I have a trajectory file from a molecular simulation that is written in netCDF format. I would like to convert this file to .csv format so that I can apply further Python-based analysis of the proximity between molecules. The trajectory file contains information corresponding to 3D Cartesian coordinates for all 6500 atoms of my simulation for each time step.
I have used the below script to convert this netCDF file to a .csv file using the netCDF4 and Pandas modules. My code is given below.
import netCDF4
import pandas as pd
fp='TEST4_simulate1.traj'
dataset = netCDF4.Dataset(fp, mode='r')
cols = list(dataset.variables.keys())
list_dataset = []
for c in cols:
list_dataset.append(list(dataset.variables[c][:]))
#print(list_dataset)
df_dataset = pd.DataFrame(list_dataset)
df_dataset = df_dataset.T
df_dataset.columns = cols
df_dataset.to_csv("file_path.csv", index = False)
A small selection of the output .csv file is given below. Notice that a set of ellipses are given between the first and last set of 3 atomic coordinates.
time,spatial,coordinates
12.0,b'x',"[[ 33.332325 -147.24976 -107.131 ]
[ 34.240444 -147.80115 -107.4043 ]
[ 33.640083 -146.47362 -106.41945 ]
...
[ 70.31757 -16.499006 -186.13313 ]
[ 98.310844 65.95696 76.43664 ]
[ 84.08772 52.676186 145.48856 ]]"
How can I modify this code so that the entirety of my atomic coordinates are written to my .csv file?
