lingyuzeng/analysis_pdb
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hotwa
2024-01-12 11:27:04 +08:00
parent 52ead0d941
commit 36020e9e34
1 changed files with 2 additions and 2 deletions
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4
modelbuilder.py
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@@ -89,7 +89,7 @@ class LoopModelBuilder:
def split_chains(self) -> dict: def split_chains(self) -> dict:
split_dict = {} split_dict = {}
for chain_id in self.analyzer_instance.chain_id_list: for chain_id in self.analyzer_instance.chain_id_list:
self.logger.info(f"Chain {chain_id} info: \n{self.analyzer_instance.extract_sequences(chain_id)}") self.logger.info(f"Chain {chain_id} info(from file not fasta): \n{self.sequences[chain_id]}")
chain_file = self.output_dir.joinpath(f"{self.analyzer_instance.pid}_{chain_id}.pdb") chain_file = self.output_dir.joinpath(f"{self.analyzer_instance.pid}_{chain_id}.pdb")
self.analyzer_instance.split_chain(chain_id).to_pdb(chain_file.as_posix()) self.analyzer_instance.split_chain(chain_id).to_pdb(chain_file.as_posix())
split_dict[chain_id] = chain_file.read_text() split_dict[chain_id] = chain_file.read_text()
@@ -112,7 +112,7 @@ class LoopModelBuilder:
self.logger.info(f'Missing residues info for {self.pdb_file}:\n {self.missing_info}') self.logger.info(f'Missing residues info for {self.pdb_file}:\n {self.missing_info}')
split_dict = {} # split all chains split_dict = {} # split all chains
for j in self.analyzer_instance.chain_id_list: for j in self.analyzer_instance.chain_id_list:
self.logger.info(f"Chain {j} info: \n{self.analyzer_instance.extract_sequences(j)}") self.logger.info(f"Chain {j} info(from file not fasta): \n{self.sequences[j]}")
fn = self.output_dir.joinpath(f"{self.analyzer_instance.pid}_{j}.pdb") fn = self.output_dir.joinpath(f"{self.analyzer_instance.pid}_{j}.pdb")
self.analyzer_instance.split_chain(j).to_pdb(fn.as_posix()) self.analyzer_instance.split_chain(j).to_pdb(fn.as_posix())
split_dict[j]=fn.read_text() split_dict[j]=fn.read_text()