This CafePy is a tool for analyzing CafeMol outputs. CafeMol is one of the greatest Molecluar Dynamics simulation Software. The software provides a large time scale and a big structure scale simulation by using Coarse-Grained methods.
CafePy provides ..
- Reading some files [PDB, DCD, NINFO]
- calcurating Center of Mass from [PDB, DCD]
- python3 >= 3.5.1
- Numpy
- Scipy
- Matplotlib
git clone https://github.com/Moguf/cafepy.git
# or
pip install -U CafePy
Install virtualenv. (RECOMMEND:for protecting your Home environment.)
python3 -m pip install -U pip setuptools
python3 -m pip install virtualenv
# or
pip3 install virtualenv
activate virtualenv
virtualenv -p python3 venv
source venv/bin/activate
# Removing virtual environment
# (venv) deactivate
python3 -m pip install -r requirements.txt
# or
pip3 install -r requirements.txt
build & install
cd cafepy
python3 setup.py build
python3 setup.py install
## or
cd cafepy
pip3 install -e .
cd cafepy/docs
make html
Command Line Usage
python3 -m cafepy com -f filename.dcd -o output.file
Script Usage Samples
- Read dcd file.
from cafepy.files import DCD
dcd = DCD('test.dcd')
# you can get a coordinate of protein with list format.
print(dcd[0])
# you can get a coordinate of 1th atom with list format.
print(dcd[0][0])
- Read Ninfo file.
from cafepy.files import Ninfo
ntmp = Ninfo('test.ninfo')
print(ntmp)
# return data from interaction type.
bond_data = ntmp['bond']
# return list format.
angle_data = ntmp['angle']
del ntmp['bond'][0]
ntmp.write('out.file')
# don't support write() yet.
You can get a lot of information from below.
- Python codes
- C++ codes ( faster than python codes )
.. toctree:: :maxdepth: 1 cafepy
- CafeMol Project.