From e18b417ae822fb9913e99711b38fa76695886e38 Mon Sep 17 00:00:00 2001
From: Brandon Duane Walker <walkerbd@UPDATEME.HOSTNAME.COM>
Date: Mon, 13 May 2024 14:54:00 -0400
Subject: [PATCH] elm

---
 docking/elm.wic | 83 +++++++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 83 insertions(+)
 create mode 100644 docking/elm.wic

diff --git a/docking/elm.wic b/docking/elm.wic
new file mode 100644
index 00000000..fa64110b
--- /dev/null
+++ b/docking/elm.wic
@@ -0,0 +1,83 @@
+steps:
+  download_pdb.wic:
+    in:
+      #pdb_id: !ii 1r4l # ACE2
+      #pdb_id: !ii 1ntp # trypsin
+      pdb_id: !ii 1uao # chignolin (for speed)
+  setup_pdb.wic:
+    in:
+      input_pdb_path: !* protein.pdb
+      pdb_path: !ii pdb.pdbqt
+      box_path: !ii box.pdb
+      box_buffer: !ii 20 # Angstroms
+      water_type: !ii spce
+      forcefield: !ii amber99sb-ildn
+    out:
+    - pdb_path: !& pdb.pdbqt
+    - box_path: !& box.pdb
+  download_ligand_database:
+    in:
+      database: !ii /NCIOpen.sdf
+  extract_molecules_sdf:
+    in:
+      first_molecule: !ii 1
+      last_molecule: !ii 1
+    # out:
+    # - output_sdf_path: !& ligands.sdf
+# NOTE: We need to extract the models first, before splitting them into separate files.
+# If we try to do both simultaneously, obabel ignores -f and -l and outputs ALL models.
+  split_sdf:
+#    in:
+#      input_path: !* ligands.sdf
+    out:
+    - output_sdf_path: !& ligand.sdf # Array type
+  docking_stability.wic:
+    scatter: [sdf_path]
+    in:
+      # NOTE: sdf_path is currently only necessary
+      # due to a limitation of the inlineing implementation.
+      sdf_path: !* ligand.sdf
+# NOTE: Do not add scattering arguments here, add them to the wic: metadata annotations.
+# (We want this information at the call site, not inserted within the subworkflow.)
+
+wic:
+  steps:
+    (1, download_pdb.wic):
+      wic:
+        inlineable: False
+    (2, setup_pdb.wic):
+      wic:
+        inlineable: True
+    (4, extract_molecules_sdf):
+      wic:
+        graphviz:
+          label: Choose Ligands from\nCheminformatics Database
+    (5, split_sdf):
+      wic:
+        graphviz:
+          label: Split Ligands into\nSeparate Files
+    (6, docking_stability.wic):
+      wic:
+        # Scattering changes the input/output types and thus creates a barrier to inlineing.
+        inlineable: False
+
+# Beware 0 vs 1 -based indexing! JavaScript (and thus CWL) uses 0-based indices.
+# If you accidentally use 1-based indices, the last array access will be out of
+# bounds and return null, which causes the following nasty error message:
+
+# Cannot make job: Expression evaluation error:
+# Expecting value: line 1 column 1 (char 0)
+# script was:
+# ...
+#     "index": 2
+# };
+# var self = [
+# ...
+# ];
+# var runtime = {
+#     "tmpdir": null,
+#     "outdir": null
+# };
+# (function(){return ((self[inputs.__index__]));})()
+# stdout was: 'undefined'
+# stderr was: ''