44 lines
1.2 KiB
Python
44 lines
1.2 KiB
Python
#!/usr/bin/env python
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# -*- coding: utf-8 -*-
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import os
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from rdkit import Chem
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# 当前目录路径
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current_dir = os.path.dirname(os.path.abspath(__file__))
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# 输入SDF文件路径
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sdf_file = os.path.join(current_dir, 'fgbar_vina_SP_1_pv.sdf')
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# 输出SMILES文件路径
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smiles_file = os.path.join(current_dir, 'molecules.txt')
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def sdf_to_smiles(sdf_path, output_path):
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"""读取SDF文件中的分子并将其转换为SMILES格式保存到文本文件"""
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# 读取SDF文件
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suppl = Chem.SDMolSupplier(sdf_path)
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# 计数有效分子数量
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valid_mol_count = 0
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# 打开输出文件
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with open(output_path, 'w') as f:
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# 遍历所有分子
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for i, mol in enumerate(suppl):
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if mol is not None: # 确保分子有效
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# 获取SMILES
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smiles = Chem.MolToSmiles(mol)
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# 写入文件
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f.write(f"{smiles}\n")
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valid_mol_count += 1
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return valid_mol_count
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def main():
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print(f"正在读取SDF文件: {sdf_file}")
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mol_count = sdf_to_smiles(sdf_file, smiles_file)
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print(f"成功处理了 {mol_count} 个分子")
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print(f"SMILES已保存到: {smiles_file}")
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if __name__ == "__main__":
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main() |