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Bonds #41

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merged 10 commits into from
Apr 23, 2024
Merged

Bonds #41

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92662dc
New implementation for the function define_bonds() and the correspond…
pinedaps Mar 21, 2024
06cb158
The function define.bond will work by providing the type_bond, a dict…
pinedaps Apr 17, 2024
f58cd13
Merge conflicts solved
pinedaps Apr 18, 2024
d3e1362
Implemetation of new define_bond function in the sample scripts, test…
pinedaps Apr 18, 2024
88c6b52
Implementation of Raise ValueError when missing some of the parameter…
pinedaps Apr 19, 2024
6d53385
Additional test for define_default_bond function implemented
pinedaps Apr 20, 2024
0742332
Merge branch 'pyMBE-dev:main' into bonds
pinedaps Apr 22, 2024
dd1340e
Changing olf nomenclature in the new tests
pinedaps Apr 22, 2024
7b3c8f2
Changing define_default_bond by define_bond funtion and deleting the …
pinedaps Apr 22, 2024
6ff4df2
Add test for bonds to CI, add additional checks to test, adapt load_i…
pm-blanco Apr 23, 2024
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1 change: 1 addition & 0 deletions Makefile
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Expand Up @@ -10,6 +10,7 @@ docs:
tests:
python3 testsuite/lj_tests.py
python3 testsuite/set_particle_acidity_test.py
python3 testsuite/bond_tests.py
python3 testsuite/generate_perpendicular_vectors_test.py
python3 testsuite/create_molecule_position_test.py
python3 testsuite/read-write-df_test.py
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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -150,7 +150,7 @@ To make sure your code is valid, please run the testsuite before submitting your

```sh
source pymbe/bin/activate
make testsuite
make tests
deactivate
```

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18 changes: 9 additions & 9 deletions parameters/peptides/Avogadro_parametrization.txt
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Expand Up @@ -8,12 +8,12 @@
{"object_type":"particle", "name": "n", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "H", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "K", "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"}}
{"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"}}
{"object_type":"bond", "name1": "CA", "name2": "Y", "bond_type": "harmonic", "r_0": {"value":0.648, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
{"object_type":"bond", "name1": "CA", "name2": "n", "bond_type": "harmonic", "r_0": {"value":0.146, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
{"object_type":"bond", "name1": "CA", "name2": "H", "bond_type": "harmonic", "r_0": {"value":0.452, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
{"object_type":"bond", "name1": "CA", "name2": "K", "bond_type": "harmonic", "r_0": {"value":0.558, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
{"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"}}}
{"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"}}}
{"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"}}}
{"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"}}}
{"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"}}}
{"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"}}}
{"object_type":"bond", "bond_type": "harmonic", "particle_pairs": [["CA","A"]] , "bond_parameters" : {"r_0": {"value":0.153, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}}
{"object_type":"bond", "bond_type": "harmonic", "particle_pairs": [["CA","c"]] , "bond_parameters" : {"r_0": {"value":0.246, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}}
{"object_type":"bond", "bond_type": "harmonic", "particle_pairs": [["CA","n"]] , "bond_parameters" : {"r_0": {"value":0.146, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}}
23 changes: 1 addition & 22 deletions parameters/peptides/Blanco2020.txt
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Expand Up @@ -11,25 +11,4 @@
{"object_type":"particle", "name": "G", "q":0, "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "F", "q":0, "sigma": {"value":0.4, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "c", "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"}}
{"object_type":"bond", "name1": "H", "name2": "A", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "A", "name2": "K", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "E", "name2": "H", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "E", "name2": "K", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "K", "name2": "R", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "K", "name2": "H", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "R", "name2": "H", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "H", "name2": "H", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "H", "name2": "G", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "G", "name2": "Y", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "Y", "name2": "K", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "R", "name2": "K", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "K", "name2": "F", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "H", "name2": "S", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "H", "name2": "F", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "H", "name2": "R", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "R", "name2": "G", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "Y", "name2": "G", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"object_type":"bond", "name1": "Y", "name2": "c", "bond_type": "harmonic", "r_0": {"value":0.4, "units":"nm"}, "k": {"value": 0.41, "units":"N / m"}}
{"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"]]}
12 changes: 6 additions & 6 deletions parameters/peptides/Lunkad2021.txt
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Expand Up @@ -5,9 +5,9 @@
{"object_type":"particle", "name": "H", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "Y", "sigma": {"value":0.35, "units":"nm"}, "epsilon":{"value":1, "units":"reduced_energy"}}
{"object_type":"particle", "name": "K", "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"}}
{"object_type":"bond", "name1": "CA", "name2": "H", "bond_type": "harmonic", "r_0": {"value":0.452, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
{"object_type":"bond", "name1": "CA", "name2": "Y", "bond_type": "harmonic", "r_0": {"value":0.648, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
{"object_type":"bond", "name1": "CA", "name2": "K", "bond_type": "harmonic", "r_0": {"value":0.558, "units":"nm"}, "k": {"value": 400, "units":"reduced_energy / nm**2"}}
{"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"}}}
{"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"}}}
{"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"}}}
{"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"}}}
{"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"}}}
{"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"}}}
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