Adjusting command format for design_macrocyclic_binder.sh and design_macrocyclic_monomer.sh

Author: woodsh17

examples/design_macrocyclic_binder.sh

@@ -1,18 +1,15 @@
 #!/bin/bash
 
-prefix=./outputs/diffused_binder_cyclic2
+# Note that in the example below the indices in the
+# input_pdbs/7zkr_GABARAP.pdb file have been shifted
+# by +2 in chain A relative to pdbID 7zkr.
 
-# Note that the indices in this pdb file have been 
-# shifted by +2 in chain A relative to pdbID 7zkr.
-pdb='./input_pdbs/7zkr_GABARAP.pdb'
-
-num_designs=10
-script="../scripts/run_inference.py"
-$script --config-name base \
-inference.output_prefix=$prefix \
-inference.num_designs=$num_designs \
+../scripts/run_inference.py \
+--config-name base \
+inference.output_prefix=example_outputs/diffused_binder_cyclic2 \
+inference.num_designs=10 \
 'contigmap.contigs=[12-18 A3-117/0]' \
-inference.input_pdb=$pdb \
+inference.input_pdb=/input_pdbs/7zkr_GABARAP.pdb \
 inference.cyclic=True \
 diffuser.T=50 \
 inference.cyc_chains='a' \

examples/design_macrocyclic_monomer.sh

@@ -1,17 +1,15 @@
 #!/bin/bash 
 
-prefix=./outputs/uncond_cycpep
-# Note that the indices in this pdb file have been 
-# shifted by +2 in chain A relative to pdbID 7zkr.
-pdb='./input_pdbs/7zkr_GABARAP.pdb'
+# Note that in the example below the indices in the 
+# input_pdbs/7zkr_GABARAP.pdb file have been shifted
+# by +2 in chain A relative to pdbID 7zkr.
 
-num_designs=10
-script="../scripts/run_inference.py"
-$script --config-name base \
-inference.output_prefix=$prefix \
-inference.num_designs=$num_designs \
+../scripts/run_inference.py \
+--config-name base \
+inference.output_prefix=example_outputs/uncond_cycpep \
+inference.num_designs=10 \
 'contigmap.contigs=[12-18]' \
-inference.input_pdb=$pdb \
+inference.input_pdb=input_pdbs/7zkr_GABARAP.pdb \
 inference.cyclic=True \
 diffuser.T=50 \
 inference.cyc_chains='a'