diff --git a/poetry.lock b/poetry.lock
index 4fd9b51..956c9ee 100644
--- a/poetry.lock
+++ b/poetry.lock
@@ -188,13 +188,13 @@ testing = ["jaraco.test", "pytest (!=8.0.*)", "pytest (>=6,!=8.1.*)", "pytest-ch
 
 [[package]]
 name = "beautifulsoup4"
-version = "4.13.3"
+version = "4.13.4"
 description = "Screen-scraping library"
 optional = true
 python-versions = ">=3.7.0"
 files = [
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-    {file = "beautifulsoup4-4.13.3.tar.gz", hash = "sha256:1bd32405dacc920b42b83ba01644747ed77456a65760e285fbc47633ceddaf8b"},
+    {file = "beautifulsoup4-4.13.4-py3-none-any.whl", hash = "sha256:9bbbb14bfde9d79f38b8cd5f8c7c85f4b8f2523190ebed90e950a8dea4cb1c4b"},
+    {file = "beautifulsoup4-4.13.4.tar.gz", hash = "sha256:dbb3c4e1ceae6aefebdaf2423247260cd062430a410e38c66f2baa50a8437195"},
 ]
 
 [package.dependencies]
@@ -361,13 +361,13 @@ files = [
 
 [[package]]
 name = "certifi"
-version = "2025.1.31"
+version = "2025.4.26"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
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-    {file = "certifi-2025.1.31.tar.gz", hash = "sha256:3d5da6925056f6f18f119200434a4780a94263f10d1c21d032a6f6b2baa20651"},
+    {file = "certifi-2025.4.26-py3-none-any.whl", hash = "sha256:30350364dfe371162649852c63336a15c70c6510c2ad5015b21c2345311805f3"},
+    {file = "certifi-2025.4.26.tar.gz", hash = "sha256:0a816057ea3cdefcef70270d2c515e4506bbc954f417fa5ade2021213bb8f0c6"},
 ]
 
 [[package]]
@@ -473,103 +473,103 @@ files = [
 
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 name = "charset-normalizer"
-version = "3.4.1"
+version = "3.4.2"
 description = "The Real First Universal Charset Detector. Open, modern and actively maintained alternative to Chardet."
 optional = false
 python-versions = ">=3.7"
 files = [
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 [[package]]
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 [[package]]
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+version = "1.8.14"
 description = "An implementation of the Debug Adapter Protocol for Python"
 optional = false
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 ]
 
 [[package]]
@@ -1139,13 +1139,13 @@ dev = ["flake8", "markdown", "twine", "wheel"]
 
 [[package]]
 name = "griffe"
-version = "1.7.2"
+version = "1.7.3"
 description = "Signatures for entire Python programs. Extract the structure, the frame, the skeleton of your project, to generate API documentation or find breaking changes in your API."
 optional = true
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -1153,29 +1153,29 @@ colorama = ">=0.4"
 
 [[package]]
 name = "h11"
-version = "0.14.0"
+version = "0.16.0"
 description = "A pure-Python, bring-your-own-I/O implementation of HTTP/1.1"
 optional = true
-python-versions = ">=3.7"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
 name = "httpcore"
-version = "1.0.7"
+version = "1.0.9"
 description = "A minimal low-level HTTP client."
 optional = true
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
 certifi = "*"
-h11 = ">=0.13,<0.15"
+h11 = ">=0.16"
 
 [package.extras]
 asyncio = ["anyio (>=4.0,<5.0)"]
@@ -1209,13 +1209,13 @@ zstd = ["zstandard (>=0.18.0)"]
 
 [[package]]
 name = "identify"
-version = "2.6.9"
+version = "2.6.10"
 description = "File identification library for Python"
 optional = true
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.extras]
@@ -1237,13 +1237,13 @@ all = ["flake8 (>=7.1.1)", "mypy (>=1.11.2)", "pytest (>=8.3.2)", "ruff (>=0.6.2
 
 [[package]]
 name = "importlib-metadata"
-version = "8.6.1"
+version = "8.7.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -1363,21 +1363,21 @@ test-extra = ["curio", "matplotlib (!=3.2.0)", "nbformat", "numpy (>=1.22)", "pa
 
 [[package]]
 name = "ipywidgets"
-version = "8.1.5"
+version = "8.1.6"
 description = "Jupyter interactive widgets"
 optional = true
 python-versions = ">=3.7"
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 [package.dependencies]
 comm = ">=0.1.3"
 ipython = ">=6.1.0"
-jupyterlab-widgets = ">=3.0.12,<3.1.0"
+jupyterlab_widgets = ">=3.0.14,<3.1.0"
 traitlets = ">=4.3.1"
-widgetsnbextension = ">=4.0.12,<4.1.0"
+widgetsnbextension = ">=4.0.14,<4.1.0"
 
 [package.extras]
 test = ["ipykernel", "jsonschema", "pytest (>=3.6.0)", "pytest-cov", "pytz"]
@@ -1578,13 +1578,13 @@ format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-
 
 [[package]]
 name = "jsonschema-specifications"
-version = "2024.10.1"
+version = "2025.4.1"
 description = "The JSON Schema meta-schemas and vocabularies, exposed as a Registry"
 optional = true
 python-versions = ">=3.9"
 files = [
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 [package.dependencies]
@@ -1731,13 +1731,13 @@ test = ["jupyter-server (>=2.0.0)", "pytest (>=7.0)", "pytest-jupyter[server] (>
 
 [[package]]
 name = "jupyterlab"
-version = "4.4.0"
+version = "4.4.1"
 description = "JupyterLab computational environment"
 optional = true
 python-versions = ">=3.9"
 files = [
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 ]
 
 [package.dependencies]
@@ -1758,7 +1758,7 @@ tornado = ">=6.2.0"
 traitlets = "*"
 
 [package.extras]
-dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.9.9)"]
+dev = ["build", "bump2version", "coverage", "hatch", "pre-commit", "pytest-cov", "ruff (==0.11.4)"]
 docs = ["jsx-lexer", "myst-parser", "pydata-sphinx-theme (>=0.13.0)", "pytest", "pytest-check-links", "pytest-jupyter", "sphinx (>=1.8,<8.2.0)", "sphinx-copybutton"]
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@@ -1803,13 +1803,13 @@ test = ["hatch", "ipykernel", "openapi-core (>=0.18.0,<0.19.0)", "openapi-spec-v
 
 [[package]]
 name = "jupyterlab-widgets"
-version = "3.0.13"
+version = "3.0.14"
 description = "Jupyter interactive widgets for JupyterLab"
 optional = true
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
@@ -1991,20 +1991,20 @@ files = [
 
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 name = "markdown"
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+version = "3.8"
 description = "Python implementation of John Gruber's Markdown."
 optional = true
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 [package.dependencies]
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 [package.extras]
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 testing = ["coverage", "pyyaml"]
 
 [[package]]
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 ]
 
 [package.dependencies]
@@ -2143,13 +2156,15 @@ contourpy = ">=1.0.1"
 cycler = ">=0.10"
 fonttools = ">=4.22.0"
 importlib-resources = {version = ">=3.2.0", markers = "python_version < \"3.10\""}
-kiwisolver = ">=1.0.1"
-numpy = ">=1.21,<2"
+kiwisolver = ">=1.3.1"
+numpy = ">=1.23"
 packaging = ">=20.0"
-pillow = ">=6.2.0"
+pillow = ">=8"
 pyparsing = ">=2.3.1"
 python-dateutil = ">=2.7"
-setuptools_scm = ">=7"
+
+[package.extras]
+dev = ["meson-python (>=0.13.1,<0.17.0)", "numpy (>=1.25)", "pybind11 (>=2.6,!=2.13.3)", "setuptools (>=64)", "setuptools_scm (>=7)"]
 
 [[package]]
 name = "matplotlib-inline"
@@ -2423,13 +2438,13 @@ test = ["coverage"]
 
 [[package]]
 name = "more-itertools"
-version = "10.6.0"
+version = "10.7.0"
 description = "More routines for operating on iterables, beyond itertools"
 optional = true
 python-versions = ">=3.9"
 files = [
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 ]
 
 [[package]]
@@ -2560,13 +2575,13 @@ reports = ["lxml"]
 
 [[package]]
 name = "mypy-extensions"
-version = "1.0.0"
+version = "1.1.0"
 description = "Type system extensions for programs checked with the mypy type checker."
 optional = true
-python-versions = ">=3.5"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [[package]]
@@ -2752,13 +2767,13 @@ files = [
 
 [[package]]
 name = "notebook"
-version = "7.4.0"
+version = "7.4.1"
 description = "Jupyter Notebook - A web-based notebook environment for interactive computing"
 optional = true
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -2898,34 +2913,50 @@ wheel = "*"
 
 [[package]]
 name = "openbabel-wheel"
-version = "3.1.1.19"
+version = "3.1.1.21"
 description = "An unofficial repository to distribute OpenBabel prebuilt wheels through Pypi.."
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [[package]]
@@ -2941,13 +2972,13 @@ files = [
 
 [[package]]
 name = "packaging"
-version = "24.2"
+version = "25.0"
 description = "Core utilities for Python packages"
 optional = false
 python-versions = ">=3.8"
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 [[package]]
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 ]
 
 [package.extras]
-docs = ["furo", "olefile", "sphinx (>=8.1)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
+docs = ["furo", "olefile", "sphinx (>=8.2)", "sphinx-copybutton", "sphinx-inline-tabs", "sphinxext-opengraph"]
 fpx = ["olefile"]
 mic = ["olefile"]
+test-arrow = ["pyarrow"]
 tests = ["check-manifest", "coverage (>=7.4.2)", "defusedxml", "markdown2", "olefile", "packaging", "pyroma", "pytest", "pytest-cov", "pytest-timeout", "trove-classifiers (>=2024.10.12)"]
 typing = ["typing-extensions"]
 xmp = ["defusedxml"]
@@ -3309,13 +3351,13 @@ twisted = ["twisted"]
 
 [[package]]
 name = "prompt-toolkit"
-version = "3.0.50"
+version = "3.0.51"
 description = "Library for building powerful interactive command lines in Python"
 optional = false
-python-versions = ">=3.8.0"
+python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -3446,13 +3488,13 @@ windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
 name = "pymdown-extensions"
-version = "10.14.3"
+version = "10.15"
 description = "Extension pack for Python Markdown."
 optional = true
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -4281,28 +4323,6 @@ core = ["importlib-metadata (>=6)", "importlib-resources (>=5.10.2)", "jaraco.te
 doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "pygments-github-lexers (==0.0.5)", "pyproject-hooks (!=1.1)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-favicon", "sphinx-inline-tabs", "sphinx-lint", "sphinx-notfound-page (>=1,<2)", "sphinx-reredirects", "sphinxcontrib-towncrier"]
 test = ["build[virtualenv] (>=1.0.3)", "filelock (>=3.4.0)", "importlib-metadata", "ini2toml[lite] (>=0.14)", "jaraco.develop (>=7.21)", "jaraco.envs (>=2.2)", "jaraco.path (>=3.2.0)", "jaraco.test", "mypy (==1.11.*)", "packaging (>=23.2)", "pip (>=19.1)", "pyproject-hooks (!=1.1)", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-home (>=0.5)", "pytest-mypy", "pytest-perf", "pytest-ruff (<0.4)", "pytest-ruff (>=0.2.1)", "pytest-ruff (>=0.3.2)", "pytest-subprocess", "pytest-timeout", "pytest-xdist (>=3)", "tomli", "tomli-w (>=1.0.0)", "virtualenv (>=13.0.0)", "wheel"]
 
-[[package]]
-name = "setuptools-scm"
-version = "8.2.0"
-description = "the blessed package to manage your versions by scm tags"
-optional = true
-python-versions = ">=3.8"
-files = [
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-]
-
-[package.dependencies]
-packaging = ">=20"
-setuptools = ">=61"
-tomli = {version = ">=1", markers = "python_version < \"3.11\""}
-typing-extensions = {version = "*", markers = "python_version < \"3.10\""}
-
-[package.extras]
-docs = ["entangled-cli (>=2.0,<3.0)", "mkdocs", "mkdocs-entangled-plugin", "mkdocs-material", "mkdocstrings[python]", "pygments"]
-rich = ["rich"]
-test = ["build", "pytest", "rich", "typing-extensions", "wheel"]
-
 [[package]]
 name = "six"
 version = "1.17.0"
@@ -4338,13 +4358,13 @@ files = [
 
 [[package]]
 name = "soupsieve"
-version = "2.6"
+version = "2.7"
 description = "A modern CSS selector implementation for Beautiful Soup."
 optional = true
 python-versions = ">=3.8"
 files = [
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-    {file = "soupsieve-2.6.tar.gz", hash = "sha256:e2e68417777af359ec65daac1057404a3c8a5455bb8abc36f1a9866ab1a51abb"},
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+    {file = "soupsieve-2.7.tar.gz", hash = "sha256:ad282f9b6926286d2ead4750552c8a6142bc4c783fd66b0293547c8fe6ae126a"},
 ]
 
 [[package]]
@@ -4640,13 +4660,13 @@ urllib3 = ">=2"
 
 [[package]]
 name = "typing-extensions"
-version = "4.13.1"
+version = "4.13.2"
 description = "Backported and Experimental Type Hints for Python 3.8+"
 optional = false
 python-versions = ">=3.8"
 files = [
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+    {file = "typing_extensions-4.13.2-py3-none-any.whl", hash = "sha256:a439e7c04b49fec3e5d3e2beaa21755cadbbdc391694e28ccdd36ca4a1408f8c"},
+    {file = "typing_extensions-4.13.2.tar.gz", hash = "sha256:e6c81219bd689f51865d9e372991c540bda33a0379d5573cddb9a3a23f7caaef"},
 ]
 
 [[package]]
@@ -4696,13 +4716,13 @@ dev = ["flake8", "flake8-annotations", "flake8-bandit", "flake8-bugbear", "flake
 
 [[package]]
 name = "urllib3"
-version = "2.3.0"
+version = "2.4.0"
 description = "HTTP library with thread-safe connection pooling, file post, and more."
 optional = false
 python-versions = ">=3.9"
 files = [
-    {file = "urllib3-2.3.0-py3-none-any.whl", hash = "sha256:1cee9ad369867bfdbbb48b7dd50374c0967a0bb7710050facf0dd6911440e3df"},
-    {file = "urllib3-2.3.0.tar.gz", hash = "sha256:f8c5449b3cf0861679ce7e0503c7b44b5ec981bec0d1d3795a07f1ba96f0204d"},
+    {file = "urllib3-2.4.0-py3-none-any.whl", hash = "sha256:4e16665048960a0900c702d4a66415956a584919c03361cac9f1df5c5dd7e813"},
+    {file = "urllib3-2.4.0.tar.gz", hash = "sha256:414bc6535b787febd7567804cc015fee39daab8ad86268f1310a9250697de466"},
 ]
 
 [package.extras]
@@ -4866,13 +4886,13 @@ test = ["pytest (>=6.0.0)", "setuptools (>=65)"]
 
 [[package]]
 name = "widgetsnbextension"
-version = "4.0.13"
+version = "4.0.14"
 description = "Jupyter interactive widgets for Jupyter Notebook"
 optional = true
 python-versions = ">=3.7"
 files = [
-    {file = "widgetsnbextension-4.0.13-py3-none-any.whl", hash = "sha256:74b2692e8500525cc38c2b877236ba51d34541e6385eeed5aec15a70f88a6c71"},
-    {file = "widgetsnbextension-4.0.13.tar.gz", hash = "sha256:ffcb67bc9febd10234a362795f643927f4e0c05d9342c727b65d2384f8feacb6"},
+    {file = "widgetsnbextension-4.0.14-py3-none-any.whl", hash = "sha256:4875a9eaf72fbf5079dc372a51a9f268fc38d46f767cbf85c43a36da5cb9b575"},
+    {file = "widgetsnbextension-4.0.14.tar.gz", hash = "sha256:a3629b04e3edb893212df862038c7232f62973373869db5084aed739b437b5af"},
 ]
 
 [[package]]
@@ -4904,4 +4924,4 @@ viz = ["matplotlib", "nglview"]
 [metadata]
 lock-version = "2.0"
 python-versions = ">=3.9,<4.0"
-content-hash = "7368ec2e5cdf8521190c7c4d067651e62e73b450bf229e1fb66cfb048848636f"
+content-hash = "ee6d795a958900c224eaf1fc9dc88bb721b0ee7e3ab0160aa286ff30c45b5d4a"
diff --git a/pyproject.toml b/pyproject.toml
index a5f3b2d..6b0ff99 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -1,7 +1,7 @@
 [tool]
 [tool.poetry]
 name = "procaliper"
-version = "0.2.0"
+version = "0.2.1"
 homepage = "https://github.com/LifeWorks/procaliper"
 description = "Skeleton project created by Python Project Wizard (ppw)."
 authors = ["AlphaMeter <song.feng@pnnl.gov>"]
@@ -19,7 +19,7 @@ packages = [{ include = "procaliper" }, { include = "tests", format = "sdist" }]
 [tool.poetry.dependencies]
 python = ">=3.9,<4.0"
 biopython = ">=1.84,<2"
-openbabel-wheel = "3.1.1.19"   # note: might want to change to official openbabel if/when install issues are fixed
+openbabel-wheel = ">=3.1.1.21"   # note: might want to change to official openbabel if/when install issues are fixed
 biopandas = ">=0.5.1,<1"
 uniprot-id-mapper = ">=1.1.2,<2"
 propka = ">=3.5.1,<4"
@@ -31,7 +31,7 @@ pypka = { version = "2.10.0", optional = true }
 numpy = { version = "1.26.4", optional = true }
 
 nglview = { version = ">=3.0.8, < 4", optional = true }
-matplotlib = { version = "3.8.0", optional = true }
+matplotlib = { version = ">=3.8.0", optional = true }
 
 black = { version = "24.8.0", optional = true }
 isort = { version = "5.10.1", optional = true }