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Port details on branch 2026Q1
mmdb2 C++ toolkit for working with macromolecular coordinate files
2.0.22 science on this many watch lists=0 search for ports that depend on this port Find issues related to this port Report an issue related to this port View this port on Repology. pkg-fallout 2.0.22Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2026-03-13 08:27:11
Last Update: 2026-03-13 08:26:19
Commit Hash: a1876f5
License: GPLv3 LGPL3
WWW:
https://launchpad.net/mmdb
Description:
MMDB is designed to assist developers in working with macromolecular coordinate files. The library handles both PDB and mmCIF format files. The Library also features an internal binary format, portable between different platforms. This is achieved at uniformity of the Library's interface functions, so that there is no difference in handling different formats. MMDB provides various high-level tools for working with coordinate files, including reading and writing, orthogonal-fractional transforms, generation of symmetry mates, editing the molecular structure and more. MMDB is written by Eugene Krissinel, and is distributed as a part of the CCP4 suite. This project maintains a current stand-alone version of the library.
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb - no subversion history for this port

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (46 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/mmdb2-2.0.22/catalog.mk
  3. /usr/local/share/licenses/mmdb2-2.0.22/LICENSE
  4. /usr/local/share/licenses/mmdb2-2.0.22/GPLv3
  5. /usr/local/share/licenses/mmdb2-2.0.22/LGPL3
  6. include/mmdb2/hybrid_36.h
  7. include/mmdb2/mmdb_atom.h
  8. include/mmdb2/mmdb_bondmngr.h
  9. include/mmdb2/mmdb_chain.h
  10. include/mmdb2/mmdb_cifdefs.h
  11. include/mmdb2/mmdb_coormngr.h
  12. include/mmdb2/mmdb_cryst.h
  13. include/mmdb2/mmdb_defs.h
  14. include/mmdb2/mmdb_ficif.h
  15. include/mmdb2/mmdb_io_file.h
  16. include/mmdb2/mmdb_io_stream.h
  17. include/mmdb2/mmdb_machine_.h
  18. include/mmdb2/mmdb_manager.h
  19. include/mmdb2/mmdb_mask.h
  20. include/mmdb2/mmdb_math_.h
  21. include/mmdb2/mmdb_math_align.h
  22. include/mmdb2/mmdb_math_bfgsmin.h
  23. include/mmdb2/mmdb_math_fft.h
  24. include/mmdb2/mmdb_math_graph.h
  25. include/mmdb2/mmdb_math_linalg.h
  26. include/mmdb2/mmdb_math_rand.h
  27. include/mmdb2/mmdb_mattype.h
  28. include/mmdb2/mmdb_mmcif_.h
  29. include/mmdb2/mmdb_model.h
  30. include/mmdb2/mmdb_root.h
  31. include/mmdb2/mmdb_rwbrook.h
  32. include/mmdb2/mmdb_selmngr.h
  33. include/mmdb2/mmdb_seqsuperpose.h
  34. include/mmdb2/mmdb_symop.h
  35. include/mmdb2/mmdb_tables.h
  36. include/mmdb2/mmdb_title.h
  37. include/mmdb2/mmdb_uddata.h
  38. include/mmdb2/mmdb_utils.h
  39. include/mmdb2/mmdb_xml_.h
  40. lib/libmmdb2.so
  41. lib/libmmdb2.so.0
  42. lib/libmmdb2.so.0.0.0
  43. libdata/pkgconfig/mmdb2.pc
  44. @owner
  45. @group
  46. @mode
Collapse this list.
USE_RC_SUBR (Service Scripts)
  • no SUBR information found for this port
Dependency lines:
  • mmdb2>0:science/mmdb2
To install the port:
cd /usr/ports/science/mmdb2/ && make install clean
To add the package, run one of these commands:
  • pkg install science/mmdb2
  • pkg install mmdb2
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: mmdb2
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1651333778 SHA256 (mmdb2-2.0.22.tar.gz) = a9646933ce9f34633e1ae4901f2383af0e5318d6490851328f5b6aa06195ab51 SIZE (mmdb2-2.0.22.tar.gz) = 737837
Packages (timestamps in pop-ups are UTC):
mmdb2
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest2.0.222.0.222.0.202.0.222.0.22n/an/an/a
FreeBSD:13:quarterly2.0.222.0.222.0.222.0.222.0.22n/an/an/a
FreeBSD:14:latest2.0.222.0.222.0.222.0.222.0.222.0.22-2.0.22
FreeBSD:14:quarterly2.0.222.0.22-2.0.222.0.222.0.222.0.222.0.22
FreeBSD:15:latest2.0.222.0.22n/a2.0.22n/an/a2.0.222.0.22
FreeBSD:15:quarterly2.0.222.0.22n/a-n/an/a--
FreeBSD:16:latest2.0.222.0.22n/a-n/an/a--
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. gmake>=4.4.1 : devel/gmake
There are no ports dependent upon this port
Configuration Options:
No options to configure
Options name:
science_mmdb2
USES:
gmake libtool
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://www2.mrc-lmb.cam.ac.uk/personal/pemsley/coot/dependencies/
Collapse this list.

Number of commits found: 1

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
2.0.22
13 Mar 2026 08:26:19
commit hash: a1876f54a5a7dc46e0a7e89540ef1a35166afd30commit hash: a1876f54a5a7dc46e0a7e89540ef1a35166afd30commit hash: a1876f54a5a7dc46e0a7e89540ef1a35166afd30commit hash: a1876f54a5a7dc46e0a7e89540ef1a35166afd30 files touched by this commit		 Dimitry Andric (dim) search for other commits by this committer 
science/mmdb2: fix build with libc++ 21

With libc++ 21 science/mmdb2 fails to build, with errors similar to:

    In file included from mmdb2/mmdb_machine_.cpp:41:
    mmdb2/mmdb_machine_.h:296:13: error: unknown type name 'size_t'; did you
mean 'std::size_t'?
      296 |     typedef size_t fpstr_size_t;
          |             ^~~~~~
          |             std::size_t
    /usr/include/c++/v1/__cstddef/size_t.h:20:7: note: 'std::size_t' declared
here
       20 | using size_t = decltype(sizeof(int));
          |       ^

This is because mmdb2 apparently relies on transitive includes getting
the declaration of size_t, but with libc++ 21 this no longer works. Add
an include of <stddef.h> to work around it.

PR:		293180
Approved by:	maintainer timeout (2 weeks)
MFH:		2026Q1

(cherry picked from commit 27612e339b813fd512365febb70d669cce20a53b)

Number of commits found: 1
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Last processed:
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