Update Python wf

bioexcel · Jan 14, 2025 · a13f645 · a13f645
1 parent 34fd61c
commit a13f645
Show file tree

Hide file tree

Showing 46 changed files with 188,327 additions and 2 deletions.
diff --git a/biobb_wf_md_setup/python/workflow.py b/biobb_wf_md_setup/python/workflow.py
@@ -25,7 +25,6 @@
 def main(config, system=None):
     start_time = time.time()
     conf = settings.ConfReader(config, system)
-    print(conf.properties)
     global_log, _ = fu.get_logs(path=conf.get_working_dir_path(), light_format=True)
     global_prop = conf.get_prop_dic(global_log=global_log)
     global_paths = conf.get_paths_dic()
@@ -105,7 +104,7 @@ def main(config, system=None):
     global_log.info("step23_rmsd_exp: Generate RMSd (against exp.) plot for the resulting setup trajectory from the free md step")
     gmx_rms(**global_paths["step23_rmsd_exp"], properties=global_prop["step23_rmsd_exp"])
 
-    if conf.properties['run_md']:
+    if conf.properties['global_properties']['run_md']:
         global_log.info("step24_grompp_md: Preprocess long MD simulation after setup")
         grompp(**global_paths["step24_grompp_md"], properties=global_prop["step24_grompp_md"])
 

diff --git a/biobb_wf_md_setup/tests/python/ions.pdb b/biobb_wf_md_setup/tests/python/ions.pdb
@@ -0,0 +1 @@
+TER
diff --git a/biobb_wf_md_setup/tests/python/reference/step00_cat_pdb/protein.ions.pdb b/biobb_wf_md_setup/tests/python/reference/step00_cat_pdb/protein.ions.pdb
diff --git a/biobb_wf_md_setup/tests/python/reference/step0_reduce_remove_hydrogens/structure.noH.pdb b/biobb_wf_md_setup/tests/python/reference/step0_reduce_remove_hydrogens/structure.noH.pdb
diff --git a/biobb_wf_md_setup/tests/python/reference/step100_make_ndx/str_index.ndx b/biobb_wf_md_setup/tests/python/reference/step100_make_ndx/str_index.ndx
diff --git a/biobb_wf_md_setup/tests/python/reference/step10_mdrun_min/min.edr b/biobb_wf_md_setup/tests/python/reference/step10_mdrun_min/min.edr
diff --git a/biobb_wf_md_setup/tests/python/reference/step10_mdrun_min/min.gro b/biobb_wf_md_setup/tests/python/reference/step10_mdrun_min/min.gro
diff --git a/biobb_wf_md_setup/tests/python/reference/step10_mdrun_min/min.log b/biobb_wf_md_setup/tests/python/reference/step10_mdrun_min/min.log
diff --git a/biobb_wf_md_setup/tests/python/reference/step10_mdrun_min/min.trr b/biobb_wf_md_setup/tests/python/reference/step10_mdrun_min/min.trr
diff --git a/biobb_wf_md_setup/tests/python/reference/step11_grompp_nvt/gppnvt.tpr b/biobb_wf_md_setup/tests/python/reference/step11_grompp_nvt/gppnvt.tpr
diff --git a/biobb_wf_md_setup/tests/python/reference/step12_mdrun_nvt/nvt.cpt b/biobb_wf_md_setup/tests/python/reference/step12_mdrun_nvt/nvt.cpt
diff --git a/biobb_wf_md_setup/tests/python/reference/step12_mdrun_nvt/nvt.edr b/biobb_wf_md_setup/tests/python/reference/step12_mdrun_nvt/nvt.edr
diff --git a/biobb_wf_md_setup/tests/python/reference/step12_mdrun_nvt/nvt.gro b/biobb_wf_md_setup/tests/python/reference/step12_mdrun_nvt/nvt.gro
diff --git a/biobb_wf_md_setup/tests/python/reference/step12_mdrun_nvt/nvt.log b/biobb_wf_md_setup/tests/python/reference/step12_mdrun_nvt/nvt.log
diff --git a/biobb_wf_md_setup/tests/python/reference/step12_mdrun_nvt/nvt.trr b/biobb_wf_md_setup/tests/python/reference/step12_mdrun_nvt/nvt.trr
diff --git a/biobb_wf_md_setup/tests/python/reference/step13_grompp_npt/gppnpt.tpr b/biobb_wf_md_setup/tests/python/reference/step13_grompp_npt/gppnpt.tpr
diff --git a/biobb_wf_md_setup/tests/python/reference/step14_mdrun_npt/npt.cpt b/biobb_wf_md_setup/tests/python/reference/step14_mdrun_npt/npt.cpt
diff --git a/biobb_wf_md_setup/tests/python/reference/step14_mdrun_npt/npt.edr b/biobb_wf_md_setup/tests/python/reference/step14_mdrun_npt/npt.edr
diff --git a/biobb_wf_md_setup/tests/python/reference/step14_mdrun_npt/npt.gro b/biobb_wf_md_setup/tests/python/reference/step14_mdrun_npt/npt.gro
diff --git a/biobb_wf_md_setup/tests/python/reference/step14_mdrun_npt/npt.log b/biobb_wf_md_setup/tests/python/reference/step14_mdrun_npt/npt.log
diff --git a/biobb_wf_md_setup/tests/python/reference/step14_mdrun_npt/npt.trr b/biobb_wf_md_setup/tests/python/reference/step14_mdrun_npt/npt.trr
diff --git a/biobb_wf_md_setup/tests/python/reference/step15_grompp_md/gppmd.tpr b/biobb_wf_md_setup/tests/python/reference/step15_grompp_md/gppmd.tpr
diff --git a/biobb_wf_md_setup/tests/python/reference/step16_mdrun_md/md.cpt b/biobb_wf_md_setup/tests/python/reference/step16_mdrun_md/md.cpt
diff --git a/biobb_wf_md_setup/tests/python/reference/step16_mdrun_md/md.edr b/biobb_wf_md_setup/tests/python/reference/step16_mdrun_md/md.edr
diff --git a/biobb_wf_md_setup/tests/python/reference/step16_mdrun_md/md.gro b/biobb_wf_md_setup/tests/python/reference/step16_mdrun_md/md.gro