src\bundles\add_charge\src\process_lib.py:60:6: SyntaxError: Expected a module name | 58 | return heavy_synonyms.get(heavy, []) 59 | 60 | from .5p_data import heavy_data, hyd_data | ^ 61 | for lib in sys.argv[1:]: 62 | f = open(lib, "r") | src\bundles\add_charge\src\process_lib.py:60:8: SyntaxError: Simple statements must be separated by newlines or semicolons | 58 | return heavy_synonyms.get(heavy, []) 59 | 60 | from .5p_data import heavy_data, hyd_data | ^ 61 | for lib in sys.argv[1:]: 62 | f = open(lib, "r") | src\bundles\add_charge\src\process_lib.py:60:15: SyntaxError: Simple statements must be separated by newlines or semicolons | 58 | return heavy_synonyms.get(heavy, []) 59 | 60 | from .5p_data import heavy_data, hyd_data | ^ 61 | for lib in sys.argv[1:]: 62 | f = open(lib, "r") | src\bundles\alphafold\src\alphafold21_predict_colab.py:78:5: SyntaxError: Expected a statement | 77 | # The -x option logs each command with a prompt in front of it. 78 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 79 | if _exit_code != 0: 80 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\alphafold21_predict_colab.py:78:14: SyntaxError: Simple statements must be separated by newlines or semicolons | 77 | # The -x option logs each command with a prompt in front of it. 78 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 79 | if _exit_code != 0: 80 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\alphafold21_predict_colab.py:78:46: SyntaxError: Simple statements must be separated by newlines or semicolons | 77 | # The -x option logs each command with a prompt in front of it. 78 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 79 | if _exit_code != 0: 80 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\alphafold21_predict_colab.py:78:48: SyntaxError: Expected an expression | 77 | # The -x option logs each command with a prompt in front of it. 78 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 79 | if _exit_code != 0: 80 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\alphafold21_predict_colab.py:634:5: SyntaxError: Expected a statement | 633 | # Make a zip file of the predictions 634 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 635 | 636 | # Download predictions. | src\bundles\alphafold\src\alphafold21_predict_colab.py:634:9: SyntaxError: Simple statements must be separated by newlines or semicolons | 633 | # Make a zip file of the predictions 634 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 635 | 636 | # Download predictions. | src\bundles\alphafold\src\alphafold21_predict_colab.py:634:35: SyntaxError: Expected an identifier | 633 | # Make a zip file of the predictions 634 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 635 | 636 | # Download predictions. | src\bundles\alphafold\src\alphafold21_predict_colab.py:634:36: SyntaxError: Expected an identifier | 633 | # Make a zip file of the predictions 634 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 635 | 636 | # Download predictions. | src\bundles\alphafold\src\alphafold21_predict_colab.py:634:50: SyntaxError: Expected an expression | 633 | # Make a zip file of the predictions 634 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 635 | 636 | # Download predictions. 637 | from google.colab import files | src\bundles\alphafold\src\alphafold22_predict_colab.py:80:5: SyntaxError: Expected a statement | 79 | # The -x option logs each command with a prompt in front of it. 80 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 81 | if _exit_code != 0: 82 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\alphafold22_predict_colab.py:80:14: SyntaxError: Simple statements must be separated by newlines or semicolons | 79 | # The -x option logs each command with a prompt in front of it. 80 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 81 | if _exit_code != 0: 82 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\alphafold22_predict_colab.py:80:46: SyntaxError: Simple statements must be separated by newlines or semicolons | 79 | # The -x option logs each command with a prompt in front of it. 80 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 81 | if _exit_code != 0: 82 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\alphafold22_predict_colab.py:80:48: SyntaxError: Expected an expression | 79 | # The -x option logs each command with a prompt in front of it. 80 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 81 | if _exit_code != 0: 82 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\alphafold22_predict_colab.py:679:5: SyntaxError: Expected a statement | 678 | # Make a zip file of the predictions 679 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 680 | 681 | # Download predictions. | src\bundles\alphafold\src\alphafold22_predict_colab.py:679:9: SyntaxError: Simple statements must be separated by newlines or semicolons | 678 | # Make a zip file of the predictions 679 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 680 | 681 | # Download predictions. | src\bundles\alphafold\src\alphafold22_predict_colab.py:679:35: SyntaxError: Expected an identifier | 678 | # Make a zip file of the predictions 679 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 680 | 681 | # Download predictions. | src\bundles\alphafold\src\alphafold22_predict_colab.py:679:36: SyntaxError: Expected an identifier | 678 | # Make a zip file of the predictions 679 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 680 | 681 | # Download predictions. | src\bundles\alphafold\src\alphafold22_predict_colab.py:679:50: SyntaxError: Expected an expression | 678 | # Make a zip file of the predictions 679 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 680 | 681 | # Download predictions. 682 | from google.colab import files | src\bundles\alphafold\src\alphafold_predict_colab.py:76:5: SyntaxError: Expected a statement | 75 | # The -x option logs each command with a prompt in front of it. 76 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 77 | 78 | def install_hmmer(install_log = 'install_log.txt'): | src\bundles\alphafold\src\alphafold_predict_colab.py:76:14: SyntaxError: Simple statements must be separated by newlines or semicolons | 75 | # The -x option logs each command with a prompt in front of it. 76 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 77 | 78 | def install_hmmer(install_log = 'install_log.txt'): | src\bundles\alphafold\src\alphafold_predict_colab.py:76:46: SyntaxError: Simple statements must be separated by newlines or semicolons | 75 | # The -x option logs each command with a prompt in front of it. 76 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 77 | 78 | def install_hmmer(install_log = 'install_log.txt'): | src\bundles\alphafold\src\alphafold_predict_colab.py:76:48: SyntaxError: Expected an expression | 75 | # The -x option logs each command with a prompt in front of it. 76 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 77 | 78 | def install_hmmer(install_log = 'install_log.txt'): | src\bundles\alphafold\src\alphafold_predict_colab.py:567:5: SyntaxError: Expected a statement | 566 | # Make a zip file of the predictions 567 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 568 | 569 | # Download predictions. | src\bundles\alphafold\src\alphafold_predict_colab.py:567:9: SyntaxError: Simple statements must be separated by newlines or semicolons | 566 | # Make a zip file of the predictions 567 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 568 | 569 | # Download predictions. | src\bundles\alphafold\src\alphafold_predict_colab.py:567:35: SyntaxError: Expected an identifier | 566 | # Make a zip file of the predictions 567 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 568 | 569 | # Download predictions. | src\bundles\alphafold\src\alphafold_predict_colab.py:567:36: SyntaxError: Expected an identifier | 566 | # Make a zip file of the predictions 567 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 568 | 569 | # Download predictions. | src\bundles\alphafold\src\alphafold_predict_colab.py:567:50: SyntaxError: Expected an expression | 566 | # Make a zip file of the predictions 567 | !cd {output_dir} ; zip -q -r ../results.zip * | ^ 568 | 569 | # Download predictions. 570 | from google.colab import files | src\bundles\alphafold\src\colabfold_predict.py:168:3: SyntaxError: Expected a statement | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb | ^ 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | src\bundles\alphafold\src\colabfold_predict.py:168:12: SyntaxError: Simple statements must be separated by newlines or semicolons | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb | ^ 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | src\bundles\alphafold\src\colabfold_predict.py:168:19: SyntaxError: Simple statements must be separated by newlines or semicolons | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb | ^ 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | src\bundles\alphafold\src\colabfold_predict.py:168:30: SyntaxError: Expected an expression | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb | ^ 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | src\bundles\alphafold\src\colabfold_predict.py:168:35: SyntaxError: Simple statements must be separated by newlines or semicolons | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb | ^ 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | src\bundles\alphafold\src\colabfold_predict.py:169:3: SyntaxError: Expected a statement | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | ^ 170 | 171 | # Make a zip file of the predictions | src\bundles\alphafold\src\colabfold_predict.py:169:29: SyntaxError: Expected an expression | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | ^ 170 | 171 | # Make a zip file of the predictions | src\bundles\alphafold\src\colabfold_predict.py:169:35: SyntaxError: Simple statements must be separated by newlines or semicolons | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | ^ 170 | 171 | # Make a zip file of the predictions | src\bundles\alphafold\src\colabfold_predict.py:172:3: SyntaxError: Expected a statement | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict.py:172:14: SyntaxError: Simple statements must be separated by newlines or semicolons | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict.py:172:26: SyntaxError: Simple statements must be separated by newlines or semicolons | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict.py:172:39: SyntaxError: Expected an expression | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict.py:172:45: SyntaxError: Expected an expression | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict.py:172:52: SyntaxError: Expected an expression | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict.py:172:58: SyntaxError: Expected an expression | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict.py:172:63: SyntaxError: Simple statements must be separated by newlines or semicolons | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict.py:172:76: SyntaxError: Expected an expression | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict.py:195:20: SyntaxError: Expected an expression | 193 | # 194 | def report_gpu_type(): 195 | gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name | ^ 196 | gpu_name = gpu_name_lines[0] 197 | print(f'Using {gpu_name} graphics processor') | src\bundles\alphafold\src\colabfold_predict.py:195:21: SyntaxError: Invalid assignment target | 193 | # 194 | def report_gpu_type(): 195 | gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name | ^ 196 | gpu_name = gpu_name_lines[0] 197 | print(f'Using {gpu_name} graphics processor') | src\bundles\alphafold\src\colabfold_predict.py:195:45: SyntaxError: Invalid assignment target | 193 | # 194 | def report_gpu_type(): 195 | gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name | ^ 196 | gpu_name = gpu_name_lines[0] 197 | print(f'Using {gpu_name} graphics processor') | src\bundles\alphafold\src\colabfold_predict.py:222:3: SyntaxError: Expected a statement | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict.py:222:12: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict.py:222:18: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict.py:222:34: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict.py:222:40: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict.py:222:46: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict.py:222:52: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict.py:222:58: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict.py:305:3: SyntaxError: Expected a statement | 304 | # The -x option logs each command with a prompt in front of it. 305 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 306 | if _exit_code != 0: 307 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\colabfold_predict.py:305:12: SyntaxError: Simple statements must be separated by newlines or semicolons | 304 | # The -x option logs each command with a prompt in front of it. 305 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 306 | if _exit_code != 0: 307 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\colabfold_predict.py:305:44: SyntaxError: Simple statements must be separated by newlines or semicolons | 304 | # The -x option logs each command with a prompt in front of it. 305 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 306 | if _exit_code != 0: 307 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\colabfold_predict.py:305:46: SyntaxError: Expected an expression | 304 | # The -x option logs each command with a prompt in front of it. 305 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 306 | if _exit_code != 0: 307 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\colabfold_predict_test.py:168:3: SyntaxError: Expected a statement | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb | ^ 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | src\bundles\alphafold\src\colabfold_predict_test.py:168:12: SyntaxError: Simple statements must be separated by newlines or semicolons | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb | ^ 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | src\bundles\alphafold\src\colabfold_predict_test.py:168:19: SyntaxError: Simple statements must be separated by newlines or semicolons | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb | ^ 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | src\bundles\alphafold\src\colabfold_predict_test.py:168:30: SyntaxError: Expected an expression | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb | ^ 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | src\bundles\alphafold\src\colabfold_predict_test.py:168:35: SyntaxError: Simple statements must be separated by newlines or semicolons | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb | ^ 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | src\bundles\alphafold\src\colabfold_predict_test.py:169:3: SyntaxError: Expected a statement | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | ^ 170 | 171 | # Make a zip file of the predictions | src\bundles\alphafold\src\colabfold_predict_test.py:169:29: SyntaxError: Expected an expression | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | ^ 170 | 171 | # Make a zip file of the predictions | src\bundles\alphafold\src\colabfold_predict_test.py:169:35: SyntaxError: Simple statements must be separated by newlines or semicolons | 167 | relax = 'relaxed' if energy_minimize else 'unrelaxed' 168 | !cp -p *_{relax}_rank_001_*.pdb best_model.pdb 169 | !cp -p *_scores_rank_001_*.json best_model_pae.json | ^ 170 | 171 | # Make a zip file of the predictions | src\bundles\alphafold\src\colabfold_predict_test.py:172:3: SyntaxError: Expected a statement | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict_test.py:172:14: SyntaxError: Simple statements must be separated by newlines or semicolons | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict_test.py:172:26: SyntaxError: Simple statements must be separated by newlines or semicolons | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict_test.py:172:39: SyntaxError: Expected an expression | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict_test.py:172:45: SyntaxError: Expected an expression | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict_test.py:172:52: SyntaxError: Expected an expression | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict_test.py:172:58: SyntaxError: Expected an expression | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict_test.py:172:63: SyntaxError: Simple statements must be separated by newlines or semicolons | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict_test.py:172:76: SyntaxError: Expected an expression | 171 | # Make a zip file of the predictions 172 | !zip -q -r results.zip query.fasta *.csv *.json *.a3m *.pdb cite.bibtex *.png *log.txt | ^ 173 | 174 | # Download predictions. | src\bundles\alphafold\src\colabfold_predict_test.py:195:20: SyntaxError: Expected an expression | 193 | # 194 | def report_gpu_type(): 195 | gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name | ^ 196 | gpu_name = gpu_name_lines[0] 197 | print(f'Using {gpu_name} graphics processor') | src\bundles\alphafold\src\colabfold_predict_test.py:195:21: SyntaxError: Invalid assignment target | 193 | # 194 | def report_gpu_type(): 195 | gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name | ^ 196 | gpu_name = gpu_name_lines[0] 197 | print(f'Using {gpu_name} graphics processor') | src\bundles\alphafold\src\colabfold_predict_test.py:195:45: SyntaxError: Invalid assignment target | 193 | # 194 | def report_gpu_type(): 195 | gpu_name_lines = !nvidia-smi --format=csv,noheader --query-gpu=name | ^ 196 | gpu_name = gpu_name_lines[0] 197 | print(f'Using {gpu_name} graphics processor') | src\bundles\alphafold\src\colabfold_predict_test.py:222:3: SyntaxError: Expected a statement | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict_test.py:222:12: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict_test.py:222:18: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict_test.py:222:34: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict_test.py:222:40: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict_test.py:222:46: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict_test.py:222:52: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict_test.py:222:58: SyntaxError: Expected an expression | 220 | occur if different sequences are run when computing MSA. 221 | ''' 222 | !rm -rf *.pdb *.json *_ *_env *.zip *.csv *.png *.a3m *.fasta | ^ 223 | 224 | # ================================================================================================ | src\bundles\alphafold\src\colabfold_predict_test.py:305:3: SyntaxError: Expected a statement | 304 | # The -x option logs each command with a prompt in front of it. 305 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 306 | if _exit_code != 0: 307 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\colabfold_predict_test.py:305:12: SyntaxError: Simple statements must be separated by newlines or semicolons | 304 | # The -x option logs each command with a prompt in front of it. 305 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 306 | if _exit_code != 0: 307 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\colabfold_predict_test.py:305:44: SyntaxError: Simple statements must be separated by newlines or semicolons | 304 | # The -x option logs each command with a prompt in front of it. 305 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 306 | if _exit_code != 0: 307 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\alphafold\src\colabfold_predict_test.py:305:46: SyntaxError: Expected an expression | 304 | # The -x option logs each command with a prompt in front of it. 305 | !bash -x "{filename}" >> "{install_log}" 2>&1 | ^ 306 | if _exit_code != 0: 307 | raise RuntimeError('Error running shell script %s, output in log file %s' | src\bundles\atomic\src\structure.py:865:20: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead. | 863 | from numpy import unique, in1d 864 | sel_rids = unique(rids[asel]) 865 | ares = in1d(rids, sel_rids) | ^^^^ NPY201 866 | if ares.sum() > na: 867 | # Promote to entire residues | = help: Replace with `numpy.isin` src\bundles\atomic\src\structure.py:873:23: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead. | 871 | ssids = r.secondary_structure_ids 872 | sel_ssids = unique(ssids[asel]) 873 | ass = in1d(ssids, sel_ssids) | ^^^^ NPY201 874 | if ass.sum() > na: 875 | # Promote to secondary structure | = help: Replace with `numpy.isin` src\bundles\atomic\src\structure.py:887:30: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead. | 885 | cids = array(r.chain_ids) 886 | sel_cids = unique(cids[asel]) 887 | ac = in1d(cids, sel_cids) | ^^^^ NPY201 888 | if ac.sum() > na: 889 | # Promote to entire chains | = help: Replace with `numpy.isin` src\bundles\atomic\src\structure.py:1038:20: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead. | 1036 | from numpy import in1d, invert 1037 | matched_chain_ids = atoms.filter(a).unique_chain_ids 1038 | mask = in1d(atoms.chain_ids, matched_chain_ids) | ^^^^ NPY201 1039 | if '<' in operator: 1040 | expand_by = atoms.filter(mask) | = help: Replace with `numpy.isin` src\bundles\map_data\src\arrays.py:256:12: NPY201 [*] `np.product` will be removed in NumPy 2.0. Use `numpy.prod` instead. | 254 | for k in range(size[2]): 255 | indices[k,:,:,2] = k 256 | volume = product(size) | ^^^^^^^ NPY201 257 | indices = reshape(indices, (volume, 3)) 258 | return indices | = help: Replace with `numpy.prod` src\bundles\map_data\src\readarray.py:233:13: NPY201 [*] `np.product` will be removed in NumPy 2.0. Use `numpy.prod` instead. | 231 | vtype = dtype(value_type) 232 | tsize = vtype.itemsize 233 | bytes = product(size, dtype=float64)*float(tsize) | ^^^^^^^ NPY201 234 | mbytes = bytes / 2**20 235 | sz = ','.join(['%d' % s for s in size]) | = help: Replace with `numpy.prod` src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\sample.py:38:9: SyntaxError: Simple statements must be separated by newlines or semicolons | 37 | if len(sys.argv)!=2: 38 | print "Missing file argument\nUsage: sample.py FILE" | ^ 39 | sys.exit() | src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\sample.py:44:11: SyntaxError: Simple statements must be separated by newlines or semicolons | 42 | x=xdrfile(sys.argv[1]) 43 | for f in x: #iterates frames 44 | print "%8s %8s %8s %8s Step: %8d "%("Atom","X","Y","Z",f.step) #print header | ^ 45 | for i,a in enumerate(f.x): #iterate atoms 46 | print "%8d %8.1f %8.1f %8.1f"%(i+1,a[0],a[1],a[2]) #print atom number, x, y, z | src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\sample.py:46:13: SyntaxError: Simple statements must be separated by newlines or semicolons | 44 | print "%8s %8s %8s %8s Step: %8d "%("Atom","X","Y","Z",f.step) #print header 45 | for i,a in enumerate(f.x): #iterate atoms 46 | print "%8d %8.1f %8.1f %8.1f"%(i+1,a[0],a[1],a[2]) #print atom number, x, y, z | ^ | src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:49:35: SyntaxError: Simple statements must be separated by newlines or semicolons | 47 | def test(fn): 48 | x=xdrfile(fn) 49 | if x.natoms != natoms1: print "natoms != natoms1",x.natoms,natoms1 | ^ 50 | for k,f in enumerate(x): 51 | if f.step != step1+k: print "incorrect step",f.step,step1+k,k | src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:51:37: SyntaxError: Simple statements must be separated by newlines or semicolons | 49 | if x.natoms != natoms1: print "natoms != natoms1",x.natoms,natoms1 50 | for k,f in enumerate(x): 51 | if f.step != step1+k: print "incorrect step",f.step,step1+k,k | ^ 52 | if fabs(f.time-time1-k) > toler: print "incorrect time",f.time,time1+k 53 | if not x.mode&mTrr and fabs(f.prec-prec1) > toler: print "incorrect precision",f.prec,prec1 | src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:52:48: SyntaxError: Simple statements must be separated by newlines or semicolons | 50 | for k,f in enumerate(x): 51 | if f.step != step1+k: print "incorrect step",f.step,step1+k,k 52 | if fabs(f.time-time1-k) > toler: print "incorrect time",f.time,time1+k | ^ 53 | if not x.mode&mTrr and fabs(f.prec-prec1) > toler: print "incorrect precision",f.prec,prec1 54 | if x.mode&mTrr and fabs(f.lam-lam1) > toler: print "incorrect lambda",f.lam,lam1 | src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:53:66: SyntaxError: Simple statements must be separated by newlines or semicolons | 51 | if f.step != step1+k: print "incorrect step",f.step,step1+k,k 52 | if fabs(f.time-time1-k) > toler: print "incorrect time",f.time,time1+k 53 | if not x.mode&mTrr and fabs(f.prec-prec1) > toler: print "incorrect precision",f.prec,prec1 | ^ 54 | if x.mode&mTrr and fabs(f.lam-lam1) > toler: print "incorrect lambda",f.lam,lam1 55 | for i in range(DIM): | src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:54:60: SyntaxError: Simple statements must be separated by newlines or semicolons | 52 | if fabs(f.time-time1-k) > toler: print "incorrect time",f.time,time1+k 53 | if not x.mode&mTrr and fabs(f.prec-prec1) > toler: print "incorrect precision",f.prec,prec1 54 | if x.mode&mTrr and fabs(f.lam-lam1) > toler: print "incorrect lambda",f.lam,lam1 | ^ 55 | for i in range(DIM): 56 | for j in range(DIM): | src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:57:66: SyntaxError: Simple statements must be separated by newlines or semicolons | 55 | for i in range(DIM): 56 | for j in range(DIM): 57 | if fabs(f.box[i][j] - box1[i][j]) > toler: print "box incorrect",f.box[i][j],box1[i][j] | ^ 58 | for i in range(x.natoms): 59 | for j in range(DIM): | src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:61:56: SyntaxError: Simple statements must be separated by newlines or semicolons | 59 | for j in range(DIM): 60 | target = (i+1)*3.7 + (j+1) 61 | if f.x[i][j] - target > toler : print "x incorrect" | ^ 62 | print fn,"OK" | src\bundles\md_crds\gromacs\xdrfile-1.1.4\src\python\xdrfile_test.py:62:11: SyntaxError: Simple statements must be separated by newlines or semicolons | 60 | target = (i+1)*3.7 + (j+1) 61 | if f.x[i][j] - target > toler : print "x incorrect" 62 | print fn,"OK" | ^ 63 | 64 | test("../test.trr") | src\bundles\std_commands\src\align.py:312:37: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead. | 310 | for s, a in atoms.by_structure: 311 | satoms = s.atoms 312 | catoms.append(satoms.filter(in1d(satoms.chain_ids, a.unique_chain_ids))) | ^^^^ NPY201 313 | from chimerax.atomic import concatenate, Atoms 314 | return concatenate(catoms, Atoms) | = help: Replace with `numpy.isin` src\bundles\std_commands\src\sym.py:447:16: NPY201 [*] `np.in1d` will be removed in NumPy 2.0. Use `numpy.isin` instead. | 445 | mmcif_cids = mmcif_chain_ids(atoms, self.from_mmcif) 446 | from numpy import in1d, logical_not 447 | mask = in1d(mmcif_cids, chain_ids) | ^^^^ NPY201 448 | included_atoms = atoms.filter(mask) 449 | logical_not(mask,mask) | = help: Replace with `numpy.isin` Found 113 errors. [*] 8 fixable with the `--fix` option.