提取CIF文件晶胞数据至CSV时遇字段不匹配错误求助

批量提取文件夹中所有布局各异但标签统一的.cif文件内的晶胞长度、角度等数据，将每条数据写入CSV文件的一行。

更新说明 #

根据评论要求，补充说明输入CIF文件布局可变，并附上Traceback错误信息，感谢@CodeMonkey等的反馈。

示例CIF文件内容 #

#######################################################################
#
#                 Cambridge Crystallographic Data Centre
#                                CCDC 
#
#######################################################################
#
# If this CIF has been generated from an entry in the Cambridge 
# Structural Database, then it will include bibliographic, chemical, 
# crystal, experimental, refinement or atomic coordinate data resulting 
# from the CCDC's data processing and validation procedures.
#
#######################################################################

data_PYRAZI
_symmetry_cell_setting           orthorhombic
_symmetry_space_group_name_H-M   'P m n n'
_symmetry_Int_Tables_number      58
_space_group_name_Hall           '-P 2n 2'
loop_
_symmetry_equiv_pos_site_id
_symmetry_equiv_pos_as_xyz
1 x,y,z
2 1/2-x,1/2-y,1/2+z
3 x,-y,-z
4 1/2-x,1/2+y,1/2-z
5 -x,-y,-z
6 1/2+x,1/2+y,1/2-z
7 -x,y,z
8 1/2+x,1/2-y,1/2+z
_cell_length_a                   9.316(3)
_cell_length_b                   3.815(5)
_cell_length_c                   5.911(3)
_cell_angle_alpha                90
_cell_angle_beta                 90
_cell_angle_gamma                90
_cell_volume                     210.08
loop_
_atom_site_label
_atom_site_type_symbol
_atom_site_fract_x
_atom_site_fract_y
_atom_site_fract_z
N1 N 0.14850 0.00000 0.00000
C1 C 0.07280 0.11130 0.17330
H1 H 0.13000 0.19200 0.31700
C1B C 0.07280 -0.11130 -0.17330
C1F C -0.07280 0.11130 0.17330
C1D C -0.07280 -0.11130 -0.17330
H1B H 0.13000 -0.19200 -0.31700
N1D N -0.14850 0.00000 0.00000
H1F H -0.13000 0.19200 0.31700
H1D H -0.13000 -0.19200 -0.31700

#END

当前使用的Python脚本 #

import re
from pathlib import Path
import csv

writer = None
with open("out.csv", "w") as csvfile:
    for f in Path('.').glob("*.cif"):
        print(f)
        with open(f, "r") as fin:
            row = {}
            for line in fin:
                line = line.strip()
                if len(line) == 0 or line.startswith("#"):
                    # skip blank lines and comments
                    continue
                # this matches lines like "_cell_length_a   9.316(3)"
                # and splits the input into 2 variables.
                # also ignore lines like "_symmetry_equiv_pos_site_id"
                if m := re.match(r"_?(\w+)\s+(.*)", line):
                    key = m.group(1)
                    value = m.group(2)
                    if key.startswith("cell_length") or key.startswith("cell_angle"):
                        if m := re.match(r"([^)]+)\(([^)]+)\)", value):
                            # split off the uncertainty
                            value = m.group(1)
                            unc = m.group(2)
                            # add uncertainty as separate column
                            row[key + "_unc"] = unc
                            row["filename"] = f 
                        row[key] = value
            
            print(row)
            if writer is None:
                # this is the first row found
                # create the .csv file with column names
                # from the keys in the .cif file (e.g. _cell_length_a)
                writer = csv.DictWriter(csvfile, fieldnames=sorted(row.keys()))
                writer.writeheader()
            writer.writerow(row) 

遇到的错误 #

执行脚本时触发如下ValueError：

Traceback (most recent call last):
  File "C:\Users\Owner\CSD_API\unit_cell.py", line 39, in <module>
    writer.writerow(row)
  File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.1776.0_x64__qbz5n2kfra8p0\lib\csv.py", line 154, in writerow
    return self.writer.writerow(self._dict_to_list(rowdict))
  File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.10_3.10.1776.0_x64__qbz5n2kfra8p0\lib\csv.py", line 149, in _dict_to_list
    raise ValueError("dict contains fields not in fieldnames: "
ValueError: dict contains fields not in fieldnames: 'cell_angle_alpha_unc', 'cell_angle_gamma_unc'

问题 #

如何修改脚本，避免因CIF文件布局不同导致的字段不匹配错误，成功提取数据至CSV？

内容的提问来源于stack exchange，提问作者matsmcfly