# Align Molecule
Align a molecule using [Kabsch algorithm](https://en.wikipedia.org/wiki/Kabsch_algorithm).
## Description
This extension for [OVITO](https://www.ovito.org) aligns atoms across different snapshots in a trajectory using the [Kabsch algorithm](https://en.wikipedia.org/wiki/Kabsch_algorithm), allowing only rotational adjustments without any stretching or shearing.
Users can select either all atoms or a subset as the reference for alignment. Optionally, a reference frame can be specified, defaulting to the first frame of the trajectory. This frame serves as the baseline orientation for the atoms, with their [centroid](https://en.wikipedia.org/wiki/Centroid) repositioned to the origin.
### Requirements
This modifier requires unique identifiers for each atom. If these are not available the modifier assumes a consistent atom ordering throughout the trajectory.
It's crucial to provide an unwrapped trajectory to ensure accurate behavior. If your trajectory is wrapped, use the [unwrap trajectories modifier](https://www.ovito.org/docs/current/reference/pipelines/modifiers/unwrap_trajectories.html) before applying this modifier. The behavior with wrapped trajectories is unpredictable.
When operating on a subset of atoms, ensure the selection remains consistent throughout the trajectory. Utilize the [freeze property](https://www.ovito.org/docs/current/reference/pipelines/modifiers/freeze_property.html#particles-modifiers-freeze-property) modifier to maintain a consistent selection, or the modifier's output may be undefined.
### Output
The modifier calculates the root mean square deviation (RMSD) of atomic coordinates post-alignment relative to the reference frame. The RMSD for selected atoms is recorded in the `MoleculeAlign.RMSD` [global attribute](https://www.ovito.org/docs/current/reference/data_inspector/attributes.html). The RMSD for all atoms is available in the `MoleculeAlign.RMSD_all` attribute.
Additionally, it provides an RMSD value for each atom.
## Parameters
| GUI name | Python name | Description | Default Value |
|---------------------------------|-------------------|------------------------------------------------------------------|---------------|
| **Use only selected particles** | `only_selected` | Allows alignment using only selected particles as the reference. | `True` |
| **Reference frame** | `reference_frame` | Specifies the frame to use as the reference for alignment. | `0` |
## Example
Here's an example illustrating how the modifier aligns the highlighted (green) atoms throughout the trajectory.
## Installation
### pip
- OVITO Pro [integrated Python interpreter](https://docs.ovito.org/python/introduction/installation.html#ovito-pro-integrated-interpreter):
```
ovitos -m pip install --user ovitocontrib-AlignMolecule
```
The `--user` option is recommended and [installs the package in the user's site directory](https://pip.pypa.io/en/stable/user_guide/#user-installs).
- Other Python interpreters or Conda environments:
```
pip install ovitocontrib-AlignMolecule
```
### GitHub
- OVITO Pro [integrated Python interpreter](https://docs.ovito.org/python/introduction/installation.html#ovito-pro-integrated-interpreter):
```
ovitos -m pip install --user git+https://github.com/ovito-org/AlignMolecule.git
```
The `--user` option is recommended and [installs the package in the user's site directory](https://pip.pypa.io/en/stable/user_guide/#user-installs).
- Other Python interpreters or Conda environments:
```
pip install git+https://github.com/ovito-org/AlignMolecule.git
```
## Technical information / dependencies
- Tested on OVITO version 3.10.3
## Contact
Daniel Utt (utt@ovito.org)
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"description": "# Align Molecule\n\nAlign a molecule using [Kabsch algorithm](https://en.wikipedia.org/wiki/Kabsch_algorithm).\n\n## Description\n\nThis extension for [OVITO](https://www.ovito.org) aligns atoms across different snapshots in a trajectory using the [Kabsch algorithm](https://en.wikipedia.org/wiki/Kabsch_algorithm), allowing only rotational adjustments without any stretching or shearing.\n\nUsers can select either all atoms or a subset as the reference for alignment. Optionally, a reference frame can be specified, defaulting to the first frame of the trajectory. This frame serves as the baseline orientation for the atoms, with their [centroid](https://en.wikipedia.org/wiki/Centroid) repositioned to the origin.\n\n### Requirements\n\nThis modifier requires unique identifiers for each atom. If these are not available the modifier assumes a consistent atom ordering throughout the trajectory.\n\nIt's crucial to provide an unwrapped trajectory to ensure accurate behavior. If your trajectory is wrapped, use the [unwrap trajectories modifier](https://www.ovito.org/docs/current/reference/pipelines/modifiers/unwrap_trajectories.html) before applying this modifier. The behavior with wrapped trajectories is unpredictable.\n\nWhen operating on a subset of atoms, ensure the selection remains consistent throughout the trajectory. Utilize the [freeze property](https://www.ovito.org/docs/current/reference/pipelines/modifiers/freeze_property.html#particles-modifiers-freeze-property) modifier to maintain a consistent selection, or the modifier's output may be undefined.\n\n### Output\n\nThe modifier calculates the root mean square deviation (RMSD) of atomic coordinates post-alignment relative to the reference frame. The RMSD for selected atoms is recorded in the `MoleculeAlign.RMSD` [global attribute](https://www.ovito.org/docs/current/reference/data_inspector/attributes.html). The RMSD for all atoms is available in the `MoleculeAlign.RMSD_all` attribute.\n\nAdditionally, it provides an RMSD value for each atom.\n\n## Parameters\n\n| GUI name | Python name | Description | Default Value |\n|---------------------------------|-------------------|------------------------------------------------------------------|---------------|\n| **Use only selected particles** | `only_selected` | Allows alignment using only selected particles as the reference. | `True` |\n| **Reference frame** | `reference_frame` | Specifies the frame to use as the reference for alignment. | `0` |\n\n## Example\n\nHere's an example illustrating how the modifier aligns the highlighted (green) atoms throughout the trajectory.\n\n\n\n\n\n## Installation\n\n### pip\n\n- OVITO Pro [integrated Python interpreter](https://docs.ovito.org/python/introduction/installation.html#ovito-pro-integrated-interpreter):\n ```\n ovitos -m pip install --user ovitocontrib-AlignMolecule\n ``` \n The `--user` option is recommended and [installs the package in the user's site directory](https://pip.pypa.io/en/stable/user_guide/#user-installs).\n\n- Other Python interpreters or Conda environments:\n ```\n pip install ovitocontrib-AlignMolecule\n ```\n\n### GitHub\n- OVITO Pro [integrated Python interpreter](https://docs.ovito.org/python/introduction/installation.html#ovito-pro-integrated-interpreter):\n ```\n ovitos -m pip install --user git+https://github.com/ovito-org/AlignMolecule.git\n ``` \n The `--user` option is recommended and [installs the package in the user's site directory](https://pip.pypa.io/en/stable/user_guide/#user-installs).\n\n- Other Python interpreters or Conda environments:\n ```\n pip install git+https://github.com/ovito-org/AlignMolecule.git\n ```\n\n## Technical information / dependencies\n- Tested on OVITO version 3.10.3\n\n## Contact\nDaniel Utt (utt@ovito.org)\n",
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