add .sh examples, gabarap pdb, import numpy

Author: davidcjuergens

examples/design_macrocyclic_binder.sh

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+#!/bin/bash
+
+prefix=./outputs/diffused_binder_cyclic2
+
+# 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=$num_designs \
+'contigmap.contigs=[12-18 A3-117/0]' \
+inference.input_pdb=$pdb \
+inference.cyclic=True \
+diffuser.T=50 \
+inference.cyc_chains='a' \
+ppi.hotspot_res=[\'A51\',\'A52\',\'A50\',\'A48\',\'A62\',\'A65\'] \

examples/design_macrocyclic_monomer.sh

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+#!/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'
+
+num_designs=10
+script="../scripts/run_inference.py"
+$script --config-name base \
+inference.output_prefix=$prefix \
+inference.num_designs=$num_designs \
+'contigmap.contigs=[12-18]' \
+inference.input_pdb=$pdb \
+inference.cyclic=True \
+diffuser.T=50 \
+inference.cyc_chains='a'