| Name | TRAMbio JSON |
| Version |
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| Summary | Python package for Topological Rigidity Analysis in Molecular Biology (TRAMbio). |
| upload_time | 2025-09-07 16:35:20 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.8 |
| license | None |
| keywords |
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| bugtrack_url |
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No requirements were recorded.
|
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[](https://github.com/gate-tec/TRAMbio/actions/workflows/tests.yml)
[](.github/CODE_OF_CONDUCT.md)
# TRAMbio
*Topological Rigidity Analysis in Molecular Biology* (TRAMbio)
is a package based on and centered on the pebble game. It provides
functionality for general applications in graph theory including testing
for $(k,l)$-sparsity as well as determining the $(k,l)$-spanning
subgraphs, i.e., the $(k,l)$-rigid components. With regard to
molecular data, in particular proteins, TRAMbio provides tools for the
rigidity analysis on an atom or residue-level with further functionality
towards specialized tasks like (a) simulated protein unfolding ([Rader et al. 2002])
on single-state protein data and (b) time-based tracking of
rigid component changes in molecular dynamics (MD) trajectories.
[Rader et al. 2002]: https://doi.org/10.1073/pnas.062492699
- Source: https://github.com/gate-tec/TRAMbio
- Bug reports: https://github.com/gate-tec/TRAMbio/issues
<details><summary>Table of contents</summary>
- [Installation](#installation)
- [Examples](#examples)
- [CLI commands](#cli)
- [Envoronment Variables](#environment-variables)
- [Data Formats](#data-formats)
- [Component-XML Files](#component-xml-files)
- [Edge Data Files](#edge-data-files)
- [PyMol Command Files](#pymol-command-files)
- [Residue-level Component-JSON Files](#residue-level-component-json-files)
- [Licenses](#licenses)
- [Citation](#citation)
</details>
## Installation
### System requirements
- python (>=3.8)
> [!NOTE]
> If you intend to use TRAMbio for analysis of protein trajectories, please note that building Cython wheels for
> [MDAnalysis](https://pypi.org/project/MDAnalysis/) for Python 3.8 on macOS may fail.
> In that case, users are encouraged to use [mdtraj](https://pypi.org/project/mdtraj/) as an alternative.
### Install from PyPI
The default installation only carries dependencies for the [`tram-pebble`](#cli) command as well as the API of the general (k,l)-Component Pebble Game:
```bash
pip install TRAMbio
```
Additional installation profiles are as follows:
- `molecule` is required for calculations involving protein files or data in [PDB v.3 format](https://www.wwpdb.org/documentation/file-format).
- `trajectory` extends the previous profile with dependencies required for analysis of [MD Simulation trajectories](#cli). As an alternative, you can manually install [biopandas](https://pypi.org/project/biopandas) and either [MDAnalysis](https://pypi.org/project/MDAnalysis/) or [mdtraj](https://pypi.org/project/mdtraj/).
- `xml` enables utility for verifying TRAM's [XML output](#component-xml-files). As this depends on the non-python [libxml2](https://github.com/GNOME/libxml2) library, the dependency is made optional.
- `all` combines all the above profiles.
An example installation command for protein analysis and XML verification but without support for trajectories would be:
```bash
pip install TRAMbio[molecule,xml]
```
Alternatively, you can manually download TRAMbio from [GitHub](https://github.com/gate-tec/TRAMbio/releases).
To install one of these versions, unpack it and run the following from the top-level source directory using the Terminal:
```bash
pip install .[all]
```
## Examples
Execution of the general (k,l)-Pebble Game via API:
```pycon
>>> import networkx as nx # TODO
>>> from TRAMbio.pebble_game.pebble_game import run_pebble_game
>>> graph = nx.complete_graph(5)
>>> rho, _ , graph_type = run_pebble_game(graph, k=2, l=3)
>>> print(f"The graph is {graph_type} with {rho} redundant edges.")
'The graph is over-constrained with 3 redundant edges.'
```
Command-line execution of protein analysis:
```bash
# Fetch and analyse
tram-pdb --pdb 1l2y
# Convert to PyMol script
tram-pymol --pdb 1l2y --xml 1l2y_components.xml
# Visualize
pymol 1l2y_components.pml
```
## CLI
- `tram-pdb`: command for analyzing a single-state protein from a PDB file.
The notable arguments are:
- `-p`, `--pdb`: Protein input file in PDB v3 format.
- `-o`, `--out-dir`: Directory for output files. (default: next to input file)
- `-n`, `--name`: Alternate name for protein (used as output prefix).
<br/>
If not specified, name is derived from input file name.
- `tram-xtc`: command for analyzing an MD Simulation trajectory.
The notable arguments are:
- `-x`, `--xtc`: Trajectory file in XTC format.
- `-p`, `--pdb`: Protein input file in PDB v3 format.
- `-o`, `--out-dir`: Directory for output files. (default: next to input file)
- `-n`, `--name`: Alternate name for protein (used as output prefix).
<br/>
If not specified, name is derived from input file name.
- `-s`, `--stride`: Only processes every stride-th frame. (default: 50)
<br/>
Negative values result in only the first frame being processed.
- `-m`, `--module`: Base module for trajectory loading.
<br/>
Requires either module [MDAnalysis](https://pypi.org/project/MDAnalysis/) (current default) or [mdtraj](https://pypi.org/project/mdtraj/) to load trajectories.
- `tram-pymol`: command for creating a PyMol visualization from the output of above commands.
The notable arguments are:
- `-p`, `--pdb`: Protein input file in PDB v3 format.
- `-x`, `--xml`: Path to components XML resulting from the component analysis.
- `--xtc`: Trajectory file in XTC format. Required for visualizing results from `tram-trajectory`.
- `-o`, `--out-dir`: Directory for output files. (default: next to input file)
- `-n`, `--name`: Alternate name for protein (used as output prefix).
<br/>
If not specified, name is derived from input file name.
- `-b`, `--bnd-file`: Optionally, the `.bnd` file resulting from the component analysis can be provided, if hydrogen bonds should be included in the visualization. (Not recommended for trajectories)
- `-m`, `--module`: Base module for trajectory loading. Only used when `--xtc` is present. (default: MDAnalysis)
<br/>
Requires either module [MDAnalysis](https://pypi.org/project/MDAnalysis/) (current default) or [mdtraj](https://pypi.org/project/mdtraj/) to load trajectories.
- `tram-residue`: command for converting (atom-level) component results to residue-level.
The notable arguments are:
- `-x`, `--xml`: Path to components XML resulting from the component analysis.
- `-o`, `--out-dir`: Directory for output files. (default: next to input file)
- `-n`, `--name`: Alternate name for protein (used as output prefix).
<br/>
If not specified, name is derived from input file name.
- `tram-pebble`: command for applying the general (k,l)-Component Pebble Game to provided graphs.
The notable arguments are:
- `-g`, `--graph`: Path to the input file in [GRAPHML format](http://graphml.graphdrawing.org/).
- `-k`, `--k-param`: Parameter `k` of the Pebble Game. Needs to be a positive integer. (default: 2)
- `-l`, `--l-param`: Parameter `l` of the Pebble Game. Nedds to be in interval `[0,2k)` (default: 3)
- `-o`, `--out-dir`: Directory for output files. (default: next to input file)
- `-n`, `--name`: Alternate name for protein (used as output prefix).
<br/>
If not specified, name is derived from input file name.
## Environment Variables
Multiple features of the CLI commands can be customized via environment variables.
<details><summary>Environment variables for controlling atomic interactions:</summary>
T.b.a
</details>
<details><summary>Environment variables for loading PDB data:</summary>
<table>
<thead>
<tr><th>Name</th><th>Description</th><th>Data Type</th><th>Default</th></tr>
</thead>
<tbody>
<tr><td><code>TRAM_PDB_UNIQUE_BONDS</code></td><td>Whether to limit annotations for atomic edges to a single, unique label.</td><td><code>bool</code></td><td><code>false</code></td></tr>
<tr><td><code>TRAM_PDB_KEEP_HETS</code></td><td>Whether to include <code>HETATM</code> records from PDB data.</td><td><code>bool</code></td><td><code>true</code></td></tr>
</tbody>
</table>
</details>
<details><summary>Environment variables for controlling the workflows:</summary>
T.b.a
</details>
## Data Formats
### Component-XML Files
The structure analysis results are written as an XML file with a root `<graph>` tag, containing:
- `<components>` list of "atomic" components, i.e. components that are never subdivided, but instead fully present (possibly joined together).
`size` attribute describes the number of base components.
- `<omponent>` individual base component with a unique `id` and a denoted `size` (including halo). Some components have an optional `structure` attribute, if they form a known configuration.
- `<nodes>` list of nodes, that form this component
- `<node>` tag, containing the unique node-id
- `<halo>` list of nodes that should be considered part of this component (cf. hinge properties in mechanical model)
- `<node>` tag, containing the unique node-id
- `<states>` list of all states, being either configurations (dilution analysis) or individual frames (trajectory analysis)
- `<state>` list of individual components for the specific `key` attribute, being either a minimal energy threshold (dilution) or the frame number (trajectory)
- `<component>` individual component for this state
- `<halo>` [see above]
- `<components>` list of atomic components (sub-components) that build up this component
- `<component/>` tag, referencing the `id` of the respective atomic component
### Edge Data Files
Data on interactions collected during analysis is written to a tab-separated `.bnd` bond-list file with the columns:
- `node1`: first node
- `node2`: second node
- `type`: the main interaction type between these nodes
- `type_set`: the full set of possible interactions (if not filtered)
- `key`: currently only bonding energy for hydrogen bonds
- `extra`: list of additional information for certain interaction types
- hydrogen bonds: up to three values for known angles in order of theta (donor-hydrogen-acceptor), phi (hydrogen-acceptor-base), and gamma (angle between normals of the two sp²-planes)
- cation-pi interactions: interaction angle between cation and aromatic normal vector
- aromatic interactions: interaction angle between the two aromatic normal vectors followed by the two angles between the aromatic distance vector and the respective aromatic normal vector
Additionally, only for processed trajectories, the file documents interaction changes between frames, indicated by the following columns:
- `frame`: the specific frame where this interaction changed
- `_merge`: indicating the type of change,
that this interaction was either added (`right_only`) or removed (`left_only`) in this frame
### PyMol Command Files
The `tram-pymol` command generates a PDB and a `.pml` file. The latter can be directly run in a PyMol instance from its directory.
### Residue-level Component-JSON Files
The residue-level component structure resulting from `tram-residue` is stored in JSON file with the following structure:
```json
{
"KEY-1": [
[
"AMINO-ACID-1",
"AMINO-ACID-2"
],
[
"AMINO-ACID-X",
"AMINO-ACID-Y",
...
],
...
],
"KEY-2": [...]
}
```
The `KEY-X` entries are the keys of the corresponding `<state>` in the components XML. Each of them maps to a list of residue-level components.
## Licenses
- [NetworkX](https://github.com/networkx/networkx) is Revised BSD licensed.
- [BioPandas](https://github.com/BioPandas/biopandas) is Revised BSD licensed.
- TRAMbio itself is MIT licensed.
## Citation
If you use TRAMbio as part of your workflow in a scientific publication, please consider citing the TRAMbio repository as follows:
```bibtex
@unpublished{handke2025trambio,
title = {{TRAMbio}: A Flexible Python Package for Graph Rigidity Analysis of Macromolecules},
author = {Handke, Nicolas and Gatter, Thomas and Reinhardt, Franziska and Stadler, Peter F.},
year = {2025},
note = {unpublished},
}
```
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"description": "\n\n[](https://github.com/gate-tec/TRAMbio/actions/workflows/tests.yml)\n[](.github/CODE_OF_CONDUCT.md)\n\n# TRAMbio\n\n*Topological Rigidity Analysis in Molecular Biology* (TRAMbio)\nis a package based on and centered on the pebble game. It provides\nfunctionality for general applications in graph theory including testing\nfor $(k,l)$-sparsity as well as determining the $(k,l)$-spanning\nsubgraphs, i.e., the $(k,l)$-rigid components. With regard to\nmolecular data, in particular proteins, TRAMbio provides tools for the\nrigidity analysis on an atom or residue-level with further functionality\ntowards specialized tasks like (a) simulated protein unfolding ([Rader et al. 2002])\non single-state protein data and (b) time-based tracking of\nrigid component changes in molecular dynamics (MD) trajectories.\n\n[Rader et al. 2002]: https://doi.org/10.1073/pnas.062492699\n\n- Source: https://github.com/gate-tec/TRAMbio\n- Bug reports: https://github.com/gate-tec/TRAMbio/issues\n\n<details><summary>Table of contents</summary>\n\n- [Installation](#installation)\n- [Examples](#examples)\n- [CLI commands](#cli)\n- [Envoronment Variables](#environment-variables)\n- [Data Formats](#data-formats)\n - [Component-XML Files](#component-xml-files)\n - [Edge Data Files](#edge-data-files)\n - [PyMol Command Files](#pymol-command-files)\n - [Residue-level Component-JSON Files](#residue-level-component-json-files)\n- [Licenses](#licenses)\n- [Citation](#citation)\n</details>\n\n## Installation\n\n### System requirements\n- python (>=3.8)\n\n> [!NOTE]\n> If you intend to use TRAMbio for analysis of protein trajectories, please note that building Cython wheels for\n> [MDAnalysis](https://pypi.org/project/MDAnalysis/) for Python 3.8 on macOS may fail.\n> In that case, users are encouraged to use [mdtraj](https://pypi.org/project/mdtraj/) as an alternative.\n\n### Install from PyPI\nThe default installation only carries dependencies for the [`tram-pebble`](#cli) command as well as the API of the general (k,l)-Component Pebble Game:\n```bash\npip install TRAMbio\n```\nAdditional installation profiles are as follows:\n- `molecule` is required for calculations involving protein files or data in [PDB v.3 format](https://www.wwpdb.org/documentation/file-format).\n- `trajectory` extends the previous profile with dependencies required for analysis of [MD Simulation trajectories](#cli). As an alternative, you can manually install [biopandas](https://pypi.org/project/biopandas) and either [MDAnalysis](https://pypi.org/project/MDAnalysis/) or [mdtraj](https://pypi.org/project/mdtraj/).\n- `xml` enables utility for verifying TRAM's [XML output](#component-xml-files). As this depends on the non-python [libxml2](https://github.com/GNOME/libxml2) library, the dependency is made optional.\n- `all` combines all the above profiles.\n\nAn example installation command for protein analysis and XML verification but without support for trajectories would be:\n```bash\npip install TRAMbio[molecule,xml]\n```\n\nAlternatively, you can manually download TRAMbio from [GitHub](https://github.com/gate-tec/TRAMbio/releases).\nTo install one of these versions, unpack it and run the following from the top-level source directory using the Terminal:\n```bash\npip install .[all]\n```\n\n## Examples\n\nExecution of the general (k,l)-Pebble Game via API:\n```pycon\n>>> import networkx as nx # TODO\n>>> from TRAMbio.pebble_game.pebble_game import run_pebble_game\n>>> graph = nx.complete_graph(5)\n>>> rho, _ , graph_type = run_pebble_game(graph, k=2, l=3)\n>>> print(f\"The graph is {graph_type} with {rho} redundant edges.\")\n'The graph is over-constrained with 3 redundant edges.'\n```\n\nCommand-line execution of protein analysis:\n```bash\n# Fetch and analyse\ntram-pdb --pdb 1l2y\n# Convert to PyMol script\ntram-pymol --pdb 1l2y --xml 1l2y_components.xml\n# Visualize\npymol 1l2y_components.pml\n```\n\n## CLI\n\n- `tram-pdb`: command for analyzing a single-state protein from a PDB file.\n\n The notable arguments are:\n - `-p`, `--pdb`: Protein input file in PDB v3 format.\n - `-o`, `--out-dir`: Directory for output files. (default: next to input file)\n - `-n`, `--name`: Alternate name for protein (used as output prefix).\n <br/>\n If not specified, name is derived from input file name.\n- `tram-xtc`: command for analyzing an MD Simulation trajectory.\n\n The notable arguments are:\n - `-x`, `--xtc`: Trajectory file in XTC format.\n - `-p`, `--pdb`: Protein input file in PDB v3 format.\n - `-o`, `--out-dir`: Directory for output files. (default: next to input file)\n - `-n`, `--name`: Alternate name for protein (used as output prefix).\n <br/>\n If not specified, name is derived from input file name.\n - `-s`, `--stride`: Only processes every stride-th frame. (default: 50)\n <br/>\n Negative values result in only the first frame being processed.\n - `-m`, `--module`: Base module for trajectory loading.\n <br/>\n Requires either module [MDAnalysis](https://pypi.org/project/MDAnalysis/) (current default) or [mdtraj](https://pypi.org/project/mdtraj/) to load trajectories.\n- `tram-pymol`: command for creating a PyMol visualization from the output of above commands.\n\n The notable arguments are:\n - `-p`, `--pdb`: Protein input file in PDB v3 format.\n - `-x`, `--xml`: Path to components XML resulting from the component analysis.\n - `--xtc`: Trajectory file in XTC format. Required for visualizing results from `tram-trajectory`.\n - `-o`, `--out-dir`: Directory for output files. (default: next to input file)\n - `-n`, `--name`: Alternate name for protein (used as output prefix).\n <br/>\n If not specified, name is derived from input file name.\n - `-b`, `--bnd-file`: Optionally, the `.bnd` file resulting from the component analysis can be provided, if hydrogen bonds should be included in the visualization. (Not recommended for trajectories)\n - `-m`, `--module`: Base module for trajectory loading. Only used when `--xtc` is present. (default: MDAnalysis)\n <br/>\n Requires either module [MDAnalysis](https://pypi.org/project/MDAnalysis/) (current default) or [mdtraj](https://pypi.org/project/mdtraj/) to load trajectories.\n- `tram-residue`: command for converting (atom-level) component results to residue-level.\n\n The notable arguments are:\n - `-x`, `--xml`: Path to components XML resulting from the component analysis.\n - `-o`, `--out-dir`: Directory for output files. (default: next to input file)\n - `-n`, `--name`: Alternate name for protein (used as output prefix).\n <br/>\n If not specified, name is derived from input file name.\n- `tram-pebble`: command for applying the general (k,l)-Component Pebble Game to provided graphs.\n\n The notable arguments are:\n - `-g`, `--graph`: Path to the input file in [GRAPHML format](http://graphml.graphdrawing.org/).\n - `-k`, `--k-param`: Parameter `k` of the Pebble Game. Needs to be a positive integer. (default: 2)\n - `-l`, `--l-param`: Parameter `l` of the Pebble Game. Nedds to be in interval `[0,2k)` (default: 3)\n - `-o`, `--out-dir`: Directory for output files. (default: next to input file)\n - `-n`, `--name`: Alternate name for protein (used as output prefix).\n <br/>\n If not specified, name is derived from input file name.\n\n## Environment Variables\n\nMultiple features of the CLI commands can be customized via environment variables.\n\n<details><summary>Environment variables for controlling atomic interactions:</summary>\n\nT.b.a\n</details>\n\n<details><summary>Environment variables for loading PDB data:</summary>\n\n<table>\n<thead>\n<tr><th>Name</th><th>Description</th><th>Data Type</th><th>Default</th></tr>\n</thead>\n<tbody>\n<tr><td><code>TRAM_PDB_UNIQUE_BONDS</code></td><td>Whether to limit annotations for atomic edges to a single, unique label.</td><td><code>bool</code></td><td><code>false</code></td></tr>\n<tr><td><code>TRAM_PDB_KEEP_HETS</code></td><td>Whether to include <code>HETATM</code> records from PDB data.</td><td><code>bool</code></td><td><code>true</code></td></tr>\n</tbody>\n</table>\n</details>\n\n<details><summary>Environment variables for controlling the workflows:</summary>\n\nT.b.a\n</details>\n\n## Data Formats\n\n### Component-XML Files\n\nThe structure analysis results are written as an XML file with a root `<graph>` tag, containing:\n- `<components>` list of \"atomic\" components, i.e. components that are never subdivided, but instead fully present (possibly joined together).\n `size` attribute describes the number of base components.\n - `<omponent>` individual base component with a unique `id` and a denoted `size` (including halo). Some components have an optional `structure` attribute, if they form a known configuration.\n - `<nodes>` list of nodes, that form this component\n - `<node>` tag, containing the unique node-id\n - `<halo>` list of nodes that should be considered part of this component (cf. hinge properties in mechanical model)\n - `<node>` tag, containing the unique node-id\n- `<states>` list of all states, being either configurations (dilution analysis) or individual frames (trajectory analysis)\n - `<state>` list of individual components for the specific `key` attribute, being either a minimal energy threshold (dilution) or the frame number (trajectory)\n - `<component>` individual component for this state\n - `<halo>` [see above]\n - `<components>` list of atomic components (sub-components) that build up this component\n - `<component/>` tag, referencing the `id` of the respective atomic component\n\n### Edge Data Files\n\nData on interactions collected during analysis is written to a tab-separated `.bnd` bond-list file with the columns:\n- `node1`: first node\n- `node2`: second node\n- `type`: the main interaction type between these nodes\n- `type_set`: the full set of possible interactions (if not filtered)\n- `key`: currently only bonding energy for hydrogen bonds\n- `extra`: list of additional information for certain interaction types\n - hydrogen bonds: up to three values for known angles in order of theta (donor-hydrogen-acceptor), phi (hydrogen-acceptor-base), and gamma (angle between normals of the two sp\u00b2-planes)\n - cation-pi interactions: interaction angle between cation and aromatic normal vector\n - aromatic interactions: interaction angle between the two aromatic normal vectors followed by the two angles between the aromatic distance vector and the respective aromatic normal vector\n\nAdditionally, only for processed trajectories, the file documents interaction changes between frames, indicated by the following columns:\n- `frame`: the specific frame where this interaction changed\n- `_merge`: indicating the type of change,\n that this interaction was either added (`right_only`) or removed (`left_only`) in this frame\n\n### PyMol Command Files\n\nThe `tram-pymol` command generates a PDB and a `.pml` file. The latter can be directly run in a PyMol instance from its directory.\n\n### Residue-level Component-JSON Files\n\nThe residue-level component structure resulting from `tram-residue` is stored in JSON file with the following structure:\n```json\n{\n \"KEY-1\": [\n [\n \"AMINO-ACID-1\",\n \"AMINO-ACID-2\"\n ],\n [\n \"AMINO-ACID-X\",\n \"AMINO-ACID-Y\",\n ...\n ],\n ...\n ],\n \"KEY-2\": [...]\n}\n```\nThe `KEY-X` entries are the keys of the corresponding `<state>` in the components XML. Each of them maps to a list of residue-level components.\n\n## Licenses\n\n- [NetworkX](https://github.com/networkx/networkx) is Revised BSD licensed.\n- [BioPandas](https://github.com/BioPandas/biopandas) is Revised BSD licensed.\n- TRAMbio itself is MIT licensed.\n\n## Citation\n\nIf you use TRAMbio as part of your workflow in a scientific publication, please consider citing the TRAMbio repository as follows:\n\n```bibtex\n@unpublished{handke2025trambio,\n title = {{TRAMbio}: A Flexible Python Package for Graph Rigidity Analysis of Macromolecules},\n author = {Handke, Nicolas and Gatter, Thomas and Reinhardt, Franziska and Stadler, Peter F.},\n year = {2025},\n note = {unpublished},\n}\n```\n",
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