (Issue #5067, PR #5073)
+ * Parallelize `analysis.rdf.InterRDF` and `analysis.rdf.InterRDF` (Issue #4675)
+ * Support for Python 3.14 was added (PR #5121).
+ * Added support for reading and processing streamed data in `coordinates.base`
+   with new `StreamFrameIteratorSliced` and `StreamReaderBase` (Issue #4827, PR #4923)
+ * New coordinate reader: Added `IMDReader` for reading real-time streamed
+   molecular dynamics simulation data using the IMDv3 protocol - requires
+   `imdclient` package (Issue #4827, PR #4923)
+ * Added capability to calculate MSD from frames with irregular (non-linear)
+   time spacing in analysis.msd.EinsteinMSD with keyword argument
+   `non_linear=True` (Issue #5028, PR #5066)
+ * Support has been added for reading positions and velocities
+   from GROMACS TPR files, between GROMACS version 4.x and 2025
+   (Issue #464, PR #4873)
+ * Added `TemplateInferrer` and `RDKitInferrer` dataclasses to the
+   `RDKitInferring` module to be used by the RDKit converter. (PR #4305)
+ * Improve speed of GROMOS11 (TRC) reader (Issue #5079, PR #5080)
+ * Improve parsing of topology information from LAMMPS dump files to allow
+   reading of mass, charge and element attributes. (Issue #3449, PR #4995)
+ * Added timestep support for XDR writers and readers (Issue #4905, PR #4908)
+ * New feature in `Universe`: `set_groups`. This function allows updating
+   `_topology`, `residues` (ResidueGroup), `segments` (SegmentGroup) in
+   the `Universe` using user-provided atomwise `resids` and/or `segids`.
+   (Issue #4948 #2874, PR #4965)
+ * Adds an argument `force_chainids_to_segids` in `PDBParser`: this will
+   force the use of ChainID as the segID when reading PDB (it is helpful
+   if the segment IDs (segids) are partially missing in the PDB file).
+   (Issue #4948 #2874, PR #4965)
+ * Enables parallelization for analysis.lineardensity.LinearDensity
+   (Issue #4678, PR #5007)
+ * Enabled selection of backend for distance calculations in RDF classes
+   (PR #5038)
+ * Modified functions in lib.distances to add the backend keyword,
+   so that it gets passed through from the calling functions and classes
+   (PR #5038)
+ * Moved distopia checking function to common import location in
+   MDAnalysisTest.util (PR #5038)
+ * Enables parallelization for `analysis.polymer.PersistenceLength` (Issue #4671, PR #5074)
+
+
+Changes
+ * Output precision for LAMMPS Data files set to 10 decimals (PR #5053)
+ * Support for Python 3.10 was removed, in line with SPEC0 (PR #5121).
+ * Refactored the RDKit converter code to move the inferring code in a separate
+   `RDKitInferring` module. The bond order and charges inferrer has been move to
+   an `MDAnalysisInferrer` dataclass in there. (PR #4305)
+ * Removed undocumented and unused attribute
+   `analysis.lineardensity.LinearDensity.totalmass` (PR #5007)
+ * Remove `default` channel from RTD conda env. (Issue # 5036, PR # 5037)
+
+
+Deprecations
+ * The RDKit converter parameter `NoImplicit` has been deprecated in favour of
+   `implicit_hydrogens` and `inferrer` parameters. `max_iter` has been moved
+   under `MDAnalysisInferrer`. (PR #4305)
+
+
+03/11/25 IAlibay, ChiahsinChu, RMeli, tanishy7777, talagayev, tylerjereddy,
+         marinegor, hmacdope, jauy123, al42and
+
+ * 2.9.0
+
+Fixes
+ * Add support for TPR files produced by GROMACS 2024.4 and GROMACS 2025.0
+ * Fixes invalid default unit from Angstrom to Angstrom^{-3} for
+   convert_density() function. (Issue #4829)
+ * Fixes deprecation warning Array to scalar convertion. Replaced atan2()
+   with np.arctan2() (Issue #4339)
+ * Replaced mutable defaults with None and initialized them within
+   the function to prevent shared state. (Issue #4655)
+
+Enhancements
+ * Improve distopia backend support in line with new functionality available
+   in distopia >= 0.3.1 (PR #4734)
+ * Addition of 'water' token for water selection (Issue #4839)
+ * Enables parallelization for analysis.density.DensityAnalysis
+   (Issue #4677, PR #4729)
+ * Enables parallelization for analysis.contacts.Contacts (Issue #4660)
+ * Enable parallelization for analysis.nucleicacids.NucPairDist (Issue #4670)
+ * Add check and warning for empty (all zero) coordinates in RDKit converter (PR #4824)
+ * Added `precision` for XYZWriter (Issue #4775, PR #4771)
+ * Added `precision` for XYZWriter (Issue #4775, PR #4771)
+ * Add check and warning for empty (all zero) coordinates in RDKit converter
+   (PR #4824)
+ * Added `precision` for XYZWriter (Issue #4775, PR #4771)
+
+Changes
+ * MDAnalysis.analysis.psa, MDAnalysis.analysis.waterdynamics and
+   MDAnalysis.analysis.hole2 are now no longer available by default in
+   MDAnalysis. You will need to install their respective MDAKits to
+   keep using them. Please note that they will be fully removed in
+   MDAnalysis v3.0 (Issue #4899, PR #4953).
+ * Changed `fasteners` dependency to  `filelock` (Issue #4797, PR #4800)
+ * Codebase is now formatted with black (version `24`) (PR #4886)
+
+
 11/11/24 IAlibay, HeetVekariya, marinegor, lilyminium, RMeli,
          ljwoods2, aditya292002, pstaerk, PicoCentauri, BFedder,
-         tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher, 
+         tyler.je.reddy, SampurnaM, leonwehrhan, kainszs, orionarcher,
          yuxuanzhuang, PythonFZ, laksh-krishna-sharma, orbeckst, MattTDavies,
          talagayev, aya9aladdin
 
@@ -79,11 +212,11 @@ Enhancements
  * Introduce parallelization API to `AnalysisBase` and to `analysis.rms.RMSD` class
    (Issue #4158, PR #4304)
  * Enables parallelization for analysis.gnm.GNMAnalysis (Issue #4672)
- * explicitly mark `analysis.pca.PCA` as not parallelizable (Issue #4680)
- * enables parallelization for analysis.bat.BAT (Issue #4663)
- * enable parallelization for analysis.dihedrals.{Dihedral,Ramachandran,Janin}
-   (Issue #4673) 
- * enables parallelization for analysis.dssp.dssp.DSSP (Issue #4674)
+ * Explicitly mark `analysis.pca.PCA` as not parallelizable (Issue #4680)
+ * Enables parallelization for analysis.bat.BAT (Issue #4663)
+ * Enable parallelization for analysis.dihedrals.{Dihedral,Ramachandran,Janin}
+   (Issue #4673)
+ * Enables parallelization for analysis.dssp.dssp.DSSP (Issue #4674)
  * Enables parallelization for analysis.hydrogenbonds.hbond_analysis.HydrogenBondAnalysis (Issue #4664)
  * Improve error message for `AtomGroup.unwrap()` when bonds are not present.(Issue #4436, PR #4642)
  * Add `analysis.DSSP` module for protein secondary structure assignment, based on [pydssp](https://github.com/ShintaroMinami/PyDSSP)
@@ -115,9 +248,9 @@ Changes
  * As per NEP29, the minimum version of numpy has been raised to 1.23.
    We have opted to pin to 1.23.2 to ensure the same minimum numpy version
    is used from python 3.9 to 3.11 (Issue #4401, PR #4402)
- * updated tests that used assert_almost_equal(..., decimal={N}) with 
+ * updated tests that used assert_almost_equal(..., decimal={N}) with
    equivalent assert_allclose(...  rtol=0, atol=1.5e-{N}) (issue modernize
-   testing code #3743, PR Replaced numpy.testing.assert_almost_equal to 
+   testing code #3743, PR Replaced numpy.testing.assert_almost_equal to
    numpy.testing.assert_allclose #4438)
 
 Deprecations
@@ -149,8 +282,8 @@ Deprecations
    (PR #4403)
 
 
-12/26/23 IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith, 
-         richardjgowers, lilyminium, ALescoulie, hmacdope, HeetVekariya, 
+12/26/23 IAlibay, ianmkenney, PicoCentauri, pgbarletta, p-j-smith,
+         richardjgowers, lilyminium, ALescoulie, hmacdope, HeetVekariya,
          JoStoe, jennaswa, ljwoods2
 
  * 2.7.0
@@ -168,7 +301,7 @@ Fixes
     RMSD of None
   * Fixes hydrogenbonds tutorial path to point to hbonds (Issue #4285, PR #4286)
   * Fix atom charge reading in PDBQT parser (Issue #4282, PR #4283)
-  * Fix doctests failing from separated blocks of imports and 
+  * Fix doctests failing from separated blocks of imports and
     execution and incorrectly formatted test output (Issue #3925, PR #4366)
 
 Enhancements
@@ -184,8 +317,8 @@ Enhancements
   * Added a warning about charge neutrality to the documentation of
     `DielectricConstant` (Issue #4262, PR #4263)
   * Add support for reading chainID info from prmtop amber topologies (PR #4007)
-  * Add support for reading chainID info from GROMACS TPR topologies 
-    (Issue #3994, PR #4281)  
+  * Add support for reading chainID info from GROMACS TPR topologies
+    (Issue #3994, PR #4281)
   * Add support for reading chainID info from Autodock PDBQT files (Issue #4207,
     PR #4284)
 
@@ -199,7 +332,7 @@ Changes
     replacing the now deprecated `xdrlib` core Python library
     (PR #4271)
   * ConverterBase class moved from coordinates/base.py to converters/base.py (Issue #3404)
-  * Results for WatsonCrickDist nucleic acids analysis are now stored in 
+  * Results for WatsonCrickDist nucleic acids analysis are now stored in
     `analysis.nucleicacids.WatsonCrickDist.results.distances` (Issue #3720, PR #3735)
 
 Deprecations
@@ -216,7 +349,7 @@ Deprecations
     in favor of using `ResidueGroup`: using `List[Residue]` will be removed in release
     3.0.0; instead use a `ResidueGroup` (Issue #3720, PR #3735)
   * In `nucleicacids.WatsonCrickDist` the result `results.pair_distances` was
-    deprecated and will be removed in 3.0.0; use `results.distances` (Issue #3720, 
+    deprecated and will be removed in 3.0.0; use `results.distances` (Issue #3720,
     PR #3735)
 
 
@@ -268,7 +401,7 @@ Changes
     of NEP29 (PR #4108).
   * Removed `-ffast-math` compiler flag to avoid potentially incorrect
     floating point results in MDAnalysis *and* other codes when
-    MDAnalysis shared libraries are loaded --- see 
+    MDAnalysis shared libraries are loaded --- see
     https://moyix.blogspot.com/2022/09/someones-been-messing-with-my-subnormals.html
     (Issues #3821, #4211)
   * Atom ID representation order updated to match that of associated
@@ -299,7 +432,7 @@ Deprecations
     32 bit compatible versions. (Issue #3858, PR #4176)
 
 
-05/28/23 IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae, 
+05/28/23 IAlibay, pgbarletta, mglagolev, hmacdope, manuel.nuno.melo, chrispfae,
          ooprathamm, MeetB7, BFedder, v-parmar, MoSchaeffler, jbarnoud, jandom,
          xhgchen, jaclark5, DrDomenicoMarson, AHMED-salah00, schlaicha,
          SophiaRuan, g2707, p-j-smith, tylerjereddy, xiki-tempula, richardjgowers,
@@ -363,13 +496,13 @@ Enhancements
   * Add distopia distance calculation library bindings as a selectable backend
     for `calc_bonds` in `MDA.lib.distances`. (Issue #3783, PR #3914)
   * AuxReaders are now pickle-able and copy-able (Issue #1785, PR #3887)
-  * Add pickling support for Atom, Residue, Segment, ResidueGroup 
+  * Add pickling support for Atom, Residue, Segment, ResidueGroup
     and SegmentGroup. (PR #3953)
 
 Changes
   * As per NEP29 the minimum supported Python version has been raised to 3.9
     (PR #4115).
-  * einsum method for Einstein summation convention introduced to increase 
+  * einsum method for Einstein summation convention introduced to increase
     performance (Issue #2063, PR #4089)
   * Add progress bars to track the progress of _conclude() functions
     (_conclude_simple() and _conclude_fft()) in msd.py (Issue #4070, PR #4072)
@@ -429,16 +562,16 @@ Fixes
  * 2.4.0
 
 Fixes
-  * Update hbond analysis doc string to use exclusive bound language 
+  * Update hbond analysis doc string to use exclusive bound language
     (Issue #3847)
   * XTC and TRR readers now fail with IOError when a status except EOK (=0) is
     detected on reading a frame instead of silently continuing
   * Consolidate license files across MDAnalysis library packages (PR #3939)
   * Kwargs passed through to `MemoryReader` when using `transfer_to_memory()`
     and `in_memory=True`.
-  * NoDataError raised on empty atomgroup provided to `DCDReader.timeseries` 
+  * NoDataError raised on empty atomgroup provided to `DCDReader.timeseries`
     was changed to ValueError (see #3901). A matching ValueError was added to
-    `MemoryReader.timeseries`(PR #3890). 
+    `MemoryReader.timeseries`(PR #3890).
   * Removes ``pbc`` kwarg from ``AtomGroup.wrap`` (Issue #3909)
   * LAMMPSDump Reader translates the box to the origin (#3741)
   * hbond analysis: access hbonds results through new results member in count_by_ids() and count_by_type()
@@ -446,7 +579,7 @@ Fixes
     behaviour for cutoff values < -1 (PR # 3749)
   * Fixes distances.between not always returning AtomGroup (Issue #3794)
   * Upgrade to chemfiles 0.10.3 (Issue #3798)
-  * fixes guessed_attributes and read_attributes methods of the Topology class, as 
+  * fixes guessed_attributes and read_attributes methods of the Topology class, as
     those methods were giving unexpected results for some topology attributes
     (e.g. bonds, angles) (PR #3779).
 
@@ -455,12 +588,12 @@ Enhancements
     (Issue #3841, PR #3842)
   * MDAnalysis now follows PEP621 (PR #3528)
   * Added a reader for GROMACS TNG files based on PyTNG (PR #3765,
-    Issue #3237, partially addressing Issue #865) 
-  * Added ability for hbond analysis to use types when resnames are not 
+    Issue #3237, partially addressing Issue #865)
+  * Added ability for hbond analysis to use types when resnames are not
     present (Issue #3847)
   * Added explanatory warnings when hbond analysis doesn't find any hbonds
     (Issue #3847)
-  * Improve C content of libxdr Cython, add `read_direct` methods to read 
+  * Improve C content of libxdr Cython, add `read_direct` methods to read
     coordinates, velocities and forces directly into memoryviews of `Timestep`
     attributes, make `TRR` timestep have positions, velocities and forces on
     `__init__`. (Issue #3891 PR  #3892).
@@ -468,11 +601,11 @@ Enhancements
   * The timeseries method for exporting coordinates from multiple frames to a
     NumPy array was added to ProtoReader (PR #3890)
   * MDAnalysis now officially supports py3.11 (Issue #3878)
-  * LAMMPSDump Reader optionally unwraps trajectories with image flags upon 
+  * LAMMPSDump Reader optionally unwraps trajectories with image flags upon
     loading (Issue #3843)
   * LAMMPSDump Reader now imports velocities and forces (Issue #3843)
   * Minimum NumPy version for py3.11 is now set to 1.23.2.
-  * Added decorator to check for an empty atom group, applied in topological 
+  * Added decorator to check for an empty atom group, applied in topological
     attributes(Issue #3837)
   * AuxReaders now have a memory_limit parameter to control when memory usage
     warnings are issued. (PR # 3749)

{mdanalysis-2.8.0 → mdanalysis-2.10.0}/MDAnalysis/__init__.py

@@ -150,8 +150,7 @@ the OPLS/AA force field.
 
 """
 
-__all__ = ['Universe', 'Writer',
-           'AtomGroup', 'ResidueGroup', 'SegmentGroup']
+__all__ = ["Universe", "Writer", "AtomGroup", "ResidueGroup", "SegmentGroup"]
 
 import logging
 import warnings
@@ -161,10 +160,11 @@ from typing import Dict
 logger = logging.getLogger("MDAnalysis.__init__")
 
 from .version import __version__
+
 try:
     from .authors import __authors__
 except ImportError:
-    logger.info('Could not find authors.py, __authors__ will be empty.')
+    logger.info("Could not find authors.py, __authors__ will be empty.")
     __authors__ = []
 
 # Registry of Readers, Parsers and Writers known to MDAnalysis
@@ -178,16 +178,23 @@ _PARSER_HINTS: Dict = {}
 _SELECTION_WRITERS: Dict = {}
 _CONVERTERS: Dict = {}
 # Registry of TopologyAttributes
-_TOPOLOGY_ATTRS: Dict = {}   # {attrname: cls}
-_TOPOLOGY_TRANSPLANTS: Dict = {}   # {name: [attrname, method, transplant class]}
-_TOPOLOGY_ATTRNAMES: Dict = {}   # {lower case name w/o _ : name}
+_TOPOLOGY_ATTRS: Dict = {}  # {attrname: cls}
+_TOPOLOGY_TRANSPLANTS: Dict = (
+    {}
+)  # {name: [attrname, method, transplant class]}
+_TOPOLOGY_ATTRNAMES: Dict = {}  # {lower case name w/o _ : name}
 _GUESSERS: Dict = {}
 
 # custom exceptions and warnings
 from .exceptions import (
-    SelectionError, NoDataError, ApplicationError, SelectionWarning,
-    MissingDataWarning, ConversionWarning, FileFormatWarning,
-    StreamWarning
+    SelectionError,
+    NoDataError,
+    ApplicationError,
+    SelectionWarning,
+    MissingDataWarning,
+    ConversionWarning,
+    FileFormatWarning,
+    StreamWarning,
 )
 
 from .lib import log
@@ -197,8 +204,9 @@ logging.getLogger("MDAnalysis").addHandler(log.NullHandler())
 del logging
 
 # only MDAnalysis DeprecationWarnings are loud by default
-warnings.filterwarnings(action='once', category=DeprecationWarning,
-                        module='MDAnalysis')
+warnings.filterwarnings(
+    action="once", category=DeprecationWarning, module="MDAnalysis"
+)
 
 
 from . import units
@@ -213,11 +221,17 @@ from . import converters
 
 from .due import due, Doi, BibTeX
 
-due.cite(Doi("10.25080/majora-629e541a-00e"),
-         description="Molecular simulation analysis library",
-         path="MDAnalysis", cite_module=True)
-due.cite(Doi("10.1002/jcc.21787"),
-         description="Molecular simulation analysis library",
-         path="MDAnalysis", cite_module=True)
+due.cite(
+    Doi("10.25080/majora-629e541a-00e"),
+    description="Molecular simulation analysis library",
+    path="MDAnalysis",
+    cite_module=True,
+)
+due.cite(
+    Doi("10.1002/jcc.21787"),
+    description="Molecular simulation analysis library",
+    path="MDAnalysis",
+    cite_module=True,
+)
 
 del Doi, BibTeX

{mdanalysis-2.8.0 → mdanalysis-2.10.0}/MDAnalysis/analysis/__init__.py

@@ -22,31 +22,31 @@
 #
 
 __all__ = [
-    'align',
-    'backends',
-    'base',
-    'contacts',
-    'density',
-    'distances',
-    'diffusionmap',
-    'dihedrals',
-    'distances',
-    'dielectric',
-    'gnm',
-    'hbonds',
-    'helix_analysis',
-    'hole2',
-    'hydrogenbonds',
-    'leaflet',
-    'lineardensity',
-    'msd',
-    'nuclinfo',
-    'nucleicacids',
-    'polymer',
-    'pca',
-    'psa',
-    'rdf',
-    'results',
-    'rms',
-    'waterdynamics',
+    "align",
+    "backends",
+    "base",
+    "contacts",
+    "density",
+    "distances",
+    "diffusionmap",
+    "dihedrals",
+    "distances",
+    "dielectric",
+    "gnm",
+    "hbonds",
+    "helix_analysis",
+    "hole2",
+    "hydrogenbonds",
+    "leaflet",
+    "lineardensity",
+    "msd",
+    "nuclinfo",
+    "nucleicacids",
+    "polymer",
+    "pca",
+    "psa",
+    "rdf",
+    "results",
+    "rms",
+    "waterdynamics",
 ]