BSD Portsscience/smoldyn 2.75_1 FreeBSD
Biochemical simulator for molecular diffusion, surface interactions
- System
- FreeBSD
- Repository
- FreeBSD ports
- Maintainer
- [email protected]
- License
- LGPL3
- Categories
- science
- Package size
- 854.1 KiB, 4655.3 KiB installed
Description
Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system.
Smoldyn is easy to use and easy to install. It is more accurate and faster than other particle-based simulators. Smoldyn's unique features include: a "virtual experimenter" who can manipulate or measure the simulated system, support for spatial compartments, molecules with excluded volume, and simulations in 1, 2, or 3 dimensions.
In the other systems
| System | Port | Version |
|---|---|---|
| FreeBSD | science/smoldyn | 2.75_1 |
| DragonFly | science/smoldyn | 2.74 |
Install
Binary package:
pkg install smoldynFrom the ports tree:
cd /usr/ports/science/smoldyn/ && make install cleanTo depend on this port in another port's Makefile:
RUN_DEPENDS= smoldyn>0:science/smoldyn
LIB_DEPENDS= libsmoldyn_shared.so:science/smoldynPackages
The version each package repository carries. “-” means the repository builds no package of it, “n/a” that there is no such repository.
| Repository | aarch64 | amd64 | armv6 | armv7 | i386 |
|---|---|---|---|---|---|
| FreeBSD:14:latest | 2.75_1 | 2.75_1 | 2.69 | 2.75 | 2.75_1 |
| FreeBSD:14:quarterly | 2.75_1 | 2.75_1 | n/a | 2.74 | 2.75_1 |
| FreeBSD:15:latest | 2.75_1 | 2.75_1 | n/a | 2.74 | 2.75 |
| FreeBSD:15:quarterly | 2.75_1 | 2.75_1 | n/a | n/a | n/a |
| FreeBSD:16:latest | 2.75_1 | 2.75_1 | n/a | n/a | n/a |
| FreeBSD:16:quarterly | n/a | n/a | n/a | n/a | n/a |
Dependencies
As this port's Makefile names them.
Library 1
libtiff.so: graphics/tiff
Test 3
${PYTHON_PKGNAMEPREFIX}flaky>0: devel/py-flaky${PYTHON_PKGNAMEPREFIX}matplotlib>0: math/py-matplotlib${PYTHON_PKGNAMEPREFIX}numpy>=1.16: math/py-numpy
The full lists below include those, and their dependencies in turn.
Build dependencies 40
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- devel/cmake-core
- devel/gettext-runtime
- devel/jsoncpp
- devel/libffi
- devel/libunistring
- devel/libuv
- devel/ninja
- devel/readline
- dns/libidn2
- graphics/freeglut
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lerc
- graphics/libGLU
- graphics/libglvnd
- graphics/tiff
- lang/python312
- math/mpdecimal
- ports-mgmt/pkg
- print/indexinfo
- security/rhash
- textproc/expat2
- x11-toolkits/libXmu
- x11-toolkits/libXt
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXfixes
- x11/libXi
- x11/libXrandr
- x11/libXrender
- x11/libXxf86vm
- x11/libxcb
- x11/xorgproto
Run dependencies 25
- archivers/libdeflate
- archivers/liblz4
- archivers/zstd
- graphics/freeglut
- graphics/jbigkit
- graphics/jpeg-turbo
- graphics/lerc
- graphics/libGLU
- graphics/libglvnd
- graphics/tiff
- x11-toolkits/libXmu
- x11-toolkits/libXt
- x11/libICE
- x11/libSM
- x11/libX11
- x11/libXau
- x11/libXdmcp
- x11/libXext
- x11/libXfixes
- x11/libXi
- x11/libXrandr
- x11/libXrender
- x11/libXxf86vm
- x11/libxcb
- x11/xorgproto
No port depends on this one.
Configuration
Options name: science_smoldyn
| Option | Default | Description |
|---|---|---|
| PYTHON | off | Python bindings or support |
- USES
- cmake:testing compiler:c++11-lang gl localbase:ldflags python:test tar:tgz shebangfix xorg
- Service scripts
- none
Files
pkg-plist 28
- bin/smoldyn
- include/libsmoldyn.h
- include/smoldyn.h
- include/smoldynconfigure.h
- lib/libsmoldyn_shared.so
- lib/libsmoldyn_static.a
- %%PYTHON_SITELIBDIR%%/smoldyn/__init__.py
- %%PYTHON_SITELIBDIR%%/smoldyn/__main__.py
- %%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/__init__.pyc
- %%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/smoldyn.pyc
- %%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/types.pyc
- %%PYTHON_SITELIBDIR%%/smoldyn/__pycache__/utils.pyc
- %%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn.cpython-310-darwin.so
- %%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn-darwin.so
- %%PYTHON_SITELIBDIR%%/smoldyn/_smoldyn.so
- %%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__init__.py
- %%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__main__.py
- %%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/__init__.pyc
- %%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/_version.pyc
- %%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/combine.pyc
- %%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/__pycache__/data_model.pyc
- %%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/_version.py
- %%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/combine.py
- %%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/data_model.py
- %%PYTHON_SITELIBDIR%%/smoldyn/biosimulators/utils.py
- %%PYTHON_SITELIBDIR%%/smoldyn/smoldyn.py
- %%PYTHON_SITELIBDIR%%/smoldyn/types.py
- %%PYTHON_SITELIBDIR%%/smoldyn/utils.py
distinfo 1
| File | Size | SHA256 |
|---|---|---|
| smoldyn-2.75.tgz | 3.4008076e+07 | f7116e207d6ba91d3f709b6839d8054a622383ac6e0c5f81108015d083a2a094 |
Master sites 1
- https://www.smoldyn.org/
Commit history 0
No commits in the history this site was built from.