Update Python wf

bioexcel · Jan 14, 2025 · a13f645 · a13f645
1 parent 34fd61c
commit a13f645
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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
diff --git a/biobb_wf_md_setup/tests/python/reference/step16_mdrun_md/md.log b/biobb_wf_md_setup/tests/python/reference/step16_mdrun_md/md.log
diff --git a/biobb_wf_md_setup/tests/python/reference/step16_mdrun_md/md.trr b/biobb_wf_md_setup/tests/python/reference/step16_mdrun_md/md.trr
diff --git a/biobb_wf_md_setup/tests/python/reference/step17_gmx_image1/md.imaged.trr b/biobb_wf_md_setup/tests/python/reference/step17_gmx_image1/md.imaged.trr
diff --git a/biobb_wf_md_setup/tests/python/reference/step18_gmx_image2/md.imaged.rot.xtc b/biobb_wf_md_setup/tests/python/reference/step18_gmx_image2/md.imaged.rot.xtc
diff --git a/biobb_wf_md_setup/tests/python/reference/step19_gmx_trjconv_str/setup.top.pdb b/biobb_wf_md_setup/tests/python/reference/step19_gmx_trjconv_str/setup.top.pdb
diff --git a/biobb_wf_md_setup/tests/python/reference/step1_extract_molecule/protein.pdb b/biobb_wf_md_setup/tests/python/reference/step1_extract_molecule/protein.pdb
diff --git a/biobb_wf_md_setup/tests/python/reference/step20_gmx_energy/setup.energy.xvg b/biobb_wf_md_setup/tests/python/reference/step20_gmx_energy/setup.energy.xvg
@@ -0,0 +1,76 @@
+# This file was created Tue Jan 14 16:44:25 2025
+# Created by:
+#                :-) GROMACS - gmx energy, 2022.2-conda_forge (-:
+# 
+# Executable:   /home/gbayarri/anaconda3/envs/biobb_wf_md_setup/bin.AVX2_256/gmx
+# Data prefix:  /home/gbayarri/anaconda3/envs/biobb_wf_md_setup
+# Working dir:  /home/gbayarri/projects/BioBB/biobb_workflows/biobb_wf_md_setup/python
+# Command line:
+#   gmx energy -f /home/gbayarri/projects/BioBB/biobb_workflows/biobb_wf_md_setup/python/sandbox_3679c174-b9b9-4d62-8e30-0d8cd5cafd6a/md.edr -o /home/gbayarri/projects/BioBB/biobb_workflows/biobb_wf_md_setup/python/sandbox_3679c174-b9b9-4d62-8e30-0d8cd5cafd6a/setup.energy.xvg -xvg xmgr
+# gmx energy is part of G R O M A C S:
+#
+# Getting the Right Output Means no Artefacts in Calculating Stuff
+#
+@    title "GROMACS Energies"
+@    xaxis  label "Time (ps)"
+@    yaxis  label "(kJ/mol)"
+@TYPE nxy
+@ view 0.15, 0.15, 0.75, 0.85
+@ legend on
+@ legend box on
+@ legend loctype view
+@ legend 0.78, 0.8
+@ legend length 2
+@ legend string 0 "Potential"
+@ legend string 1 "Total Energy"
+    0.000000  -292210.062500  -235844.781250
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+  490.000000  -291825.593750  -236198.062500
+  500.000000  -290777.125000  -235247.375000
diff --git a/biobb_wf_md_setup/tests/python/reference/step21_gmx_rgyr/setup.rgyr.xvg b/biobb_wf_md_setup/tests/python/reference/step21_gmx_rgyr/setup.rgyr.xvg
@@ -0,0 +1,78 @@
+# This file was created Tue Jan 14 16:44:25 2025
+# Created by:
+#                :-) GROMACS - gmx gyrate, 2022.2-conda_forge (-:
+# 
+# Executable:   /home/gbayarri/anaconda3/envs/biobb_wf_md_setup/bin.AVX2_256/gmx
+# Data prefix:  /home/gbayarri/anaconda3/envs/biobb_wf_md_setup
+# Working dir:  /home/gbayarri/projects/BioBB/biobb_workflows/biobb_wf_md_setup/python
+# Command line:
+#   gmx gyrate -s /home/gbayarri/projects/BioBB/biobb_workflows/biobb_wf_md_setup/python/sandbox_297a0ad1-22af-4ca1-9ace-bb529959e859/gppmd.tpr -f /home/gbayarri/projects/BioBB/biobb_workflows/biobb_wf_md_setup/python/sandbox_297a0ad1-22af-4ca1-9ace-bb529959e859/md.imaged.rot.xtc -o /home/gbayarri/projects/BioBB/biobb_workflows/biobb_wf_md_setup/python/sandbox_297a0ad1-22af-4ca1-9ace-bb529959e859/setup.rgyr.xvg -xvg xmgr -n /home/gbayarri/projects/BioBB/biobb_workflows/biobb_wf_md_setup/python/sandbox_297a0ad1-22af-4ca1-9ace-bb529959e859/str_index.ndx
+# gmx gyrate is part of G R O M A C S:
+#
+# Getting the Right Output Means no Artefacts in Calculating Stuff
+#
+@    title "Radius of gyration (total and around axes)"
+@    xaxis  label "Time (ps)"
+@    yaxis  label "Rg (nm)"
+@TYPE nxy
+@ view 0.15, 0.15, 0.75, 0.85
+@ legend on
+@ legend box on
+@ legend loctype view
+@ legend 0.78, 0.8
+@ legend length 2
+@ legend string 0 "Rg"
+@ legend string 1 "Rg\sX\N"
+@ legend string 2 "Rg\sY\N"
+@ legend string 3 "Rg\sZ\N"
+         0     1.40465     1.20274     1.02643     1.20248
+        10      1.4098      1.2079      1.0279     1.20808
+        20     1.41866     1.21242     1.03264      1.2202
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diff --git a/biobb_wf_md_setup/tests/python/reference/step22_rmsd_first/setup.rmsd_first.xvg b/biobb_wf_md_setup/tests/python/reference/step22_rmsd_first/setup.rmsd_first.xvg
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diff --git a/biobb_wf_md_setup/tests/python/reference/step23_rmsd_exp/setup.rmsd_exp.xvg b/biobb_wf_md_setup/tests/python/reference/step23_rmsd_exp/setup.rmsd_exp.xvg
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