| Port details |
- py-rmsd Calculate root-mean-square deviation (RMSD) between coordinate sets
- 1.5.1 science
 =2      1.4_1Version of this port present on the latest quarterly branch. - Maintainer: yuri@FreeBSD.org
- Port Added: 2019-01-18 02:03:56
- Last Update: 2024-11-16 10:27:22
- Commit Hash: 397236d
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- 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.
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- 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 py311-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 py311-rmsd listed in the above command, you can pick from the names under the Packages section.- PKGNAME: py311-rmsd
- Package flavors (<flavor>: <package>)
- distinfo:
- TIMESTAMP = 1731748655
SHA256 (rmsd-1.5.1.tar.gz) = c0342821432aac10e98089877875a2cd8bbf624163971076d93686a40f10d127
SIZE (rmsd-1.5.1.tar.gz) = 19076
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-setuptools>=63.1.0 : devel/py-setuptools@py311
- python3.11 : lang/python311
- Test dependencies:
-
- python3.11 : lang/python311
- Runtime dependencies:
-
- py311-numpy>=1.16,1<1.27,1 : math/py-numpy@py311
- py311-scipy>0 : science/py-scipy@py311
- py311-setuptools>=63.1.0 : devel/py-setuptools@py311
- python3.11 : lang/python311
- This port is required by:
- for Build
-
- science/py-atomium
- for Run
-
- 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:
|
| Commit History - (may be incomplete: for full details, see links to repositories near top of page) |
| Commit | Credits | Log message |
|---|
1.5.1
16 Nov 2024 10:27:22
 |
Yuri Victorovich (yuri) |
science/py-rmsd: update 1.4 → 1.5.1
Reported by: portscout |
1.4_1
27 Jun 2023 19:34:34
|
Rene Ladan (rene) |
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
|
Gerald Pfeifer (gerald) |
*: Bump PORTREVISIONs for math/mpc update to 1.3.1 |
1.4
11 Jan 2023 15:58:34
|
Dmitry Marakasov (amdmi3) |
*/*: rename CHEESESHOP to PYPI in MASTER_SITES
PR: 267994
Differential revision: D37518
Approved by: bapt |
07 Sep 2022 21:58:51
|
Stefan Eßer (se) |
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
|
Stefan Eßer (se) |
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  ) |
1.4
07 Apr 2021 08:09:01
|
Mathieu Arnold (mat) |
One more small cleanup, forgotten yesterday.
Reported by: lwhsu |
1.4
06 Apr 2021 14:31:07
|
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
1.4
24 Dec 2020 09:03:39
 |
antoine |
scipy 1.5.4 is only compatible with python 3.6+
Reported by: pkg-fallout |
1.4
11 Nov 2020 06:00:50
|
yuri |
science/py-rmsd: Update 1.3.2 -> 1.4 |
1.3.2_2
26 Jul 2019 20:46:57
|
gerald |
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
|
yuri |
science/py-rmsd: Fix license
PR: 238134
Reported by: tobik |
1.3.2_1
10 Apr 2019 06:18:32
|
antoine |
Bump a few PORTREVISIONs after r498529
With hat: portmgr |
1.3.2
18 Jan 2019 02:07:03
|
yuri |
science/py-rmsd: Fix CATEGORIES |
1.3.2
18 Jan 2019 02:03:39
|
yuri |
New port: science/py-rmsd: Calculate root-mean-square deviation (RMSD) between
coordinate sets |
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