Get data for AF2 2.1 done.

run_af2/src/run_af2/run_singularity.py

@@ -195,11 +195,12 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     model_preset="monomer",
     is_prokaryote_list=None,
     af2_image_file=None,
-    # "/export/soft/singularity-containers/alphafold",
+    # af2_image_dir="/export/soft/singularity-containers/alphafold",
     af2_image_dir="/scicore/home/schwede/GROUP/alphafold_data/",
     snglrty_bin="/usr/bin/singularity",
     tmpdir_var="TMPDIR",
-    data_dir="/scicore/data/managed/AF2params/frozen_210805T171956/",
+    # data_dir="/scicore/data/managed/AF2params/frozen_210805T171956/",
+    data_dir="/scicore/home/schwede/GROUP/alphafold_data/",
     uniref90_database_path="/scicore/data/managed/UniProt/latest/uniref/"
     + "uniref90/uniref90.fasta",
     mgnify_database_path="/scicore/data/managed/MGnify/frozen_210805T103002/"
@@ -210,13 +211,14 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     + "frozen_210812T135116/bfd-first_non_consensus_sequences.fasta",
     uniclust30_database_path="/scicore/data/managed/Uniclust/"
     + "frozen_181015T170110/uniclust30_2018_08/uniclust30_2018_08",
-    uniprot_database_path="/scicore/home/schwede/scicore/home/schwede/GROUP/"
-    + "alphafold_data/uniprot/uniprot.fasta",
+    uniprot_database_path="/scicore/home/schwede/GROUP/alphafold_data/uniprot/"
+    + "uniprot.fasta",
     pdb70_database_path="/scicore/data/managed/PDB70/frozen_210805T142857/pdb70",
-    pdb_seqres_database_path="/scicore/home/schwede/scicore/home/schwede/GROUP/"
-    + "alphafold_data/pdb_seqres/pdb_seqres.txt",
-    template_mmcif_dir="/scicore/data/managed/PDB/latest/data/structures/all/"
-    + "mmcif_files/",
+    pdb_seqres_database_path="/scicore/home/schwede/GROUP/alphafold_data/"
+    + "pdb_seqres/pdb_seqres.txt",
+    # template_mmcif_dir="/scicore/data/managed/PDB/latest/data/structures/all/"
+    # + "mmcif_files/",
+    template_mmcif_dir="/scicore/home/schwede/GROUP/alphafold_data/pdb_mmcif",
     obsolete_pdbs_path="/scicore/data/managed/PDB/latest/data/status/"
     + "obsolete.dat",
 ):