Port details |
- checkmol Analyze molecules for the presence of functional groups
- 0.5_17 science =2 0.5_16Version of this port present on the latest quarterly branch.
- Maintainer: acm@FreeBSD.org
- Port Added: 2009-09-19 09:54:11
- Last Update: 2025-01-25 00:33:46
- Commit Hash: 71b1672
- People watching this port, also watch:: jdictionary, py311-Automat, py311-python-gdsii, py39-PyOpenGL, p5-Sane
- License: GPLv2+
- WWW:
- https://homepage.univie.ac.at/norbert.haider/cheminf/cmmm.html
- Description:
- Checkmol is a command-line utility program which reads molecular
structure files in different formats and analyzes the input
molecule for the presence of various functional groups and structural
elements. At present, approx. 200 different functional groups are
recognized. This output can be easily placed into a database table,
permitting the creation of chemical databases with a functional group
search option. Checkmol also outputs a set of statistical values derived
from a given molecule, which can also be used for quick retrieval from a
database. These values include: the number of atoms, bonds, and rings,
the number of differently hybridized carbon, oxgen, and nitrogen atoms,
the number of C=O double bonds, the number of rings of different sizes,
the number of rings containing nitrogen, oxygen, sulfur, the number of
aromatic rings, the number of heterocyclic rings, etc. The combination
of all of these values for a given molecule represents some kind of
"fingerprint" which is useful for rapid pre-selection in a database
structure/substructure search prior to a full atom-by-atom match.
Matchmol complements the capabilities of checkmol. It compares two (or
more) molecular structures and determines whether one of them is a
substructure of the other one. This is done by a full atom-by-atom
comparison of the input structures. Thus, matchmol can be used as a
back-end program for structure/substructure search operations in
chemical databases.
The port installs both checkmol and matchmol.
- ¦ ¦ ¦ ¦
- Manual pages:
- FreshPorts has no man page information for this port.
- pkg-plist: as obtained via:
make generate-plist - Dependency lines:
-
- checkmol>0:science/checkmol
- To install the port:
- cd /usr/ports/science/checkmol/ && make install clean
- To add the package, run one of these commands:
- pkg install science/checkmol
- pkg install checkmol
NOTE: If this package has multiple flavors (see below), then use one of them instead of the name specified above.- PKGNAME: checkmol
- Flavors: there is no flavor information for this port.
- ONLY_FOR_ARCHS: aarch64 amd64 i386
- distinfo:
- TIMESTAMP = 1577760992
SHA256 (checkmol) = 6913ea64238a3bfe1dc9929d979e20c87fc5f40d53e300722ad18178c0dc80f2
SIZE (checkmol) = 555927
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:
-
- as : devel/binutils
- ppcx64 : lang/fpc
- There are no ports dependent upon this port
Configuration Options:
- No options to configure
- Options name:
- science_checkmol
- USES:
- fpc
- 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 |
0.5_17 25 Jan 2025 00:33:46 |
Jose Alonso Cardenas Marquez (acm) |
*/*: Bump PORTREVISION. editors/lazarus was updated to 3.8.0 |
0.5_16 18 Sep 2024 08:22:50 |
Jose Alonso Cardenas Marquez (acm) |
*/*: Pass to fpc based ports control of ONLY_FOR_ARCHS
- science/checkmol: Add aarch64 like supported platform
- science/mol2ps: Add aarch64 like supported platform
- science/mol2ps: Fix fetch updating it to 0.4c |
0.5_15 16 Jun 2024 08:26:36 |
Jose Alonso Cardenas Marquez (acm) |
*/*: Bump PORTREVISION. lang/fpc was updated to 3.2.3 |
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) |
0.5_14 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 ) |
0.5_14 20 Jul 2022 14:22:51 |
Tobias C. Berner (tcberner) |
science: remove 'Created by' lines
A big Thank You to the original contributors of these ports:
* Andreas Fehlner <fehlner@gmx.de>
* Brad Huntting <huntting@glarp.com>
* Chao Shin <quakelee@cn.FreeBSD.org>
* Cheng-Lung Sung <clsung@FreeBSD.org>
* Chia-Hsing Yu <me@davidyu.org>
* Chris Rees <utisoft@gmail.com>
* David Naylor <dbn@FreeBSD.org>
* Dmitry Sivachenko <demon@FreeBSD.org>
* Ed Schouten <ed@FreeBSD.org>
* Eric Freeman <freebsdports@chillibear.com>
* Erik B Knudsen (Only the first 15 lines of the commit message are shown above ) |
0.5_14 21 Jun 2022 01:17:20 |
Jose Alonso Cardenas Marquez (acm) |
lang/fpc: Fix build issues building some fpc based apps
- Add missing parameter to getdirentries syscall function
- Re-build i386 and amd64 bootstrap
- Revert fpc-i386 (FPC_USE_LIBC) build to syscall build
- Bump PORTREVISION in all ports dependant of freepascal compiler |
0.5_13 18 Jun 2022 04:23:28 |
Jose Alonso Cardenas Marquez (acm) |
*/*: Bump PORTREVISION
- lang/fpc was update to new bootstrap |
0.5_12 03 Feb 2022 05:07:13 |
Jose Alonso Cardenas Marquez (acm) |
lang/fpc: Fix build issue on lazarus i386 and amd64
- Bump PORTREVISION
- Disable some default OPTIONS
Obtained
from: https://forum.lazarus.freepascal.org/index.php/topic,57752.msg429737.html#msg429737 |
0.5_11 01 Aug 2021 02:03:46 |
Jose Alonso Cardenas Marquez (acm) |
games/hedgewars: lang/nbc: science/checkmol: science/mol2ps: bump PORTREVISION
* lang/fpc was updated to 3.2.2 |
0.5_10 06 Apr 2021 14:31:07 |
Mathieu Arnold (mat) |
Remove # $FreeBSD$ from Makefiles. |
0.5_10 14 Jan 2021 21:11:15 |
acm |
- lang/fpc revert way like linker is taken by fpc compiler
- lang/fpc add binutils to RUN_DEPENDS
- editors/lazarus add binutils to RUN_DEPENDS
- editors/lazarus add gmake to RUN_DEPENDS
- editors/lazarus install fpc units like RUN_DEPENDS too
- Bump PORTREVISiON of fpc/lazarus ports
PR: 251712
Reported by: amdmi3 |
0.5_9 25 Nov 2020 03:13:18 |
acm |
- Bump PORTREVISION. fpc was updated to 3.2.0 |
0.5_8 06 Mar 2020 06:26:05 |
acm |
- Remove compat < 11 dependencies from bootstrap and compiler. It could fix
problems
when GENERIC kernel is not used.
- Rebuild bootstrap (ppcx64 and ppc386) with new changes
- Bump PORTREVISION
PR: 239135
Reported by: fbsdbugs4 at sentry.org |
0.5_7 31 Dec 2019 15:11:19 |
acm |
- Change LDPATH to FPC_LDPATH into lang/fpc/Makefile. It can be changed from
/etc/make.conf
- Add FPC_LDPATH to freepascal compiler. By default it is defined to
%%LOCALBASE%%/bin/ld.bfd but it can be changed setting FPC_LDPATH environment
variable
- Remove compatX dependencies from bootstrap and compiler. It could fix problems
when GENERIC kernel is not used [1]
- Rebuild bootstrap (ppcx64 and ppc386) with new changes
- Bump PORTREVISION
PR: 239135
Submitted by: fbsdbugs4 __at__ sentry.org |
0.5_6 06 Nov 2019 16:26:35 |
antoine |
Mark a few ports BROKEN (unfetchable) |
0.5_6 03 Sep 2019 15:51:51 |
acm |
- Rebuild bootstrap (ppcx64 and ppc386) with ld patches
- Fix build on 12-STABLE and CURRENT (amd64 and i386)
- Bump PORTREVISION for all ports that depends of lang/fpc
- Add USE_BINUTILS to fpc and lazarus based ports
- Add binutils dependency to Uses/fpc.mk and Uses/lazarus.mk
PR: 240293 239934 233413 214864
Exp-run by: antoine |
0.5_5 15 Aug 2019 16:11:27 |
acm |
- Add new fpc bootstrap (i386 and x86_64). It could need less COMPATX
dependencies in kernel
- Add patch file to solve some linking problem
- Remove LD_UNSAFE. Now it can be defined via LDPATH (/usr/bin/ld.bfd by
default). fpc is not working with lld. We will use binutils-ports when
ld.bfd is moved from base if lld not working on future version
of fpc
- Bump PORTREVISION |
0.5_4 15 Jan 2019 05:43:59 |
acm |
- Add LLD_UNSAFE
PR: 214864 |
0.5_4 05 Apr 2018 04:52:36 |
acm |
- Migrate Mk/bsd.fpc.mk to Mk/Uses/fpc.mk
- Convert all fpc-based ports to USES=fpc
PR: 227210
Reviewed by: portmgr
Approved by: portmgr
Exp-run by: antoine
Differential Revision: https://reviews.freebsd.org/D14617 |
0.5_4 01 Feb 2018 07:32:05 |
acm |
- Bump PORTREVISION. lang/fpc was updated to 3.0.4 |
0.5_3 26 Feb 2017 17:48:32 |
acm |
- Bump PORTREVISION. Freepascal was updated
- Take maintainership |
0.5_2 12 Jan 2016 16:20:32 |
amdmi3 |
Convert LICENSE= "GPLxx # or later" to "GPLxx+"
Approved by: portmgr blanket |
0.5_2 05 Nov 2015 12:36:25 |
mat |
Fix ports that confused the meaning of WRKDIR and WRKSRC.
PR: 204056
Submitted by: mat
Reviewed by: bapt
Sponsored by: Absolight
Differential Revision: https://reviews.freebsd.org/D2735 |
0.5_2 09 Aug 2015 08:06:45 |
acm |
- editors/lazarus update to 1.4.2
- Add USE_FPC_RUN to bsd.fpc.mk. It add fpc units like run dependencies.
Otherwise
fpc units only are added like build dependencies (less dependencies registered
when they are installed with pkg).
- Remove GTK1 obsolete dependencies
- Bump all ports with dependencies of fpc-* units
- Bump all ports with dependencies of lazarus ports
- Clean up |
0.5_1 10 Jun 2014 12:52:48 |
vanilla |
Stagify. |
26 Mar 2014 04:04:46
|
acm |
- Bump PORTREVISION. Freepascal compiler was updated to 2.6.4 |
0.5 20 Sep 2013 22:48:31 |
bapt |
Add NO_STAGE all over the place in preparation for the staging support (cat:
science) |
0.5 01 Jun 2013 05:10:39 |
jgh |
- worked with upstream to roll versioned source distfile
- no difference in previous distfile (ie. checksum)
- remove unneeded dist_subdir directive |
0.5 18 May 2013 20:16:55 |
jgh |
- update to 0.5
Submitted by: pointhat (erwin@) |
0.4e 07 Apr 2013 07:11:17 |
jgh |
- update to 0.4e
- unbreak as distfile is unversioned
- future mismatches should be investigated as potential software updates
Approved by: portmgr (erwin) |
0.4d 30 Mar 2013 13:19:16 |
miwi |
- Mark BROKEN checksum mismatch
Reported by: pointyhat
Approved by: portmgr |
0.4d 02 Mar 2013 06:30:56 |
miwi |
- Update to 0.4d
PR: 176547
Submitted by: ports fury |
0.4a_4 01 Oct 2012 14:45:17 |
tabthorpe |
- Reassign to the heap at maintainer's request |
0.4a_4 19 Apr 2012 06:51:44 |
acm |
- Bump PORTREVISION (freepascal ports were updated) |
0.4a_3 03 Jul 2011 13:22:25 |
ohauer |
- remove MD5 |
0.4a_3 23 Jun 2011 05:39:27 |
acm |
- Bump PORTREVISION. lang/fpc has been updated to 2.4.4 |
0.4a_2 15 Nov 2010 22:50:44 |
acm |
- Welcome to fpc 2.4.2
- Bump PORTREVISIOON |
0.4a_1 16 Aug 2010 18:46:23 |
acm |
- Bump PORTREVISION. lang/fpc was updated and now it supports amd64 |
0.4a 19 Sep 2009 09:53:55 |
miwi |
Checkmol is a command-line utility program which reads molecular
structure files in different formats and analyzes the input
molecule for the presence of various functional groups and structural
elements. At present, approx. 200 different functional groups are
recognized. This output can be easily placed into a database table,
permitting the creation of chemical databases with a functional group
search option. Checkmol also outputs a set of statistical values derived
from a given molecule, which can also be used for quick retrieval from a
database. These values include: the number of atoms, bonds, and rings,
the number of differently hybridized carbon, oxgen, and nitrogen atoms,
the number of C=O double bonds, the number of rings of different sizes,
the number of rings containing nitrogen, oxygen, sulfur, the number of
aromatic rings, the number of heterocyclic rings, etc. The combination
of all of these values for a given molecule represents some kind of
"fingerprint" which is useful for rapid pre-selection in a database
structure/substructure search prior to a full atom-by-atom match.
WWW: http://merian.pch.univie.ac.at/~nhaider/cheminf/cmmm.html
PR: ports/138670
Feature safe:yes
Submitted by: Fernan Aguero <fernan at iib.unsam.edu.ar> |