shnitsel-tools 0.0.2.dev1__tar.gz → 0.0.2.dev2__tar.gz

{shnitsel_tools-0.0.2.dev1/shnitsel_tools.egg-info → shnitsel_tools-0.0.2.dev2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: shnitsel-tools
-Version: 0.0.2.dev1
+Version: 0.0.2.dev2
 Summary: Collect, manage, process, analyse & visualize surface hopping data
 Author-email: Theodor Everley Röhrkasten <theodor.roehrkasten@fau.de>, Kevin Höllring <kevin.hoellring@fau.de>, Carolin Müller <carolin.cpc.mueller@fau.de>
 Classifier: Programming Language :: Python :: 3
@@ -22,22 +22,27 @@ Requires-Dist: jupyter>=1.0.0
 Requires-Dist: py3dmol>=2.0.4
 Requires-Dist: tqdm>=4.66.2
 Requires-Dist: pyparsing>=3.2.5
-Requires-Dist: tox-uv>=1.29.0
-Provides-Extra: extras
-Requires-Dist: plotly>=5.22.0; extra == "extras"
-Requires-Dist: seaborn>=0.13.1; extra == "extras"
-Requires-Dist: bokeh>=3.5; extra == "extras"
+Requires-Dist: fsspec
+Requires-Dist: requests
+Requires-Dist: aiohttp
+Provides-Extra: vis
+Requires-Dist: bokeh>=3.5; extra == "vis"
+Requires-Dist: datashader; extra == "vis"
+Requires-Dist: seaborn; extra == "vis"
 Provides-Extra: dev
 Requires-Dist: pytest>=5.2; extra == "dev"
 Requires-Dist: pytest-cov>=4.1.0; extra == "dev"
 Requires-Dist: hypothesis>=6; extra == "dev"
 Requires-Dist: tox>=4.10.0; extra == "dev"
+Requires-Dist: tox-uv>=1.29.0; extra == "dev"
 Requires-Dist: pre-commit>=2.20.0; extra == "dev"
 Requires-Dist: ruff==0.4.1; extra == "dev"
 Requires-Dist: mypy>=1.9.0; extra == "dev"
 Requires-Dist: pandas-stubs; extra == "dev"
 Requires-Dist: scipy-stubs; extra == "dev"
 Requires-Dist: types-tqdm; extra == "dev"
+Requires-Dist: build; extra == "dev"
+Requires-Dist: grayskull; extra == "dev"
 Requires-Dist: sphinx; extra == "dev"
 Requires-Dist: sphinx-autobuild; extra == "dev"
 Requires-Dist: sphinx-autosummary-accessors; extra == "dev"
@@ -69,23 +74,31 @@ The package leverages [Xarray](https://xarray.dev/) to benefit from efficient mu
 `shnitsel-tools` is normally used interactively via Jupyter Notebook on a local machine.
 However, some users might find it convenient to convert trajectories to NetCDF
 on-cluster, as the NetCDF file will likely download faster than the raw text files.
-Either way the following should work as usual, ideally in a virtual (e.g. `conda`) environment:
-  
+Either way the following should work as usual, ideally in a fresh virtual (e.g. `conda`) environment:
+
+<!-- TODO: remove --pre once full release out -->
   ```bash
-  pip install shnitsel-tools
+  pip install shnitsel-tools[vis]
   ```
 
+For more detailed installation instructions, see [here](#detailed-installation-instructions)
+
 ## Usage
 
-The package is organized into top-level functions for reading data,
-accessor methods available on `xr.Dataset` and `xr.DataArray` objects, plotting routines found in the `shnitsel.plot` namespace,
-and functions taking an RDKit `Mol` object as their principal argument under `shnitsel.rd`.
-The adventurous may find something useful under `shnitsel.core`, though this should be considered internal and therefore subject to change.
+For documentation including an API reference, please see https://shnitsel.github.io/tools/docs/_build/index.html.
+
+`shnitsel-tools` mostly exposes data as Xarray (`xr`) objects, so familiarity with that library is beneficial.
+Xarray is somewhat like Pandas for higher-dimensional data, or like Numpy with labels and other metadata.
+- [Overview of data structures](https://tutorial.xarray.dev/intermediate/datastructures-intermediate.html)
+- [Official quick overview](https://docs.xarray.dev/en/stable/getting-started-guide/quick-overview.html)
+- [Xarray in 45 minutes](https://tutorial.xarray.dev/overview/xarray-in-45-min.html) for a more detailed introduction
 
 ### Tutorials
 For a quick start, see the [tutorials](https://github.com/SHNITSEL/shnitsel-tools/blob/main/tutorials) directory,
 which contains Jupyter Notebooks showing the workflow for parsing, writing and loading SHNITSEL databases as well as how to postprocess and visualize the respective data.
 
+<!--
+TODO: Adapt to new tutorials!
 #### Collection & storage
 - [parsing trajcetory and initial condition data obtained by SHARC](https://github.com/SHNITSEL/shnitsel-tools/blob/main/tutorials/0_1_sharc2hdf5.ipynb)
 - [parsing trajectory data produced with Newton-X](https://github.com/SHNITSEL/shnitsel-tools/blob/main/tutorials/0_2_nx2hdf5.ipynb)
@@ -103,51 +116,112 @@ analysis of homologous/isoelectronic molecules, from filtration via dimensional
 ## Tree
 
 ```bash
-shnitsel
-├── core
-│   ├── ase.py
-│   ├── datasheet
-│   │   ├── colormaps.py
-│   │   ├── common.py
-│   │   ├── dip_trans_hist.py
-│   │   ├── hist.py
-│   │   ├── __init__.py
-│   │   ├── nacs_hist.py
-│   │   ├── oop.py
-│   │   ├── per_state_hist.py
-│   │   ├── structure.py
-│   │   └── time.py
-│   ├── filter_unphysical.py
-│   ├── filtration.py
-│   ├── indexes.py
-│   ├── __init__.py
-│   ├── parse
-│   │   ├── common.py
-│   │   ├── __init__.py
-│   │   ├── nx.py
-│   │   ├── pyrai2md.py
-│   │   ├── sharc_icond.py
-│   │   ├── sharc_traj.py
-│   │   └── xyz.py
-│   ├── plot
-│   │   ├── __init__.py
-│   │   ├── kde.py
-│   │   ├── p3mhelpers.py
-│   │   ├── pca_biplot.py
-│   │   ├── polychrom.py
-│   │   ├── select.py
-│   │   └── spectra3d.py
-│   ├── postprocess.py
-│   ├── spectra.py
-│   └── xrhelpers.py
-├── __init__.py
-├── plot
-│   └── __init__.py
-├── rd.py
-└── xarray.py
+# TODO: regenerate directory tree
+```
+-->
+
+## Detailed installation instructions
+
+### Optional dependencies
+In the following, the `[vis]` suffix causes optional plotting dependencies to be
+installed. If you are using `shnitsel-tools` on an HPC, you can omit it.
+
+If you would like to contribute to `shnitsel-tools`, you may find the development
+dependencies useful. These can be obtained by adding `[dev]` at the end of the
+package name.
+
+To install all optional dependencies, please add `[vis,dev]` after the package name.
+
+### Using conda
+Before anything else, please run:
+```bash
+conda create -n shnitsel python==3.12 pip
+conda activate shnitsel
+```
+
+#### For tutorials or development
+If you would like to work through the tutorials, please use the following commands
+while the conda environment is active:
+<!-- TODO: remove git-switch command once full release version comes out -->
+```bash
+git clone 'https://github.com/SHNITSEL/shnitsel-tools.git'
+cd shnitsel-tools
+git switch develop
+pip install .[vis]
+```
+
+If you would like changes you make to the code in the `shnitsel-tools` directory
+to be reflected in your environment, please add the `-e` flag ("editable mode") to the
+final line of the above block:
+```bash
+# Same commands as before, and then:
+pip install -e .[vis]  # or .[vis,dev] to include development tools
+```
+
+#### For ordinary use
+If you would just like to use the package, it is unnecessary to clone the repository.
+Instead, it should suffice to run the following command with the conda environment active:
+
+<!-- TODO: remove --pre once full release version comes out -->
+```bash
+pip install --pre shnitsel-tools[vis]
 ```
 
-## Development
+### Using uv
+
+This tool, available at  https://docs.astral.sh/uv/, is typically faster and
+more light-weight than `pip` and `conda`.
+Unlike `conda`, it creates traditional Python virtual environments, which are
+stored in the folder in which the command is run and activated by sourcing
+a shell-script.
+
+```bash
+git clone 'https://github.com/SHNITSEL/shnitsel-tools.git'
+cd shnitsel-tools
+
+uv pip install -e .[dev]  # install shnitsel in editable mode
+```
+
+#### For tutorials or development
+If you would like to work through the tutorials, please use the following commands:
+<!-- TODO: remove git-switch command once full release version comes out -->
+```bash
+git clone 'https://github.com/SHNITSEL/shnitsel-tools.git'
+cd shnitsel-tools
+git switch develop
+uv venv --python 3.12  # create an environment under ./.venv
+source .venv/bin/activate  # activate the new environment
+uv pip install .[vis]
+```
+
+If you would like changes you make to the code in the `shnitsel-tools` directory
+to be reflected in your environment, please add the `-e` flag ("editable mode") to the
+final line of the above block:
+```bash
+# Same commands as before, and then:
+uv pip install -e .[vis]  # or .[vis,dev] to include development tools
+```
+
+#### For command-line only use
+The following will ensure the command-line programs provided are always available,
+without requiring environments to be activated first.
+```bash
+uv tool install --pre shnitsel-tools
+```
+
+#### For ordinary use
+If you would just like to use the package, it is unnecessary to clone the repository.
+Instead, it should suffice to run the following commands:
+
+<!-- TODO: remove --pre once full release version comes out -->
+```bash
+uv venv --python 3.12 shnitsel  # creates a directory here called ./shnitsel
+source shnitsel/bin/activate  # activate the new environment
+uv pip install --pre shnitsel-tools[vis]
+```
+
+<!--
+### For developers
   
   We recommend installation using the `uv` tool, available at https://docs.astral.sh/uv/.
   Please clone this repo and run the following in the `shnitsel-tools` directory:
@@ -167,6 +241,8 @@ shnitsel
   please [fork](https://github.com/SHNITSEL/shnitsel-tools/fork) this repo,
   and make a pull request.
 
+-->
+
 ## Further Information
 
 [![Website](https://img.shields.io/badge/Website-shnitsel.github.io-yellow.svg)](https://shnitsel.github.io/)

shnitsel_tools-0.0.2.dev2/README.md

@@ -0,0 +1,197 @@
+<div align="center">
+  <h1>shnitsel-tools</h1>
+  <img src="https://raw.githubusercontent.com/SHNITSEL/shnitsel-tools/main/logo_shnitsel_tools.png" alt="SHNITSEL-TOOLS Logo" width="200px">
+  <h3>Surface Hopping Nested Instances Training Set for Excited-state Learning Tools</h3>
+  <br>
+  <a href="https://shnitsel.github.io/"><img src="https://img.shields.io/badge/Website-shnitsel.github.io-yellow.svg" alt="DOI"></a>
+  &nbsp;&nbsp;&nbsp;
+  <a href="https://shnitsel.github.io/tools/docs/_build/index.html"><img src="https://img.shields.io/badge/Docs-shnitsel.github.io-yellow.svg" alt="DOI"></a>
+</div>
+
+--------------------
+
+## About
+
+`shnitsel-tools` is designed to to support the entire data lifecycle of surface hopping (SH) trajectory data upon simulation: data managment, storage, processing, visualization and interpretation. 
+The tool is compatible with surface hopping data generated using the software packages [SHARC 3/4](https://sharc-md.org/), [Newton-X](https://newtonx.org/), and [PyRAI2MD](https://github.com/lopez-lab/PyRAI2MD).
+The package leverages [Xarray](https://xarray.dev/) to benefit from efficient multidimensional data handling, improved metadata management, and a structure that aligns naturally with the needs of quantum chemical datasets.
+
+## Installation
+
+`shnitsel-tools` is normally used interactively via Jupyter Notebook on a local machine.
+However, some users might find it convenient to convert trajectories to NetCDF
+on-cluster, as the NetCDF file will likely download faster than the raw text files.
+Either way the following should work as usual, ideally in a fresh virtual (e.g. `conda`) environment:
+
+<!-- TODO: remove --pre once full release out -->
+  ```bash
+  pip install shnitsel-tools[vis]
+  ```
+
+For more detailed installation instructions, see [here](#detailed-installation-instructions)
+
+## Usage
+
+For documentation including an API reference, please see https://shnitsel.github.io/tools/docs/_build/index.html.
+
+`shnitsel-tools` mostly exposes data as Xarray (`xr`) objects, so familiarity with that library is beneficial.
+Xarray is somewhat like Pandas for higher-dimensional data, or like Numpy with labels and other metadata.
+- [Overview of data structures](https://tutorial.xarray.dev/intermediate/datastructures-intermediate.html)
+- [Official quick overview](https://docs.xarray.dev/en/stable/getting-started-guide/quick-overview.html)
+- [Xarray in 45 minutes](https://tutorial.xarray.dev/overview/xarray-in-45-min.html) for a more detailed introduction
+
+### Tutorials
+For a quick start, see the [tutorials](https://github.com/SHNITSEL/shnitsel-tools/blob/main/tutorials) directory,
+which contains Jupyter Notebooks showing the workflow for parsing, writing and loading SHNITSEL databases as well as how to postprocess and visualize the respective data.
+
+<!--
+TODO: Adapt to new tutorials!
+#### Collection & storage
+- [parsing trajcetory and initial condition data obtained by SHARC](https://github.com/SHNITSEL/shnitsel-tools/blob/main/tutorials/0_1_sharc2hdf5.ipynb)
+- [parsing trajectory data produced with Newton-X](https://github.com/SHNITSEL/shnitsel-tools/blob/main/tutorials/0_2_nx2hdf5.ipynb)
+- [convert ASE databases](https://github.com/SHNITSEL/shnitsel-tools/blob/main/tutorials/0_4_ase2hdf5.ipynb)
+#### Management
+- [exploration of electronic properties](https://github.com/SHNITSEL/shnitsel-tools/blob/main/tutorials/2_2_PS_explore.ipynb)
+#### Postprocessing & visualization of data
+- [datasheet for trajectory data](https://github.com/SHNITSEL/shnitsel-tools/blob/main/tutorials/3_1_datasheet.ipynb)
+- [principal component analysis and trajectory classification](https://github.com/SHNITSEL/shnitsel-tools/blob/main/tutorials/1_1_GS_PCA.ipynb)
+
+### Workflow walkthrough
+Four [notebooks](https://github.com/SHNITSEL/shnitsel-tools/tree/main/tutorials/walkthrough) demonstrate a workflow for the comparative
+analysis of homologous/isoelectronic molecules, from filtration via dimensional reduction and clustering to kinetics.
+
+## Tree
+
+```bash
+# TODO: regenerate directory tree
+```
+-->
+
+## Detailed installation instructions
+
+### Optional dependencies
+In the following, the `[vis]` suffix causes optional plotting dependencies to be
+installed. If you are using `shnitsel-tools` on an HPC, you can omit it.
+
+If you would like to contribute to `shnitsel-tools`, you may find the development
+dependencies useful. These can be obtained by adding `[dev]` at the end of the
+package name.
+
+To install all optional dependencies, please add `[vis,dev]` after the package name.
+
+### Using conda
+Before anything else, please run:
+```bash
+conda create -n shnitsel python==3.12 pip
+conda activate shnitsel
+```
+
+#### For tutorials or development
+If you would like to work through the tutorials, please use the following commands
+while the conda environment is active:
+<!-- TODO: remove git-switch command once full release version comes out -->
+```bash
+git clone 'https://github.com/SHNITSEL/shnitsel-tools.git'
+cd shnitsel-tools
+git switch develop
+pip install .[vis]
+```
+
+If you would like changes you make to the code in the `shnitsel-tools` directory
+to be reflected in your environment, please add the `-e` flag ("editable mode") to the
+final line of the above block:
+```bash
+# Same commands as before, and then:
+pip install -e .[vis]  # or .[vis,dev] to include development tools
+```
+
+#### For ordinary use
+If you would just like to use the package, it is unnecessary to clone the repository.
+Instead, it should suffice to run the following command with the conda environment active:
+
+<!-- TODO: remove --pre once full release version comes out -->
+```bash
+pip install --pre shnitsel-tools[vis]
+```
+
+### Using uv
+
+This tool, available at  https://docs.astral.sh/uv/, is typically faster and
+more light-weight than `pip` and `conda`.
+Unlike `conda`, it creates traditional Python virtual environments, which are
+stored in the folder in which the command is run and activated by sourcing
+a shell-script.
+
+```bash
+git clone 'https://github.com/SHNITSEL/shnitsel-tools.git'
+cd shnitsel-tools
+
+uv pip install -e .[dev]  # install shnitsel in editable mode
+```
+
+#### For tutorials or development
+If you would like to work through the tutorials, please use the following commands:
+<!-- TODO: remove git-switch command once full release version comes out -->
+```bash
+git clone 'https://github.com/SHNITSEL/shnitsel-tools.git'
+cd shnitsel-tools
+git switch develop
+uv venv --python 3.12  # create an environment under ./.venv
+source .venv/bin/activate  # activate the new environment
+uv pip install .[vis]
+```
+
+If you would like changes you make to the code in the `shnitsel-tools` directory
+to be reflected in your environment, please add the `-e` flag ("editable mode") to the
+final line of the above block:
+```bash
+# Same commands as before, and then:
+uv pip install -e .[vis]  # or .[vis,dev] to include development tools
+```
+
+#### For command-line only use
+The following will ensure the command-line programs provided are always available,
+without requiring environments to be activated first.
+```bash
+uv tool install --pre shnitsel-tools
+```
+
+#### For ordinary use
+If you would just like to use the package, it is unnecessary to clone the repository.
+Instead, it should suffice to run the following commands:
+
+<!-- TODO: remove --pre once full release version comes out -->
+```bash
+uv venv --python 3.12 shnitsel  # creates a directory here called ./shnitsel
+source shnitsel/bin/activate  # activate the new environment
+uv pip install --pre shnitsel-tools[vis]
+```
+
+<!--
+### For developers
+  
+  We recommend installation using the `uv` tool, available at https://docs.astral.sh/uv/.
+  Please clone this repo and run the following in the `shnitsel-tools` directory:
+
+  ```bash
+  git clone 'https://github.com/SHNITSEL/shnitsel-tools.git'
+  cd shnitsel-tools
+  uv venv  # create an environment under ./.venv
+  source .venv/bin/activate  # activate the new environment
+  uv pip install -e .[dev]  # install shnitsel in editable mode
+  ```
+
+  In the above, the option `-e` installs in editable mode, meaning that Python will see changes you make
+  to the source, while `[dev]` installs the optional development dependencies.  
+
+  If you would like to contribute your changes,
+  please [fork](https://github.com/SHNITSEL/shnitsel-tools/fork) this repo,
+  and make a pull request.
+
+-->
+
+## Further Information
+
+[![Website](https://img.shields.io/badge/Website-shnitsel.github.io-yellow.svg)](https://shnitsel.github.io/)
+
+

{shnitsel_tools-0.0.2.dev1 → shnitsel_tools-0.0.2.dev2}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "shnitsel-tools"
-version = "0.0.2.dev1"
+version = "0.0.2.dev2"
 authors = [
   { name = "Theodor Everley Röhrkasten", email = "theodor.roehrkasten@fau.de" },
   { name = "Kevin Höllring", email = "kevin.hoellring@fau.de" },
@@ -29,27 +29,37 @@ dependencies = [
   "pandas>=2.2",
   "h5netcdf>=1.7.0",
   "scikit-learn>=1.5",
-  "jupyter>=1.0.0",
-  "py3dmol>=2.0.4",
+  "jupyter>=1.0.0",    # TODO: make optional?
+  "py3dmol>=2.0.4",    # TODO: make optional?
   "tqdm>=4.66.2",
   "pyparsing>=3.2.5",
-  "tox-uv>=1.29.0",
+  # To enable direct loading of remote resources:
+  "fsspec",
+  "requests",
+  "aiohttp"
 ]
 
 [project.optional-dependencies]
-extras = ["plotly>=5.22.0", "seaborn>=0.13.1", "bokeh>=3.5"]
+vis = [
+  "bokeh>=3.5",
+  "datashader",
+  "seaborn"
+]
 
 dev = [
   "pytest>=5.2",
   "pytest-cov>=4.1.0",
   "hypothesis>=6",         # ==6.127.3
   "tox>=4.10.0",
+  "tox-uv>=1.29.0",
   "pre-commit>=2.20.0",
   "ruff==0.4.1",
   "mypy>=1.9.0",
   "pandas-stubs",
   "scipy-stubs",
   "types-tqdm",
+  "build",
+  "grayskull",
 
   # Sphinx and its extensions for building documentation
   "sphinx",

{shnitsel_tools-0.0.2.dev1 → shnitsel_tools-0.0.2.dev2}/shnitsel/_generated_accessors.py

@@ -13,7 +13,7 @@ from ._accessors import DAManualAccessor, DSManualAccessor
 from ._contracts import needs
 from numpy import nan, ndarray
 from rdkit.Chem.rdchem import Mol
-from shnitsel.analyze.generic import keep_norming, norm, subtract_combinations
+from shnitsel.analyze.generic import keep_norming, norm, pwdists, subtract_combinations
 from shnitsel.analyze.lda import lda
 from shnitsel.analyze.pca import pairwise_dists_pca, pca, pca_and_hops
 from shnitsel.analyze.pls import pls, pls_ds
@@ -45,6 +45,7 @@ class DataArrayAccessor(DAManualAccessor):
         'norm',
         'subtract_combinations',
         'keep_norming',
+        'pwdists',
         'calc_confidence_interval',
         'time_grouped_confidence_interval',
         'to_xyz',
@@ -102,6 +103,10 @@ class DataArrayAccessor(DAManualAccessor):
         """Wrapper for :py:func:`shnitsel.analyze.generic.keep_norming`."""
         return keep_norming(self._obj, exclude=exclude)
 
+    def pwdists(self, mean: bool=False) -> DataArray:
+        """Wrapper for :py:func:`shnitsel.analyze.generic.pwdists`."""
+        return pwdists(self._obj, mean=mean)
+
     def calc_confidence_interval(self, confidence: float=0.95) -> ndarray:
         """Wrapper for :py:func:`shnitsel.analyze.stats.calc_confidence_interval`."""
         return calc_confidence_interval(self._obj, confidence=confidence)
@@ -112,14 +117,14 @@ class DataArrayAccessor(DAManualAccessor):
         return time_grouped_confidence_interval(self._obj, confidence=confidence)
 
     @needs(dims={'atom', 'direction'}, coords_or_vars={'atNames'}, not_dims={'frame'})
-    def to_xyz(self, comment='#') -> str:
+    def to_xyz(self, comment='#', units='angstrom') -> str:
         """Wrapper for :py:func:`shnitsel.bridges.to_xyz`."""
-        return to_xyz(self._obj, comment=comment)
+        return to_xyz(self._obj, comment=comment, units=units)
 
     @needs(dims={'atom', 'direction'}, groupable={'time'}, coords_or_vars={'atNames'})
-    def traj_to_xyz(self) -> str:
+    def traj_to_xyz(self, units='angstrom') -> str:
         """Wrapper for :py:func:`shnitsel.bridges.traj_to_xyz`."""
-        return traj_to_xyz(self._obj)
+        return traj_to_xyz(self._obj, units=units)
 
     @needs(dims={'atom', 'direction'}, coords_or_vars={'atNames'}, not_dims={'frame'})
     def to_mol(self, charge: int | None=None, covFactor: float=1.2, to2D: bool=True, molAtomMapNumber: Union=None, atomNote: Union=None, atomLabel: Union=None) -> Mol:
@@ -136,9 +141,9 @@ class DataArrayAccessor(DAManualAccessor):
         return default_mol(self._obj)
 
     @needs(dims={'atom'})
-    def pairwise_dists_pca(self, **kwargs) -> DataArray:
+    def pairwise_dists_pca(self, mean: bool=False, return_pca_object=False, **kwargs) -> DataArray:
         """Wrapper for :py:func:`shnitsel.analyze.pca.pairwise_dists_pca`."""
-        return pairwise_dists_pca(self._obj, **kwargs)
+        return pairwise_dists_pca(self._obj, mean=mean, return_pca_object=return_pca_object, **kwargs)
 
     def convert_energy(self, to: str, convert_from: str | None=None):
         """Wrapper for :py:func:`shnitsel.units.conversion.convert_energy`."""
@@ -247,7 +252,7 @@ class DataArrayAccessor(DAManualAccessor):
         return get_bats(self._obj, matches_or_mol=matches_or_mol, signed=signed, ang=ang, pyr=pyr)
 
     @needs(dims={'atom', 'direction'})
-    def kabsch(self, reference_or_indexers: xarray.core.dataarray.DataArray | dict | None=None, **indexers_kwargs):
+    def kabsch(self, reference_or_indexers: xarray.core.dataarray.DataArray | dict | None=None, **indexers_kwargs) -> DataArray:
         """Wrapper for :py:func:`shnitsel.geo.geocalc.kabsch`."""
         return kabsch(self._obj, reference_or_indexers=reference_or_indexers, **indexers_kwargs)
 
@@ -279,9 +284,9 @@ class DataArrayAccessor(DAManualAccessor):
         """Wrapper for :py:func:`shnitsel.vis.plot.p3mhelpers.trajs3Dgrid`."""
         return trajs3Dgrid(self._obj, trajids=trajids, loop=loop)
 
-    def traj_vmd(self, groupby='trajid', scale=0.5):
+    def traj_vmd(self, groupby='trajid'):
         """Wrapper for :py:func:`shnitsel.vis.vmd.traj_vmd`."""
-        return traj_vmd(self._obj, groupby=groupby, scale=scale)
+        return traj_vmd(self._obj, groupby=groupby)
 
     def pca(self, dim: str, n_components: int=2, return_pca_object: bool=False) -> tuple[xarray.core.dataarray.DataArray, sklearn.decomposition._pca.PCA] | xarray.core.dataarray.DataArray:
         """Wrapper for :py:func:`shnitsel.analyze.pca.pca`."""
@@ -328,9 +333,9 @@ class DatasetAccessor(DSManualAccessor):
     ]
 
     @needs(coords_or_vars={'astate', 'atXYZ'})
-    def pca_and_hops(self) -> tuple:
+    def pca_and_hops(self, mean: bool) -> tuple:
         """Wrapper for :py:func:`shnitsel.analyze.pca.pca_and_hops`."""
-        return pca_and_hops(self._obj)
+        return pca_and_hops(self._obj, mean)
 
     def validate(self) -> ndarray:
         """Wrapper for :py:func:`shnitsel.data.helpers.validate`."""
@@ -398,7 +403,7 @@ class DatasetAccessor(DSManualAccessor):
         """Wrapper for :py:func:`shnitsel.data.multi_indices.stack_trajs`."""
         return stack_trajs(self._obj)
 
-    def write_shnitsel_file(self, savepath: str | os.PathLike | pathlib._local.Path, complevel: int=9):
+    def write_shnitsel_file(self, savepath: str | os.PathLike, complevel: int=9):
         """Wrapper for :py:func:`shnitsel.io.shnitsel.write.write_shnitsel_file`."""
         return write_shnitsel_file(self._obj, savepath, complevel=complevel)
 
@@ -411,17 +416,17 @@ class DatasetAccessor(DSManualAccessor):
         """Wrapper for :py:func:`shnitsel.clean.filter_energy.energy_filtranda`."""
         return energy_filtranda(self._obj, etot_drift=etot_drift, etot_step=etot_step, epot_step=epot_step, ekin_step=ekin_step, hop_epot_step=hop_epot_step, units=units)
 
-    def sanity_check(self, cut: Union='truncate', units='eV', etot_drift: float=nan, etot_step: float=nan, epot_step: float=nan, ekin_step: float=nan, hop_epot_step: float=nan):
+    def sanity_check(self, cut: Union='truncate', units='eV', etot_drift: float=nan, etot_step: float=nan, epot_step: float=nan, ekin_step: float=nan, hop_epot_step: float=nan, plot_thresholds: Union=False, plot_populations: Union=False):
         """Wrapper for :py:func:`shnitsel.clean.filter_energy.sanity_check`."""
-        return sanity_check(self._obj, cut=cut, units=units, etot_drift=etot_drift, etot_step=etot_step, epot_step=epot_step, ekin_step=ekin_step, hop_epot_step=hop_epot_step)
+        return sanity_check(self._obj, cut=cut, units=units, etot_drift=etot_drift, etot_step=etot_step, epot_step=epot_step, ekin_step=ekin_step, hop_epot_step=hop_epot_step, plot_thresholds=plot_thresholds, plot_populations=plot_populations)
 
-    def bond_length_filtranda(self, search_dict: dict[str, numbers.Number] | None=None, units='angstrom'):
+    def bond_length_filtranda(self, search_dict: dict[str, numbers.Number] | None=None, units='angstrom', mol: rdkit.Chem.rdchem.Mol | None=None):
         """Wrapper for :py:func:`shnitsel.clean.filter_geo.bond_length_filtranda`."""
-        return bond_length_filtranda(self._obj, search_dict=search_dict, units=units)
+        return bond_length_filtranda(self._obj, search_dict=search_dict, units=units, mol=mol)
 
-    def filter_by_length(self, cut: Union='truncate', search_dict: dict[str, numbers.Number] | None=None):
+    def filter_by_length(self, cut: Union='truncate', search_dict: dict[str, numbers.Number] | None=None, units: str='angstrom', plot_thresholds: Union=False, plot_populations: Union=False, mol: rdkit.Chem.rdchem.Mol | None=None):
         """Wrapper for :py:func:`shnitsel.clean.filter_geo.filter_by_length`."""
-        return filter_by_length(self._obj, cut=cut, search_dict=search_dict)
+        return filter_by_length(self._obj, cut=cut, search_dict=search_dict, units=units, plot_thresholds=plot_thresholds, plot_populations=plot_populations, mol=mol)
 
     def omit(self):
         """Wrapper for :py:func:`shnitsel.clean.common.omit`."""