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Port details
py-rmsd Calculate root-mean-square deviation (RMSD) between coordinate sets
1.4_1 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 1.4_1Version of this port present on the latest quarterly branch.
Maintainer: yuri@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2019-01-18 02:03:56
Last Update: 2023-06-27 19:34:34
Commit Hash: 3d9a815
License: BSD2CLAUSE
WWW:
https://github.com/charnley/rmsd
Description:
Calculate Root-mean-square deviation (RMSD) of Two Molecules Using Rotation. The root-mean-square deviation (RMSD) is calculated, using Kabsch algorithm (1976) or Quaternion algorithm (1991) for rotation, between two Cartesian coordinates in either .xyz or .pdb format, resulting in the minimal RMSD.
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
There is no configure plist information for this port.
Dependency lines:
  • ${PYTHON_PKGNAMEPREFIX}rmsd>0:science/py-rmsd@${PY_FLAVOR}
To install the port:
cd /usr/ports/science/py-rmsd/ && make install clean
To add the package, run one of these commands:
  • pkg install science/py-rmsd
  • pkg install py39-rmsd
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.
NOTE: This is a Python port. Instead of py39-rmsd listed in the above command, you can pick from the names under the Packages section.
PKGNAME: py39-rmsd
Package flavors (<flavor>: <package>)
  • py39: py39-rmsd
distinfo:
TIMESTAMP = 1605074347 SHA256 (rmsd-1.4.tar.gz) = 16a84a5f919faa0f2361e55ad4009a7c28e19a21ee9cc3bdb83f28ffb566563f SIZE (rmsd-1.4.tar.gz) = 18001

Packages (timestamps in pop-ups are UTC):
py311-rmsd
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest1.4_11.4_1-1.4_11.4_1---
FreeBSD:13:quarterly1.4_11.4_1-1.4_11.4_1---
FreeBSD:14:latest1.4_11.4_1-1.4_11.4_1---
FreeBSD:14:quarterly-1.4_1--1.4_1---
FreeBSD:15:latest1.4_11.4_1n/a-n/a---
 

py39-rmsd
ABIaarch64amd64armv6armv7i386powerpcpowerpc64powerpc64le
FreeBSD:13:latest--------
FreeBSD:13:quarterly------1.4_1-
FreeBSD:14:latest--------
FreeBSD:14:quarterly1.4_1--1.4_1--1.4_1-
FreeBSD:15:latest--n/a-n/a-1.4_11.4_1
 

Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  2. python3.9 : lang/python39
Test dependencies:
  1. python3.9 : lang/python39
Runtime dependencies:
  1. py39-numpy>=1.16,1<1.25,1 : math/py-numpy@py39
  2. py39-scipy>0 : science/py-scipy@py39
  3. py39-setuptools>=63.1.0 : devel/py-setuptools@py39
  4. python3.9 : lang/python39
This port is required by:
for Build
  1. science/py-atomium
for Run
  1. science/py-atomium

Configuration Options:
No options to configure
Options name:
science_py-rmsd
USES:
python
FreshPorts was unable to extract/find any pkg message
Master Sites:
Expand this list (2 items)
Collapse this list.
  1. https://files.pythonhosted.org/packages/source/r/rmsd/
  2. https://pypi.org/packages/source/r/rmsd/
Collapse this list.

Number of commits found: 14

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
1.4_1
27 Jun 2023 19:34:34
commit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacbcommit hash: 3d9a815d9c5acbb71f4bb07738bdeab4879feacb files touched by this commit
Rene Ladan (rene) search for other commits by this committer
all: remove explicit versions in USES=python for "3.x+"

The logic in USES=python will automatically convert this to 3.8+ by
itself.

Adjust two ports that only had Python 3.7 mentioned but build fine
on Python 3.8 too.

finance/quickfix: mark BROKEN with PYTHON

libtool: compile:  c++ -DHAVE_CONFIG_H -I. -I../.. -I -I. -I.. -I../.. -I../C++
-DLIBICONV_PLUG -DPYTHON_MAJOR_VERSION=3 -Wno-unused-variable
-Wno-maybe-uninitialized -O2 -pipe -DLIBICONV_PLUG -fstack-protector-strong
-fno-strict-aliasing -DLIBICONV_PLUG -Wall -ansi
-Wno-unused-command-line-argument -Wpointer-arith -Wwrite-strings
-Wno-overloaded-virtual -Wno-deprecated-declarations -Wno-deprecated -std=c++0x
-MT _quickfix_la-QuickfixPython.lo -MD -MP -MF
.deps/_quickfix_la-QuickfixPython.Tpo -c QuickfixPython.cpp  -fPIC -DPIC -o
.libs/_quickfix_la-QuickfixPython.o
warning: unknown warning option '-Wno-maybe-uninitialized'; did you mean
'-Wno-uninitialized'? [-Wunknown-warning-option]
QuickfixPython.cpp:175:11: fatal error: 'Python.h' file not found
          ^~~~~~~~~~
1 warning and 1 error generated.

Reviewed by:	portmgr, vishwin, yuri
Differential Revision:	<https://reviews.freebsd.org/D40568>
1.4_1
23 Apr 2023 09:09:58
commit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5bcommit hash: 8d3e020ed032a8db00208994d0db646de7dc6f5b files touched by this commit
Gerald Pfeifer (gerald) search for other commits by this committer
*: Bump PORTREVISIONs for math/mpc update to 1.3.1
1.4
11 Jan 2023 15:58:34
commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656commit hash: 77d68471aded6907dbbcb5ef50d557e4c69db656 files touched by this commit
Dmitry Marakasov (amdmi3) search for other commits by this committer
*/*: rename CHEESESHOP to PYPI in MASTER_SITES

PR:			267994
Differential revision:	D37518
Approved by:		bapt
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)
1.4
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)
1.4
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
1.4
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.
1.4
24 Dec 2020 09:03:39
Revision:559053Original commit files touched by this commit
antoine search for other commits by this committer
scipy 1.5.4 is only compatible with python 3.6+

Reported by:	pkg-fallout
1.4
11 Nov 2020 06:00:50
Revision:554876Original commit files touched by this commit
yuri search for other commits by this committer
science/py-rmsd: Update 1.3.2 -> 1.4
1.3.2_2
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
1.3.2_1
26 May 2019 18:17:15
Revision:502739Original commit files touched by this commit
yuri search for other commits by this committer
science/py-rmsd: Fix license

PR:		238134
Reported by:	tobik
1.3.2_1
10 Apr 2019 06:18:32
Revision:498530Original commit files touched by this commit
antoine search for other commits by this committer
Bump a few PORTREVISIONs after r498529

With hat:	portmgr
1.3.2
18 Jan 2019 02:07:03
Revision:490619Original commit files touched by this commit
yuri search for other commits by this committer
science/py-rmsd: Fix CATEGORIES
1.3.2
18 Jan 2019 02:03:39
Revision:490618Original commit files touched by this commit
yuri search for other commits by this committer
New port: science/py-rmsd: Calculate root-mean-square deviation (RMSD) between
coordinate sets

Number of commits found: 14