CCPBioSim · harryswift01 · Sep 18, 2026 · Sep 17, 2026 · Sep 18, 2026
diff --git a/.gitignore b/.gitignore
@@ -49,10 +49,10 @@
 *.app
 
 # SIST build outputs
-trans_three/qsidd
-trans_compete/qsidd
-trans_three/depend
-trans_compete/depend
+src/trans_three/qsidd
+src/trans_compete/qsidd
+src/trans_three/depend
+src/trans_compete/depend
 
 # Debug information files
 *.dwo

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -3,37 +3,37 @@ project(code)
 
 set(CMAKE_CXX_STANDARD 14)
 
-include_directories(trans_compete)
-include_directories(trans_three)
+include_directories(src/trans_compete)
+include_directories(src/trans_three)
 
 add_executable(code
-        trans_compete/G_x.cpp
-        trans_compete/G_x.h
-        trans_compete/qsidd.cpp
-        trans_compete/SIDD_1R.cpp
-        trans_compete/SIDD_1R.h
-        trans_compete/SIDD_2R.cpp
-        trans_compete/SIDD_2R.h
-        trans_compete/SIDD_3R.cpp
-        trans_compete/SIDD_3R.h
-        trans_compete/SIDD_4R.cpp
-        trans_compete/SIDD_4R.h
-        trans_compete/SIDD_Base.cpp
-        trans_compete/SIDD_Base.h
-        trans_compete/stat_1R.cpp
-        trans_compete/stat_1R.h
-        trans_three/G_x.cpp
-        trans_three/G_x.h
-        trans_three/qsidd.cpp
-        trans_three/SIDD_1R.cpp
-        trans_three/SIDD_1R.h
-        trans_three/SIDD_2R.cpp
-        trans_three/SIDD_2R.h
-        trans_three/SIDD_3R.cpp
-        trans_three/SIDD_3R.h
-        trans_three/SIDD_4R.cpp
-        trans_three/SIDD_4R.h
-        trans_three/SIDD_Base.cpp
-        trans_three/SIDD_Base.h
-        trans_three/stat_1R.cpp
-        trans_three/stat_1R.h)
+        src/trans_compete/G_x.cpp
+        src/trans_compete/G_x.h
+        src/trans_compete/qsidd.cpp
+        src/trans_compete/SIDD_1R.cpp
+        src/trans_compete/SIDD_1R.h
+        src/trans_compete/SIDD_2R.cpp
+        src/trans_compete/SIDD_2R.h
+        src/trans_compete/SIDD_3R.cpp
+        src/trans_compete/SIDD_3R.h
+        src/trans_compete/SIDD_4R.cpp
+        src/trans_compete/SIDD_4R.h
+        src/trans_compete/SIDD_Base.cpp
+        src/trans_compete/SIDD_Base.h
+        src/trans_compete/stat_1R.cpp
+        src/trans_compete/stat_1R.h
+        src/trans_three/G_x.cpp
+        src/trans_three/G_x.h
+        src/trans_three/qsidd.cpp
+        src/trans_three/SIDD_1R.cpp
+        src/trans_three/SIDD_1R.h
+        src/trans_three/SIDD_2R.cpp
+        src/trans_three/SIDD_2R.h
+        src/trans_three/SIDD_3R.cpp
+        src/trans_three/SIDD_3R.h
+        src/trans_three/SIDD_4R.cpp
+        src/trans_three/SIDD_4R.h
+        src/trans_three/SIDD_Base.cpp
+        src/trans_three/SIDD_Base.h
+        src/trans_three/stat_1R.cpp
+        src/trans_three/stat_1R.h)
diff --git a/conda-recipe/build.sh b/conda-recipe/build.sh
@@ -1,16 +1,16 @@
 #!/usr/bin/env bash
 set -euxo pipefail
 
-make -C trans_three clean
-make -C trans_three
+make -C src/trans_three clean
+make -C src/trans_three
 
-make -C trans_compete clean
-make -C trans_compete
+make -C src/trans_compete clean
+make -C src/trans_compete
 
 install -d "${PREFIX}/bin"
 install -d "${PREFIX}/libexec/sist"
-install -d "${PREFIX}/libexec/sist/trans_three"
-install -d "${PREFIX}/libexec/sist/trans_compete"
+install -d "${PREFIX}/libexec/sist/src/trans_three"
+install -d "${PREFIX}/libexec/sist/src/trans_compete"
 
 install -m 755 \
     master.pl \
@@ -21,12 +21,12 @@ install -m 755 \
     "${PREFIX}/libexec/sist/IR_finder.pl"
 
 install -m 755 \
-    trans_three/qsidd \
-    "${PREFIX}/libexec/sist/trans_three/qsidd"
+    src/trans_three/qsidd \
+    "${PREFIX}/libexec/sist/src/trans_three/qsidd"
 
 install -m 755 \
-    trans_compete/qsidd \
-    "${PREFIX}/libexec/sist/trans_compete/qsidd"
+    src/trans_compete/qsidd \
+    "${PREFIX}/libexec/sist/src/trans_compete/qsidd"
 
 cat > "${PREFIX}/bin/sist" << 'EOF'
 #!/usr/bin/env bash

diff --git a/docs/source/development.rst b/docs/source/development.rst
@@ -11,10 +11,10 @@ Build the C++ components from the repository root:
 
 .. code-block:: bash
 
-   make -C trans_three clean
-   make -C trans_three
-   make -C trans_compete clean
-   make -C trans_compete
+   make -C src/trans_three clean
+   make -C src/trans_three
+   make -C src/trans_compete clean
+   make -C src/trans_compete
 
 The Makefiles are also used by the Conda build and accept the compiler and
 linker settings supplied by the Conda toolchain.

diff --git a/docs/source/installation.rst b/docs/source/installation.rst
@@ -59,8 +59,8 @@ Build both C++ components from the repository root:
 
 .. code-block:: bash
 
-   make -C trans_three
-   make -C trans_compete
+   make -C src/trans_three
+   make -C src/trans_compete
 
 The source-tree pipeline can then be run with:
 

diff --git a/docs/source/source-usage.rst b/docs/source/source-usage.rst
@@ -19,11 +19,11 @@ Source components
    repeat information required for cruciform calculations, including start
    positions, possible extrusion lengths, and cruciform formation energies.
 
-``trans_three/``
+``src/trans_three/``
    C++ implementation for analysing strand separation, Z-DNA, and cruciform
    extrusion independently.
 
-``trans_compete/``
+``src/trans_compete/``
    C++ implementation for analysing competition between strand separation,
    Z-DNA, and cruciform extrusion.
 
@@ -75,13 +75,13 @@ Compile the C++ implementations with:
 
 .. code-block:: bash
 
-   make -C trans_three
-   make -C trans_compete
+   make -C src/trans_three
+   make -C src/trans_compete
 
 After compilation, each directory contains a ``qsidd`` executable.
 
 Running ``qsidd`` without the required arguments displays its detailed usage
-information. For example, from ``trans_three``:
+information. For example, from ``src/trans_three``:
 
 .. code-block:: bash
 
@@ -99,13 +99,13 @@ Run ``IR_finder.pl`` first:
 
    perl IR_finder.pl temperature shape sequence_file
 
-For a cruciform calculation using ``trans_three``:
+For a cruciform calculation using ``src/trans_three``:
 
 .. code-block:: bash
 
    ./qsidd -C -X "string" -f sequence_file
 
-For a competition calculation using ``trans_compete``:
+For a competition calculation using ``src/trans_compete``:
 
 .. code-block:: bash
 

diff --git a/master.pl b/master.pl
@@ -23,8 +23,8 @@
 "Script analyzes superhelically induced structural transition probabilities for each base pair.\n".
 "Algorithm types: M (melting), Z (Z-DNA), C (cruciforms), and A (competition between all three).\n".
 "Sequence file will be converted to the format required by the algorithm.\n".
-"Code in directory trans_three/ will handle M, Z, and C algorithm types.\n".
-"Code in directory trans_compete/ will handle A algorithm type.\n".
+"Code in directory src/trans_three/ will handle M, Z, and C algorithm types.\n".
+"Code in directory src/trans_compete/ will handle A algorithm type.\n".
 "For algorithm type options -a C and -a A user will need an Inverted Repeat Finder (IRF) executable compatible with user's operating system.\n".
 "IRF download page: http://tandem.bu.edu/irf/irf.download.html.\n".
 "Selected output will be printed to the screen.\n\n".
@@ -73,8 +73,8 @@
 
 
 my @name = split("/",$file);
-my $single_exe = "$RealBin/trans_three/qsidd";
-my $compete_exe = "$RealBin/trans_compete/qsidd";
+my $single_exe = "$RealBin/src/trans_three/qsidd";
+my $compete_exe = "$RealBin/src/trans_compete/qsidd";
 
 my $output_IR;
 if ($trans eq "M") {

diff --git a/trans_compete/G_x.cpp → src/trans_compete/G_x.cpp b/trans_compete/G_x.cpp → src/trans_compete/G_x.cpp
diff --git a/trans_compete/G_x.h → src/trans_compete/G_x.h b/trans_compete/G_x.h → src/trans_compete/G_x.h
diff --git a/trans_compete/Makefile → src/trans_compete/Makefile b/trans_compete/Makefile → src/trans_compete/Makefile
diff --git a/trans_compete/SIDD_1R.cpp → src/trans_compete/SIDD_1R.cpp b/trans_compete/SIDD_1R.cpp → src/trans_compete/SIDD_1R.cpp
diff --git a/trans_compete/SIDD_1R.h → src/trans_compete/SIDD_1R.h b/trans_compete/SIDD_1R.h → src/trans_compete/SIDD_1R.h
diff --git a/trans_compete/SIDD_2R.cpp → src/trans_compete/SIDD_2R.cpp b/trans_compete/SIDD_2R.cpp → src/trans_compete/SIDD_2R.cpp
diff --git a/trans_compete/SIDD_2R.h → src/trans_compete/SIDD_2R.h b/trans_compete/SIDD_2R.h → src/trans_compete/SIDD_2R.h
diff --git a/trans_compete/SIDD_3R.cpp → src/trans_compete/SIDD_3R.cpp b/trans_compete/SIDD_3R.cpp → src/trans_compete/SIDD_3R.cpp
diff --git a/trans_compete/SIDD_3R.h → src/trans_compete/SIDD_3R.h b/trans_compete/SIDD_3R.h → src/trans_compete/SIDD_3R.h
diff --git a/trans_compete/SIDD_4R.cpp → src/trans_compete/SIDD_4R.cpp b/trans_compete/SIDD_4R.cpp → src/trans_compete/SIDD_4R.cpp
diff --git a/trans_compete/SIDD_4R.h → src/trans_compete/SIDD_4R.h b/trans_compete/SIDD_4R.h → src/trans_compete/SIDD_4R.h
diff --git a/trans_compete/SIDD_Base.cpp → src/trans_compete/SIDD_Base.cpp b/trans_compete/SIDD_Base.cpp → src/trans_compete/SIDD_Base.cpp
diff --git a/trans_compete/SIDD_Base.h → src/trans_compete/SIDD_Base.h b/trans_compete/SIDD_Base.h → src/trans_compete/SIDD_Base.h
diff --git a/trans_compete/qsidd.cpp → src/trans_compete/qsidd.cpp b/trans_compete/qsidd.cpp → src/trans_compete/qsidd.cpp
diff --git a/trans_compete/stat_1R.cpp → src/trans_compete/stat_1R.cpp b/trans_compete/stat_1R.cpp → src/trans_compete/stat_1R.cpp
diff --git a/trans_compete/stat_1R.h → src/trans_compete/stat_1R.h b/trans_compete/stat_1R.h → src/trans_compete/stat_1R.h
diff --git a/trans_three/G_x.cpp → src/trans_three/G_x.cpp b/trans_three/G_x.cpp → src/trans_three/G_x.cpp
diff --git a/trans_three/G_x.h → src/trans_three/G_x.h b/trans_three/G_x.h → src/trans_three/G_x.h
diff --git a/trans_three/Makefile → src/trans_three/Makefile b/trans_three/Makefile → src/trans_three/Makefile
diff --git a/trans_three/SIDD_1R.cpp → src/trans_three/SIDD_1R.cpp b/trans_three/SIDD_1R.cpp → src/trans_three/SIDD_1R.cpp
diff --git a/trans_three/SIDD_1R.h → src/trans_three/SIDD_1R.h b/trans_three/SIDD_1R.h → src/trans_three/SIDD_1R.h
diff --git a/trans_three/SIDD_2R.cpp → src/trans_three/SIDD_2R.cpp b/trans_three/SIDD_2R.cpp → src/trans_three/SIDD_2R.cpp
diff --git a/trans_three/SIDD_2R.h → src/trans_three/SIDD_2R.h b/trans_three/SIDD_2R.h → src/trans_three/SIDD_2R.h
diff --git a/trans_three/SIDD_3R.cpp → src/trans_three/SIDD_3R.cpp b/trans_three/SIDD_3R.cpp → src/trans_three/SIDD_3R.cpp
diff --git a/trans_three/SIDD_3R.h → src/trans_three/SIDD_3R.h b/trans_three/SIDD_3R.h → src/trans_three/SIDD_3R.h
diff --git a/trans_three/SIDD_4R.cpp → src/trans_three/SIDD_4R.cpp b/trans_three/SIDD_4R.cpp → src/trans_three/SIDD_4R.cpp
diff --git a/trans_three/SIDD_4R.h → src/trans_three/SIDD_4R.h b/trans_three/SIDD_4R.h → src/trans_three/SIDD_4R.h
diff --git a/trans_three/SIDD_Base.cpp → src/trans_three/SIDD_Base.cpp b/trans_three/SIDD_Base.cpp → src/trans_three/SIDD_Base.cpp
diff --git a/trans_three/SIDD_Base.h → src/trans_three/SIDD_Base.h b/trans_three/SIDD_Base.h → src/trans_three/SIDD_Base.h
diff --git a/trans_three/qsidd.cpp → src/trans_three/qsidd.cpp b/trans_three/qsidd.cpp → src/trans_three/qsidd.cpp
diff --git a/trans_three/stat_1R.cpp → src/trans_three/stat_1R.cpp b/trans_three/stat_1R.cpp → src/trans_three/stat_1R.cpp
diff --git a/trans_three/stat_1R.h → src/trans_three/stat_1R.h b/trans_three/stat_1R.h → src/trans_three/stat_1R.h
diff --git a/tests/conftest.py b/tests/conftest.py
@@ -87,7 +87,7 @@ def build_sist(
         ),
     )
 
-    for directory in ("trans_three", "trans_compete"):
+    for directory in ("src/trans_three", "src/trans_compete"):
         clean_result = run_command(
             ["make", "-C", directory, "clean"],
             cwd=working_copy,