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Port details
dsr-pdb Simple C++ PDB reader (reads the protein description format)
1.0.3_15 biology on this many watch lists=2 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 1.0.3_14Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-01-29 07:57:18
Last Update: 2025-02-14 03:17:22
Commit Hash: fa53920
People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
License: LGPL21
WWW:
https://graphics.stanford.edu/~drussel/pdb/
Description:
dsr-pdb is a simple C++ PDB reader along with a couple of programs which use it to manipulate pdb files (applying a rigid transform or splitting/merging). The are aimed at people interested in proteins from a geometric viewpoint as they allow easy access to the geometry and bond structure in addition of the biological information. The reader has two modes for reading/writing a pdb file. The simplest one, through the Protein class just reads and writes a single protein from/to a pdb file (which must have only one chain, but can have multiple models). The second, through the PDB class can handle pdb files with multiple models and herogens (although these are just passed through and not currently interpreted).
Homepage    cgit ¦ Codeberg ¦ GitHub ¦ GitLab ¦ SVNWeb

Manual pages:
FreshPorts has no man page information for this port.
pkg-plist: as obtained via: make generate-plist
Expand this list (35 items)
Collapse this list.
  1. @ldconfig
  2. /usr/local/share/licenses/dsr-pdb-1.0.3_15/catalog.mk
  3. /usr/local/share/licenses/dsr-pdb-1.0.3_15/LICENSE
  4. /usr/local/share/licenses/dsr-pdb-1.0.3_15/LGPL21
  5. bin/pdb_align
  6. bin/pdb_align_points
  7. bin/pdb_cat
  8. bin/pdb_distance
  9. bin/pdb_distance_matrix
  10. bin/pdb_split
  11. bin/pdb_stats
  12. bin/pdb_transform
  13. include/dsrpdb/Atom.h
  14. include/dsrpdb/Matrix.h
  15. include/dsrpdb/Model.h
  16. include/dsrpdb/PDB.h
  17. include/dsrpdb/PDB_index.h
  18. include/dsrpdb/Point.h
  19. include/dsrpdb/Protein.h
  20. include/dsrpdb/Residue.h
  21. include/dsrpdb/Transform.h
  22. include/dsrpdb/align.h
  23. include/dsrpdb/config.h
  24. include/dsrpdb/distance.h
  25. include/dsrpdb/geometry.h
  26. include/dsrpdb/geometry_internal.h
  27. include/dsrpdb/iterator.h
  28. include/dsrpdb/label.h
  29. include/dsrpdb/labeled_index.h
  30. include/dsrpdb/small_map.h
  31. lib/libdsrpdb.a
  32. lib/libdsrpdb.so
  33. @owner
  34. @group
  35. @mode
Collapse this list.
Dependency lines:
  • dsr-pdb>0:biology/dsr-pdb
To install the port:
cd /usr/ports/biology/dsr-pdb/ && make install clean
To add the package, run one of these commands:
  • pkg install biology/dsr-pdb
  • pkg install dsr-pdb
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
PKGNAME: dsr-pdb
Flavors: there is no flavor information for this port.
distinfo:
TIMESTAMP = 1548747311 SHA256 (dsr-pdb-1.0.3/dsr-pdb.tgz) = e9fea9c4b8fc0255ee0e2bca11ab267d10cc9687cf5ba515c704875bcee21837 SIZE (dsr-pdb-1.0.3/dsr-pdb.tgz) = 958360
Packages (timestamps in pop-ups are UTC):
dsr-pdb
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest-1.0.3_151.0.3_51.0.3_151.0.3_15-1.0.3_5-
FreeBSD:13:quarterly-1.0.3_141.0.3_101.0.3_141.0.3_141.0.3_111.0.3_111.0.3_11
FreeBSD:14:latest-1.0.3_151.0.3_81.0.3_151.0.3_151.0.3_10-1.0.3_10
FreeBSD:14:quarterly-1.0.3_14-1.0.3_141.0.3_141.0.3_111.0.3_111.0.3_11
FreeBSD:15:latest-1.0.3_15n/a1.0.3_15n/a1.0.3_111.0.3_111.0.3_12
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
Library dependencies:
  1. libboost_program_options.so : devel/boost-libs
There are no ports dependent upon this port
Configuration Options:
No options to configure
Options name:
biology_dsr-pdb
USES:
compiler:c++11-lang gmake libtool localbase:ldflags tar:tgz
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (1 items)
Collapse this list.
  1. https://graphics.stanford.edu/~drussel/
Collapse this list.

Number of commits found: 22

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.0.3_15
14 Feb 2025 03:17:22
commit hash: fa53920e7219d4246816f65034ad058e81de3353commit hash: fa53920e7219d4246816f65034ad058e81de3353commit hash: fa53920e7219d4246816f65034ad058e81de3353commit hash: fa53920e7219d4246816f65034ad058e81de3353 files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
devel/boost: bump consumers after Boost-1.87 update

Sponsored by:	Future Crew, LLC
1.0.3_14
20 Nov 2024 10:05:25
commit hash: 312ee18b022b4abcb14973bb10894ba152b8f60bcommit hash: 312ee18b022b4abcb14973bb10894ba152b8f60bcommit hash: 312ee18b022b4abcb14973bb10894ba152b8f60bcommit hash: 312ee18b022b4abcb14973bb10894ba152b8f60b files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
devel/boost: bump consu,ers after update Boost to 1.86 release

Sponsored by:	Future Crew, LLC
1.0.3_13
03 Oct 2024 10:25:14
commit hash: 55cfbcf56c31f949cd93e4012c1d705c1094a5c6commit hash: 55cfbcf56c31f949cd93e4012c1d705c1094a5c6commit hash: 55cfbcf56c31f949cd93e4012c1d705c1094a5c6commit hash: 55cfbcf56c31f949cd93e4012c1d705c1094a5c6 files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
*/*: bump consumers after devel/boost* update

With hat:	office
Sponsored by:	Future Crew, LLC
1.0.3_12
13 Feb 2024 14:44:22
commit hash: db616534ff99d6268997e2f30858891e20641a1ecommit hash: db616534ff99d6268997e2f30858891e20641a1ecommit hash: db616534ff99d6268997e2f30858891e20641a1ecommit hash: db616534ff99d6268997e2f30858891e20641a1e files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
devel/boost: bump consumers after library update
1.0.3_11
27 Sep 2023 14:36:30
commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487commit hash: 21d8008e86830262f2a33a6dca9ddf2478cd6487 files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
devel/boost*: bump all consumers after 1.83.0
1.0.3_10
27 Apr 2023 18:25:55
commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6commit hash: 3e45e8e24481fab02384c55a1e655d1dc1b781c6 files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
*/*: bump all direct Boost cunsumers
1.0.3_9
16 Jan 2023 19:32:07
commit hash: e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash: e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash: e1287d0d1228d93e469256fa6c4c824b9d20426bcommit hash: e1287d0d1228d93e469256fa6c4c824b9d20426b files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
*/*:	bump libboost*.so libraries consumert after Boost upgrade
07 Sep 2022 21:58:51
commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4commit hash: fb16dfecae4a6efac9f3a78e0b759fb7a3c53de4 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
Remove WWW entries moved into port Makefiles

Commit b7f05445c00f has added WWW entries to port Makefiles based on
WWW: lines in pkg-descr files.

This commit removes the WWW: lines of moved-over URLs from these
pkg-descr files.

Approved by:		portmgr (tcberner)
1.0.3_8
07 Sep 2022 21:10:59
commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52commit hash: b7f05445c00f2625aa19b4154ebcbce5ed2daa52 files touched by this commit		 Stefan Eßer (se) search for other commits by this committer 
Add WWW entries to port Makefiles

It has been common practice to have one or more URLs at the end of the
ports' pkg-descr files, one per line and prefixed with "WWW:". These
URLs should point at a project website or other relevant resources.

Access to these URLs required processing of the pkg-descr files, and
they have often become stale over time. If more than one such URL was
present in a pkg-descr file, only the first one was tarnsfered into
the port INDEX, but for many ports only the last line did contain the
port specific URL to further information.

There have been several proposals to make a project URL available as
a macro in the ports' Makefiles, over time.
(Only the first 15 lines of the commit message are shown above View all of this commit message)
1.0.3_8
12 Aug 2022 14:46:53
commit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5edcommit hash: 4cf39decb348615b9c8a28370d987a85d1b8a5ed files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
*/*: bump all consumers after recent boost upgrade
1.0.3_7
22 May 2022 20:17:16
commit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cdcommit hash: b082b3d13e8c4872b73fb681eb99b261926ac9cd files touched by this commit		 Dima Panov (fluffy) search for other commits by this committer 
devel/boost-all: bump all library consumers after boost upgrade

PR:	246106
1.0.3_6
22 Mar 2022 00:07:11
commit hash: 929ed699367f119574a299b211b395ac2b2d74c9commit hash: 929ed699367f119574a299b211b395ac2b2d74c9commit hash: 929ed699367f119574a299b211b395ac2b2d74c9commit hash: 929ed699367f119574a299b211b395ac2b2d74c9 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/dsr-pdb: Remove -pg (mcount instrumentation) flag

This causes failure on aarch64:
https://bugs.freebsd.org/bugzilla/show_bug.cgi?id=262709
1.0.3_5
21 Mar 2022 19:25:25
commit hash: ed0ea3f13498154aad38b6ec5f1290a19d525c13commit hash: ed0ea3f13498154aad38b6ec5f1290a19d525c13commit hash: ed0ea3f13498154aad38b6ec5f1290a19d525c13commit hash: ed0ea3f13498154aad38b6ec5f1290a19d525c13 files touched by this commit		 Yuri Victorovich (yuri) search for other commits by this committer 
biology/dsr-pdb: Broken on aarch64

Reported by:	fallout
1.0.3_5
07 Apr 2021 08:09:01
commit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455ccommit hash: cf118ccf875508b9a1c570044c93cfcc82bd455c files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
One more small cleanup, forgotten yesterday.
Reported by:	lwhsu
1.0.3_5
06 Apr 2021 14:31:07
commit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344ebcommit hash: 305f148f482daf30dcf728039d03d019f88344eb files touched by this commit		 Mathieu Arnold (mat) search for other commits by this committer 
Remove # $FreeBSD$ from Makefiles.
1.0.3_5
11 Dec 2019 17:53:49
Revision:519824Original commit files touched by this commit		 jbeich search for other commits by this committer 
devel/boost-*: update to 1.72.0

Changes:	http://www.boost.org/users/history/version_1_72_0.html
PR:		241449
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D22136
1.0.3_4
19 Aug 2019 15:35:28
Revision:509290Original commit files touched by this commit		 jbeich search for other commits by this committer 
devel/boost-*: update to 1.71.0

Changes:	http://www.boost.org/users/history/version_1_71_0.html
PR:		238827
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D20774
1.0.3_3
26 Jul 2019 20:46:57
Revision:507372Original commit files touched by this commit		 gerald search for other commits by this committer 
Bump PORTREVISION for ports depending on the canonical version of GCC
as defined in Mk/bsd.default-versions.mk which has moved from GCC 8.3
to GCC 9.1 under most circumstances now after revision 507371.

This includes ports
 - with USE_GCC=yes or USE_GCC=any,
 - with USES=fortran,
 - using Mk/bsd.octave.mk which in turn features USES=fortran, and
 - with USES=compiler specifying openmp, nestedfct, c11, c++0x, c++11-lang,
   c++11-lib, c++14-lang, c++17-lang, or gcc-c++11-lib
plus, everything INDEX-11 shows with a dependency on lang/gcc9 now.

PR:		238330
1.0.3_2
12 Apr 2019 06:36:31
Revision:498698Original commit files touched by this commit		 jbeich search for other commits by this committer 
devel/boost-*: update to 1.70.0

Changes:	http://www.boost.org/users/history/version_1_70_0.html
PR:		235956
Exp-run by:	antoine
Differential Revision:	https://reviews.freebsd.org/D19303
1.0.3_1
05 Feb 2019 19:02:00
Revision:492270Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/dsr-pdb: Correct typo
1.0.3
05 Feb 2019 19:00:37
Revision:492269Original commit files touched by this commit		 yuri search for other commits by this committer 
biology/dsr-pdb: Add c++11 flags because boost isn't found without it

Also add patches for missing includes that only gcc complains about.

PR:		235519
Reported by:	Piotr Kubaj <pkubaj@anongoth.pl>
1.0.3
29 Jan 2019 07:56:30
Revision:491546Original commit files touched by this commit		 yuri search for other commits by this committer 
New port: biology/dsr-pdb: Simple C++ PDB reader (reads the protein description
format)

Number of commits found: 22
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