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.
*/*: 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
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)
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 )
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
- 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
- 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
- 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
- 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: 240293239934233413214864
Exp-run by: antoine
- 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
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
- 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
- update to 0.4e
- unbreak as distfile is unversioned
- future mismatches should be investigated as potential software updates
Approved by: portmgr (erwin)
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>
