update regex pattern for diff check

tests/check_intermediate.sh

@@ -29,13 +29,13 @@ for path_to_cif in Resources/KnownCIFs/*.cif; do
     echo -e "${GREEN}CHECKING${NC} $cif..."
     output_path="Output/$cif"
     known_path="Resources/KnownCIFs/Outputs/$cif"
-    # In order, a-zA-Z# -> a-zA-Z, NODE# -> "", Lines with # -> "", # -> 1 decimal place
-    pattern="s/([a-zA-Z]+)[0-9]+/\1/g; s/NODE [0-9]+/NODE/g; s/^[ \t]*#.*//g; s/([0-9]+)(.[0-9])?[0-9]+/\1\2/g"
+    # In order, a-zA-Z# -> a-zA-Z, NODE# -> "", Lines with # -> "", # -> 1 decimal place, #_#+ -> "", condense whitespace
+    pattern="s/([a-zA-Z]+)[0-9]+/\1/g; s/NODE [0-9]+/NODE/g; s/^[ \t]*#.*//g; s/([0-9]+)(.[0-9])?[0-9]+/\1\2/g; s/[0-9]_[0-9]+//g; s/[ \t]+/\t/g"
     # Check orig_mol.cif
-    diff -b <(sed -E "$pattern" $known_path/orig_mol.cif | sort) <(sed -E "$pattern" $output_path/orig_mol.cif | sort) > /dev/null
+    diff -yw <(sed -E "$pattern" $known_path/orig_mol.cif | sort) <(sed -E "$pattern" $output_path/orig_mol.cif | sort) > /dev/null
     if [[ $? -ne 0 ]]; then
         echo -e "${RED}WARNING:${NC} orig_mol.cif is different" 
-        diff -yb --suppress-common-lines <(sed -E "$pattern" $known_path/orig_mol.cif | sort) <(sed -E "$pattern" $output_path/orig_mol.cif | sort) | colordiff
+        diff -yw --suppress-common-lines <(sed -E "$pattern" $known_path/orig_mol.cif | sort) <(sed -E "$pattern" $output_path/orig_mol.cif | sort) | colordiff
         mkdir -p Mismatch/$cif/
         cp -u Output/$cif/orig_mol.cif Mismatch/$cif/orig_mol.cif
     fi
@@ -44,15 +44,15 @@ for path_to_cif in Resources/KnownCIFs/*.cif; do
         # Currently only checks CIF files
         for path_to_file in $path_to_dir/*.cif; do
             file="$(basename $path_to_file)"
-            diff -b <(sed -E "$pattern" $path_to_file | sort) <(sed -E "$pattern" $output_path/$dir/$file | sort) > /dev/null
+            diff -yw <(sed -E "$pattern" $path_to_file | sort) <(sed -E "$pattern" $output_path/$dir/$file | sort) > /dev/null
             exit_code="$?"
             if [[ $exit_code -ne 0 ]]; then
                 echo -e "${YELLOW}INVESTIGATING:${NC} $cif/$dir/$file may be different..."
                 #python tests/check_file.py "$path_to_file" "$output_path/$dir/$file"
                 bin/compare "$path_to_file" "$output_path/$dir/$file"
                 if [[ $? -ne 0 ]]; then
                     echo -e "${RED}WARNING:${NC} $cif/$dir/$file is different"
-                    diff -yb --suppress-common-lines <(sed -E "$pattern" $path_to_file | sort) <(sed -E "$pattern" $output_path/$dir/$file | sort) | colordiff
+                    diff -yw --suppress-common-lines <(sed -E "$pattern" $path_to_file | sort) <(sed -E "$pattern" $output_path/$dir/$file | sort) | colordiff
                     mkdir -p Mismatch/$cif/$dir/
                     cp -u Output/$cif/$dir/$file Mismatch/$cif/$dir/$file
                 else