codebase cleanup, repo reorganization & SambVca cross-validation

- Format with ruff, fix bare excepts, boolean comparisons & dead code
- Rename dbstep/examples/ to dbstep/data/, move images/ and sterimol.f
- Remove DBLOOP, mcgowan.csv (data moved to constants.py)
- Update H Bondi radius from 1.20 to 1.09 Å
- Add SambVca 2.1 cross-validation tests (21 molecules, tolerance 0.2%)
- Add .claude/ to .gitignore

Author: bobbypaton

.gitignore

@@ -28,3 +28,6 @@ htmlcov/
 # Tools
 .mypy_cache/
 .ruff_cache/
+
+# Claude Code
+.claude/

CLAUDE.md

@@ -17,7 +17,7 @@ DBSTEP (DFT-Based Steric Parameters) is a Python package for computing steric pa
   - `writer.py` — Output formatting and file writing
   - `__init__.py` — Package init, `__version__`, `__all__`
   - `__main__.py` — Module entry point for `python -m dbstep`
-  - `examples/` — Example molecular structure files (xyz format)
+  - `data/` — Benchmark molecular structure files (xyz format)
 - `tests/` — Pytest test suite
   - `test_dbstep.py` — Sterimol parameter validation against Verloop's reference values
   - `test_calculator.py` — Unit tests for rotation/geometry math

README.md

@@ -1,4 +1,4 @@
-![DBSTEP](DBSTEP_banner.png)
+![DBSTEP](images/DBSTEP_banner.png)
 ===
 
 # DBSTEP
@@ -37,7 +37,7 @@ Calculate Sterimol parameters<sup>1</sup> (L, Bmin, Bmax), %Buried Volume<sup>2<
 
 ## Requirements & Dependencies
 * Python 3.9 or greater
-* Non-standard dependencies will be installed along with DBSTEP, but include [numpy](https://numpy.org/), [numba](https://numba.pydata.org/), [scipy](https://www.scipy.org/), and [cclib](https://cclib.github.io/).
+* Non-standard dependencies will be installed along with DBSTEP, but include [numpy](https://numpy.org/), [scipy](https://www.scipy.org/), and [cclib](https://cclib.github.io/).
 
 ## Install
 
@@ -111,7 +111,7 @@ H	0.76	2.03	-1.25
 
 A visualization of these parameters can be shown in the program PyMOL using the two output files created by DBSTEP, showing the L parameter in blue, Bmin parameter in green and Bmax parameter in red. 
 
-![Example1](Example1.png)
+![Example1](images/Example1.png)
 
 2. Sterimol2Vec Parameters for Ph
 
@@ -133,7 +133,7 @@ A visualization of these parameters can be shown in the program PyMOL using the
 ```
 
  Displayed in PyMOL, each new Bmin and Bmax axis is added along the L axis. 
- ![Example2](Example2.png)
+ ![Example2](images/Example2.png)
 
 
 3. Percent Buried Volume 
@@ -147,7 +147,7 @@ A visualization of these parameters can be shown in the program PyMOL using the
  ```
 
  For percent buried volume, the PyMOL script will overlay an appropriate sized sphere where measurement took place.
-  ![Example3](Example3.png)
+  ![Example3](images/Example3.png)
 
 4. Vol2Vec Parameters