BioBB WF MD Setup Mutations

bioexcel · Jan 17, 2025 · d8db266 · d8db266
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diff --git a/biobb_wf_dna_helparms/README.md b/biobb_wf_dna_helparms/README.md
@@ -36,8 +36,8 @@ This tutorial aims to illustrate the process of **extracting structural and dyna
 ## Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

diff --git a/biobb_wf_dna_helparms/tests/python/reference/step1_biobb_curves/curves.out.cda b/biobb_wf_dna_helparms/tests/python/reference/step1_biobb_curves/curves.out.cda
diff --git a/biobb_wf_flexdyn/README.md b/biobb_wf_flexdyn/README.md
@@ -97,8 +97,8 @@ The particular structure used is the **complex between ADENYLATE KINASE from Esc
 ## Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

diff --git a/biobb_wf_flexserv/README.md b/biobb_wf_flexserv/README.md
@@ -60,8 +60,8 @@ The codes wrapped are the ***FlexServ*** and ***PCAsuite*** tools:
 ## Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

diff --git a/biobb_wf_godmd/README.md b/biobb_wf_godmd/README.md
@@ -48,8 +48,8 @@ The code wrapped is the ***GOdMD*** method, developed in the **[Molecular Modeli
 ## Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

diff --git a/biobb_wf_ligand_parameterization/README.md b/biobb_wf_ligand_parameterization/README.md
@@ -42,8 +42,8 @@ This tutorial aims to illustrate the process of **ligand parameterization** for
 ## Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

diff --git a/biobb_wf_md_setup/README.md b/biobb_wf_md_setup/README.md
@@ -42,8 +42,8 @@ This tutorial aims to illustrate the process of **setting up a simulation** syst
 ## Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

diff --git a/biobb_wf_md_setup/tests/python/biobb_wf_md_setup.py b/biobb_wf_md_setup/tests/python/biobb_wf_md_setup.py
@@ -381,7 +381,7 @@ def step23_rmsd_exp(config, remove=False, system=None):
     # assert fx.equal(global_paths["step23_rmsd_exp"]["output_xvg_path"], f'reference/step23_rmsd_exp/{Path(global_paths["step23_rmsd_exp"]["output_xvg_path"]).name}')
 
     if remove:
-        tmp_files = [conf.get_working_dir_path(), 'fort.7', 'gridout', 'restart']
+        tmp_files = [conf.get_working_dir_path()]
         tmp_files.extend(glob.glob('sandbox_*'))
         fu.rm_file_list(tmp_files)
 

diff --git a/biobb_wf_md_setup_mutations/README.md b/biobb_wf_md_setup_mutations/README.md
@@ -30,8 +30,8 @@ This tutorial aims to illustrate the process of **setting up a simulation** syst
 ## Copyright & Licensing
 This software has been developed in the [MMB group](http://mmb.irbbarcelona.org) at the [BSC](http://www.bsc.es/) & [IRB](https://www.irbbarcelona.org/) for the [European BioExcel](http://bioexcel.eu/), funded by the European Commission (EU H2020 [823830](http://cordis.europa.eu/projects/823830), EU H2020 [675728](http://cordis.europa.eu/projects/675728)).
 
-* (c) 2015-2024 [Barcelona Supercomputing Center](https://www.bsc.es/)
-* (c) 2015-2024 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
+* (c) 2015-2025 [Barcelona Supercomputing Center](https://www.bsc.es/)
+* (c) 2015-2025 [Institute for Research in Biomedicine](https://www.irbbarcelona.org/)
 
 Licensed under the
 [Apache License 2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file LICENSE for details.

diff --git a/biobb_wf_md_setup_mutations/python/workflow.py b/biobb_wf_md_setup_mutations/python/workflow.py
@@ -22,6 +22,7 @@
 from biobb_analysis.gromacs.gmx_image import gmx_image
 from biobb_analysis.gromacs.gmx_rms import gmx_rms
 
+
 def main(config, system=None):
     start_time = time.time()
     conf = settings.ConfReader(config, system)
@@ -41,9 +42,9 @@ def main(config, system=None):
     global_log.info("step2_fix_side_chain: Modeling the missing heavy atoms in the structure side chains")
     fix_side_chain(**global_paths["step2_fix_side_chain"], properties=global_prop["step2_fix_side_chain"])
 
-    for mutation_number, mutation in enumerate(conf.properties['mutations']):
+    for mutation_number, mutation in enumerate(conf.properties['global_properties']['mutations']):
         global_log.info('')
-        global_log.info("Mutation: %s  %d/%d" % (mutation, mutation_number+1, len(conf.properties['mutations'])))
+        global_log.info("Mutation: %s  %d/%d" % (mutation, mutation_number+1, len(conf.properties['global_properties']['mutations'])))
         global_log.info('')
         prop = conf.get_prop_dic(prefix=mutation, global_log=global_log)
         paths = conf.get_paths_dic(prefix=mutation)
@@ -116,7 +117,7 @@ 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(**paths["step23_rmsd_exp"], properties=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(**paths["step24_grompp_md"], properties=prop["step24_grompp_md"])
 
@@ -132,6 +133,7 @@ def main(config, system=None):
     global_log.info('Elapsed time: %.1f minutes' % (elapsed_time/60))
     global_log.info('')
 
+
 if __name__ == '__main__':
     parser = argparse.ArgumentParser(description="Based on the official Gromacs tutorial")
     parser.add_argument('--config', required=True)

diff --git a/biobb_wf_md_setup_mutations/python/workflow.yml b/biobb_wf_md_setup_mutations/python/workflow.yml
@@ -2,8 +2,7 @@ global_properties:
   working_dir_path: biobb_wf_md_setup_mutations
   can_write_console_log: False
   run_md: true
-
-mutations: ["A:Gly4Lys","A:Leu8Met","A:Tyr20Gln"]
+  mutations: ["A:Gly4Lys","A:Leu8Met","A:Tyr20Gln"]
 
 step0_reduce_remove_hydrogens:
   tool: reduce_remove_hydrogens