init

2023-12-04 09:00:16 +08:00
commit f71d0d81a2
3 changed files with 676 additions and 0 deletions
--- a/build_modellel.py
+++ b/build_modellel.py
@@ -0,0 +1,111 @@
+from pathlib import Path
+from modeller import *
+from modeller.automodel import *    # 加载 AutoModel 类
+import time
+import os
+# micromamba create -n modeller modeller biopython pymol-open-source biopandas -y -c conda-forge -c salilab
+# 注册码：MODELIRANJE
+# python /opt/software/docking_pipeline/scripts/protein_structure/modeller/build_modellel.py -s /mnt/AppData/task-27/ProteinCompletion/protein.pdb -f /mnt/AppData/task-27/ProteinCompletion/seq.fasta -o ./ -n 1 -m refine.fast
+
+def make_model(structure_file,
+               sequence_file,
+               outdir: str,
+               chain: str,
+               num_loop: int = 2,
+               md_level: str = 'refine.fast'
+               ):
+    
+    print("***************************************************")
+    print("md_level ====",md_level)
+    print("***************************************************")
+
+    p_struct = Path(structure_file)
+    p_seq = Path(sequence_file)
+    structure = p_struct.stem
+    sequence = p_seq.stem
+    # 开始时间
+    time_start = time.time()
+    # 对齐蛋白质结构和序列
+    env1 = Environ()
+    # 从 PDB 文件中读取模型并将其加入对齐对象中
+    mdl = Model(env1, file=structure_file, model_segment=(f'FIRST:{chain}', f'LAST:{chain}'))
+    # print(mdl)
+    aln = Alignment(env1)
+    # print(aln)
+    aln.append_model(mdl, align_codes=structure, atom_files=structure_file)
+    # 将序列添加到对齐对象中
+    aln.append(file=sequence_file, align_codes=sequence)
+    # 进行 2D 对齐
+    aln.align2d()
+    # 将对齐结果写入文件
+    aln.write(file=f'{outdir}/alignment.ali', alignment_format='PIR')
+    aln.write(file=f'{outdir}/alignment.pap', alignment_format='PAP')
+
+    log.verbose()
+
+    # 重建蛋白质结构
+    env2 = Environ()
+    # 设置输入原子文件的目录
+    env2.io.atom_files_directory = ['.']
+    # 生成模型，使用自动调整模型类 LoopModel
+    loop_model = LoopModel(env2,
+                           alnfile=f'{outdir}/alignment.ali',
+                           knowns=structure,
+                           sequence=sequence,
+                           loop_assess_methods=(assess.DOPE, assess.GA341))
+    # 设置模型数量
+    # loop_model.starting_model = 1
+    # loop_model.ending_model = int(num_loop)
+
+    # 设置循环模型数量
+    # 数量规则：(end - start) + 1
+    loop_model.loop.starting_model = 1
+    loop_model.loop.ending_model = int(num_loop)
+    # 设置 MD 优化函数为 "refine.slow" 或 "refine.fast
+    if md_level.strip() == 'refine.slow':
+        loop_model.loop.md_level = refine.slow
+    elif md_level.strip() == 'refine.very_fast':
+        loop_model.loop.md_level = refine.very_fast
+    elif md_level.strip() == 'refine.fast':
+        loop_model.loop.md_level = refine.fast
+        
+    # 生成模型
+    loop_model.make()
+    end_time = time.time()
+    print(f"Time cost: {end_time - time_start}s")
+
+
+def fasta_to_ali(fasta_file, outdir):
+    if os.path.exists(outdir) is False:
+        os.makedirs(outdir)
+
+    p_fasta = Path(fasta_file)
+    sequence = p_fasta.stem
+    with open(fasta_file, 'r') as f:
+        seq = f.readlines()
+    seq = seq[1].strip()
+    ali_file = f'{outdir}/{sequence}_full.ali'
+    with open(ali_file, 'w') as f:
+        f.write(f'>P1;{sequence}_full\n')
+        f.write(f'sequence:{sequence}_full:::::::0.00: 0.00\n')
+        f.write(f'{seq}*')
+    return ali_file
+
+if __name__ == "__main__":
+    import argparse
+    parser = argparse.ArgumentParser(description="Build model by Modeller")
+    parser.add_argument("-s", "--structure", help="Structure file")
+    parser.add_argument("-o", "--outdir", help="Output directory")
+    parser.add_argument("-f", "--fasta", help="Fasta file")
+    parser.add_argument("-n", "--num_loop", help="Number of loop model")
+    parser.add_argument("-m", "--md_level", help="MD level")
+    parser.add_argument("-c", "--chain", help="your fix chain ID")
+    args = parser.parse_args()
+
+    sequence_file = fasta_to_ali(args.fasta, args.outdir)
+
+    make_model(args.structure, sequence_file,
+               args.outdir, args.chain,args.num_loop, args.md_level)
+
+# python build_modellel.py -s 5sws_fixer.pdb -o ./5swsmodellerfix -f rcsb_pdb_5SWS.fasta -n 1 -m refine.fast -c A
+# python build_modellel.py -s ../5sws_fixer.pdb -o ./5swsmodellerfix -f ../rcsb_pdb_5SWS.fasta -n 1 -m refine.fast -c D