From 94b7a6058c3cb2377d8e4ded943ad1a07fe5def7 Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 21 Sep 2022 15:53:06 -0400
Subject: [PATCH 01/11] basic idea implemented - add tests

---
 py2sambvca/py2sambvca.py            | 112 ++--------------------------
 py2sambvca/radii_tables/__init__.py |   1 +
 py2sambvca/radii_tables/default.py  | 105 ++++++++++++++++++++++++++
 3 files changed, 112 insertions(+), 106 deletions(-)
 create mode 100644 py2sambvca/radii_tables/__init__.py
 create mode 100644 py2sambvca/radii_tables/default.py

diff --git a/py2sambvca/py2sambvca.py b/py2sambvca/py2sambvca.py
index 72f1c4a..f66df92 100644
--- a/py2sambvca/py2sambvca.py
+++ b/py2sambvca/py2sambvca.py
@@ -5,6 +5,9 @@
 from typing import List
 from warnings import warn
 
+from py2sambvca.radii_tables import (
+    default_table,
+)
 
 class py2sambvca():
     """
@@ -44,7 +47,9 @@ def __init__(self,
                  write_surf_files: int = 1,
                  path_to_sambvcax: str = "sambvca.exe",
                  working_dir: str = os.getcwd(),
-                 verbose: int = 1):
+                 verbose: int = 1,
+                 radii_table: str = "default",
+                 ):
         """
         Wrapper class for py2sambvca functions.
 
@@ -482,108 +487,3 @@ def run(self):
         return self.total_results, self.quadrant_results, self.octant_results
 
 
-radii_table = [
-    'H       1.28\n',
-    'HE      1.64\n',
-    'LI      2.13\n',
-    'BE      1.79\n',
-    'B       2.25\n',
-    'C       1.99\n',
-    'N       1.81\n',
-    'O       1.78\n',
-    'F       1.72\n',
-    'NE      1.80\n',
-    'NA      2.66\n',
-    'MG      2.02\n',
-    'AL      2.15\n',
-    'SI      2.46\n',
-    'P       2.11\n',
-    'S       2.11\n',
-    'CL      2.05\n',
-    'AR      2.20\n',
-    'K       3.22\n',
-    'CA      2.70\n',
-    'SC      2.52\n',
-    'TI      2.47\n',
-    'V       2.42\n',
-    'CR      2.41\n',
-    'MN      2.40\n',
-    'FE      2.39\n',
-    'CO      2.34\n',
-    'NI      1.91\n',
-    'CU      1.64\n',
-    'ZN      1.63\n',
-    'GA      2.19\n',
-    'GE      2.47\n',
-    'AS      2.16\n',
-    'SE      2.22\n',
-    'BR      2.16\n',
-    'KR      2.36\n',
-    'RB      3.55\n',
-    'SR      2.91\n',
-    'Y       2.71\n',
-    'ZR      2.61\n',
-    'NB      2.55\n',
-    'MO      2.54\n',
-    'TC      2.53\n',
-    'RU      2.49\n',
-    'RH      2.46\n',
-    'PD      1.91\n',
-    'AG      2.01\n',
-    'CD      1.85\n',
-    'IN      2.26\n',
-    'SN      2.54\n',
-    'SB      2.41\n',
-    'TE      2.41\n',
-    'I       2.32\n',
-    'XE      2.53\n',
-    'CS      4.01\n',
-    'BA      3.14\n',
-    'LA      2.84\n',
-    'CE      2.83\n',
-    'PR      2.81\n',
-    'ND      2.80\n',
-    'PM      2.78\n',
-    'SM      2.76\n',
-    'EU      2.75\n',
-    'GD      2.74\n',
-    'TB      2.73\n',
-    'DY      2.70\n',
-    'HO      2.69\n',
-    'ER      2.68\n',
-    'TM      2.66\n',
-    'YB      2.64\n',
-    'LU      2.62\n',
-    'HF      2.61\n',
-    'TA      2.60\n',
-    'W       2.55\n',
-    'RE      2.53\n',
-    'OS      2.53\n',
-    'IR      2.49\n',
-    'PT      2.01\n',
-    'AU      1.94\n',
-    'HG      1.81\n',
-    'TL      2.29\n',
-    'PB      2.36\n',
-    'BI      2.42\n',
-    'PO      2.30\n',
-    'AT      2.36\n',
-    'RN      2.57\n',
-    'FR      4.07\n',
-    'RA      3.31\n',
-    'AC      2.89\n',
-    'TH      2.87\n',
-    'PA      2.84\n',
-    'U       2.18\n',
-    'NP      2.80\n',
-    'PU      2.84\n',
-    'AM      2.85\n',
-    'CM      2.87\n',
-    'BK      2.85\n',
-    'CF      2.87\n',
-    'ES      2.87\n',
-    'FM      2.87\n',
-    'M       2.88\n',
-    'NO      2.88\n',
-    'LR      2.88\n'
-]
diff --git a/py2sambvca/radii_tables/__init__.py b/py2sambvca/radii_tables/__init__.py
new file mode 100644
index 0000000..49cb1ea
--- /dev/null
+++ b/py2sambvca/radii_tables/__init__.py
@@ -0,0 +1 @@
+from default import radii_table as default_table
diff --git a/py2sambvca/radii_tables/default.py b/py2sambvca/radii_tables/default.py
new file mode 100644
index 0000000..db7bc49
--- /dev/null
+++ b/py2sambvca/radii_tables/default.py
@@ -0,0 +1,105 @@
+radii_table = [
+    'H       1.28\n',
+    'HE      1.64\n',
+    'LI      2.13\n',
+    'BE      1.79\n',
+    'B       2.25\n',
+    'C       1.99\n',
+    'N       1.81\n',
+    'O       1.78\n',
+    'F       1.72\n',
+    'NE      1.80\n',
+    'NA      2.66\n',
+    'MG      2.02\n',
+    'AL      2.15\n',
+    'SI      2.46\n',
+    'P       2.11\n',
+    'S       2.11\n',
+    'CL      2.05\n',
+    'AR      2.20\n',
+    'K       3.22\n',
+    'CA      2.70\n',
+    'SC      2.52\n',
+    'TI      2.47\n',
+    'V       2.42\n',
+    'CR      2.41\n',
+    'MN      2.40\n',
+    'FE      2.39\n',
+    'CO      2.34\n',
+    'NI      1.91\n',
+    'CU      1.64\n',
+    'ZN      1.63\n',
+    'GA      2.19\n',
+    'GE      2.47\n',
+    'AS      2.16\n',
+    'SE      2.22\n',
+    'BR      2.16\n',
+    'KR      2.36\n',
+    'RB      3.55\n',
+    'SR      2.91\n',
+    'Y       2.71\n',
+    'ZR      2.61\n',
+    'NB      2.55\n',
+    'MO      2.54\n',
+    'TC      2.53\n',
+    'RU      2.49\n',
+    'RH      2.46\n',
+    'PD      1.91\n',
+    'AG      2.01\n',
+    'CD      1.85\n',
+    'IN      2.26\n',
+    'SN      2.54\n',
+    'SB      2.41\n',
+    'TE      2.41\n',
+    'I       2.32\n',
+    'XE      2.53\n',
+    'CS      4.01\n',
+    'BA      3.14\n',
+    'LA      2.84\n',
+    'CE      2.83\n',
+    'PR      2.81\n',
+    'ND      2.80\n',
+    'PM      2.78\n',
+    'SM      2.76\n',
+    'EU      2.75\n',
+    'GD      2.74\n',
+    'TB      2.73\n',
+    'DY      2.70\n',
+    'HO      2.69\n',
+    'ER      2.68\n',
+    'TM      2.66\n',
+    'YB      2.64\n',
+    'LU      2.62\n',
+    'HF      2.61\n',
+    'TA      2.60\n',
+    'W       2.55\n',
+    'RE      2.53\n',
+    'OS      2.53\n',
+    'IR      2.49\n',
+    'PT      2.01\n',
+    'AU      1.94\n',
+    'HG      1.81\n',
+    'TL      2.29\n',
+    'PB      2.36\n',
+    'BI      2.42\n',
+    'PO      2.30\n',
+    'AT      2.36\n',
+    'RN      2.57\n',
+    'FR      4.07\n',
+    'RA      3.31\n',
+    'AC      2.89\n',
+    'TH      2.87\n',
+    'PA      2.84\n',
+    'U       2.18\n',
+    'NP      2.80\n',
+    'PU      2.84\n',
+    'AM      2.85\n',
+    'CM      2.87\n',
+    'BK      2.85\n',
+    'CF      2.87\n',
+    'ES      2.87\n',
+    'FM      2.87\n',
+    'M       2.88\n',
+    'NO      2.88\n',
+    'LR      2.88\n'
+]

From a9609e999c3e9cf583cb3e6de357c5b2a1955c60 Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 21 Sep 2022 16:01:07 -0400
Subject: [PATCH 02/11] provide table lookup, need to also reorder input args
 to base class

---
 py2sambvca/py2sambvca.py            | 44 +++++++++++++++--------------
 py2sambvca/radii_tables/__init__.py |  6 +++-
 2 files changed, 28 insertions(+), 22 deletions(-)

diff --git a/py2sambvca/py2sambvca.py b/py2sambvca/py2sambvca.py
index f66df92..7052c7e 100644
--- a/py2sambvca/py2sambvca.py
+++ b/py2sambvca/py2sambvca.py
@@ -5,9 +5,7 @@
 from typing import List
 from warnings import warn
 
-from py2sambvca.radii_tables import (
-    default_table,
-)
+from py2sambvca.radii_tables import table_lookup
 
 class py2sambvca():
     """
@@ -33,23 +31,24 @@ class py2sambvca():
     verbose (int): 0 for no output, 1 for some output, 2 for the most output
     """
 
-    def __init__(self,
-                 xyz_filepath: str,
-                 sphere_center_atom_ids: List[int],
-                 z_ax_atom_ids: List[int],
-                 xz_plane_atoms_ids: List[int],
-                 atoms_to_delete_ids: List[int] = None,
-                 sphere_radius: float = 3.5,
-                 displacement: float = 0.0,
-                 mesh_size: float = 0.10,
-                 remove_H: int = 1,
-                 orient_z: int = 1,
-                 write_surf_files: int = 1,
-                 path_to_sambvcax: str = "sambvca.exe",
-                 working_dir: str = os.getcwd(),
-                 verbose: int = 1,
-                 radii_table: str = "default",
-                 ):
+    def __init__(
+        self,
+        xyz_filepath: str,
+        sphere_center_atom_ids: List[int],
+        z_ax_atom_ids: List[int],
+        xz_plane_atoms_ids: List[int],
+        atoms_to_delete_ids: List[int] = None,
+        sphere_radius: float = 3.5,
+        displacement: float = 0.0,
+        mesh_size: float = 0.10,
+        remove_H: int = 1,
+        orient_z: int = 1,
+        write_surf_files: int = 1,
+        path_to_sambvcax: str = "sambvca.exe",
+        working_dir: str = os.getcwd(),
+        verbose: int = 1,
+        radii_table: str = "default",
+        ):
         """
         Wrapper class for py2sambvca functions.
 
@@ -117,6 +116,9 @@ def __init__(self,
         self.quadrant_results = None
         self.octant_results = None
 
+        # data table
+        self.__radii_table = table_lookup(radii_table)
+
     def write_input(self):
         """
         Write input for the Sambvca buried-volume Fortran calculator based on the data entered
@@ -154,7 +156,7 @@ def write_input(self):
                 "103\n"
             ])
             # write radii
-            file.writelines(radii_table)
+            file.writelines(self.__radii_table)
             # write the atom coordinates
             file.writelines(self.xyz_data)
 
diff --git a/py2sambvca/radii_tables/__init__.py b/py2sambvca/radii_tables/__init__.py
index 49cb1ea..2acd708 100644
--- a/py2sambvca/radii_tables/__init__.py
+++ b/py2sambvca/radii_tables/__init__.py
@@ -1 +1,5 @@
-from default import radii_table as default_table
+from py2sambvca.radii_tables.default import radii_table as default
+
+table_lookup = {
+    "default": default,
+}
\ No newline at end of file

From e2661cd70e55e2b1bf61c415bcf04bc944e01e65 Mon Sep 17 00:00:00 2001
From: JacksonBurns <33505528+JacksonBurns@users.noreply.github.com>
Date: Wed, 21 Sep 2022 16:02:25 -0400
Subject: [PATCH 03/11] i've been doing too much matlab

---
 py2sambvca/py2sambvca.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py2sambvca/py2sambvca.py b/py2sambvca/py2sambvca.py
index 7052c7e..bcbd7a2 100644
--- a/py2sambvca/py2sambvca.py
+++ b/py2sambvca/py2sambvca.py
@@ -117,7 +117,7 @@ def __init__(
         self.octant_results = None
 
         # data table
-        self.__radii_table = table_lookup(radii_table)
+        self.__radii_table = table_lookup[radii_table]
 
     def write_input(self):
         """

From cbe3d1170acd78f9714896be9e015d485efd7c66 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Sat, 3 Jun 2023 15:32:58 -0400
Subject: [PATCH 04/11] add a function to format dictionaries into the way
 sambvca expects

---
 py2sambvca/radii_tables/format_table.py | 20 ++++++++++++++++++++
 1 file changed, 20 insertions(+)
 create mode 100644 py2sambvca/radii_tables/format_table.py

diff --git a/py2sambvca/radii_tables/format_table.py b/py2sambvca/radii_tables/format_table.py
new file mode 100644
index 0000000..b95c34a
--- /dev/null
+++ b/py2sambvca/radii_tables/format_table.py
@@ -0,0 +1,20 @@
+def format_radii_table(radii_table: dict):
+    """Formats a dictionary of atomic symbol: radii to a list of strings for sambvca
+
+    Args:
+        radii_table (dict): Mapping of atomic symbols to radii, i.e. {'H':1.0,'LI':1.1}
+    """
+    output_list = []
+    for element, radius in radii_table.items():
+        # sambvca expects each row in the radii table to look like this:
+        # "C       1.11" with _exactly_ six spaces for elements with two letter
+        # abbreviations and _exactly_ seven for elements with one letter
+        # abbreviations, and then three digits for the radius
+        output_list.append(
+            element
+            + (" " if len(element) == 1 else "")
+            + "      "
+            + str(round(radius, 2))
+            + "\n"
+        )
+    return output_list

From d138ab7006a86957e6a9ad147a4e81b1d323987d Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Sat, 3 Jun 2023 15:33:19 -0400
Subject: [PATCH 05/11] add default and van der waals radii options

---
 py2sambvca/radii_tables/__init__.py    |   9 +-
 py2sambvca/radii_tables/default.py     | 212 +++++++++++++------------
 py2sambvca/radii_tables/vanDerWaals.py |   8 +
 3 files changed, 121 insertions(+), 108 deletions(-)
 create mode 100644 py2sambvca/radii_tables/vanDerWaals.py

diff --git a/py2sambvca/radii_tables/__init__.py b/py2sambvca/radii_tables/__init__.py
index 2acd708..49de8c9 100644
--- a/py2sambvca/radii_tables/__init__.py
+++ b/py2sambvca/radii_tables/__init__.py
@@ -1,5 +1,8 @@
-from py2sambvca.radii_tables.default import radii_table as default
+from py2sambvca.radii_tables.default import default_radii_table
+from py2sambvca.radii_tables.vanDerWaals import vdw_radii_table
+from py2sambvca.radii_tables.format_table import format_radii_table
 
 table_lookup = {
-    "default": default,
-}
\ No newline at end of file
+    "default": default_radii_table,
+    "vdw": vdw_radii_table,
+}
diff --git a/py2sambvca/radii_tables/default.py b/py2sambvca/radii_tables/default.py
index db7bc49..2906a58 100644
--- a/py2sambvca/radii_tables/default.py
+++ b/py2sambvca/radii_tables/default.py
@@ -1,105 +1,107 @@
-radii_table = [
-    'H       1.28\n',
-    'HE      1.64\n',
-    'LI      2.13\n',
-    'BE      1.79\n',
-    'B       2.25\n',
-    'C       1.99\n',
-    'N       1.81\n',
-    'O       1.78\n',
-    'F       1.72\n',
-    'NE      1.80\n',
-    'NA      2.66\n',
-    'MG      2.02\n',
-    'AL      2.15\n',
-    'SI      2.46\n',
-    'P       2.11\n',
-    'S       2.11\n',
-    'CL      2.05\n',
-    'AR      2.20\n',
-    'K       3.22\n',
-    'CA      2.70\n',
-    'SC      2.52\n',
-    'TI      2.47\n',
-    'V       2.42\n',
-    'CR      2.41\n',
-    'MN      2.40\n',
-    'FE      2.39\n',
-    'CO      2.34\n',
-    'NI      1.91\n',
-    'CU      1.64\n',
-    'ZN      1.63\n',
-    'GA      2.19\n',
-    'GE      2.47\n',
-    'AS      2.16\n',
-    'SE      2.22\n',
-    'BR      2.16\n',
-    'KR      2.36\n',
-    'RB      3.55\n',
-    'SR      2.91\n',
-    'Y       2.71\n',
-    'ZR      2.61\n',
-    'NB      2.55\n',
-    'MO      2.54\n',
-    'TC      2.53\n',
-    'RU      2.49\n',
-    'RH      2.46\n',
-    'PD      1.91\n',
-    'AG      2.01\n',
-    'CD      1.85\n',
-    'IN      2.26\n',
-    'SN      2.54\n',
-    'SB      2.41\n',
-    'TE      2.41\n',
-    'I       2.32\n',
-    'XE      2.53\n',
-    'CS      4.01\n',
-    'BA      3.14\n',
-    'LA      2.84\n',
-    'CE      2.83\n',
-    'PR      2.81\n',
-    'ND      2.80\n',
-    'PM      2.78\n',
-    'SM      2.76\n',
-    'EU      2.75\n',
-    'GD      2.74\n',
-    'TB      2.73\n',
-    'DY      2.70\n',
-    'HO      2.69\n',
-    'ER      2.68\n',
-    'TM      2.66\n',
-    'YB      2.64\n',
-    'LU      2.62\n',
-    'HF      2.61\n',
-    'TA      2.60\n',
-    'W       2.55\n',
-    'RE      2.53\n',
-    'OS      2.53\n',
-    'IR      2.49\n',
-    'PT      2.01\n',
-    'AU      1.94\n',
-    'HG      1.81\n',
-    'TL      2.29\n',
-    'PB      2.36\n',
-    'BI      2.42\n',
-    'PO      2.30\n',
-    'AT      2.36\n',
-    'RN      2.57\n',
-    'FR      4.07\n',
-    'RA      3.31\n',
-    'AC      2.89\n',
-    'TH      2.87\n',
-    'PA      2.84\n',
-    'U       2.18\n',
-    'NP      2.80\n',
-    'PU      2.84\n',
-    'AM      2.85\n',
-    'CM      2.87\n',
-    'BK      2.85\n',
-    'CF      2.87\n',
-    'ES      2.87\n',
-    'FM      2.87\n',
-    'M       2.88\n',
-    'NO      2.88\n',
-    'LR      2.88\n'
-]
+# These are the radii used in the original Cavallo paper, which are just the vDW
+# radii multiplied by 1.17
+default_radii_table = {
+    "H": 1.28,
+    "HE": 1.64,
+    "LI": 2.13,
+    "BE": 1.79,
+    "B": 2.25,
+    "C": 1.99,
+    "N": 1.81,
+    "O": 1.78,
+    "F": 1.72,
+    "NE": 1.80,
+    "NA": 2.66,
+    "MG": 2.02,
+    "AL": 2.15,
+    "SI": 2.46,
+    "P": 2.11,
+    "S": 2.11,
+    "CL": 2.05,
+    "AR": 2.20,
+    "K": 3.22,
+    "CA": 2.70,
+    "SC": 2.52,
+    "TI": 2.47,
+    "V": 2.42,
+    "CR": 2.41,
+    "MN": 2.40,
+    "FE": 2.39,
+    "CO": 2.34,
+    "NI": 1.91,
+    "CU": 1.64,
+    "ZN": 1.63,
+    "GA": 2.19,
+    "GE": 2.47,
+    "AS": 2.16,
+    "SE": 2.22,
+    "BR": 2.16,
+    "KR": 2.36,
+    "RB": 3.55,
+    "SR": 2.91,
+    "Y": 2.71,
+    "ZR": 2.61,
+    "NB": 2.55,
+    "MO": 2.54,
+    "TC": 2.53,
+    "RU": 2.49,
+    "RH": 2.46,
+    "PD": 1.91,
+    "AG": 2.01,
+    "CD": 1.85,
+    "IN": 2.26,
+    "SN": 2.54,
+    "SB": 2.41,
+    "TE": 2.41,
+    "I": 2.32,
+    "XE": 2.53,
+    "CS": 4.01,
+    "BA": 3.14,
+    "LA": 2.84,
+    "CE": 2.83,
+    "PR": 2.81,
+    "ND": 2.80,
+    "PM": 2.78,
+    "SM": 2.76,
+    "EU": 2.75,
+    "GD": 2.74,
+    "TB": 2.73,
+    "DY": 2.70,
+    "HO": 2.69,
+    "ER": 2.68,
+    "TM": 2.66,
+    "YB": 2.64,
+    "LU": 2.62,
+    "HF": 2.61,
+    "TA": 2.60,
+    "W": 2.55,
+    "RE": 2.53,
+    "OS": 2.53,
+    "IR": 2.49,
+    "PT": 2.01,
+    "AU": 1.94,
+    "HG": 1.81,
+    "TL": 2.29,
+    "PB": 2.36,
+    "BI": 2.42,
+    "PO": 2.30,
+    "AT": 2.36,
+    "RN": 2.57,
+    "FR": 4.07,
+    "RA": 3.31,
+    "AC": 2.89,
+    "TH": 2.87,
+    "PA": 2.84,
+    "U": 2.18,
+    "NP": 2.80,
+    "PU": 2.84,
+    "AM": 2.85,
+    "CM": 2.87,
+    "BK": 2.85,
+    "CF": 2.87,
+    "ES": 2.87,
+    "FM": 2.87,
+    "M": 2.88,
+    "NO": 2.88,
+    "LR": 2.88,
+}
diff --git a/py2sambvca/radii_tables/vanDerWaals.py b/py2sambvca/radii_tables/vanDerWaals.py
new file mode 100644
index 0000000..fc9b065
--- /dev/null
+++ b/py2sambvca/radii_tables/vanDerWaals.py
@@ -0,0 +1,8 @@
+# this radius table just returns to the plain old van Der Waals radii,
+# which are the radii reported in the original Cavallo paper divided by
+# 1.17
+from py2sambvca.radii_tables.default import default_radii_table
+
+vdw_radii_table = {
+    element: radius / 1.17 for element, radius in default_radii_table.items()
+}

From 36ce13c0c77034b2c149db22507c18b7dc1ad2f6 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Sat, 3 Jun 2023 15:33:45 -0400
Subject: [PATCH 06/11] update readme, test, and docstrings to cover new radii
 table option

---
 README.md                |  9 +++++----
 py2sambvca/py2sambvca.py | 14 +++++++++-----
 test/test_py2sambvca.py  |  1 +
 3 files changed, 15 insertions(+), 9 deletions(-)

diff --git a/README.md b/README.md
index 91a3fb0..2679e32 100644
--- a/README.md
+++ b/README.md
@@ -22,12 +22,12 @@
 pip install py2sambvca
 ```
 
-`py2sambvca` has __zero__ external depdencies.
+`py2sambvca` has __zero__ external dependencies.
 
-### Downloading and Compiling `Sambvca`
-`py2sambvca` can read and write input and output files for `Sambvca` without the actual program in place, but in order to run input files you must have an executable `sambvca21.exe` (or similar) somewhere on your machine.
+### Downloading and Compiling `SambVca`
+`py2sambvca` can read and write input and output files for `SambVca` without the actual program in place, but in order to run input files you must have an executable `sambvca21.exe` (or similar) somewhere on your machine.
 
-You can download the source code [on the `Sambvca` webserver](https://www.molnac.unisa.it/OMtools/sambvca2.1/download/download.html) and compile it using [`gfortran`](https://gcc.gnu.org/wiki/GFortranBinaries).
+You can download the source code [on the `SambVca` webserver](https://www.molnac.unisa.it/OMtools/sambvca2.1/download/download.html) and compile it using [`gfortran`](https://gcc.gnu.org/wiki/GFortranBinaries).
 
 By default, `py2sambvca` expects the executable to be present in the `cwd` and named `sambvca21.exe` on Windows or `sambvca21.x` on Unix-based systems. optionally, the filepath to your executable can be specified as shown below.
 
@@ -62,6 +62,7 @@ The following parameters are optional and will be filled with default values if
  - `path_to_sambvcax` (str): Path to the SambVca executable. Only needed to use py2sambvca.calc()(default "sambvca.exe")
  - `working_dir` (path): Path to the working directory where the output and input files are generated (default os.getcwd())
  - `verbose` (int): 0 for no output, 1 for some output, 2 for the most output (default 1)
+ - `radii_table` (dict or str): a dictionary of atomic symbols and their radii (angstroms), or "default" for the radii used in the original implementation
 
 
 From here, running can be done stepwise or with a single function:
diff --git a/py2sambvca/py2sambvca.py b/py2sambvca/py2sambvca.py
index ded89a8..b581080 100644
--- a/py2sambvca/py2sambvca.py
+++ b/py2sambvca/py2sambvca.py
@@ -2,10 +2,11 @@
 import re
 import glob
 import os
-from typing import List
+from typing import List, Union
 from warnings import warn
 
-from py2sambvca.radii_tables import table_lookup
+from py2sambvca.radii_tables import table_lookup, format_radii_table
+
 
 class py2sambvca:
     """
@@ -29,6 +30,7 @@ class py2sambvca:
     path_to_sambvcax (str): Path to the SambVca executable. Only needed to use py2sambvca.calc()( default "/path/to/executable/sambvca.x")
     working_dir (path): Path to the working directory where the output and input files are generated (default os.getcwd())
     verbose (int): 0 for no output, 1 for some output, 2 for the most output
+    radii_table: Dictionary of atomic symbols (H, N, LI, etc.) and their radii in Angstrom, "default" (bondii/vDW radii * 1.17), or "vdw" for van Der Waals
     """
 
     def __init__(
@@ -47,7 +49,7 @@ def __init__(
         path_to_sambvcax: str = "sambvca.exe",
         working_dir: str = os.getcwd(),
         verbose: int = 1,
-        radii_table: str = "default",
+        radii_table: Union[str, dict] = "default",
     ):
         """
         Wrapper class for py2sambvca functions.
@@ -70,6 +72,7 @@ def __init__(
         path_to_sambvcax (str): Path to the SambVca executable. Only needed to use py2sambvca.calc()( default "/path/to/executable/sambvca.x")
         working_dir (path): Path to the working directory where the output and input files are generated (default os.getcwd())
         verbose (int): 0 for no output, 1 for some output, 2 for the most output
+        radii_table: Dictionary of atomic symbols (H, N, LI, etc.) and their radii in Angstrom, "default" (bondii/vDW radii * 1.17), or "vdw" for van Der Waals
         """
         # if atoms are requested to be deleted, assign them and the number of them
         if atoms_to_delete_ids is not None:
@@ -117,7 +120,9 @@ def __init__(
         self.octant_results = None
 
         # data table
-        self.__radii_table = table_lookup[radii_table]
+        self.__radii_table = format_radii_table(
+            table_lookup[radii_table] if type(radii_table) is str else radii_table
+        )
 
     def write_input(self):
         """
@@ -516,4 +521,3 @@ def run(self):
         self.parse_output()
         self.clean_files()
         return self.total_results, self.quadrant_results, self.octant_results
-
diff --git a/test/test_py2sambvca.py b/test/test_py2sambvca.py
index 757a2ef..c977a6d 100644
--- a/test/test_py2sambvca.py
+++ b/test/test_py2sambvca.py
@@ -108,6 +108,7 @@ def test_full_init(self):
             self.orient_Z,
             self.write_surf_files,
             self.exe_path,
+            "default",
         )
         self.assertEqual(
             self.sphere_ids,

From cb84c900745d8da93fad1cbf639f958a5614153e Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Sat, 3 Jun 2023 15:35:39 -0400
Subject: [PATCH 07/11] edit docstring for line length restriction

---
 py2sambvca/py2sambvca.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py2sambvca/py2sambvca.py b/py2sambvca/py2sambvca.py
index b581080..f674728 100644
--- a/py2sambvca/py2sambvca.py
+++ b/py2sambvca/py2sambvca.py
@@ -30,7 +30,7 @@ class py2sambvca:
     path_to_sambvcax (str): Path to the SambVca executable. Only needed to use py2sambvca.calc()( default "/path/to/executable/sambvca.x")
     working_dir (path): Path to the working directory where the output and input files are generated (default os.getcwd())
     verbose (int): 0 for no output, 1 for some output, 2 for the most output
-    radii_table: Dictionary of atomic symbols (H, N, LI, etc.) and their radii in Angstrom, "default" (bondii/vDW radii * 1.17), or "vdw" for van Der Waals
+    radii_table (dict or str): atomic symbols (ie. H, LI) and radii (Angstrom), "default" (bondii radii*1.17), or "vdw" for van Der Waals
     """
 
     def __init__(

From 818604440ecd64c8b2ceca51ead38a0d2d423e5e Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Sat, 3 Jun 2023 15:38:37 -0400
Subject: [PATCH 08/11] additional line length fix

---
 py2sambvca/py2sambvca.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py2sambvca/py2sambvca.py b/py2sambvca/py2sambvca.py
index f674728..fdc7bb1 100644
--- a/py2sambvca/py2sambvca.py
+++ b/py2sambvca/py2sambvca.py
@@ -72,7 +72,7 @@ def __init__(
         path_to_sambvcax (str): Path to the SambVca executable. Only needed to use py2sambvca.calc()( default "/path/to/executable/sambvca.x")
         working_dir (path): Path to the working directory where the output and input files are generated (default os.getcwd())
         verbose (int): 0 for no output, 1 for some output, 2 for the most output
-        radii_table: Dictionary of atomic symbols (H, N, LI, etc.) and their radii in Angstrom, "default" (bondii/vDW radii * 1.17), or "vdw" for van Der Waals
+        radii_table (dict or str): atomic symbols (ie. H, LI) and radii (Angstrom), "default" (bondii radii*1.17), or "vdw" for van Der Waals
         """
         # if atoms are requested to be deleted, assign them and the number of them
         if atoms_to_delete_ids is not None:

From 307a717121a00e3c9c65a66363f7c05ee96404ab Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Sat, 3 Jun 2023 15:40:28 -0400
Subject: [PATCH 09/11] add explicit export of radii table directory

---
 py2sambvca/radii_tables/__init__.py | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/py2sambvca/radii_tables/__init__.py b/py2sambvca/radii_tables/__init__.py
index 49de8c9..b0c6c34 100644
--- a/py2sambvca/radii_tables/__init__.py
+++ b/py2sambvca/radii_tables/__init__.py
@@ -6,3 +6,5 @@
     "default": default_radii_table,
     "vdw": vdw_radii_table,
 }
+
+__all__ = ["format_radii_table", "table_lookup"]

From bec14cc0af1d2942fe360a500097d351133aa209 Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Sat, 3 Jun 2023 15:47:57 -0400
Subject: [PATCH 10/11] add ci aggregation step

---
 .github/workflows/run_tests.yml | 15 +++++++++++++++
 1 file changed, 15 insertions(+)

diff --git a/.github/workflows/run_tests.yml b/.github/workflows/run_tests.yml
index a4bfdf0..2405f72 100644
--- a/.github/workflows/run_tests.yml
+++ b/.github/workflows/run_tests.yml
@@ -51,3 +51,18 @@ jobs:
       - name: Show Coverage
         run: |
           coverage report -m
+
+  # This allows us to have a branch protection rule for tests and deploys with matrix
+  # 
+  # taken from https://github.com/orgs/community/discussions/4324#discussioncomment-3477871
+  ci-report-status:
+    runs-on: ubuntu-latest
+    needs: build
+    if: always()
+    steps:
+      - name: Successful CI
+        if: ${{ !(contains(needs.build.result, 'failure')) }}
+        run: exit 0
+      - name: Failing CI
+        if: ${{ contains(needs.build.result, 'failure') }}
+        run: exit 1 

From e39cd74ef3c15ba5fc1befbc47cdc8ae6d9efecc Mon Sep 17 00:00:00 2001
From: Jackson Burns <jwburns@mit.edu>
Date: Sat, 3 Jun 2023 15:48:02 -0400
Subject: [PATCH 11/11] bump version

---
 py2sambvca/__init__.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/py2sambvca/__init__.py b/py2sambvca/__init__.py
index 54ec9b2..715e0d2 100644
--- a/py2sambvca/__init__.py
+++ b/py2sambvca/__init__.py
@@ -2,4 +2,4 @@
 
 __all__ = ["p2s"]
 
-__version__ = "1.3.4"
+__version__ = "1.4.0"