lcao commit

qDNA/__init__.py

@@ -9,6 +9,7 @@
 from .tools import *
 from .utils import *
 
+from .lcao import *
 from .dna_seq import *
 from .model import *
 from .hamiltonian import *

qDNA/data/raw/config.json

@@ -1 +1,13 @@
-{"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": {}}
+{
+    "data": {
+      "DNA_BASES": ["A", "T", "G", "C", "F"],
+      "TB_MODELS": ["WM", "LM", "ELM", "FWM", "FLM", "FELM", "FC"],
+      "SOURCES": ["Hawke2010", "Simserides2014", "Mantela2021", "Simserides2024", "Herb2024", "1BNA"],
+      "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": {}
+  }

qDNA/data/raw/lcao_params/HKS.json

@@ -0,0 +1,8 @@
+{
+    "chi_pppi":-0.63,
+    "chi_sssigma":2.22,
+    "E_CP":-6.7,
+    "E_Np_2":-7.9,
+    "E_Np_3":-10.9,
+    "E_Op":-11.8
+}

qDNA/data/raw/lcao_params/MMTS.json

@@ -0,0 +1,8 @@
+{
+    "chi_pppi":-0.77,
+    "chi_sssigma":2.22,
+    "E_CP":-6.56,
+    "E_Np_2":-9.62,
+    "E_Np_3":-11.48,
+    "E_Op":-10.35
+}

qDNA/data/raw/lcao_params/MSF.json

@@ -0,0 +1,18 @@
+{
+    "chi_sssigma": -1.32,
+    "chi_spsigma": -1.42,
+    "chi_pppi": -0.73,
+    "chi_ppsigma": 2.22,
+    "E_Hs": -13.638,
+    "E_Cs": -13.18,
+    "E_Cp": -6.7,
+    "E_Ns": -14.51,
+    "E_Np": -9.55,
+    "E_Os": -15.03,
+    "E_Op": -11.52,
+    "b": 0.7,
+    "d0": 1.35,
+    "d0H": 1.0,
+    "cutoff_radius": 1.59,
+    "cutoff_radius_H": 2.651
+}

qDNA/data/raw/tb_params/1BNA_electron_LM.json

@@ -0,0 +1 @@
+{"data": {"t_01C02G": 31.61, "h_01C24G": -1.85, "h_02G23C": -0.61, "t_23C24G": 36.86, "E_01C": -4407.5, "E_02G": -4122.11, "E_23C": -4396.97, "E_24G": -4117.5, "t_02G03C": 85.75, "h_03C22G": -0.3, "t_22G23C": 43.8, "E_03C": -4406.16, "E_22G": -4121.57, "t_03C04G": -25.49, "h_04G21C": -1.87, "t_21C22G": -34.44, "E_04G": -4110.29, "E_21C": -4400.93, "t_04G05A": -30.57, "h_05A20T": 13.08, "t_20T21C": -3.65, "E_05A": -4299.77, "E_20T": -4381.16, "t_05A06A": -33.36, "h_06A19T": -9.93, "t_19T20T": -19.71, "E_06A": -4300.28, "E_19T": -4388.51, "t_06A07T": 9.05, "h_07T18A": -11.19, "t_18A19T": 14.78, "E_07T": -4398.61, "E_18A": -4292.44, "t_07T08T": 22.16, "h_08T17A": 11.05, "t_17A18A": 33.66, "E_08T": -4390.88, "E_17A": -4312.89, "t_08T09C": -7.94, "h_09C16G": 0.2, "t_16G17A": 8.84, "E_09C": -4396.15, "E_16G": -4110.66, "t_09C10G": 35.12, "h_10G15C": 0.97, "t_15C16G": 19.17, "E_10G": -4118.87, "E_15C": -4403.71, "t_10G11C": 32.44, "h_11C14G": 0.24, "t_14G15C": 76.22, "E_11C": -4405.89, "E_14G": -4114.6, "t_11C12G": 27.56, "h_12G13C": -0.48, "t_13C14G": -21.64, "E_12G": -4116.63, "E_13C": -4400.85}, "metadata": {"source": "1BNA", "particle": "electron", "tb_model_name": "LM", "unit": "meV", "notes": "Geometries from RCSB 1BNA"}}

qDNA/data/raw/tb_params/1BNA_hole_LM.json

@@ -0,0 +1 @@
+{"data": {"t_01C02G": 51.74, "h_01C24G": 42.72, "h_02G23C": 40.54, "t_23C24G": 44.51, "E_01C": -8688.17, "E_02G": -8245.54, "E_23C": -8703.52, "E_24G": -8254.17, "t_02G03C": -62.15, "h_03C22G": 52.42, "t_22G23C": 2.81, "E_03C": -8702.17, "E_22G": -8255.1, "t_03C04G": -13.71, "h_04G21C": -46.31, "t_21C22G": 12.87, "E_04G": -8236.57, "E_21C": -8699.98, "t_04G05A": -1.17, "h_05A20T": -18.15, "t_20T21C": 118.09, "E_05A": -8426.53, "E_20T": -9118.54, "t_05A06A": -54.27, "h_06A19T": 9.74, "t_19T20T": -70.44, "E_06A": -8429.44, "E_19T": -9106.04, "t_06A07T": 75.06, "h_07T18A": 9.32, "t_18A19T": 134.35, "E_07T": -9117.11, "E_18A": -8426.33, "t_07T08T": -61.12, "h_08T17A": -26.37, "t_17A18A": -75.88, "E_08T": -9100.56, "E_17A": -8412.01, "t_08T09C": -137.39, "h_09C16G": -36.16, "t_16G17A": -63.02, "E_09C": -8689.41, "E_16G": -8230.12, "t_09C10G": 17.8, "h_10G15C": 52.62, "t_15C16G": 10.69, "E_10G": -8243.86, "E_15C": -8698.44, "t_10G11C": -20.68, "h_11C14G": -25.11, "t_14G15C": -25.39, "E_11C": -8697.09, "E_14G": -8234.53, "t_11C12G": -51.3, "h_12G13C": -37.6, "t_13C14G": -36.93, "E_12G": -8242.82, "E_13C": -8687.74}, "metadata": {"source": "1BNA", "particle": "hole", "tb_model_name": "LM", "unit": "meV", "notes": "Geometries from RCSB 1BNA"}}

qDNA/data/raw/tb_params/Herb2024_electron_ELM.json

@@ -0,0 +1 @@
+{"data": {"t_AA": -37.42, "h_AT": 31.81, "t_TT": -168.33, "E_A": -8496.74, "E_T": -9120.92, "r+_AT": 10.3, "r-_AT": -4.3, "t_AC": -43.28, "h_CG": 45.25, "t_GT": -121.25, "E_C": -8668.94, "E_G": -8307.66, "r+_AG": 9.23, "r-_CT": 1.19, "t_AG": 33.27, "h_GC": 45.21, "t_CT": -130.61, "r+_AC": 21.24, "r-_GT": 17.1, "t_AT": 98.82, "h_TA": -31.8, "r+_AA": -41.07, "r-_TT": 1.49, "t_CA": -83.24, "t_TG": 61.79, "r+_CT": -4.57, "r-_AG": 8.63, "t_CC": -130.55, "t_GG": 112.4, "r+_CG": -8.07, "r-_CG": -12.13, "t_CG": 68.53, "r+_CC": -8.91, "r-_GG": 54.82, "r+_CA": 21.21, "r-_TG": -17.11, "t_GA": 143.72, "t_TC": -165.64, "r+_GT": 4.0, "r-_AC": 0.51, "t_GC": 44.35, "r+_GG": 13.02, "r-_CC": -1.17, "r+_GC": 8.09, "r-_GC": -12.12, "r+_GA": -9.24, "r-_TC": -1.19, "t_TA": -65.61, "r+_TT": -2.34, "r-_AA": 50.46, "r+_TG": -3.99, "r-_CA": -0.51, "r+_TC": -4.57, "r-_GA": -8.58, "r+_TA": 10.28, "r-_TA": -4.29}, "metadata": {"source": "Herb2024", "particle": "electron", "tb_model_name": "ELM", "unit": "meV", "notes": "Geometries from Biovia"}}

qDNA/data/raw/tb_params/Herb2024_electron_LM.json

@@ -0,0 +1 @@
+{"data": {"t_AA": -37.42, "h_AT": 31.81, "t_TT": -168.33, "E_A": -8496.74, "E_T": -9120.92, "t_AC": -43.28, "h_CG": 45.25, "t_GT": -121.25, "E_C": -8668.94, "E_G": -8307.66, "t_AG": 33.27, "h_GC": 45.21, "t_CT": -130.61, "t_AT": 98.82, "h_TA": -31.8, "t_CA": -83.24, "t_TG": 61.79, "t_CC": -130.55, "t_GG": 112.4, "t_CG": 68.53, "t_GA": 143.72, "t_TC": -165.64, "t_GC": 44.35, "t_TA": -65.61}, "metadata": {"source": "Herb2024", "particle": "electron", "tb_model_name": "LM", "unit": "meV", "notes": "Geometries from Biovia"}}

qDNA/data/raw/tb_params/Herb2024_electron_WM.json

@@ -0,0 +1 @@
+{"data": {"t_AA": -38.42, "E_A": -8489.8, "t_AC": 16.32, "E_C": -8299.74, "t_AG": 36.81, "E_G": -8299.63, "t_AT": 49.76, "E_T": -8489.79, "t_CA": -27.47, "t_CC": -115.79, "t_CG": 75.23, "t_CT": -36.58, "t_GA": 142.03, "t_GC": -9.92, "t_GG": -115.92, "t_GT": -16.35, "t_TA": -37.07, "t_TC": 142.14, "t_TG": -27.46, "t_TT": 38.28}, "metadata": {"source": "Herb2024", "particle": "electron", "tb_model_name": "WM", "unit": "meV", "notes": "Geometries from Biovia"}}

qDNA/data/raw/tb_params/Herb2024_hole_ELM.json

@@ -0,0 +1 @@
+{"data": {"t_AA": 106.22, "h_AT": -95.62, "t_TT": 27.22, "E_A": -10079.62, "E_T": -10457.82, "r+_AT": -10.38, "r-_AT": -37.52, "t_AC": 103.71, "h_CG": -151.55, "t_GT": 139.95, "E_C": -9994.06, "E_G": -9931.62, "r+_AG": 58.36, "r-_CT": 4.43, "t_AG": -132.6, "h_GC": -151.49, "t_CT": 76.92, "r+_AC": -14.34, "r-_GT": -75.84, "t_AT": -76.94, "h_TA": 95.76, "r+_AA": -54.33, "r-_TT": 4.38, "t_CA": -117.9, "t_TG": 19.97, "r+_CT": -7.51, "r-_AG": -174.12, "t_CC": -29.54, "t_GG": -173.77, "r+_CG": 17.96, "r-_CG": 70.64, "t_CG": 8.78, "r+_CC": -10.72, "r-_GG": -227.32, "r+_CA": -14.32, "r-_TG": 75.76, "t_GA": -144.78, "t_TC": -88.64, "r+_GT": -12.34, "r-_AC": 32.09, "t_GC": -84.2, "r+_GG": 89.16, "r-_CC": -4.56, "r+_GC": -17.99, "r-_GC": 70.74, "r+_GA": -58.36, "r-_TC": -4.44, "t_TA": -137.71, "r+_TT": -5.39, "r-_AA": 72.05, "r+_TG": 12.32, "r-_CA": -32.13, "r+_TC": -7.51, "r-_GA": 174.12, "r+_TA": -10.37, "r-_TA": -37.58}, "metadata": {"source": "Herb2024", "particle": "hole", "tb_model_name": "ELM", "unit": "meV", "notes": "Geometries from Biovia"}}

qDNA/data/raw/tb_params/Herb2024_hole_LM.json

@@ -0,0 +1 @@
+{"data": {"t_AA": 106.22, "h_AT": -95.62, "t_TT": 27.22, "E_A": -10079.62, "E_T": -10457.82, "t_AC": 103.71, "h_CG": -151.55, "t_GT": 139.95, "E_C": -9994.06, "E_G": -9931.62, "t_AG": -132.6, "h_GC": -151.49, "t_CT": 76.92, "t_AT": -76.94, "h_TA": 95.76, "t_CA": -117.9, "t_TG": 19.97, "t_CC": -29.54, "t_GG": -173.77, "t_CG": 8.78, "t_GA": -144.78, "t_TC": -88.64, "t_GC": -84.2, "t_TA": -137.71}, "metadata": {"source": "Herb2024", "particle": "hole", "tb_model_name": "LM", "unit": "meV", "notes": "Geometries from Biovia"}}

qDNA/data/raw/tb_params/Herb2024_hole_WM.json

@@ -0,0 +1 @@
+{"data": {"t_AA": -169.25, "E_A": -9120.27, "t_AC": -17.13, "E_C": -8667.3, "t_AG": 127.49, "E_G": -8667.34, "t_AT": -14.44, "E_T": -9119.98, "t_CA": -16.1, "t_CC": -127.66, "t_CG": 21.3, "t_CT": -126.73, "t_GA": 166.31, "t_GC": 7.31, "t_GG": -128.53, "t_GT": 17.09, "t_TA": 11.54, "t_TC": 165.26, "t_TG": -16.07, "t_TT": 168.32}, "metadata": {"source": "Herb2024", "particle": "hole", "tb_model_name": "WM", "unit": "meV", "notes": "Geometries from Biovia"}}

qDNA/data/raw/tb_params/Simserides2024_electron_ELM.json

@@ -1,8 +1,94 @@
 {
-"data": {
-"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 'F' "
-}
+    "data": {
+        "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,
+        "r-_AF": 0.023,
+        "r-_FA": 0.023,
+        "r-_FT": 0.009,
+        "r-_TF": 0.009,
+        "r+_AF": 0.042,
+        "r+_FA": 0.042,
+        "r+_FT": 0.024,
+        "r+_TF": 0.024,
+        "t_AF": 0.077,
+        "t_FA": 0.017,
+        "t_FT": 0.049,
+        "t_TF": 0.018
+    },
+    "metadata": {
+        "source": "Simserides2024",
+        "particle": "electron",
+        "tb_model_name": "ELM",
+        "unit": "eV",
+        "notes": "includes 5'-methylated cytosine denoted as 'F' "
+    }
 }

qDNA/data/raw/tb_params/Simserides2024_electron_FELM.json

@@ -1,8 +1,101 @@
 {
-"data": {
-"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 'F' and sugar-phosphate backbone denoted as 'B' "
-}
+    "data": {
+        "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,
+        "r-_AF": 0.023,
+        "r-_FA": 0.023,
+        "r-_FT": 0.009,
+        "r-_TF": 0.009,
+        "r+_AF": 0.042,
+        "r+_FA": 0.042,
+        "r+_FT": 0.024,
+        "r+_TF": 0.024,
+        "t_AF": 0.077,
+        "t_FA": 0.017,
+        "t_FT": 0.049,
+        "t_TF": 0.018
+    },
+    "metadata": {
+        "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' "
+    }
 }

qDNA/data/raw/tb_params/Simserides2024_hole_ELM.json

@@ -1,8 +1,94 @@
 {
-"data": {
-"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 'F' "
-}
+    "data": {
+        "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,
+        "r-_AF": 0.017,
+        "r-_FA": 0.017,
+        "r-_FT": 0.002,
+        "r-_TF": 0.002,
+        "r+_AF": 0.002,
+        "r+_FA": 0.002,
+        "r+_FT": 0.000,
+        "r+_TF": 0.000,
+        "t_AF": 0.119,
+        "t_FA": 0.034,
+        "t_FT": 0.059,
+        "t_TF": 0.150
+    },
+    "metadata": {
+        "source": "Simserides2024",
+        "particle": "hole",
+        "tb_model_name": "ELM",
+        "unit": "eV",
+        "notes": "includes 5'-methylated cytosine denoted as 'F' "
+    }
 }