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Port details
checkmol Analyze molecules for the presence of functional groups
0.5_14 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 0.5_14Version of this port present on the latest quarterly branch.
Maintainer: acm@FreeBSD.org search for ports maintained by this maintainer
Port Added: 2009-09-19 09:54:11
Last Update: 2022-09-07 21:58:51
Commit Hash: fb16dfe
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.
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 (5 items)
Collapse this list.
  1. bin/checkmol
  2. bin/matchmol
  3. /usr/local/share/licenses/checkmol-0.5_14/catalog.mk
  4. /usr/local/share/licenses/checkmol-0.5_14/LICENSE
  5. /usr/local/share/licenses/checkmol-0.5_14/GPLv2+
Collapse this list.
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.
distinfo:
TIMESTAMP = 1577760992 SHA256 (checkmol) = 6913ea64238a3bfe1dc9929d979e20c87fc5f40d53e300722ad18178c0dc80f2 SIZE (checkmol) = 555927

Packages (timestamps in pop-ups are UTC):
checkmol
ABIlatestquarterly
FreeBSD:13:aarch64--
FreeBSD:13:amd640.5_140.5_14
FreeBSD:13:armv6--
FreeBSD:13:armv7--
FreeBSD:13:i3860.5_140.5_14
FreeBSD:13:powerpc--
FreeBSD:13:powerpc64--
FreeBSD:13:powerpc64le--
FreeBSD:14:aarch64--
FreeBSD:14:amd640.5_140.5_14
FreeBSD:14:armv6--
FreeBSD:14:armv7--
FreeBSD:14:i3860.5_140.5_14
FreeBSD:14:powerpc--
FreeBSD:14:powerpc64--
FreeBSD:14:powerpc64le--
FreeBSD:15:aarch64--
FreeBSD:15:amd640.5_14-
FreeBSD:15:armv7--
FreeBSD:15:powerpc--
FreeBSD:15:powerpc64--
FreeBSD:15:powerpc64le--
 
Dependencies
NOTE: FreshPorts displays only information on required and default dependencies. Optional dependencies are not covered.
Build dependencies:
  1. as : devel/binutils
  2. 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:
Expand this list (1 items)
Collapse this list.
  1. https://homepage.univie.ac.at/norbert.haider/download/chemistry/checkmol/
Collapse this list.

Number of commits found: 37

Commit History - (may be incomplete: for full details, see links to repositories near top of page)
CommitCreditsLog message
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)
0.5_14
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)
0.5_14
20 Jul 2022 14:22:51
commit hash: 46196047a4df0f85aaee442799209fdaacf03361commit hash: 46196047a4df0f85aaee442799209fdaacf03361commit hash: 46196047a4df0f85aaee442799209fdaacf03361commit hash: 46196047a4df0f85aaee442799209fdaacf03361 files touched by this commit
Tobias C. Berner (tcberner) search for other commits by this committer
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 View all of this commit message)
0.5_14
21 Jun 2022 01:17:20
commit hash: c77c31909fb042682ba8aed7ca69419de9332804commit hash: c77c31909fb042682ba8aed7ca69419de9332804commit hash: c77c31909fb042682ba8aed7ca69419de9332804commit hash: c77c31909fb042682ba8aed7ca69419de9332804 files touched by this commit
Jose Alonso Cardenas Marquez (acm) search for other commits by this committer
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
commit hash: 121ccc3d2933cc7fba5c5b4ef78926541dfa9066commit hash: 121ccc3d2933cc7fba5c5b4ef78926541dfa9066commit hash: 121ccc3d2933cc7fba5c5b4ef78926541dfa9066commit hash: 121ccc3d2933cc7fba5c5b4ef78926541dfa9066 files touched by this commit
Jose Alonso Cardenas Marquez (acm) search for other commits by this committer
*/*: Bump PORTREVISION

- lang/fpc was update to new bootstrap
0.5_12
03 Feb 2022 05:07:13
commit hash: 0de5507c162d2a04212efa2770a1a9ed56626030commit hash: 0de5507c162d2a04212efa2770a1a9ed56626030commit hash: 0de5507c162d2a04212efa2770a1a9ed56626030commit hash: 0de5507c162d2a04212efa2770a1a9ed56626030 files touched by this commit
Jose Alonso Cardenas Marquez (acm) search for other commits by this committer
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
commit hash: 20948f4616704cb77eb942569eaf874288b29d02commit hash: 20948f4616704cb77eb942569eaf874288b29d02commit hash: 20948f4616704cb77eb942569eaf874288b29d02commit hash: 20948f4616704cb77eb942569eaf874288b29d02 files touched by this commit
Jose Alonso Cardenas Marquez (acm) search for other commits by this committer
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
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.
0.5_10
14 Jan 2021 21:11:15
Revision:561593Original commit files touched by this commit
acm search for other commits by this committer
- 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
Revision:556262Original commit files touched by this commit
acm search for other commits by this committer
- Bump PORTREVISION. fpc was updated to 3.2.0
0.5_8
06 Mar 2020 06:26:05
Revision:527858Original commit files touched by this commit
acm search for other commits by this committer
- 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
Revision:521624Original commit files touched by this commit
acm search for other commits by this committer
- 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
Revision:516897Original commit files touched by this commit
antoine search for other commits by this committer
Mark a few ports BROKEN (unfetchable)
0.5_6
03 Sep 2019 15:51:51
Revision:510956Original commit files touched by this commit
acm search for other commits by this committer
- 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
Revision:509004Original commit files touched by this commit
acm search for other commits by this committer
- 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
Revision:490347Original commit files touched by this commit
acm search for other commits by this committer
- Add LLD_UNSAFE

PR:		214864
0.5_4
05 Apr 2018 04:52:36
Revision:466532Original commit files touched by this commit
acm search for other commits by this committer
- 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
Revision:460573Original commit files touched by this commit
acm search for other commits by this committer
- Bump PORTREVISION. lang/fpc was updated to 3.0.4
0.5_3
26 Feb 2017 17:48:32
Revision:434899Original commit files touched by this commit
acm search for other commits by this committer
- Bump PORTREVISION. Freepascal was updated
- Take maintainership
0.5_2
12 Jan 2016 16:20:32
Revision:405891Original commit files touched by this commit
amdmi3 search for other commits by this committer
Convert LICENSE= "GPLxx # or later" to "GPLxx+"

Approved by:	portmgr blanket
0.5_2
05 Nov 2015 12:36:25
Revision:400848Original commit files touched by this commit
mat search for other commits by this committer
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
Revision:393766Original commit files touched by this commit
acm search for other commits by this committer
- 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
Revision:357307Original commit files touched by this commit
vanilla search for other commits by this committer
Stagify.
26 Mar 2014 04:04:46
Revision:349223Original commit files touched by this commit Sanity Test Failure Refresh
acm search for other commits by this committer
- Bump PORTREVISION. Freepascal compiler was updated to 2.6.4
0.5
20 Sep 2013 22:48:31
Revision:327767Original commit files touched by this commit
bapt search for other commits by this committer
Add NO_STAGE all over the place in preparation for the staging support (cat:
science)
0.5
01 Jun 2013 05:10:39
Revision:319554Original commit files touched by this commit
jgh search for other commits by this committer
- 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
Revision:318449Original commit files touched by this commit
jgh search for other commits by this committer
- update to 0.5

Submitted by:	pointhat (erwin@)
0.4e
07 Apr 2013 07:11:17
Revision:315750Original commit files touched by this commit
jgh search for other commits by this committer
- 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
Revision:315612Original commit files touched by this commit
miwi search for other commits by this committer
- Mark BROKEN  checksum mismatch

Reported by:	pointyhat
Approved by:	portmgr
0.4d
02 Mar 2013 06:30:56
Revision:313208Original commit files touched by this commit
miwi search for other commits by this committer
- Update to 0.4d

PR:		176547
Submitted by:	ports fury
0.4a_4
01 Oct 2012 14:45:17
Revision:305130Original commit files touched by this commit
tabthorpe search for other commits by this committer
- Reassign to the heap at maintainer's request
0.4a_4
19 Apr 2012 06:51:44
Original commit files touched by this commit
acm search for other commits by this committer
- Bump PORTREVISION (freepascal ports were updated)
0.4a_3
03 Jul 2011 13:22:25
Original commit files touched by this commit
ohauer search for other commits by this committer
 - remove MD5
0.4a_3
23 Jun 2011 05:39:27
Original commit files touched by this commit
acm search for other commits by this committer
- Bump PORTREVISION. lang/fpc has been updated to 2.4.4
0.4a_2
15 Nov 2010 22:50:44
Original commit files touched by this commit
acm search for other commits by this committer
- Welcome to fpc 2.4.2
- Bump PORTREVISIOON
0.4a_1
16 Aug 2010 18:46:23
Original commit files touched by this commit
acm search for other commits by this committer
- Bump PORTREVISION. lang/fpc was updated and now it supports amd64
0.4a
19 Sep 2009 09:53:55
Original commit files touched by this commit
miwi search for other commits by this committer
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>

Number of commits found: 37