Commit 2b1e7997 authored by Martin Larralde's avatar Martin Larralde
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Improve `README.md` with list of features and reference to documentation

parent a5efc8a6
...@@ -4,11 +4,11 @@ ...@@ -4,11 +4,11 @@
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...@@ -27,6 +27,29 @@ some additional features from [EMBOSS](http://emboss.bioinformatics.nl/cgi-bin/e ...@@ -27,6 +27,29 @@ some additional features from [EMBOSS](http://emboss.bioinformatics.nl/cgi-bin/e
This library has no external dependency and is available for all modern Python This library has no external dependency and is available for all modern Python
versions (3.6+). versions (3.6+).
### 📋 Features
A non-exhaustive list of available features:
- Peptide statistics: amino acid counts and frequencies.
- **QSAR** descriptors: BLOSUM indices, Cruciani properties, FASGAI vectors, Kidera factors, MS-WHIM scores, PCP descriptors, ProtFP descriptors, Sneath vectors, ST-scales, T-scales, VHSE-scales, Z-scales.
- Sequence profiles: hydrophobicity, hydrophobic moment, membrane position.
- Physicochemical properties: aliphatic index, instability index, theoretical net charge, isoelectric point, molecular weight (with isotope labelling support).
- Biological properties: structural class prediction.
*If this library is missing a useful statistic or descriptor, feel free to
reach out and open a feature request on the [issue tracker](https://github.com/althonos/peptides.py/issues)
of the [project repository](https://github.com/althonos/peptides.py).*
### 🧊 Vectorization
Most of the descriptors for a protein sequence are simple averages of values
taken in a lookup table, so computing them can be done in a vectorized manner.
If [`numpy`](https://numpy.org/) can be imported, relevant functions
(like `numpy.sum` or `numpy.take`) will be used, otherwise a fallback
implementation using [`array.array`](https://docs.python.org/3/library/array.html#array.array)
from the standard library is available.
## 🔧 Installing ## 🔧 Installing
Install the `peptides` package directly from [PyPi](https://pypi.org/project/peptides) Install the `peptides` package directly from [PyPi](https://pypi.org/project/peptides)
...@@ -42,6 +65,16 @@ package: ...@@ -42,6 +65,16 @@ package:
$ conda install -c bioconda peptides-py $ conda install -c bioconda peptides-py
``` --> ``` -->
## 📖 Documentation
A complete [API reference](https://peptides.readthedocs.io/en/stable/api.html)
can be found in the [online documentation](https://peptides.readthedocs.io/),
or directly from the command line using
[`pydoc`](https://docs.python.org/3/library/pydoc.html):
```console
$ pydoc peptides.Peptide
```
## 💡 Example ## 💡 Example
Start by creating a `Peptide` object from a protein sequence: Start by creating a `Peptide` object from a protein sequence:
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...@@ -93,7 +93,7 @@ A non-exhaustive list of available features: ...@@ -93,7 +93,7 @@ A non-exhaustive list of available features:
- Hydrophobic moment profile based on `Eisenberg, Weiss and Terwilliger (1984) <https://doi.org/10.1073/pnas.81.1.140>`_. - Hydrophobic moment profile based on `Eisenberg, Weiss and Terwilliger (1984) <https://doi.org/10.1073/pnas.81.1.140>`_.
- Membrane position based on `Eisenberg (1984) <https://doi.org/10.1146/annurev.bi.53.070184.003115>`_. - Membrane position based on `Eisenberg (1984) <https://doi.org/10.1146/annurev.bi.53.070184.003115>`_.
- Physico-chemical properties: - Physical-chemical properties:
- Aliphatic index proposed in `Ikai (1980) <https://pubmed.ncbi.nlm.nih.gov/7462208/>`_. - Aliphatic index proposed in `Ikai (1980) <https://pubmed.ncbi.nlm.nih.gov/7462208/>`_.
- Instability index proposed in `Boman (2003) <https://doi.org/10.1046/j.1365-2796.2003.01228.x>`_. - Instability index proposed in `Boman (2003) <https://doi.org/10.1046/j.1365-2796.2003.01228.x>`_.
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