Skip to content

Commit

Permalink
Merge pull request #27 from pyMBE-dev/refactor-lj-parameters
Browse files Browse the repository at this point in the history 
Refactor lj parameters
  • Loading branch information
@pm-blanco
pm-blanco authored Apr 1, 2024
2 parents 87b73b0 + 09c9257 commit b787b89
Show file tree
Hide file tree
Showing 16 changed files with 1,794 additions and 263 deletions.
1 change: 1 addition & 0 deletions Makefile
View file
Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@ docs:
pdoc ./pyMBE.py -o ./documentation --docformat google

tests:
python3 testsuite/lj_tests.py
python3 testsuite/peptide_tests.py

sample:
Expand Down
18 changes: 9 additions & 9 deletions parameters/peptides/Avogadro_parametrization.txt
View file
Original file line number Diff line number Diff line change
@@ -1,13 +1,13 @@
# Parameters from Lunkad, R. et al. Molecular Systems Design & Engineering (2021), 6(2), 122-131.
{"object_type":"particle", "name": "CA", "q":0, "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "A", "q":0, "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "c", "acidity": "acidic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "D", "acidity": "acidic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "E", "acidity": "acidic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "Y", "acidity": "acidic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "n", "acidity": "basic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "H", "acidity": "basic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "K", "acidity": "basic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "CA", "q":0, "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "A", "q":0, "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "c", "acidity": "acidic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "D", "acidity": "acidic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "E", "acidity": "acidic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "Y", "acidity": "acidic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "n", "acidity": "basic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "H", "acidity": "basic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "K", "acidity": "basic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"bond", "name1": "CA", "name2": "CA", "bond_type": "harmonic", "r_0": {"value":0.382, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
{"object_type":"bond", "name1": "CA", "name2": "A", "bond_type": "harmonic", "r_0": {"value":0.153, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
{"object_type":"bond", "name1": "CA", "name2": "c", "bond_type": "harmonic", "r_0": {"value":0.246, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
Expand Down
24 changes: 12 additions & 12 deletions parameters/peptides/Blanco2020.txt
View file
Original file line number Diff line number Diff line change
@@ -1,16 +1,16 @@
# Parameters from Blanco et al. Soft Matter, 17(3), 655-669, 2021.
{"object_type":"particle", "name": "D", "acidity": "acidic", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "E", "acidity": "acidic", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "n", "acidity": "basic", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "S", "q":0, "acidity": "inert", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "H", "acidity": "basic", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "A", "q":0,"acidity": "inert", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "K", "acidity": "basic", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "Y", "acidity": "acidic", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "R", "acidity": "basic", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "G", "q":0,"acidity": "inert", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "F", "q":0,"acidity": "inert", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "c", "acidity": "acidic", "diameter": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "D", "acidity": "acidic", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "E", "acidity": "acidic", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "n", "acidity": "basic", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "S", "q":0, "acidity": "inert", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "H", "acidity": "basic", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "A", "q":0,"acidity": "inert", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "K", "acidity": "basic", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "Y", "acidity": "acidic", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "R", "acidity": "basic", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "G", "q":0,"acidity": "inert", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "F", "q":0,"acidity": "inert", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "c", "acidity": "acidic", "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"bond", "name1": "n", "name2": "D", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "S", "name2": "D", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "S", "name2": "H", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
Expand Down
12 changes: 6 additions & 6 deletions parameters/peptides/Lunkad2021.txt
View file
Original file line number Diff line number Diff line change
@@ -1,10 +1,10 @@
# Parameters from Lunkad, R. et al. Molecular Systems Design & Engineering (2021), 6(2), 122-131.
{"object_type":"particle", "name": "CA", "q":0, "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "D", "acidity": "acidic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "E", "acidity": "acidic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "H", "acidity": "basic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "Y", "acidity": "acidic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "K", "acidity": "basic", "diameter": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "CA", "q":0, "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "D", "acidity": "acidic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "E", "acidity": "acidic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "H", "acidity": "basic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "Y", "acidity": "acidic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "K", "acidity": "basic", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"bond", "name1": "CA", "name2": "CA", "bond_type": "harmonic", "r_0": {"value":0.382, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
{"object_type":"bond", "name1": "CA", "name2": "D", "bond_type": "harmonic", "r_0": {"value":0.329, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
{"object_type":"bond", "name1": "CA", "name2": "E", "bond_type": "harmonic", "r_0": {"value":0.435, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
Expand Down
Loading

0 comments on commit b787b89

Please sign in to comment.