vacuum minimization

ndonyapour · ndonyapour · commit b16ab61d1e85 · 2024-03-18T12:03:14.000-04:00
diff --git a/cwl_adapters/combine_structure.cwl b/cwl_adapters/combine_structure.cwl
@@ -12,7 +12,7 @@ baseCommand: ['python', '/combine_structure.py']
 
 hints:
   DockerRequirement:
-    dockerPull: ndonyapour/combine_structure
+    dockerPull: ndonyapour/combine_structure_zip
 
 inputs:
   input_structure1:
@@ -40,6 +40,20 @@ inputs:
     - edam:format_3877 
     inputBinding:
       prefix: --input_structure2
+  
+  input_top_zip_path:
+    label: Input zip file
+    doc: |-
+      Input zip file
+      Type: string
+      File type: input
+      Accepted formats: zip
+      Example file: https://github.com/bioexcel/biobb_md/blob/master/biobb_md/test/data/gromacs/genion.zip
+    type: File
+    format:
+    - edam:format_3987
+    inputBinding:
+      prefix: --input_top_zip_path
 
   output_structure_path:
     label: Output combined PDB file path
diff --git a/examples/config_ci.json b/examples/config_ci.json
@@ -10,7 +10,11 @@
         "vs_demo_2_weekly",
         "vs_demo_3_weekly",
         "vs_demo_4_weekly",
-        "docking_rescoring_weekly"
+        "docking_rescoring_weekly",
+        "stability",
+        "docking_stability",
+        "nmr",
+        "tutorial"
     ],
     // NOTE: Most of the workflows in this list have free variables because they are subworkflows
     // i.e. if you try to run them, you will get "Missing required input parameter"
diff --git a/examples/docking/docking.yml b/examples/docking/docking.yml
@@ -90,6 +90,7 @@ steps:
       in:
         input_structure1: '*receptor.xyz' # '*receptor_hydrogens.pdb'
         input_structure2: '*pose_ligand.xyz'
+        input_top_zip_path: '*complex_vac.zip'
         output_structure_path: '&complex_vac.pdb'
 
 wic:
diff --git a/examples/docking/docking_stability.yml b/examples/docking/docking_stability.yml
@@ -29,14 +29,31 @@ wic:
         inlineable: True
     (2, stability.yml):
       wic:
-        inlineable: True
+        inlineable: False
         steps:
+          (1, setup_vac_min.yml):
+            wic:
+              steps:
+                (3, solv_ion.yml):
+                  wic:
+                    steps:
+                      (4, genion):
+                        in:
+                          output_top_zip_path: '&genion_complex.zip'
           (2, basic.yml):
+            in:
+              top_zip_path: '*genion_complex.zip'
             wic:
               steps:
                 (3, prod.yml):
                   wic:
                     steps:
+                      (2, grompp):
+                        in:
+                          input_top_zip_path: '*genion_complex.zip'
+                      (3, mdrun):
+                        in:
+                          output_crd_path: '&prod_complex.gro'
                       (4, cwl_watcher_analysis.yml):
                         wic:
                           backend: complex
@@ -45,4 +62,7 @@ wic:
               steps:
                 (1, analysis_realtime.yml):
                   wic:
-                    backend:  complex
+                    backend: complex
+                (2, analysis_final.yml):
+                  wic:
+                    backend: complex
diff --git a/examples/docking/gen_topol_params.yml b/examples/docking/gen_topol_params.yml
@@ -70,6 +70,7 @@ steps:
     in:
       input_structure1: ~input_receptor_xyz_path
       input_structure2: '*pose_ligand.xyz'
+      input_top_zip_path: '*complex_vac.zip'
       output_structure_path: '&complex_vac.pdb'
 
 wic:
diff --git a/examples/docking/vs_demo_2.yml b/examples/docking/vs_demo_2.yml
@@ -146,13 +146,18 @@ wic:
       wic:
         inlineable: False
         steps:
-          (1, setup.yml):
+          (1, setup_vac_min.yml):
             wic:
               steps:
-                (4, genion):
-                  in:
-                    output_top_zip_path: '&genion_complex.zip'
+                (3, solv_ion.yml):
+                  wic:
+                    steps:
+                      (4, genion):
+                        in:
+                          output_top_zip_path: '&genion_complex.zip'
           (2, basic.yml):
+            in:
+              top_zip_path: '*genion_complex.zip'
             wic:
               steps:
                 (3, prod.yml):
diff --git a/examples/docking/vs_demo_3.yml b/examples/docking/vs_demo_3.yml
@@ -124,13 +124,18 @@ wic:
       wic:
         inlineable: False
         steps:
-          (1, setup.yml):
+          (1, setup_vac_min.yml):
             wic:
               steps:
-                (4, genion):
-                  in:
-                    output_top_zip_path: '&genion_complex.zip'
+                (3, solv_ion.yml):
+                  wic:
+                    steps:
+                      (4, genion):
+                        in:
+                          output_top_zip_path: '&genion_complex.zip'
           (2, basic.yml):
+            in:
+              top_zip_path: '*genion_complex.zip'
             wic:
               steps:
                 (3, prod.yml):
diff --git a/examples/docking/vs_demo_4.yml b/examples/docking/vs_demo_4.yml
@@ -191,13 +191,18 @@ wic:
       wic:
         inlineable: False
         steps:
-          (1, setup.yml):
+          (1, setup_vac_min.yml):
             wic:
               steps:
-                (4, genion):
-                  in:
-                    output_top_zip_path: '&genion_complex.zip'
+                (3, solv_ion.yml):
+                  wic:
+                    steps:
+                      (4, genion):
+                        in:
+                          output_top_zip_path: '&genion_complex.zip'
           (2, basic.yml):
+            in:
+              top_zip_path: '*genion_complex.zip'
             wic:
               steps:
                 (3, prod.yml):
diff --git a/examples/gromacs/basic.yml b/examples/gromacs/basic.yml
@@ -1,4 +1,8 @@
 inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
   nsteps:
     type: int
   dt:
@@ -16,6 +20,8 @@ steps:
 # to this level and use the following syntax to pass it to only one call site.
 # (Moreover, the former will create multiple definitions of &min.tpr, which is not allowed.)
   - min.yml:
+      in:
+        top_zip_path: ~top_zip_path
   - equil.yml:
   - prod.yml:
       in:
diff --git a/examples/gromacs/cg.yml b/examples/gromacs/cg.yml
@@ -1,6 +1,13 @@
+inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 steps:
   - grompp:
       in:
+        input_top_zip_path: ~top_zip_path
         config:
           mdp:
             integrator: cg
diff --git a/examples/gromacs/min.yml b/examples/gromacs/min.yml
@@ -1,9 +1,19 @@
+inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 steps:
   - steep.yml:
+      in:
+        top_zip_path: ~top_zip_path
 # Fatal error:
 # The coordinates could not be constrained. Minimizer 'cg' can not handle
 # constraint failures, use minimizer 'steep' before using 'cg'.
   - cg.yml:
+      in:
+        top_zip_path: ~top_zip_path
 # Fatal error:
 # The combination of constraints and L-BFGS minimization is not implemented.
 # Either do not use constraints, or use another minimizer (e.g. steepest
diff --git a/examples/gromacs/setup.yml b/examples/gromacs/setup.yml
@@ -10,13 +10,6 @@ inputs:
     - edam:format_3987
 
 steps:
-# - editconf:
-#     in:
-#       input_crd_path: ~crd_path
-#       #input_crd_path: '*complex_vac.pdb'
-#       config:
-#         box_type: cubic
-#         distance_to_molecule: 1.2
 - gmx_editconf:
     in:
       input_crd_path: ~crd_path
diff --git a/examples/gromacs/setup_vac_min.yml b/examples/gromacs/setup_vac_min.yml
@@ -1,8 +1,37 @@
+inputs:
+  crd_path:
+    type: File
+    format:
+    - edam:format_1476
+    - edam:format_2033
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 steps:
   - topology.yml:
+      in:
+        crd_path: ~crd_path
   - min.yml: # Minimize in vacuum first, then in solvent.
+      in:
+        top_zip_path: ~top_zip_path
   - solv_ion.yml:
-
+      in:
+        top_zip_path: ~top_zip_path
 wic:
   graphviz:
-    label: System Setup
+    label: System Setup
+  steps:
+    (1, topology.yml):
+      wic:
+        graphviz:
+          label: 'Initialize\nPeriodic Box'
+    (2, min.yml):
+      wic:
+        graphviz:
+          label: 'Vacuum Minimization'
+    (3, solv_ion.yml):
+      wic:
+        graphviz:
+          label: 'Add Water\nSolvent'
diff --git a/examples/gromacs/solv_ion.yml b/examples/gromacs/solv_ion.yml
@@ -1,12 +1,19 @@
+inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 steps:
-  - editconf:
+  - gmx_editconf:
       in:
-        config:
-          box_type: cubic
-          distance_to_molecule: 1.0
+        #input_crd_path: ~crd_path
+        align_principal_axes: 0
+        box_type: cubic
+        distance_to_molecule: 1.2
   - solvate:
       in:
-        input_top_zip_path: '*complex_vac.zip'
+        input_top_zip_path: ~top_zip_path
         output_crd_path: '&solvate.gro'
         output_top_zip_path: '&solvate.zip'
   - grompp:
@@ -28,10 +35,10 @@ wic:
   graphviz:
     label: Solvation & Ionization
     ranksame:
-    - (1, editconf)
+    - (1, gmx_editconf)
     - (4, genion)
   steps:
-    (1, editconf):
+    (1, gmx_editconf):
       wic:
         graphviz:
           label: 'Initialize\nPeriodic Box'
diff --git a/examples/gromacs/stability.yml b/examples/gromacs/stability.yml
@@ -18,12 +18,13 @@ inputs:
     - edam:format_3987
 
 steps:
-  - setup.yml:
+  - setup_vac_min.yml:
       in:
         crd_path: ~crd_path
         top_zip_path: ~top_zip_path
   - basic.yml:
       in:
+        top_zip_path: '*genion.zip'
         nsteps: ~nsteps
         dt: ~dt
         ref-t: ~temperature
diff --git a/examples/gromacs/steep.yml b/examples/gromacs/steep.yml
@@ -1,10 +1,17 @@
+inputs:
+  top_zip_path:
+    type: File
+    format:
+    - edam:format_3987
+
 # On my machine, 10 iterations of steepest descent is sufficient to prevent
 # conjugate gradient from crashing. (i.e. pytest works for me!)
 # But using only 10 iterations is causing the tests on github actions to fail!
 # 25 seems to work, but let's just set it to 100.
 steps:
   - grompp:
       in:
+        input_top_zip_path: ~top_zip_path
         config:
           mdp:
             integrator: steep
diff --git a/examples/gromacs/topology.yml b/examples/gromacs/topology.yml
@@ -1,10 +1,17 @@
+inputs:
+  crd_path:
+    type: File
+    format:
+    - edam:format_1476
+    - edam:format_2033
+
 steps:
 # We want to perform vacuum minimization first, before solvation and ionization.
 # NOTE: Gromacs no longer supports non-periodic boundary conditions (!!!),
 # so we must emulate a vacuum by using a very large (1000 Angstrom) box.
   - editconf:
       in:
-        input_crd_path: '*complex_vac.pdb'
+        input_crd_path: ~crd_path
         output_crd_path: '&complex_box.g96'
         config:
           box_type: cubic
diff --git a/examples/gromacs/tutorial.yml b/examples/gromacs/tutorial.yml
@@ -6,7 +6,7 @@ steps:
       in:
         crd_path: '*complex_vac.pdb'
         top_zip_path: '*complex_vac.zip'
-        nsteps: 100000
+        nsteps: 10000
         dt: 0.002
         temperature: 298.0
         pressure: 1.0
diff --git a/examples/scripts/Dockerfile_combine_structure b/examples/scripts/Dockerfile_combine_structure
@@ -1,7 +1,7 @@
 FROM condaforge/mambaforge
 # NOT mambaforge-pypy3 (rdkit is incompatible with pypy)
 
-RUN mamba install -c conda-forge rdkit
+RUN mamba install -c conda-forge rdkit mdanalysis gromacs
 
 ADD combine_structure.py .
 ADD Dockerfile_combine_structure .
diff --git a/examples/scripts/combine_structure.py b/examples/scripts/combine_structure.py
