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# PypKa
A python module for flexible Poisson-Boltzmann based pKa calculations with proton tautomerism
# Dependencies
delphi4py #1.0.0
libgfortran4
gawk
pytest
numpy
# License
pypka is distributed under a LGPL-3.0, however delphi4py depends on DelPhi which is proprietary. To use DelPhi the user is required to download the DelPhi license [here](https://honiglab.c2b2.columbia.edu/software/cgi-bin/software.pl?input=DelPhi)
# Documentation
Documentation can be found [here](https://pypka.readthedocs.io/en/latest/). (Under development)
# Installation
pip install pypka
apt install gawk gcc gfortran libgfortran4
# Contacts
Please submit a github issue to report bugs and to request new features. Alternatively you may find the developer [here](mailto:pdreis@fc.ul.pt). Please visit ou [website](http://mms.rd.ciencias.ulisboa.pt/) for more information.
# Change Log
- ## v0.4
API development
code level documentation improvement
documentation wiki developement with tutorial
test suite implementation
- ## v0.3
integration with delphi4py
integration with PDB2PQR
additional testing
- ## v0.2
DelPhi is now divided into two python modules imported by delphiT.py
input arguments are defined in delphiT.py
DelPhi routines for reading input files are bundled in delphi1_module
delphi1_module returns DelPhi’s internal data structure
delphi2_module does not do any I/O
delphi2_module returns solvation energies and potential map
delphiT.py calculates intrinsic pka and interactions energies
delphiT.py supports multiprocessing and Nanoshaper usage
delphiT.py supports membrane systems
delphiT.py supports double/single precision
- ## v0.1
migration from DelPhi 5.0 to DelPhi 5.1_Patched
delphiT calls delphiT.py
delphiT.py calls DelPhi 5.1_Patched
added benchmark process and small test set
- ## original version
delphiT calls directly DelPhi 5.0
1 maintainer
Metadata
1 maintainer
Release files for pypka 0.0.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| pypka-0.0.6.tar.gz | 1.9 MB | Details |
Built distributions (wheels)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| pypka-0.0.6-py3-none-any.whl | Python 3 | none | any | Details |
| pypka-0.0.6-py2-none-any.whl | Python 2 | none | any | Details |
Total release size: 6.0 MB
Release files / pypka-0.0.6.tar.gz
| Download URL | pypka-0.0.6.tar.gz |
|---|---|
| Size | 1.9 MB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
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No |
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twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.1.0 requests-toolbelt/0.9.1 tqdm/4.33.0 CPython/3.6.8
|
Release files / pypka-0.0.6-py3-none-any.whl
| Download URL | pypka-0.0.6-py3-none-any.whl |
|---|---|
| Size | 2.0 MB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
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twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.1.0 requests-toolbelt/0.9.1 tqdm/4.33.0 CPython/3.6.8
|
Release files / pypka-0.0.6-py2-none-any.whl
| Download URL | pypka-0.0.6-py2-none-any.whl |
|---|---|
| Size | 2.0 MB |
| Tags | Python 2 |
|
SHA-256 checksum How to use checksums |
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| Uploaded via |
twine/1.13.0 pkginfo/1.5.0.1 requests/2.22.0 setuptools/41.1.0 requests-toolbelt/0.9.1 tqdm/4.33.0 CPython/3.6.8
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