From ffe70a75d332cf02f2d62802c40c86cc8ba45897 Mon Sep 17 00:00:00 2001
From: Ninjani <janani.durairaj@gmail.com>
Date: Fri, 26 Jan 2024 13:42:11 +0100
Subject: [PATCH] switch pdbx to mmcif library
---
PDBValidation/PDBXReader.py | 2 +-
README.md | 14 +++-----------
setup.py | 2 +-
3 files changed, 5 insertions(+), 13 deletions(-)
diff --git a/PDBValidation/PDBXReader.py b/PDBValidation/PDBXReader.py
index 95b8bbb..060e2f1 100644
--- a/PDBValidation/PDBXReader.py
+++ b/PDBValidation/PDBXReader.py
@@ -3,7 +3,7 @@ import gzip
import pandas as pd
import ost
-from pdbx.reader.PdbxReader import PdbxReader
+from mmcif.io.PdbxReader import PdbxReader
from .utils import *
diff --git a/README.md b/README.md
index 970513a..6441358 100644
--- a/README.md
+++ b/README.md
@@ -242,19 +242,11 @@ See [Ligand Options](#ligand-options).
- Python 3
- lxml
- pandas
-- PDBx Python Parser
+- py-mmcif (mmCIF Core Access Library)
- OpenStructure
-The lxml and pandas dependencies will be automatically installed upon installation with pip.
-The PDBx and OpenStructure packages aren't available through PyPI
-
-### PDBx Python Parser
-The wwPDB PDBx Python Parser must be installed manually as explained on the documentation page, and the PYTHONPATH
-entry set correctly:
-<http://mmcif.wwpdb.org/docs/sw-examples/python/html/index.html>
-
-A Python 3-compatible version is available in the CAMEO checkout:
-<https://git.scicore.unibas.ch/schwede/CAMEO/-/tree/master/modules/pdbx>
+The lxml, pandas and mmcif dependencies will be automatically installed upon installation with pip.
+The OpenStructure package isn't available through PyPI
### Compound Library
A working compound library is required. If it is not know by OpenStructure (which it should if OST was
diff --git a/setup.py b/setup.py
index 4725bee..52f32f8 100644
--- a/setup.py
+++ b/setup.py
@@ -18,7 +18,7 @@ setuptools.setup(
"License :: ???",
"Operating System :: OS Independent",
],
- install_requires=['lxml', 'pandas'],
+ install_requires=['lxml', 'pandas', 'mmcif'],
test_suite="PDBValidation.tests",
packages=['PDBValidation', 'PDBValidation/presets'],
scripts=['bin/PDBValidation', 'bin/PDBValidationExtract'],
--
GitLab