将NETCDF转换为CSV时，如何显示所有数据（无椭圆）？

发布于 2025-01-26 02:31:07 字数 1017 浏览 6 评论 0原文

我有一个以NetCDF格式编写的分子模拟的轨迹文件。我想将此文件转换为.csv格式，以便我可以对分子之间的接近度进行进一步的基于Python的分析。该轨迹文件包含与每个时间步长的所有6500个原子的3D笛卡尔坐标相对应的信息。

我已经使用以下脚本使用 netcdf4 和 pandas 模块将此NetCDF文件转换为.csv文件。我的代码在下面给出。

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)

下面给出了一小部分输出.CSV文件。请注意，在3个原子坐标的第一组和最后一组之间给出了一组椭圆。

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 ]]"

如何修改此代码，以便将整个原子坐标写入我的.CSV文件？

原文

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?

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