From 512cdcfd3a30092e0aea9135b11f8872dda469aa Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Fri, 20 Sep 2024 10:28:18 +0200 Subject: [PATCH 1/4] [UPDATE](biobb_wf_md_setup): Update wf to the new configReader --- biobb_wf_md_setup_mutations/python/workflow.py | 6 ++++-- .../python/workflow.yml | 18 ++++++++++-------- 2 files changed, 14 insertions(+), 10 deletions(-) mode change 100644 => 100755 biobb_wf_md_setup_mutations/python/workflow.py diff --git a/biobb_wf_md_setup_mutations/python/workflow.py b/biobb_wf_md_setup_mutations/python/workflow.py old mode 100644 new mode 100755 index f3c121f1..d7f20a57 --- 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) @@ -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 index 0b44acd4..8ba826b7 100644 --- a/biobb_wf_md_setup_mutations/python/workflow.yml +++ b/biobb_wf_md_setup_mutations/python/workflow.yml @@ -1,13 +1,15 @@ -working_dir_path: biobb_wf_md_setup_mutations -can_write_console_log: False -run_md: true - -mutations: ["A:Gly4Lys","A:Leu8Met","A:Tyr20Gln"] +global_properties: + working_dir_path: biobb_wf_md_setup_mutations + can_write_console_log: False + run_md: true + disable_sandbox: False + timeout: 5 + mutations: ["A:Gly4Lys","A:Leu8Met","A:Tyr20Gln"] step0_reduce_remove_hydrogens: tool: reduce_remove_hydrogens paths: - input_path: /path/to/inputs/structure.pdb + input_path: /Users/pau/projects/biobb_workflows/biobb_wf_md_setup_mutations/python/structure.pdb output_path: structure.noH.pdb step1_extract_molecule: @@ -20,7 +22,7 @@ step00_cat_pdb: tool: cat_pdb paths: input_structure1: dependency/step1_extract_molecule/output_molecule_path - input_structure2: /path/to/inputs/ions.pdb + input_structure2: /Users/pau/projects/biobb_workflows/biobb_wf_md_setup_mutations/python/ions.pdb output_structure_path: protein.ions.pdb step2_fix_side_chain: @@ -210,7 +212,7 @@ step18_gmx_image2: output_traj_path: md.imaged.rot.xtc properties: fit_selection: "Protein" - output_selection: System + output_selection: System fit: rot+trans step19_gmx_trjconv_str: From acf35e754f22b9574ec534bab28cf7a313228ffe Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Fri, 20 Sep 2024 10:29:00 +0200 Subject: [PATCH 2/4] [UPDATE](biobb_wf_md_setup): Update wf to the new configReader --- biobb_wf_md_setup_mutations/python/workflow.yml | 2 -- 1 file changed, 2 deletions(-) diff --git a/biobb_wf_md_setup_mutations/python/workflow.yml b/biobb_wf_md_setup_mutations/python/workflow.yml index 8ba826b7..b4918f55 100644 --- a/biobb_wf_md_setup_mutations/python/workflow.yml +++ b/biobb_wf_md_setup_mutations/python/workflow.yml @@ -2,8 +2,6 @@ global_properties: working_dir_path: biobb_wf_md_setup_mutations can_write_console_log: False run_md: true - disable_sandbox: False - timeout: 5 mutations: ["A:Gly4Lys","A:Leu8Met","A:Tyr20Gln"] step0_reduce_remove_hydrogens: From 949ba098c73cb522f14be1dd50f7d8b56c5abbb0 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Fri, 20 Sep 2024 10:42:03 +0200 Subject: [PATCH 3/4] [FIX](biobb_wf_md_setup_mutations): Remove local paths --- biobb_wf_md_setup_mutations/python/workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/biobb_wf_md_setup_mutations/python/workflow.yml b/biobb_wf_md_setup_mutations/python/workflow.yml index b4918f55..ef22e642 100644 --- a/biobb_wf_md_setup_mutations/python/workflow.yml +++ b/biobb_wf_md_setup_mutations/python/workflow.yml @@ -7,7 +7,7 @@ global_properties: step0_reduce_remove_hydrogens: tool: reduce_remove_hydrogens paths: - input_path: /Users/pau/projects/biobb_workflows/biobb_wf_md_setup_mutations/python/structure.pdb + input_path: /path/to/structure.pdb output_path: structure.noH.pdb step1_extract_molecule: @@ -20,7 +20,7 @@ step00_cat_pdb: tool: cat_pdb paths: input_structure1: dependency/step1_extract_molecule/output_molecule_path - input_structure2: /Users/pau/projects/biobb_workflows/biobb_wf_md_setup_mutations/python/ions.pdb + input_structure2: /path/to/ions.pdb output_structure_path: protein.ions.pdb step2_fix_side_chain: From ec8bfdd22c3662b53ea40a19dfede7fdb420eb71 Mon Sep 17 00:00:00 2001 From: Pau Andrio Date: Fri, 20 Sep 2024 10:43:19 +0200 Subject: [PATCH 4/4] [FIX](biobb_wf_md_setup_mutations): Remove local paths --- biobb_wf_md_setup_mutations/python/workflow.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/biobb_wf_md_setup_mutations/python/workflow.yml b/biobb_wf_md_setup_mutations/python/workflow.yml index ef22e642..b5c69be3 100644 --- a/biobb_wf_md_setup_mutations/python/workflow.yml +++ b/biobb_wf_md_setup_mutations/python/workflow.yml @@ -7,7 +7,7 @@ global_properties: step0_reduce_remove_hydrogens: tool: reduce_remove_hydrogens paths: - input_path: /path/to/structure.pdb + input_path: /path/to/inputs/structure.pdb output_path: structure.noH.pdb step1_extract_molecule: @@ -20,7 +20,7 @@ step00_cat_pdb: tool: cat_pdb paths: input_structure1: dependency/step1_extract_molecule/output_molecule_path - input_structure2: /path/to/ions.pdb + input_structure2: /path/to/inputs/ions.pdb output_structure_path: protein.ions.pdb step2_fix_side_chain: