Making parameter files JSON-compliant (#52)

* WIP making parameter files JSON-compliant

* Make test future-proof

* Add citekeys

* Refactor peptide interaction parameters

* remove verbose from CI

* remove Avogadro dataset

---------

Co-authored-by: Jean-Noël Grad <[email protected]>
Co-authored-by: pm-blanco<[email protected]>

Makefile

@@ -15,6 +15,7 @@ tests:
 	python3 testsuite/create_molecule_position_test.py
 	python3 testsuite/seed_test.py
 	python3 testsuite/read-write-df_test.py
+	python3 testsuite/parameter_test.py
 	python3 testsuite/henderson_hasselbalch_tests.py
 	python3 testsuite/cph_ideal_tests.py
 	python3 testsuite/grxmc_ideal_tests.py

parameters/peptides/Blanco2021.json

@@ -0,0 +1,23 @@
+{
+	"metadata": {
+		"summary": "Interaction parameters from Blanco et al.",
+		"source": "Blanco et al. Soft Matter, 17(3), 655-669, 2021.",
+		"doi": "10.1039/d0sm01475c", 
+		"citekey": "blanco2021a"
+	},
+	"data": {
+		"D": {"object_type":"particle", "name": "D", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"E": {"object_type":"particle", "name": "E", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"n": {"object_type":"particle", "name": "n", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"S": {"object_type":"particle", "name": "S", "q":0, "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"H": {"object_type":"particle", "name": "H", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"A": {"object_type":"particle", "name": "A", "q":0, "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"K": {"object_type":"particle", "name": "K", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"Y": {"object_type":"particle", "name": "Y", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"R": {"object_type":"particle", "name": "R", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"G": {"object_type":"particle", "name": "G", "q":0, "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"F": {"object_type":"particle", "name": "F", "q":0, "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"c": {"object_type":"particle", "name": "c", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"bond": {"object_type":"bond",  "bond_type": "harmonic", "bond_parameters" : {"r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N/m"}}, "particle_pairs": [["n","D"],["S","D"],["S","H"],["H","A"],["A","K"],["E","H"],["E","K"],["K","R"],["K","H"],["R","H"],["H","H"],["H","G"],["G","Y"],["Y","K"],["R","K"],["K","F"],["H","S"],["H","F"],["H","R"],["R","G"],["Y","G"],["Y","c"]]}
+	}
+}

parameters/peptides/Lunkad2021.json

@@ -0,0 +1,22 @@
+{
+	"metadata": {
+		"summary": "Interaction parameters from Lunkad et al.",
+		"source": "Lunkad, R. et al.  Molecular Systems Design & Engineering (2021), 6(2), 122-131.",
+		"doi": "10.1039/D0ME00147C", 
+		"citekey": "lunkad2021a"
+	},
+	"data": {
+		"CA": {"object_type":"particle", "name": "CA", "q":0, "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"D": {"object_type":"particle", "name": "D",  "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"E": {"object_type":"particle", "name": "E",  "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"H": {"object_type":"particle", "name": "H",  "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"Y": {"object_type":"particle", "name": "Y",  "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"K": {"object_type":"particle", "name": "K", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}},
+		"bond_CA_CA": {"object_type":"bond",  "bond_type": "harmonic", "particle_pairs": [["CA","CA"]] , "bond_parameters" : {"r_0": {"value":0.382, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}},
+		"bond_CA_D": {"object_type":"bond",  "bond_type": "harmonic", "particle_pairs": [["CA","D"]] , "bond_parameters" : {"r_0": {"value":0.329, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}},
+		"bond_CA_E": {"object_type":"bond",  "bond_type": "harmonic", "particle_pairs": [["CA","E"]] , "bond_parameters" : {"r_0": {"value":0.435, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}},
+		"bond_CA_H": {"object_type":"bond",  "bond_type": "harmonic", "particle_pairs": [["CA","H"]] , "bond_parameters" : {"r_0": {"value":0.452, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}},
+		"bond_CA_Y": {"object_type":"bond",  "bond_type": "harmonic", "particle_pairs": [["CA","Y"]] , "bond_parameters" : {"r_0": {"value":0.648, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}},
+		"bondd_CA_K": {"object_type":"bond",  "bond_type": "harmonic", "particle_pairs": [["CA","K"]] , "bond_parameters" : {"r_0": {"value":0.558, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}}
+	}
+}

parameters/pka_sets/Bienkiewicz1999.json

@@ -0,0 +1,13 @@
+{
+	"metadata": {
+		"summary": "pKa-values for phosphorilated aminoacids J U and Z from Bienkiewicz & K.J. Lumb",
+		"source": "Bienkiewicz & K.J. Lumb, J Biomol NMR 15: 203-206 (1999).", 
+		"doi": "10.1023/A:1008375029746",
+		"citekey": "bienkiewicz1999a" 
+	},
+	"data": {
+		"J": {"pka_value": 5.96, "acidity": "acidic"},
+		"U": {"pka_value": 6.30, "acidity": "acidic"},
+		"Z": {"pka_value": 5.96, "acidity": "acidic"}
+	}
+}

parameters/pka_sets/CRC1991.json

@@ -0,0 +1,19 @@
+{
+	"metadata": {
+		"summary": "pKa-values from CRC 72nd edition",
+		"source": "Handbook of Chemistry and Physics, 72nd Edition, CRC Press, Boca Raton, FL, 1991.",
+		"isbn": "0-8493-0565-9",
+		"citekey": "lide1991a"
+	},
+	"data": {
+		"D": {"pka_value": 3.65, "acidity": "acidic"},
+		"E": {"pka_value": 4.25, "acidity": "acidic"},
+		"Y": {"pka_value": 10.07, "acidity": "acidic"},
+		"C": {"pka_value": 8.18, "acidity": "acidic"},
+		"H": {"pka_value": 6.00, "acidity": "basic"},
+		"K": {"pka_value": 10.54, "acidity": "basic"},
+		"R": {"pka_value": 12.48, "acidity": "basic"},
+		"n": {"pka_value": 8.0, "acidity": "basic"},
+		"c": {"pka_value": 3.6, "acidity": "acidic"}
+	}
+}

parameters/pka_sets/Dobrev2020.json

@@ -0,0 +1,15 @@
+{
+	"metadata": {
+		"summary": "pKa-values from Dobrev",
+		"source": "Dobrev P., Probing the Accuracy of Explicit Solvent Constant pH Molecular Dynamics Simulations for Peptides, J. Chem. Theory Comput. 2020, 16, 2561−2569", 
+		"notes": "n and c were added from Nozaki pKa set",
+		"doi": "10.1021/acs.jctc.9b01232",
+		"citekey": "dobrev2020a"
+	},
+	"data": {
+		"E" : {"pka_value": 4.08, "acidity": "acidic"},
+		"H" : {"pka_value": 6.54, "acidity": "basic"},
+		"n" : {"pka_value": 7.5, "acidity": "basic"},
+		"c" : {"pka_value": 3.8, "acidity": "acidic"}
+	}
+}

parameters/pka_sets/Hass2015.json

@@ -0,0 +1,19 @@
+{
+	"metadata": {
+		"summary": "pKa-values of Hass et al.",
+		"source": "Hass MA, Mulder FAA. Contemporary NMR Studies of Protein Electrostatics. Annu Rev Biophys. 2015;44:53-75.", 
+		"doi": "10.1146/annurev-biophys-083012-130351",
+		"citekey": "hass2015a"
+	},
+	"data": {
+		"D": {"pka_value": 4.0, "acidity": "acidic"},
+		"E": {"pka_value": 4.4, "acidity": "acidic"},
+		"Y": {"pka_value": 9.6, "acidity": "acidic"},
+		"C": {"pka_value": 8.3, "acidity": "acidic"},
+		"H": {"pka_value": 6.8, "acidity": "basic"},
+		"K": {"pka_value": 10.4, "acidity": "basic"},
+		"R": {"pka_value": 13.5, "acidity": "basic"},
+		"n": {"pka_value": 8.0, "acidity": "basic"},
+		"c": {"pka_value": 3.6, "acidity": "acidic"}
+	}
+}

parameters/pka_sets/Nozaki1967.json

@@ -0,0 +1,19 @@
+{
+	"metadata": {
+		"summary": "pKa-values from Nozaki et al.",
+		"source": "Y. Nozaki and C. Tanford, Methods Enzymol., 1967, 11, 715–734.",
+		"doi": "10.1016/S0076-6879(67)11088-4",
+		"citekey": "nozaki1967a"
+	},
+	"data": {
+		"D": {"pka_value": 4.0, "acidity": "acidic"},
+		"E": {"pka_value": 4.4, "acidity": "acidic"},
+		"Y": {"pka_value": 9.6, "acidity": "acidic"},
+		"C": {"pka_value": 9.5, "acidity": "acidic"},
+		"H": {"pka_value": 6.3, "acidity": "basic"},
+		"K": {"pka_value": 10.4, "acidity": "basic"},
+		"R": {"pka_value": 12.0, "acidity": "basic"},
+		"n": {"pka_value": 7.5, "acidity": "basic"},
+		"c": {"pka_value": 3.8, "acidity": "acidic"}
+	}
+}

parameters/pka_sets/Platzer2014.json

@@ -0,0 +1,19 @@
+{
+	"metadata": {
+		"summary": "pKa-values from Platzer et al.",
+		"source": "Platzer G, Okon M, McIntosh LP. 2014.  J. Biomol. NMR 60:109–29", 
+		"doi": "10.1007/s10858-014-9862-y",
+		"citekey": "platzer2014a"
+	},
+	"data": {
+		"D" : {"pka_value": 3.86, "acidity": "acidic"},
+		"E" : {"pka_value": 4.34, "acidity": "acidic"},
+		"Y" : {"pka_value": 9.76, "acidity": "acidic"},
+		"C" : {"pka_value": 8.49, "acidity": "acidic"},
+		"H" : {"pka_value": 6.45, "acidity": "basic"},
+		"K" : {"pka_value": 10.34, "acidity": "basic"},
+		"R" : {"pka_value": 13.9, "acidity": "basic"},
+		"n" : {"pka_value": 8.23, "acidity": "basic"},
+		"c" : {"pka_value": 3.55, "acidity": "acidic"}
+	}
+}

parameters/pka_sets/Thurlkill2006.json

@@ -0,0 +1,18 @@
+{
+	"metadata": {
+		"summary": "pKa-values from Thurlkill et al.", 
+		"source": "Thurlkill RL, Grimsley GR, Scholtz JM, Pace CN. pK values of the ionizable groups of proteins. Protein Sci. 2006 May;15(5):1214-8", 
+		"doi": "10.1110/ps.051840806",
+		"citekey": "thurlkill2006a"
+	},
+	"data": {
+		"D" : {"pka_value": 3.67, "acidity": "acidic"},
+		"E" : {"pka_value": 4.25, "acidity": "acidic"},
+		"Y" : {"pka_value": 9.84, "acidity": "acidic"},
+		"C" : {"pka_value": 8.55, "acidity": "acidic"},
+		"H" : {"pka_value": 6.54, "acidity": "basic"},
+		"K" : {"pka_value": 10.40, "acidity": "basic"},
+		"n" : {"pka_value": 8.00, "acidity": "basic"},
+		"c" : {"pka_value": 3.67, "acidity": "acidic"}
+	}
+}