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[bug#58261] [PATCH 00/11] Add rdkit.
From: |
David Elsing |
Subject: |
[bug#58261] [PATCH 00/11] Add rdkit. |
Date: |
Sun, 2 Oct 2022 22:55:26 +0000 |
Hello!
This patch series adds rdkit and its new dependencies.
Most optional components are enabled, except for the additional wrappers,
the "StructChecker" and the "compressed MolSuppliers".
All bundled software in External/ is unbundled and the included pickled data
(only used for a few tests) is removed.
freesasa is built as a shared library and the flex and bison files are
generated.
For yaehmop-tightbind, I removed the transpiled Fortran->C files and built the
Fortran parts with GFortran instead.
gemmi included a patched version of sajson where numbers are kept as the
original strings, so I made a package variant and added a check for
sajson::TYPE_INTEGER in gemmi.
sajson also requires another small patch
(gnu/packages/patches/sajson-parse_flags-linking.patch) which I took from the
unmerged upstream pull request
https://github.com/chadaustin/sajson/pull/54/files, is that ok?
The packages were reproducible after two rounds (when setting the environment
variables as in python-build-system for rdkit), but I only built them on
x86_64 as emulation would take quite long.
David Elsing (11):
gnu: Add fast-float.
gnu: Add pocketfft.
gnu: Add sajson.
gnu: Add tinydir.
gnu: Add optionparser.
gnu: Add gemmi.
gnu: Add freesasa.
gnu: Add maeparser.
gnu: Add coordgenlibs.
gnu: Add yaehmop-tightbind.
gnu: Add rdkit.
gnu/packages/chemistry.scm | 531 ++++++++++++++++++
gnu/packages/cpp.scm | 201 +++++++
.../patches/gemmi-fix-sajson-types.patch | 11 +
.../rdkit-cmake-external-dependencies.patch | 102 ++++
.../sajson-for-gemmi-numbers-as-strings.patch | 195 +++++++
.../patches/sajson-parse_flags-linking.patch | 45 ++
6 files changed, 1085 insertions(+)
create mode 100644 gnu/packages/patches/gemmi-fix-sajson-types.patch
create mode 100644 gnu/packages/patches/rdkit-cmake-external-dependencies.patch
create mode 100644
gnu/packages/patches/sajson-for-gemmi-numbers-as-strings.patch
create mode 100644 gnu/packages/patches/sajson-parse_flags-linking.patch
--
2.37.0
- [bug#58261] [PATCH 00/11] Add rdkit.,
David Elsing <=