prot-rsa 1.0.1__py3-none-any.whl

prot_rsa-1.0.1.dist-info/METADATA

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+Metadata-Version: 2.4
+Name: prot-rsa
+Version: 1.0.1
+Summary: Fast protein residue surface-area calculation in Python
+Author: Junjun Mao
+License-Expression: MIT
+Project-URL: Homepage, https://github.com/newbooks/prot-rsa
+Project-URL: Repository, https://github.com/newbooks/prot-rsa
+Project-URL: Issues, https://github.com/newbooks/prot-rsa/issues
+Project-URL: Changelog, https://github.com/newbooks/prot-rsa/blob/main/HISTORY.md
+Project-URL: Documentation, https://github.com/newbooks/prot-rsa/blob/main/README.md
+Keywords: bioinformatics,computational biology,protein,residue surface area,structural biology
+Classifier: Development Status :: 5 - Production/Stable
+Classifier: Intended Audience :: Science/Research
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3 :: Only
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Programming Language :: Python :: 3.14
+Classifier: Programming Language :: Python :: 3
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy
+Requires-Dist: scipy
+Requires-Dist: numba
+Dynamic: license-file
+
+# prot-rsa
+
+Fast protein residue surface-area calculation in Python.
+
+## Installation
+
+Install the distribution from PyPI:
+
+```bash
+pip install prot-rsa
+```
+
+## Command-line use
+
+Run the installed application with:
+
+```bash
+prot-rsa structure.pdb
+# optionally choose a lower sampling resolution (minimum 122 points)
+prot-rsa structure.pdb --sphere-points 480
+```
+
+Run `prot-rsa --help` to see the supported PDB/mmCIF input suffixes, calculation
+options, defaults, and derived output filenames.
+
+The command writes `<base>.atom_sas.tsv` and `<base>.res_sas.tsv` as TSV files, plus a
+normalized `<base>.pqr` containing the selected radii and placeholder charge
+`0.000`. The production calculation uses cKDTree neighbor pruning; the
+deliberately naive serial implementation remains available as a correctness
+reference.
+
+## Python use
+
+The application can also be imported as the `protrsa` module so its functions
+and constants can be used directly:
+
+```python
+import protrsa
+```
+
+The distribution and command are named `prot-rsa`. The import name is
+`protrsa` because Python module names cannot contain hyphens.
+
+## Residue exposure
+
+Residue solvent-accessible surface area will be calculated by summing the
+already computed atom SASAs for each residue. The residue report will contain
+both complete-residue (`ALL`) and side-chain (`SIDE`) **Contextual Exposure
+Fraction (CEF)** values rather than conventional RSA:
+
+```text
+CEF = selected-atom SASA in the complete protein
+      / SASA of the same selected residue conformation in isolation
+```
+
+The denominator is a naked-residue calculation using the same selected atoms,
+atomic radii, probe radius, and sphere points, but without other residues
+present. The compact output columns are `all`, `a_ref`, `a_cef`, `side`,
+`s_ref`, and `s_cef`; leading `#` comment lines explain every field. CEF therefore represents
+the fraction of the selected residue surface retained in its protein context.
+It is distinct from conventional RSA, which normally uses a fixed residue-type
+reference or maximum ASA.
+
+Residues without retained side-chain atoms, such as glycine under the
+canonical backbone definition, use `NA` for the three SIDE fields.
+
+CEF lies in `[0, 1]` up to floating-point roundoff. The complete residue
+output contract is documented in `docs/specs/residue-cef.md`.
+
+
+## Optimization Comparison
+
+This program targets the speed optimization of residue surface solvent exposure calculation.
+
+The table below compares protein RSA calculation times under each
+optimization. Execution times are reported in seconds; lower values are
+better.
+
+| Optimization | Sphere points | Time (small) | Time (medium) | Time (large) | Atom-SASA MAE vs `*.sas.baseline` (small / medium / large, Ų) |
+| --- | ---: | ---: | ---: | ---: | ---: |
+| Naive | 960 | 551 | 2185 | 11634 | 0.000 / 0.000 / 0.000 |
+| cKDTree | 960 | 19.490 | 40.644 | 86.590 | 0.000 / 0.000 / 0.000 |
+| Vectorized mask | 960 | 0.609 | 1.285 | 2.820 | 0.000 / 0.000 / 0.000 |
+| Occlusion-ordered neighbors | 960 | 0.319 | 0.630 | 1.620 | 0.000 / 0.000 / 0.000 |
+| Cache | 960 | 0.276 | 0.536 | 1.393 | 0.000 / 0.000 / 0.000 |
+| Numba CPU | 960 | 0.328 | 0.388 | 0.735 | 0.000 / 0.000 / 0.000 |
+| Reduced points | 480 | 0.358 | 0.382 | 0.494 | 0.164 / 0.145 / 0.184 |
+
+Benchmark structures are **small** — 1LYZ (129 residues); **medium** — 1CA2
+(256 residues); **large** — 1UOR (580 residues). Residue counts are the numbers
+of unique residues represented by `ATOM` records; waters, ions, and other
+`HETATM` records are excluded.

prot_rsa-1.0.1.dist-info/RECORD

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+protrsa.py,sha256=swuXEoBwoGw9J6-6xgz7lo6mOEOE35B_VFylKkj32-k,62665
+prot_rsa-1.0.1.dist-info/licenses/LICENSE,sha256=oCSOht5ssI7Bw-fHeIPV6VssFgNAvXnYo4cyNxenMYc,1067
+prot_rsa-1.0.1.dist-info/METADATA,sha256=Nl9236Uowx4__MY_DHFFXHWK58IK32Xv9WbDgvypNNM,4957
+prot_rsa-1.0.1.dist-info/WHEEL,sha256=YVMoNqKzERt-wjUZwJ33xBGAwnFl-4cqbYkTtWa4itE,91
+prot_rsa-1.0.1.dist-info/entry_points.txt,sha256=ZOcjS_Cx_mgW3kHgD94BVjBJxPlSbHJqXGMYJ-qhA68,42
+prot_rsa-1.0.1.dist-info/top_level.txt,sha256=0NScA00sZEK-eDEyd_cXdTkWpFJU97Qrz8G7FbeNK7E,8
+prot_rsa-1.0.1.dist-info/RECORD,,

prot_rsa-1.0.1.dist-info/WHEEL

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+Wheel-Version: 1.0
+Generator: setuptools (84.0.0)
+Root-Is-Purelib: true
+Tag: py3-none-any
+

prot_rsa-1.0.1.dist-info/entry_points.txt

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+[console_scripts]
+prot-rsa = protrsa:main

prot_rsa-1.0.1.dist-info/licenses/LICENSE

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+MIT License
+
+Copyright (c) 2026 Junjun Mao
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

prot_rsa-1.0.1.dist-info/top_level.txt

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+protrsa