Specific versions, add testing

oxpig · Jul 26, 2024 · a7a7a06 · a7a7a06
1 parent 8f528b5
commit a7a7a06
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diff --git a/requirements.txt b/requirements.txt
@@ -2,5 +2,5 @@ torch_geometric==2.4.0
 biopython==1.83
 biotite==0.38
 pygam==0.9.*
-numpy
-pandas
+numpy==1.26.*
+pandas==2.*
diff --git a/testing/test.sh b/testing/test.sh
@@ -0,0 +1,57 @@
+#!/bin/bash
+set -e
+set -o nounset
+set -o pipefail
+if [[ ${TRACE-0} == "1" ]]; then
+  set -o xtrace
+fi
+
+NUM_TESTS=7
+
+# Run AntiFold on single PDB/CIF file
+# Nb: Assumes first chain heavy, second chain light
+echo -e "\n### Test 1 / $NUM_TESTS ###"
+python antifold/main.py \
+    --pdb_file data/pdbs/6y1l_imgt.pdb
+
+# Antibody-antigen complex
+echo -e "\n### Test 2 / $NUM_TESTS ###"
+python antifold/main.py \
+    --pdb_file data/antibody_antigen/3hfm.pdb \
+    --heavy_chain H \
+    --light_chain L \
+    --antigen_chain Y
+
+# Nanobody or single-chain
+echo -e "\n### Test 3 / $NUM_TESTS ###"
+python antifold/main.py \
+    --pdb_file data/nanobody/8oi2_imgt.pdb \
+    --nanobody_chain B
+
+# Folder of PDB/CIFs
+# Nb: Assumes first chain heavy, second light
+echo -e "\n### Test 4 / $NUM_TESTS ###"
+python antifold/main.py \
+    --pdb_dir data/pdbs
+
+# Specify chains to run in a CSV file (e.g. antibody-antigen complex)
+echo -e "\n### Test 5 / $NUM_TESTS ###"
+python antifold/main.py \
+    --pdb_dir data/antibody_antigen \
+    --pdbs_csv data/antibody_antigen.csv
+
+# Sample sequences 10x
+echo -e "\n### Test 6 / $NUM_TESTS ###"
+python antifold/main.py \
+    --pdb_file data/pdbs/6y1l_imgt.pdb \
+    --heavy_chain H \
+    --light_chain L \
+    --num_seq_per_target 10 \
+    --sampling_temp "0.2" \
+    --regions "CDR1 CDR2 CDR3"
+
+# Run all chains with ESM-IF1 model weights
+echo -e "\n### Test 7 / $NUM_TESTS ###"
+python antifold/main.py \
+    --pdb_dir data/pdbs \
+    --esm_if1_mode