science/py-gemmi 0.7.5_1 FreeBSD

Macromolecular crystallography library and utilities

System: FreeBSD
Repository: FreeBSD ports
Maintainer: [email protected]
Last update: 2026-09-23
Commit: 7e67b1988f
License: MPL20
Categories: science, python
Package size: 1168.2 KiB, 3696.0 KiB installed

Description

Gemmi is a library, accompanied by a set of programs, developed primarily for use in macromolecular crystallography (MX). For working with: * macromolecular models (content of PDB, PDBx/mmCIF and mmJSON files), * refinement restraints (CIF files), * reflection data (MTZ and mmCIF formats), * data on a 3D grid (electron density maps, masks, MRC/CCP4 format) * crystallographic symmetry.

In the other systems

System

Port

Version

FreeBSD

science/py-gemmi

0.7.5_1

DragonFly

science/py-gemmi

0.7.1

Install

Binary package:

pkg install py312-gemmi

From the ports tree:

cd /usr/ports/science/py-gemmi/ && make install clean

To depend on this port in another port's Makefile:

RUN_DEPENDS=	py312-gemmi>0:science/py-gemmi

Packages

The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.

Repository

aarch64

amd64

armv6

armv7

i386

FreeBSD:14:latest

0.7.5_1

0.5.8

0.7.3

0.7.5_1

FreeBSD:14:quarterly

0.7.5_1

n/a

0.7.1

0.7.5_1

FreeBSD:15:latest

0.7.5_1

n/a

0.7.3

FreeBSD:15:quarterly

0.7.5_1

n/a

FreeBSD:16:latest

0.7.5_1

n/a

FreeBSD:16:quarterly

n/a

Dependencies

As this port's Makefile names them.

Build 4

${PYTHON_PKGNAMEPREFIX}pip>0 : devel/py-pip
${PYTHON_PKGNAMEPREFIX}nanobind>0 : devel/py-nanobind
${PYTHON_PKGNAMEPREFIX}wheel>0 : devel/py-wheel
pybind11>=2.6 : devel/pybind11

Library 1

libgemmi_cpp.so : science/gemmi

Test 1

${PYTHON_PKGNAMEPREFIX}biopython>0 : biology/py-biopython

The full lists below include those, and their dependencies in turn.

Build dependencies 24

Run dependencies 8

No port depends on this one.

Configuration

No options to configure.

USES: cmake compiler:c++17-lang localbase:ldflags python
Service scripts: none

Files

pkg-plist 32

%%PYTHON_SITELIBDIR%%/gemmi/__init__.py
%%PYTHON_SITELIBDIR%%/gemmi/__init__.pyi
%%PYTHON_SITELIBDIR%%/gemmi/cif.pyi
%%PYTHON_SITELIBDIR%%/gemmi/examples/aafreq.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/ccd_gi.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/ccd_subgraph.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/cif_i_sigi.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/col_order.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/from_json.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/long_geom.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/map2mtz.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/maskcheck.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/maskdiff.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/matthews.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/merge_mtz_mmcif.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/monomers.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/mtrix_iso.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/mtz_i_sigi.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/multiproc.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/patterson_slice.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/qq-plot.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/rama_gather.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/rama_plot.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/read_cif.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/refln-stats.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/simple_search.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/sub_ccd.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/to_rdkit.py
%%PYTHON_SITELIBDIR%%/gemmi/examples/weight.py
%%PYTHON_SITELIBDIR%%/gemmi/fetch.py
%%PYTHON_SITELIBDIR%%/gemmi/gemmi_ext.so
%%PYTHON_SITELIBDIR%%/gemmi/py.typed

distinfo 1

File

Size

SHA256

project-gemmi-gemmi-v0.7.5_GH0.tar.gz

2.096501e+06

9e2a8a51e62c69bf43f62aadf527ca4312860de8a36c12a8747d3e8ae556f0b3

Commit history 2

Date Commit Credits Log message

2026-09-23

7e67b1988f

Yuri Victorovich

science/py-gemmi: unbreak by backporting new patch to support nanobind-3.x

Also: fix the only failing testcase

2026-09-21 114e0397dd Yuri Victorovich devel/py-nanobind: update 2.13.0 → 3.1.0