_ _ _

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
  • https://github.com/mash-it/CafeMolAnalysis
  • https://github.com/naotohori/cafysis
• C++ codes ( faster than python codes )
  • https://github.com/noinil/pinang
  • https://github.com/ToruNiina/Coffee-mill

• http://www.mdanalysis.org
• http://mdtraj.org

• CafeMol Project.

• genindex
• modindex
• search