Port details
py-atomium Molecular modeller and file parser
1.0.11_6 science Σ 1.0.11_5Version of this port present on the latest quarterly branch. Maintainer: yuri@FreeBSD.org Port Added: 2022-10-04 04:09:29Last Update: 2026-05-05 19:29:37Commit Hash: 2bf3834 Also Listed In: biology python License: MITWWW: https://atomium.bio/ Description: # atomium is a molecular modeller and file parser, capable of reading from and
writing to .pdb, .cif and .mmtf files. Manual pages: # FreshPorts has no man page information for this port.
pkg-plist: make generate-plist # There is no configure plist information for this port. USE_RC_SUBR (Service Scripts)
no SUBR information found for this port
Dependency lines :
${PYTHON_PKGNAMEPREFIX}atomium>0:science/py-atomium@${PY_FLAVOR} To install the port : # cd /usr/ports/science/py-atomium/ && make install clean To add the package , run one of these commands: pkg install science/py-atomium pkg install py311-atomium py311-atomium listed in the above command, you can pick from the names under the Packages section.PKGNAME: py311-atomium Package flavors (<flavor>: <package> ) # distinfo: # TIMESTAMP = 1664851734
SHA256 (samirelanduk-atomium-v1.0.11_GH0.tar.gz) = f26fec07ab7777032e2f829e4338021543f5ccbd76f59dc47c12decc9b1ebe88
SIZE (samirelanduk-atomium-v1.0.11_GH0.tar.gz) = 21454532
Packages (timestamps in pop-ups are UTC): #
Dependencies # NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered. Build dependencies: #
py311-coveralls>0 : devel/py-coveralls@py311 py311-msgpack>=0.6.1 : devel/py-msgpack@py311 py311-numpy>=1.16 : math/py-numpy@py311 py311-paramiko>0 : security/py-paramiko@py311 py311-requests>0 : www/py-requests@py311 py311-rmsd>0 : science/py-rmsd@py311 py311-sphinx>0 : textproc/py-sphinx@py311 py311-sphinx_rtd_theme>0 : textproc/py-sphinx_rtd_theme@py311 py311-tqdm>0 : misc/py-tqdm@py311 py311-valerius>=0.2 : biology/py-valerius@py311 py311-setuptools>=63.1.0 : devel/py-setuptools@py311 python3.11 : lang/python311
Test dependencies: #
py311-pytest>=7,1 : devel/py-pytest@py311 python3.11 : lang/python311
Runtime dependencies: #
py311-coveralls>0 : devel/py-coveralls@py311 py311-msgpack>=0.6.1 : devel/py-msgpack@py311 py311-numpy>=1.16 : math/py-numpy@py311 py311-paramiko>0 : security/py-paramiko@py311 py311-requests>0 : www/py-requests@py311 py311-rmsd>0 : science/py-rmsd@py311 py311-sphinx>0 : textproc/py-sphinx@py311 py311-sphinx_rtd_theme>0 : textproc/py-sphinx_rtd_theme@py311 py311-tqdm>0 : misc/py-tqdm@py311 py311-valerius>=0.2 : biology/py-valerius@py311 python3.11 : lang/python311
There are no ports dependent upon this port # Configuration Options : # No options to configure Options name : # science_py-atomium USES: # python
pkg-message: # FreshPorts was unable to extract/find any pkg message Master Sites: #
Commit History - (may be incomplete: for full details, see links to repositories near top of page) Commit Credits Log message 1.0.11_6 Max Brazhnikov (makc) */*: bump PORTREVISION after switching to NumPy 2.x 1.0.11_5 Max Brazhnikov (makc) */*: Switch to NumPy 2.x
PR: 294328
Exp-run: antoine 1.0.11_5 Charlie Li (vishwin) python.mk: retire ${PYNUMPY}
With both math/py-numpy (2) and math/py-numpy1, the variable stopped
making sense. Also remove the upper version bound. 1.0.11_5 Charlie Li (vishwin) math/py-numpy1: bump more RUN_DEPENDS consumers
These specify numpy indirectly using a different variable.
PR: 281470 1.0.11_4 Vsevolod Stakhov (vsevolod) security/libsodium: Update to 1.0.21
The API remains compatible but bumping all dependent ports as SHLIB
has changed.
Changelog: https://github.com/jedisct1/libsodium/releases/tag/1.0.21-RELEASE
Security: https://00f.net/2025/12/30/libsodium-vulnerability/
PR: 279347 1.0.11_3 Charlie Li (vishwin) python: bump all USE_PYTHON=distutils consumers after RUN_DEPENDS removal
Any missed ports, feel free to bump.
Any ports that need setuptools at runtime can have the devel/py-setuptools
manually added back to RUN_DEPENDS, but understand that this practice
is deprecated; see CHANGES for details. 1.0.11_2 Vsevolod Stakhov (vsevolod) security/libsodium: update to 1.0.19, bump dependent ports
PR: 278259
Reported by: Andrey Korobkov <alster-vinterdalen.se> 1.0.11_1 Gerald Pfeifer (gerald) *: Bump PORTREVISIONs for math/mpc update to 1.3.1 1.0.11 Yuri Victorovich (yuri) science/py-atomium: New port: Molecular modeller and file parser
