From 56202cf1b71932adf043dddd12566f42b8f6d1c2 Mon Sep 17 00:00:00 2001
From: Alex Morehead <acmwhb@missouri.edu>
Date: Tue, 13 Aug 2024 15:34:06 -0500
Subject: [PATCH] Remove PWD

---
 scripts/build_inference_script.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/scripts/build_inference_script.py b/scripts/build_inference_script.py
index 92eac57..28d1aa8 100644
--- a/scripts/build_inference_script.py
+++ b/scripts/build_inference_script.py
@@ -287,22 +287,22 @@ def build_inference_script(
         # Prepare input files
         if "prepare_input" in commands:
             diffdock_casp15_input_suffix = (
-                " input_data_dir='$PWD'/data/casp15_set/targets input_protein_structure_dir='$PWD'/data/casp15_set/casp15_holo_aligned_predicted_structures"
+                " input_data_dir=data/casp15_set/targets input_protein_structure_dir=data/casp15_set/casp15_holo_aligned_predicted_structures"
                 if method == "diffdock" and dataset == "casp15"
                 else ""
             )
             dynamicbind_casp15_input_suffix = (
-                " input_data_dir='$PWD'/data/casp15_set/targets"
+                " input_data_dir=data/casp15_set/targets"
                 if method == "dynamicbind" and dataset == "casp15"
                 else ""
             )
             neuralplexer_casp15_input_suffix = (
-                " input_data_dir='$PWD'/data/casp15_set/targets input_receptor_structure_dir='$PWD'/data/casp15_set/casp15_holo_aligned_predicted_structures"
+                " input_data_dir=data/casp15_set/targets input_receptor_structure_dir=data/casp15_set/casp15_holo_aligned_predicted_structures"
                 if method == "neuralplexer" and dataset == "casp15"
                 else ""
             )
             rfaa_casp15_input_suffix = (
-                " input_data_dir='$PWD'/data/casp15_set/targets"
+                " input_data_dir=data/casp15_set/targets"
                 if method == "rfaa" and dataset == "casp15"
                 else ""
             )
@@ -325,7 +325,7 @@ def build_inference_script(
                 " batch_size=1" if method == "diffdock" and dataset == "casp15" else ""
             )
             dynamicbind_casp15_inference_suffix = (
-                " batch_size=1 input_data_dir='$PWD'/data/casp15_set/casp15_holo_aligned_predicted_structures"
+                " batch_size=1 input_data_dir=data/casp15_set/casp15_holo_aligned_predicted_structures"
                 if method == "dynamicbind" and dataset == "casp15"
                 else ""
             )