| """ |
| Run all full examples in a row. |
| |
| This script should be executed from inside the haddock3/examples/ folder. |
| |
| This script runs the `*-full.cfg` files. These test cases are not fetched |
| automatically. If you want to add/remove cases you need to edit this script. |
| The HADDOCK3 team has defined here only those test cases that are part of the |
| integration tests. |
| |
| This script will delete existing run directories which names overlap with those |
| defined in the test configuration files. |
| |
| If you see errors related to python import statements, make sure you have |
| the HADDOCK3 environment activated. |
| |
| A breaking example means something is wrong in the HADDOCK3 core workflow. |
| You should work towards solving that problem or contact the HADDOCK3 team. |
| |
| USAGE: |
| |
| $ python run_examples-full.py -h |
| $ python run_examples-full.py # runs all examples regardless of errors |
| $ python run_examples-full.py -b # stops asap an error is found |
| """ |
| import argparse |
| import subprocess |
| import sys |
| from shutil import rmtree |
|
|
|
|
| try: |
| from haddock.gear.config import load as read_config |
| from haddock.libs.libio import working_directory |
| except Exception: |
| print( |
| "Haddock3 could not be imported. " |
| "Please activate the haddock3 python environment.", |
| file=sys.stderr, |
| ) |
| sys.exit(1) |
|
|
|
|
| |
| |
| |
| examples = ( |
| ("docking-protein-DNA" , "docking-protein-DNA-full.cfg"), |
| ("docking-protein-DNA" , "docking-protein-DNA-cltsel-full.cfg"), |
| ("docking-protein-DNA" , "docking-protein-DNA-mdref-full.cfg"), |
| ("docking-protein-homotrimer" , "docking-protein-homotrimer-full.cfg"), |
| ("docking-protein-ligand" , "docking-protein-ligand-full.cfg"), |
| ("docking-protein-ligand-shape", "docking-protein-ligand-shape-full.cfg"), |
| ("docking-protein-peptide" , "docking-protein-peptide-full.cfg"), |
| ("docking-protein-peptide" , "docking-protein-peptide-cltsel-full.cfg"), |
| ("docking-protein-peptide" , "docking-protein-peptide-mdref-full.cfg"), |
| ("docking-protein-protein" , "docking-protein-protein-full.cfg"), |
| ("docking-protein-protein" , "docking-protein-protein-cltsel-full.cfg"), |
| ("docking-protein-protein" , "docking-protein-protein-mdref-full.cfg"), |
| ("docking-multiple-ambig" , "docking-multiple-tbls-clt-full.cfg"), |
| ("docking-antibody-antigen" , "docking-antibody-antigen-CDR-NMR-CSP-full.cfg"), |
| ("docking-antibody-antigen" , "docking-antibody-antigen-CDR-accessible-full.cfg"), |
| ("docking-antibody-antigen" , "docking-antibody-antigen-CDR-accessible-clt-full.cfg"), |
| ("docking-antibody-antigen" , "docking-antibody-antigen-ranairCDR-full.cfg"), |
| ("docking-antibody-antigen" , "docking-antibody-antigen-ranairCDR-clt-full.cfg"), |
| ("peptide-cyclisation" , "cyclise-peptide-full.cfg"), |
| ) |
|
|
|
|
| ap = argparse.ArgumentParser( |
| description=__doc__, |
| formatter_class=argparse.RawDescriptionHelpFormatter, |
| ) |
|
|
| ap.add_argument( |
| '-b', |
| '--break-on-errors', |
| action='store_true', |
| help=( |
| "Stop execution as soon an example gives an error. " |
| "If not given, runs all examples regardless of errors." |
| ), |
| ) |
|
|
|
|
| def load_args(): |
| """Load argparse arguments.""" |
| return ap.parse_args() |
|
|
|
|
| def main(examples, break_on_errors=True): |
| """Run all the examples.""" |
| for folder, file_ in examples: |
|
|
| print() |
| print(f" {file_.upper()} ".center(80, "*")) |
| print() |
|
|
| with working_directory(folder): |
| |
| all_params = read_config(file_) |
| rundir = all_params['final_cfg']["run_dir"] |
| |
| rmtree(rundir, ignore_errors=True) |
|
|
| |
| subprocess.run( |
| f"haddock3 {file_}", |
| shell=True, |
| check=break_on_errors, |
| stdout=sys.stdout, |
| stderr=sys.stderr, |
| ) |
|
|
| return |
|
|
|
|
| if __name__ == "__main__": |
| cmd = load_args() |
| main(examples, **vars(cmd)) |
|
|
