从蛋白质结构文件pdb中提取序列和骨架原子坐标

pdb文件是蛋白质结构存储的标准文件，用txt打开其主要内容如下所示

上图部分是model1下的蛋白原子分布，序号1所在列是原子序号，序号2所在列是氨基酸种类，序号3所在列是氨基酸序号，序号4所在三列是原子的三维坐标，序号5所在列是原子种类

用python实现提取序列：

from Bio import PDB
'''本文件用于提取单个pdb文件的氨基酸'''
parser = PDB.PDBParser()
io = PDB.PDBIO()
fileName_save = 'HHH_b1_00224.fasta'

nameOfFile_read = 'HHH_b1_00224.pdb'
'''下面将氨基酸全称改为简写'''
longToShort = {'GLY': 'G', 'ALA': 'A', 'VAL': 'V', 'LEU': 'L', 'ILE': 'I', 'PHE': 'F', 'TRP': 'W', 'TYR': 'Y','ASP': 'D' ,'HIS': 'H', 'ASN': 'N', 'GLU': 'E', 'LYS': 'K', 'GLN': 'Q', 'MET': 'M', 'ARG': 'R', 'SER': 'S', 'THR': 'T', 'CYS': 'C', 'PRO': 'P', 'SEC': 'U', 'PYL': 'O'}

struct = parser.get_structure('aaaa', nameOfFile_read) '''此处的aaaa是结构名，无实际意义'''
    with open(fileName_save, 'a+') as f_w:
        f_w.write('>sequence' + str(i+1) + '\n')
        for model in struct: #遍历所有model
            for chain in model: #遍历model中的所有chain
                for residue in chain: #遍历chain中的所有残基
                    resname = residue.get_resname() #读取氨基酸
                    f_w.write(longToShort[resname])

若要读取原子坐标，只需在 for residue in chain下增加一个遍历所有原子即可，下述代码实现读取骨架原子坐标

for model in struct:
    for chain in model:
        for residue in chain:
            for atom in residue:
                if(num < 3):
                    x,y,z = atom.get_coord()
                    with open(filename, 'a+') as file_object:
                        #file_object.write('NaN' + ", " + 'NaN' + ", " + 'NaN' + "], [")
                        file_object.write(str(x) + ", " + str(y) + ", " + str(z) + "], [")
                    num = num + 1
                elif(num == 3):
                    x, y, z = atom.get_coord()
                    with open(filename, 'a+') as file_object:
                        #file_object.write('NaN' + ", " + 'NaN' + ", " + 'NaN' + "]]")
                        file_object.write(str(x) + ", " + str(y) + ", " + str(z) + "]]")
                    num = num + 1