生成PDB文件通常需要根据蛋白质的氨基酸序列、原子坐标(xyz)、占有率(occupancy)和B因子(B-factor)等信息来格式化输出。
示例代码,展示如何根据这些信息生成PDB文件。
RES_NAMES = [
'ALA','ARG','ASN','ASP','CYS',
'GLN','GLU','GLY','HIS','ILE',
'LEU','LYS','MET','PHE','PRO',
'SER','THR','TRP','TYR','VAL'
]
RES_NAMES_1 = 'ARNDCQEGHILKMFPSTWYV'
#to1letter = {aaa:a for a,aaa in zip(RES_NAMES_1,RES_NAMES)}
#to3letter = {a:aaa for a,aaa in zip(RES_NAMES_1,RES_NAMES)}
ATOM_NAMES = [
("N", "CA", "C", "O", "CB"), # ala
("N", "CA", "C", "O", "CB", "CG", "CD", "NE", "CZ", "NH1", "NH2"), # arg
("N", "CA"