preparing for new release

dehe1011 · Nov 11, 2024 · 7bc2f8b · 7bc2f8b
1 parent ca1d866
commit 7bc2f8b
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Showing 17 changed files with 404 additions and 98 deletions.
diff --git a/MANIFEST.in b/MANIFEST.in
@@ -16,6 +16,7 @@ include qDNA/defaults.yaml
 
 # Include specific data files
 include qDNA/data/data_paper/*.json
-include qDNA/data/figures_paper/*.pdf *.png
+include qDNA/data/figures_paper/*.pdf
+include qDNA/data/figures_paper/*.png
 include qDNA/data/raw/tb_params/*.json
 include qDNA/data/raw/*.json
diff --git a/README.md b/README.md
@@ -12,7 +12,7 @@
         <img src="https://readthedocs.org/projects/quantumdna/badge/?version=latest"
             alt="Documentation Status"></a>
     <a href="https://github.com/dehe1011/QuantumDNA/releases">
-        <img src="https://img.shields.io/badge/version-0.1.7-blue"
+        <img src="https://img.shields.io/badge/version-0.1.10-blue"
             alt="Release"></a>
     <a href='https://coveralls.io/github/dehe1011/QuantumDNA?branch=main'>
         <img src='https://coveralls.io/repos/github/dehe1011/QuantumDNA/badge.svg?branch=main'

diff --git a/pyproject.toml b/pyproject.toml
@@ -27,6 +27,7 @@ dependencies = [
     "tqdm==4.66.4",
     "customtkinter==5.2.2",
     "scipy==1.11.4",
+    "openpyxl==3.1.5",
 ]
 
 [project.urls]

diff --git a/qDNA/__init__.py b/qDNA/__init__.py
@@ -1,4 +1,4 @@
-__version__ = "0.1.7"
+__version__ = "0.1.10"
 
 import pathlib
 import os

diff --git a/qDNA/data/logs/qDNA.log b/qDNA/data/logs/qDNA.log
diff --git a/qDNA/data/raw/config.json b/qDNA/data/raw/config.json
@@ -1,14 +1 @@
-{
-"data": {
-    "DNA_BASES": ["A", "T", "G", "C", "c"],
-    "TB_MODELS": ["WM", "LM", "ELM", "FWM", "FLM", "FELM", "FC"],
-    "SOURCES": ["Hawke2010", "Simserides2014", "Mantela2021", "Simserides2024"],
-    "DESCRIPTIONS": ["1P", "2P"],
-    "PARTICLES": ["electron", "hole", "exciton"],
-    "UNITS": ["meV", "eV", "100meV", "rad/ps", "rad/fs", "1/cm", "K", "J", "1/fs", "1/ps"],
-    "T_UNITS": ["fs", "ps"],
-    "SPECTRAL_DENSITIES": ["debye", "ohmic"]
-    },
-"metadata": {
-    }
-}
+{"data": {"DNA_BASES": ["A", "T", "G", "C", "F"], "TB_MODELS": ["WM", "LM", "ELM", "FWM", "FLM", "FELM", "FC"], "SOURCES": ["Hawke2010", "Simserides2014", "Mantela2021", "Simserides2024", "MMYY"], "DESCRIPTIONS": ["1P", "2P"], "PARTICLES": ["electron", "hole", "exciton"], "UNITS": ["meV", "eV", "100meV", "rad/ps", "rad/fs", "1/cm", "K", "J", "1/fs", "1/ps"], "T_UNITS": ["fs", "ps"], "SPECTRAL_DENSITIES": ["debye", "ohmic"]}, "metadata": {}}
diff --git a/qDNA/data/raw/tb_models.json b/qDNA/data/raw/tb_models.json
@@ -1,48 +1,48 @@
 {
-"data": {
-    "WM": {
-        "backbone": false,
-        "double_stranded": false,
-        "num_strands": 1,
-        "diagonal_hopping": false
-    },
-    "LM": {
-        "backbone": false,
-        "double_stranded": true,
-        "num_strands": 2,
-        "diagonal_hopping": false
-    },
-    "ELM": {
-        "backbone": false,
-        "double_stranded": true,
-        "num_strands": 2,
-        "diagonal_hopping": true
-    },
-    "FWM": {
-        "backbone": true,
-        "double_stranded": false,
-        "num_strands": 3,
-        "diagonal_hopping": false
-    },
-    "FLM": {
-        "backbone": true,
-        "double_stranded": true,
-        "num_strands": 4,
-        "diagonal_hopping": false
-    },
-    "FELM": {
-        "backbone": true,
-        "double_stranded": true,
-        "num_strands": 4,
-        "diagonal_hopping": true
-    },
-    "FC": {
-        "backbone": true,
-        "double_stranded": true,
-        "num_strands": 4,
-        "diagonal_hopping": true
+    "data": {
+        "WM": {
+            "backbone": false,
+            "double_stranded": false,
+            "num_strands": 1,
+            "diagonal_hopping": false
+        },
+        "LM": {
+            "backbone": false,
+            "double_stranded": true,
+            "num_strands": 2,
+            "diagonal_hopping": false
+        },
+        "ELM": {
+            "backbone": false,
+            "double_stranded": true,
+            "num_strands": 2,
+            "diagonal_hopping": true
+        },
+        "FWM": {
+            "backbone": true,
+            "double_stranded": false,
+            "num_strands": 3,
+            "diagonal_hopping": false
+        },
+        "FLM": {
+            "backbone": true,
+            "double_stranded": true,
+            "num_strands": 4,
+            "diagonal_hopping": false
+        },
+        "FELM": {
+            "backbone": true,
+            "double_stranded": true,
+            "num_strands": 4,
+            "diagonal_hopping": true
+        },
+        "FC": {
+            "backbone": true,
+            "double_stranded": true,
+            "num_strands": 4,
+            "diagonal_hopping": true
+        }
+        },
+    "metadata": {
+        }
     }
-    },
-"metadata": {
-    }
-}
diff --git a/qDNA/data/raw/tb_params/Simserides2024_electron_ELM.json b/qDNA/data/raw/tb_params/Simserides2024_electron_ELM.json
@@ -1,8 +1,8 @@
 {
 "data": {
-"E_A": -0.130, "E_T": -0.350, "E_G": -0.520, "E_C": -0.290, "E_c": -0.290, "t_GG": 0.206, "t_CC": 0.099, "t_AA": 0.074, "t_TT": 0.035, "t_GC": 0.007, "t_CG": 0.031, "t_AT": 0.071, "t_TA": 0.011, "t_CT": 0.071, "t_AG": 0.017, "t_TC": 0.077, "t_GA": 0.008, "t_CA": 0.020, "t_TG": 0.004, "t_AC": 0.021, "t_GT": 0.022, "t_cc": 0.056, "t_Cc": 0.067, "t_cC": 0.091, "t_cG": 0.031, "t_Gc": 0.002, "h_GC": 0.073, "h_Gc": 0.069, "h_AT": 0.002, "r-_GG": 0.021, "r-_CC": 0.090, "r-_AA": 0.081, "r-_TT": 0.009, "r-_GC": 0.097, "r-_CG": 0.097, "r-_AT": 0.005, "r-_TA": 0.005, "r-_CT": 0.010, "r-_AG": 0.051, "r-_TC": 0.010, "r-_GA": 0.051, "r-_CA": 0.023, "r-_TG": 0.017, "r-_AC": 0.023, "r-_GT": 0.017, "r-_cc": 0.097, "r-_Cc": 0.094, "r-_cC": 0.094, "r-_cG": 0.084, "r-_Gc": 0.084, "r+_GG": 0.212, "r+_CC": 0.181, "r+_AA": 0.037, "r+_TT": 0.009, "r+_GC": 0.019, "r+_CG": 0.019, "r+_AT": 0.008, "r+_TA": 0.008, "r+_CT": 0.023, "r+_AG": 0.043, "r+_TC": 0.023, "r+_GA": 0.043, "r+_CA": 0.041, "r+_TG": 0.031, "r+_AC": 0.041, "r+_GT": 0.031, "r+_cc": 0.192, "r+_Cc": 0.186, "r+_cC": 0.186, "r+_cG": 0.030, "r+_Gc": 0.030
+"E_A": -0.130, "E_T": -0.350, "E_G": -0.520, "E_C": -0.290, "E_F": -0.290, "t_GG": 0.206, "t_CC": 0.099, "t_AA": 0.074, "t_TT": 0.035, "t_GC": 0.007, "t_CG": 0.031, "t_AT": 0.071, "t_TA": 0.011, "t_CT": 0.071, "t_AG": 0.017, "t_TC": 0.077, "t_GA": 0.008, "t_CA": 0.020, "t_TG": 0.004, "t_AC": 0.021, "t_GT": 0.022, "t_FF": 0.056, "t_CF": 0.067, "t_FC": 0.091, "t_FG": 0.031, "t_GF": 0.002, "h_GC": 0.073, "h_GF": 0.069, "h_AT": 0.002, "r-_GG": 0.021, "r-_CC": 0.090, "r-_AA": 0.081, "r-_TT": 0.009, "r-_GC": 0.097, "r-_CG": 0.097, "r-_AT": 0.005, "r-_TA": 0.005, "r-_CT": 0.010, "r-_AG": 0.051, "r-_TC": 0.010, "r-_GA": 0.051, "r-_CA": 0.023, "r-_TG": 0.017, "r-_AC": 0.023, "r-_GT": 0.017, "r-_FF": 0.097, "r-_CF": 0.094, "r-_FC": 0.094, "r-_FG": 0.084, "r-_GF": 0.084, "r+_GG": 0.212, "r+_CC": 0.181, "r+_AA": 0.037, "r+_TT": 0.009, "r+_GC": 0.019, "r+_CG": 0.019, "r+_AT": 0.008, "r+_TA": 0.008, "r+_CT": 0.023, "r+_AG": 0.043, "r+_TC": 0.023, "r+_GA": 0.043, "r+_CA": 0.041, "r+_TG": 0.031, "r+_AC": 0.041, "r+_GT": 0.031, "r+_FF": 0.192, "r+_CF": 0.186, "r+_FC": 0.186, "r+_FG": 0.030, "r+_GF": 0.030
 },
 "metadata": {
-"source": "Simserides2024", "particle": "electron", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' "
+"source": "Simserides2024", "particle": "electron", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'F' "
 }
 }
diff --git a/qDNA/data/raw/tb_params/Simserides2024_electron_FELM.json b/qDNA/data/raw/tb_params/Simserides2024_electron_FELM.json
@@ -1,8 +1,8 @@
 {
 "data": {
-"E_A": -0.130, "E_T": -0.350, "E_G": -0.520, "E_C": -0.290, "E_c": -0.290, "E_B": -5.000, "t_GG": 0.206, "t_CC": 0.099, "t_AA": 0.074, "t_TT": 0.035, "t_GC": 0.007, "t_CG": 0.031, "t_AT": 0.071, "t_TA": 0.011, "t_CT": 0.071, "t_AG": 0.017, "t_TC": 0.077, "t_GA": 0.008, "t_CA": 0.020, "t_TG": 0.004, "t_AC": 0.021, "t_GT": 0.022, "t_cc": 0.056, "t_Cc": 0.067, "t_cC": 0.091, "t_cG": 0.031, "t_Gc": 0.002, "t_BB": 0.700, "h_GC": 0.073, "h_Gc": 0.069, "h_AT": 0.002, "h_cB": 0.066, "h_GB": 0.092, "h_CB": 0.047, "h_AB": 0.260, "h_TB": 0.079, "r-_GG": 0.021, "r-_CC": 0.090, "r-_AA": 0.081, "r-_TT": 0.009, "r-_GC": 0.097, "r-_CG": 0.097, "r-_AT": 0.005, "r-_TA": 0.005, "r-_CT": 0.010, "r-_AG": 0.051, "r-_TC": 0.010, "r-_GA": 0.051, "r-_CA": 0.023, "r-_TG": 0.017, "r-_AC": 0.023, "r-_GT": 0.017, "r-_cc": 0.097, "r-_Cc": 0.094, "r-_cC": 0.094, "r-_cG": 0.084, "r-_Gc": 0.084, "r+_GG": 0.212, "r+_CC": 0.181, "r+_AA": 0.037, "r+_TT": 0.009, "r+_GC": 0.019, "r+_CG": 0.019, "r+_AT": 0.008, "r+_TA": 0.008, "r+_CT": 0.023, "r+_AG": 0.043, "r+_TC": 0.023, "r+_GA": 0.043, "r+_CA": 0.041, "r+_TG": 0.031, "r+_AC": 0.041, "r+_GT": 0.031, "r+_cc": 0.192, "r+_Cc": 0.186, "r+_cC": 0.186, "r+_cG": 0.030, "r+_Gc": 0.030
+"E_A": -0.130, "E_T": -0.350, "E_G": -0.520, "E_C": -0.290, "E_F": -0.290, "E_B": -5.000, "t_GG": 0.206, "t_CC": 0.099, "t_AA": 0.074, "t_TT": 0.035, "t_GC": 0.007, "t_CG": 0.031, "t_AT": 0.071, "t_TA": 0.011, "t_CT": 0.071, "t_AG": 0.017, "t_TC": 0.077, "t_GA": 0.008, "t_CA": 0.020, "t_TG": 0.004, "t_AC": 0.021, "t_GT": 0.022, "t_FF": 0.056, "t_CF": 0.067, "t_FC": 0.091, "t_FG": 0.031, "t_GF": 0.002, "t_BB": 0.700, "h_GC": 0.073, "h_GF": 0.069, "h_AT": 0.002, "h_FB": 0.066, "h_GB": 0.092, "h_CB": 0.047, "h_AB": 0.260, "h_TB": 0.079, "r-_GG": 0.021, "r-_CC": 0.090, "r-_AA": 0.081, "r-_TT": 0.009, "r-_GC": 0.097, "r-_CG": 0.097, "r-_AT": 0.005, "r-_TA": 0.005, "r-_CT": 0.010, "r-_AG": 0.051, "r-_TC": 0.010, "r-_GA": 0.051, "r-_CA": 0.023, "r-_TG": 0.017, "r-_AC": 0.023, "r-_GT": 0.017, "r-_FF": 0.097, "r-_CF": 0.094, "r-_FC": 0.094, "r-_FG": 0.084, "r-_GF": 0.084, "r+_GG": 0.212, "r+_CC": 0.181, "r+_AA": 0.037, "r+_TT": 0.009, "r+_GC": 0.019, "r+_CG": 0.019, "r+_AT": 0.008, "r+_TA": 0.008, "r+_CT": 0.023, "r+_AG": 0.043, "r+_TC": 0.023, "r+_GA": 0.043, "r+_CA": 0.041, "r+_TG": 0.031, "r+_AC": 0.041, "r+_GT": 0.031, "r+_FF": 0.192, "r+_CF": 0.186, "r+_FC": 0.186, "r+_FG": 0.030, "r+_GF": 0.030
 },
 "metadata": {
-"source": "Simserides2024", "particle": "electron", "tb_model_name": "FELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' and sugar-phosphate backbone denoted as 'B' "
+"source": "Simserides2024", "particle": "electron", "tb_model_name": "FELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'F' and sugar-phosphate backbone denoted as 'B' "
 }
 }
diff --git a/qDNA/data/raw/tb_params/Simserides2024_hole_ELM.json b/qDNA/data/raw/tb_params/Simserides2024_hole_ELM.json
@@ -1,8 +1,8 @@
 {
 "data": {
-"E_A": -7.610, "E_T": -8.240, "E_G": -7.130, "E_C": -7.900, "E_c": -7.630, "t_GG": 0.126, "t_CC": 0.064, "t_AA": 0.028, "t_TT": 0.120, "t_GC": 0.151, "t_CG": 0.025, "t_AT": 0.073, "t_TA": 0.081, "t_CT": 0.048, "t_AG": 0.059, "t_TC": 0.092, "t_GA": 0.131, "t_CA": 0.030, "t_TG": 0.079, "t_AC": 0.074, "t_GT": 0.132, "t_cc": 0.105, "t_Cc": 0.098, "t_cC": 0.067, "t_cG": 0.029, "t_Gc": 0.208, "h_GC": 0.026, "h_Gc": 0.028, "h_AT": 0.034, "r-_GG": 0.030, "r-_CC": 0.004, "r-_AA": 0.082, "r-_TT": 0.002, "r-_GC": 0.027, "r-_CG": 0.027, "r-_AT": 0.008, "r-_TA": 0.008, "r-_CT": 0.002, "r-_AG": 0.014, "r-_TC": 0.002, "r-_GA": 0.014, "r-_CA": 0.018, "r-_TG": 0.018, "r-_AC": 0.018, "r-_GT": 0.018, "r-_cc": 0.004, "r-_Cc": 0.004, "r-_cC": 0.004, "r-_cG": 0.027, "r-_Gc": 0.027, "r+_GG": 0.028, "r+_CC": 0.000, "r+_AA": 0.043, "r+_TT": 0.002, "r+_GC": 0.001, "r+_CG": 0.001, "r+_AT": 0.013, "r+_TA": 0.013, "r+_CT": 0.000, "r+_AG": 0.018, "r+_TC": 0.000, "r+_GA": 0.018, "r+_CA": 0.000, "r+_TG": 0.007, "r+_AC": 0.000, "r+_GT": 0.007, "r+_cc": 0.000, "r+_Cc": 0.000, "r+_cC": 0.000, "r+_cG": 0.002, "r+_Gc": 0.002
+"E_A": -7.610, "E_T": -8.240, "E_G": -7.130, "E_C": -7.900, "E_F": -7.630, "t_GG": 0.126, "t_CC": 0.064, "t_AA": 0.028, "t_TT": 0.120, "t_GC": 0.151, "t_CG": 0.025, "t_AT": 0.073, "t_TA": 0.081, "t_CT": 0.048, "t_AG": 0.059, "t_TC": 0.092, "t_GA": 0.131, "t_CA": 0.030, "t_TG": 0.079, "t_AC": 0.074, "t_GT": 0.132, "t_FF": 0.105, "t_CF": 0.098, "t_FC": 0.067, "t_FG": 0.029, "t_GF": 0.208, "h_GC": 0.026, "h_GF": 0.028, "h_AT": 0.034, "r-_GG": 0.030, "r-_CC": 0.004, "r-_AA": 0.082, "r-_TT": 0.002, "r-_GC": 0.027, "r-_CG": 0.027, "r-_AT": 0.008, "r-_TA": 0.008, "r-_CT": 0.002, "r-_AG": 0.014, "r-_TC": 0.002, "r-_GA": 0.014, "r-_CA": 0.018, "r-_TG": 0.018, "r-_AC": 0.018, "r-_GT": 0.018, "r-_FF": 0.004, "r-_CF": 0.004, "r-_FC": 0.004, "r-_FG": 0.027, "r-_GF": 0.027, "r+_GG": 0.028, "r+_CC": 0.000, "r+_AA": 0.043, "r+_TT": 0.002, "r+_GC": 0.001, "r+_CG": 0.001, "r+_AT": 0.013, "r+_TA": 0.013, "r+_CT": 0.000, "r+_AG": 0.018, "r+_TC": 0.000, "r+_GA": 0.018, "r+_CA": 0.000, "r+_TG": 0.007, "r+_AC": 0.000, "r+_GT": 0.007, "r+_FF": 0.000, "r+_CF": 0.000, "r+_FC": 0.000, "r+_FG": 0.002, "r+_GF": 0.002
 },
 "metadata": {
-"source": "Simserides2024", "particle": "hole", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' "
+"source": "Simserides2024", "particle": "hole", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'F' "
 }
 }
diff --git a/qDNA/data/raw/tb_params/Simserides2024_hole_FELM.json b/qDNA/data/raw/tb_params/Simserides2024_hole_FELM.json
@@ -1,8 +1,8 @@
 {
 "data": {
-"E_A": -7.610, "E_T": -8.240, "E_G": -7.130, "E_C": -7.900, "E_c": -7.630, "E_B": -9.400, "t_GG": 0.126, "t_CC": 0.064, "t_AA": 0.028, "t_TT": 0.120, "t_GC": 0.151, "t_CG": 0.025, "t_AT": 0.073, "t_TA": 0.081, "t_CT": 0.048, "t_AG": 0.059, "t_TC": 0.092, "t_GA": 0.131, "t_CA": 0.030, "t_TG": 0.079, "t_AC": 0.074, "t_GT": 0.132, "t_cc": 0.105, "t_Cc": 0.098, "t_cC": 0.067, "t_cG": 0.029, "t_Gc": 0.208, "t_BB": 0.026, "h_GC": 0.026, "h_Gc": 0.028, "h_AT": 0.034, "h_cB": 0.178, "h_GB": 0.016, "h_CB": 0.173, "h_AB": 0.024, "h_TB": 0.179, "r-_GG": 0.030, "r-_CC": 0.004, "r-_AA": 0.082, "r-_TT": 0.002, "r-_GC": 0.027, "r-_CG": 0.027, "r-_AT": 0.008, "r-_TA": 0.008, "r-_CT": 0.002, "r-_AG": 0.014, "r-_TC": 0.002, "r-_GA": 0.014, "r-_CA": 0.018, "r-_TG": 0.018, "r-_AC": 0.018, "r-_GT": 0.018, "r-_cc": 0.004, "r-_Cc": 0.004, "r-_cC": 0.004, "r-_cG": 0.027, "r-_Gc": 0.027, "r+_GG": 0.028, "r+_CC": 0.000, "r+_AA": 0.043, "r+_TT": 0.002, "r+_GC": 0.001, "r+_CG": 0.001, "r+_AT": 0.013, "r+_TA": 0.013, "r+_CT": 0.000, "r+_AG": 0.018, "r+_TC": 0.000, "r+_GA": 0.018, "r+_CA": 0.000, "r+_TG": 0.007, "r+_AC": 0.000, "r+_GT": 0.007, "r+_cc": 0.000, "r+_Cc": 0.000, "r+_cC": 0.000, "r+_cG": 0.002, "r+_Gc": 0.002
+"E_A": -7.610, "E_T": -8.240, "E_G": -7.130, "E_C": -7.900, "E_F": -7.630, "E_B": -9.400, "t_GG": 0.126, "t_CC": 0.064, "t_AA": 0.028, "t_TT": 0.120, "t_GC": 0.151, "t_CG": 0.025, "t_AT": 0.073, "t_TA": 0.081, "t_CT": 0.048, "t_AG": 0.059, "t_TC": 0.092, "t_GA": 0.131, "t_CA": 0.030, "t_TG": 0.079, "t_AC": 0.074, "t_GT": 0.132, "t_FF": 0.105, "t_CF": 0.098, "t_FC": 0.067, "t_FG": 0.029, "t_GF": 0.208, "t_BB": 0.026, "h_GC": 0.026, "h_GF": 0.028, "h_AT": 0.034, "h_FB": 0.178, "h_GB": 0.016, "h_CB": 0.173, "h_AB": 0.024, "h_TB": 0.179, "r-_GG": 0.030, "r-_CC": 0.004, "r-_AA": 0.082, "r-_TT": 0.002, "r-_GC": 0.027, "r-_CG": 0.027, "r-_AT": 0.008, "r-_TA": 0.008, "r-_CT": 0.002, "r-_AG": 0.014, "r-_TC": 0.002, "r-_GA": 0.014, "r-_CA": 0.018, "r-_TG": 0.018, "r-_AC": 0.018, "r-_GT": 0.018, "r-_FF": 0.004, "r-_CF": 0.004, "r-_FC": 0.004, "r-_FG": 0.027, "r-_GF": 0.027, "r+_GG": 0.028, "r+_CC": 0.000, "r+_AA": 0.043, "r+_TT": 0.002, "r+_GC": 0.001, "r+_CG": 0.001, "r+_AT": 0.013, "r+_TA": 0.013, "r+_CT": 0.000, "r+_AG": 0.018, "r+_TC": 0.000, "r+_GA": 0.018, "r+_CA": 0.000, "r+_TG": 0.007, "r+_AC": 0.000, "r+_GT": 0.007, "r+_FF": 0.000, "r+_CF": 0.000, "r+_FC": 0.000, "r+_FG": 0.002, "r+_GF": 0.002
 },
 "metadata": {
-"source": "Simserides2024", "particle": "hole", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'c' and the sugar-phosphate backbone denoted as 'B' "
+"source": "Simserides2024", "particle": "hole", "tb_model_name": "ELM", "unit": "eV", "notes": "includes 5'-methylated cytosine denoted as 'F' and the sugar-phosphate backbone denoted as 'B' "
 }
 }
diff --git a/qDNA/defaults.yaml b/qDNA/defaults.yaml
@@ -16,7 +16,7 @@ diss_kwargs_default:
     glob_deph_rate: 0. # rad/fs
     uniform_relaxation: True
     relax_rate: 0. # rad/fs
-    relax_rates: {'A': 0, 'T': 0, 'G': 0, 'C': 0, 'B': 0}
+    relax_rates: {'A': 0, 'T': 0, 'G': 0, 'C': 0, 'F':0, 'B': 0}
     loc_therm: False
     glob_therm: False
     deph_rate: 7. # in rad/ps

diff --git a/qDNA/dna_seq.py b/qDNA/dna_seq.py
@@ -88,7 +88,7 @@ def __init__(self, upper_strand, tb_model_name, methylated=True, lower_strand=No
             "T": "A",
             "G": "C",
             "C": "G",
-            "c": "G",
+            "F": "G",
         }
         # Generate the DNA sequence
         self.dna_seq = self._create_dna_seq()
@@ -162,17 +162,17 @@ def _create_dna_seq(self):
     def _add_methylation(self):
         """
         Adds methylation to the lower DNA strand according to the fragile X syndrome.
-        This method searches for occurrences of the sequence "cG" in the upper DNA strand.
+        This method searches for occurrences of the sequence "FG" in the upper DNA strand.
         For each occurrence, it modifies the corresponding position in the lower DNA strand
-        by changing the character following the match to "c".
+        by changing the character following the match to "F".
         """
         # Find all occurrences of "cG" in the upper DNA strand
-        matches = [match.start() for match in re.finditer("cG", self.upper_strand)]
+        matches = [match.start() for match in re.finditer("FG", self.upper_strand)]
 
         # Modify the lower DNA strand based on the matches
         lower_strand_list = list(self.lower_strand)
         for match in matches:
-            lower_strand_list[match + 1] = "c"
+            lower_strand_list[match + 1] = "F"
         self.lower_strand = "".join(lower_strand_list)
 
 

diff --git a/qDNA/plotting/__init__.py b/qDNA/plotting/__init__.py
@@ -7,11 +7,11 @@
 
 plt.rcParams.update(
     {
-        "text.usetex": True,
-        "font.family": "serif",
-        "font.serif": ["Times"],  # used in elsarticle (Elsevier)
+        # "text.usetex": True,
+        # "font.family": "serif",
+        # "font.serif": ["Times"],  # used in elsarticle (Elsevier)
         # "font.serif": ["Computer Modern Roman"], # used in revtex4-2 (APS)
-        "text.latex.preamble": r"\usepackage{amsmath}\usepackage{siunitx}",
+        # "text.latex.preamble": r"\usepackage{amsmath}\usepackage{siunitx}",
         "legend.fontsize": 20,
         "xtick.labelsize": 20,
         "ytick.labelsize": 20,

diff --git a/qDNA/plotting/plot_dna_base_frequency.py b/qDNA/plotting/plot_dna_base_frequency.py
@@ -51,7 +51,7 @@ def plot_dna_base_frequency(lifetime_dict, cutoff_num=10):
 
     # calculation
     lifetimes = np.array(list(lifetime_dict.values())[cutoff_num:])  # in fs
-    lifetime *= 1e-3  # Convert fs to ps
+    lifetimes *= 1e-3  # Convert fs to ps
 
     base_freq_dict = {}
     for base in ["A", "T", "G", "C"]: