我正在尝试合并两个文本格式 (PDB) 文件。一个（较大的）包含描述蛋白质的完整数据集，第二个包含非常小的数据集，仅更改一小部分（坐标集）。
例子：
基本文件（部分）：
ATOM 605 CD2 LEU A 92 11.727 14.051 55.011 1.00 75.51 4pxz C
ATOM 606 N ARG A 93 10.555 10.636 58.260 1.00 62.79 4pxz N
ATOM 607 CA ARG A 93 11.357 9.429 58.493 1.00 59.89 4pxz C
ATOM 608 C ARG A 93 10.429 8.207 58.562 1.00 62.83 4pxz C
ATOM 609 O ARG A 93 10.760 7.168 57.994 1.00 61.39 4pxz O
ATOM 610 CB ARG A 93 12.236 9.564 59.757 1.00 58.23 4pxz C
ATOM 611 CG ARG A 93 13.088 8.333 60.120 1.00 60.51 4pxz C
ATOM 612 CD ARG A 93 13.985 7.822 58.995 1.00 61.21 4pxz C
ATOM 613 NE ARG A 93 14.503 6.485 59.295 1.00 60.36 4pxz N
ATOM 614 CZ ARG A 93 15.012 5.642 58.400 1.00 66.21 4pxz C
ATOM 615 NH1 ARG A 93 15.074 5.979 57.116 1.00 52.54 4pxz N
ATOM 616 NH2 ARG A 93 15.455 4.453 58.780 1.00 48.93 4pxz N
ATOM 617 N THR A 94 9.247 8.357 59.192 1.00 60.68 4pxz N
ATOM 618 CA THR A 94 8.227 7.305 59.271 1.00 59.92 4pxz C
辅助文件（带有要替换的坐标集）：
ATOM 39 CA ARG A 93 11.357 9.429 58.493 1.00 59.89 hatp C
ATOM 40 CB ARG A 93 12.236 9.564 59.757 1.00 58.23 hatp C
ATOM 41 CG ARG A 93 11.569 9.166 61.087 1.00 60.51 hatp C
ATOM 42 CD ARG A 93 12.319 8.102 61.886 1.00 61.21 hatp C
ATOM 43 NE ARG A 93 11.978 6.754 61.425 1.00 60.36 hatp N
ATOM 44 CZ ARG A 93 11.731 5.714 62.217 1.00 66.21 hatp C
ATOM 45 NH2 ARG A 93 11.430 4.535 61.694 1.00 48.93 hatp N
ATOM 46 NH1 ARG A 93 11.793 5.843 63.538 1.00 52.54 hatp N
预期结果：-> 改变坐标 <-
ATOM 604 CD1 LEU A 92 9.685 13.033 54.000 1.00 73.10 4pxz C
ATOM 605 CD2 LEU A 92 11.727 14.051 55.011 1.00 75.51 4pxz C
ATOM 606 N ARG A 93 10.555 10.636 58.260 1.00 62.79 4pxz N
ATOM 607 CA ARG A 93 -> 11.357 9.429 58.493<- 1.00 59.89 4pxz C
ATOM 608 C ARG A 93 10.429 8.207 58.562 1.00 62.83 4pxz C
ATOM 609 O ARG A 93 10.760 7.168 57.994 1.00 61.39 4pxz O
ATOM 610 CB ARG A 93 -> 12.236 9.564 59.757<- 1.00 58.23 4pxz C
ATOM 611 CG ARG A 93 -> 11.569 9.166 61.087<- 1.00 60.51 4pxz C
ATOM 612 CD ARG A 93 -> 12.319 8.102 61.886<- 1.00 61.21 4pxz C
ATOM 613 NE ARG A 93 -> 11.978 6.754 61.425<- 1.00 60.36 4pxz N
ATOM 614 CZ ARG A 93 -> 11.731 5.714 62.217<- 1.00 66.21 4pxz C
ATOM 615 NH1 ARG A 93 -> 11.793 5.843 63.538<- 1.00 52.54 4pxz N
ATOM 616 NH2 ARG A 93 -> 11.430 4.535 61.694<- 1.00 48.93 4pxz N
ATOM 617 N THR A 94 9.247 8.357 59.192 1.00 60.68 4pxz N
ATOM 618 CA THR A 94 8.227 7.305 59.271 1.00 59.92 4pxz C
我尝试通过以下方式这样做：
构建列表并将每一行附加为两个文件的单个条目
从两个文件中提取原子类型、残基名称、链和残基编号（例如 CD1 LEU A 92，分别）并附加到另一个列表
比较提取列表
根据第 3 点，从第 1 点写入包含混合列表的文件。
代码：
import re
aminoacid_pattern = re.compile(r"\w.{2,3}.\b(\w[A-Z]\w*)\b\s.\s\d+")
coords_pattern = re.compile(r"\w.{2,3}.\b(\w[A-Z]\w*)\b\s.\s\d+")
class fileSaver:
protein = "4pxzclean.pdb"
flexres = "ARGA93.pdb.tmp"
def __init__(self):
pass
def aminoacid_to_substitute(self, flexres, data = []):
with open(flexres, 'r') as flex:
for line in flex:
if aminoacid_pattern != None:
data.append(line)
return data
def parse_rigid(self, rigidprot, test = []):
with open(rigidprot, 'r') as rigid:
for line in rigid:
if aminoacid_pattern != None:
test.append(line)
return test
class fileComparer:
def __init__(self):
pass
def compare_data(self, data_flex, data_rigid, cleanflex = [], cleanrigid = []):
for el in data_flex:
if aminoacid_pattern != None:
cleanflex.append(re.findall(r".\w\s+\w.{2,3}\s\w\s*\d{2,3}",str(el)))
for el in data_rigid:
if aminoacid_pattern != None:
cleanrigid.append(re.findall(r".\w\s+\w.{2,3}\s\w\s*\d{2,3}",str(el)))
with open("test.txt", 'a+') as test:
for rig_el in data_rigid:
for flex_el in data_flex:
for rg_el in cleanrigid:
if rg_el not in cleanflex:
test.write(rig_el)
if rg_el in cleanflex:
test.write(flex_el)
if __name__ == '__main__':
initialize = fileSaver()
flex = initialize.aminoacid_to_substitute("ARGA93.pdb.tmp")
rigid = initialize.parse_rigid("4pxzclean.pdb")
comparer = fileComparer()
comparer.compare_data(flex,rigid)
不幸的是，它提供了无限长的文件，没有任何更改的行。你能告诉我哪里出错了吗？