colvar-toolkit 0.2.0

A Python library for PLUMED-style colvar files

A Python package to read and write PLUMED colvar files.

• Free software: MIT license

Installation

You can either install via pip:

pip install colvar-toolkit

Or install from the repository:

pip install git+https://github.com/k9cdt/colvar-toolkit.git

Example usage

Basic read/write operations:

from cvtoolkit import Colvar

# Read a colvar file
cv = Colvar.from_file('colvar.dat')

# Access data
bias = cv["metad.bias"]
cv["metad.rct"] = my_array
del cv["metad.acc"]

# Write a new colvar file
cv.write('new_colvar.dat')

Joining two files, and column-wise actions:

cv1 = Colvar.from_file('colvar1.dat')
cv2 = Colvar.from_file('colvar2.dat')
cv3 = Colvar.from_file('colvar3.dat').choose("rmsd")

# Append time-wise
# Throws an error if cv2 does not have all keys in cv1
cv1.tappend(cv2)

# Append key-wise
# Throws an error if number of rows don't match
cv1.kappend(cv3)