Commit bfbe856a authored by Lukas Pravda's avatar Lukas Pravda
Browse files

changes to address ccdutils is now installable from PYPI

parent 1fce31a4
......@@ -27,7 +27,7 @@
* Once you have installed RDKit, as described above then install pdbeccdutils using pip:
```console
pip install git+https://github.com/PDBeurope/ccdutils.git
pip install pdbeccdutils
```
## Features
......
......@@ -4,21 +4,27 @@
# Introduction
The `pdbeccdutils` is presently under development and new functionality is added regularly as well as its functionality is being revised and updated. When properly installed all the code should have documentation. All the *public* methods do have [static typing](http://mypy-lang.org/) introduced in Python 3.5. All the interfaces should be well documented.
The `pdbeccdutils` is under development and new functionality is added regularly as well as its functionality is being revised and updated. When properly installed all the code should have documentation. All the *public* methods do have [static typing](http://mypy-lang.org/) introduced in Python 3.5. All the interfaces should be well documented.
## Installation
The `pdbeccdutils` can be presently obtained from the [EBI Gitlab](https://gitlab.ebi.ac.uk/pdbe/ccdutils.git) using the following command:
The `pdbeccdutils` can be presently obtained from [PYPI](https://pypi.org/project/pdbeccdutils/) using the following command:
```console
pip install git+https://gitlab.ebi.ac.uk/pdbe/ccdutils.git
pip install pdbeccdutils
```
Alternativelly, you can install the reposotory from [Github](https://github.com/PDBeurope/ccdutils) using the following command:
```console
pip install git+https://github.com/PDBeurope/ccdutils.git@master#egg=pdbeccdutils
```
If you want to contribute to the project please fork it first and then do a pull request.
# Getting started
The centerpoint of the `pdbecccdutils` package is a `Component` object, which is a wrapper around the default `rdkit.Chem.rdchem.Mol` object (object property `,mol`) providing most of the functionality and access to its properties. All the conformers are stored in the `rdkit.Chem.rdchem.Mol` with the exception of 2D depiction, as this one does not contain hydrogen atoms. `pdbeccdutils.core.modes.ConformerType` object allows accessing all of them.
The centerpoint of the `pdbecccdutils` package is a `Component` object, which is a wrapper around the default `rdkit.Chem.rdchem.Mol` object (object property `mol`) providing most of the functionality and access to its properties. All the conformers are stored in the `rdkit.Chem.rdchem.Mol` with the exception of 2D depiction, as this one does not contain explicit hydrogens. `pdbeccdutils.core.modes.ConformerType` object allows accessing all of them.
Below you can find a few typical use cases.
......@@ -35,7 +41,8 @@ rdkit_mol = component.mol
The `rdkit.Chem.rdchem.Mol` object is sanitized already.
### Chemical component dictionary
### Chemical component dictionary
Chemical component dictionary can be read in a single command and `rdkit.Chem.rdchem.Mol` representations obtained immediately. Resulting data structure of `ccd_reader.read_pdb_components_file` function is `Dict<str,pdbeccdutils.core.Component>` keyed on component ID as provided by the `data_XXX` element in the respective mmCIF file.
```python
......
__version__ = '0.5.4'
__version__ = '0.5.5'
from setuptools import setup, find_namespace_packages
import pdbeccdutils
import os
from setuptools import find_namespace_packages, setup
def read(fname):
return open(os.path.join(os.path.dirname(__file__), fname)).read()
def get_version(rel_path):
for line in read(rel_path).splitlines():
if line.startswith('__version__'):
delim = '"' if '"' in line else "'"
return line.split(delim)[1]
else:
raise RuntimeError("Unable to find version string.")
setup(
name="pdbeccdutils",
version=pdbeccdutils.__version__,
version=get_version('pdbeccdutils/__init__.py'),
description="Toolkit to deal with wwPDB chemical components definitions for small molecules.",
long_description=read("README.md"),
long_description_content_type='text/markdown',
project_urls={
"Source code": "https://github.com/PDBeurope/ccdutils",
"Documentation": "https://pdbeurope.github.io/ccdutils/",
......@@ -13,14 +29,16 @@ setup(
author_email="pdbehelp@ebi.ac.uk",
license="Apache License 2.0.",
keywords="PDB CCD wwPDB small molecule",
url="http://pypi.python.org/pypi/pdbeccdutils/",
packages=find_namespace_packages(),
zip_safe=False,
include_package_data=True,
python_requires='>=3.6',
install_requires=[
"Pillow",
"scipy",
"numpy",
"pdbecif @ git+https://github.com/PDBeurope/pdbecif.git@master#egg=pdbecif",
"pdbecif>=1.5",
],
tests_require=["pytest"],
entry_points={
......@@ -29,4 +47,21 @@ setup(
"setup_pubchem_library=pdbeccdutils.scripts.setup_pubchem_library_cli:main",
]
},
classifiers=[
"License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
"Programming Language :: Python",
"Programming Language :: Python :: 3",
"Programming Language :: Python :: 3.6",
"Programming Language :: Python :: 3.7",
"Programming Language :: Python :: Implementation :: CPython",
"Programming Language :: Python :: Implementation :: PyPy",
"Operating System :: Unix",
"Operating System :: MacOS",
"Operating System :: POSIX",
"Intended Audience :: Science/Research",
"Intended Audience :: Developers",
"Topic :: Scientific/Engineering :: Bio-Informatics",
"Development Status :: 5 - Production/Stable",
],
)
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment