Naming the complex PDB file after the original PDB file. This greatly…

… simplifies the workflow.

snakefiles/antibody-complexes.smk

@@ -1,33 +1,27 @@
-def complexes():
+def complexes(wildcards):
     from glob import glob
-    from subprocess import Popen, PIPE
-    complexes = []
-    for pdbid in glob_wildcards(output_dir + "vorocontacts/{pdbid}.tab").pdbid:
-        child = Popen('bin/contact-graph {}vorocontacts/{}.tab --pdb {}pdb/P0DTC2/{}.pdb --output-complexes --most-contacts'.format(output_dir, pdbid, output_dir, pdbid), stdin=PIPE, stdout=PIPE, stderr=PIPE, shell=True, text=True, env={'PYTHONPATH': '.'})
-        child.stdin.close()
-        complexes += [pdbid + '_' + x.strip() for x in child.stdout.readlines()]
-    return complexes
+    checkpoint_output = checkpoints.download_pdb_all.get(**wildcards).output[0]
+    return expand(output_dir + "pdb/antibodies/complexes/{pdbid}.pdb", pdbid=glob_wildcards(checkpoint_output + '/{pdbid}.pdb').pdbid)
 
 rule extract_complexes:
     input:
-        expand(output_dir + "pdb/antibodies/complexes/{complex}.pdb", complex=complexes())
-    output:
-        output_dir + "pdb/antibodies/complexes/out.log"
-    shell:
-        "touch {output}"
+        complexes
 
 rule extract_complex:
     input:
-        output_dir + "pdb/P0DTC2/{pdbid}.pdb"
+        pdb = output_dir + "pdb/P0DTC2/{pdbid}.pdb",
+        vorocontacts = output_dir + "vorocontacts/{pdbid}.tab"
     output:
-        output_dir + "pdb/antibodies/complexes/{pdbid}_{chains}.pdb"
+        output_dir + "pdb/antibodies/complexes/{pdbid}.pdb"
     singularity:
         "container.sif"
     shell:
         """
         mkdir --parents $(dirname {output})
-        bin/pdb_select --chain $(echo {wildcards.chains} | cut -c 1) --chain $(echo {wildcards.chains} | cut -c 2) --chain $(echo {wildcards.chains} | cut -c 3) {input} \
-            | PYTHONPATH=. bin/pdb_rename_chains --map $(echo {wildcards.chains} | cut -c 1):A --map $(echo {wildcards.chains} | cut -c 2):H --map $(echo {wildcards.chains} | cut -c 3):L > {output}
+        COMPLEX=$(PYTHONPATH=. bin/contact-graph {input.vorocontacts} --pdb {input.pdb} --output-complexes --most-contacts)
+        bin/pdb_select --chain $(echo $COMPLEX | cut -c 1) --chain $(echo $COMPLEX | cut -c 2) --chain $(echo $COMPLEX | cut -c 3) {input.pdb} \
+            | PYTHONPATH=. bin/pdb_rename_chains --map $(echo $COMPLEX | cut -c 1):A --map $(echo $COMPLEX | cut -c 2):H --map $(echo $COMPLEX | cut -c 3):L > {output}
+        echo COMPLX $COMPLEX >> {output}
         """
 
 rule renumbered: