我有1000个pdb, 每个pdb氨基酸数目为14，我需要写一个python程序实现计算1000个pdb各自内部氨基酸的距离矩阵。
使用Biopython库来解析PDB文件并计算氨基酸之间的距离矩阵。
python
from Bio import PDB
import numpy as np
def calculate_distance(atom1, atom2):
"""Calculate the Euclidean distance between two atoms."""
return np.linalg.norm(atom1.coord - atom2.coord)
def calculate_distance_matrix(structure):
"""Calculate the distance matrix for a given PDB structure."""
atoms = list(structure.get_atoms())
num_atoms = len(atoms)
distance_matrix = np.zeros((num_atoms, num_atoms))
for i in range(num_atoms):
for j in range(i, num_atoms):
distance = calculate_distance(atoms[i], atoms[j])
distance_matrix[i, j] = distance
distance_matrix[j, i] = distance
return distance_matrix
def process_pdb_file(pdb_file_path):
"""Process a single PDB file."""
parser = PDB.PDBParser(QUIET=True)
structure = parser.get_structure("protein", pdb_file_path)
distance_matrix = calculate_distance_matrix(structure)
return distance_matrix
def main():
pdb_file_paths = ["pdb1.pdb", "pdb2.pdb", "pdb3.pdb", ...] # Replace with your PDB file paths
distance_matrices = []
for pdb_file_path in pdb_file_paths:
distance_matrix = process_pdb_file(pdb_file_path)
distance_matrices.append(distance_matrix)
# distance_matrices now contains the distance matrices for each PDB file
# You can further analyze or save the results as needed.
if __name__ == "__main__":
main()将pdb1.pdb, pdb2.pdb, pdb3.pdb, ... 替换为你实际的PDB文件路径。这个程序将计算每个PDB文件中氨基酸之间的距离矩阵，并将它们存储在distance_matrices 列表中。你可以根据实际需要进一步处理或保存这些距离矩阵。