hps.parameters package

Submodules

hps.parameters.model_parameters module

Dictionary contains parameters for hps model. First level is the model name

HPS-Kr scale was taken from:

Dignon, G. L., Zheng, W., Kim, Y. C., Best, R. B., ; Mittal, J. (2018). Sequence determinants of protein phase behavior from a coarse-grained model. PLoS Computational Biology, 1–23. https://doi.org/10.1101/238170
Parameter for Nucleic acids (KR scale):

Regy, R. M., Dignon, G. L., Zheng, W., Kim, Y. C., Mittal, J. (2020). Sequence dependent phase separation of protein-polynucleotide mixtures elucidated using molecular simulations. Nucleic Acids Research, 48(22), 12593–12603. https://doi.org/10.1093/nar/gkaa1099

Phosphorylation version of some residues for KR scale are taken from:

Perdikari, T. M., Jovic, N., Dignon, G. L., Kim, Y. C., Fawzi, N. L., Mittal, J. (2021). A predictive coarse-grained model for position-specific effects of post-translational modifications. Biophysical Journal, 120(7), 1187–1197. https://doi.org/10.1016/j.bpj.2021.01.034

Note on hps (lambda) in urry scale:

# These parameters were shifted by 0.08 from original parameters directly.

in the original paper: Regy, R. M., Thompson, J., Kim, Y. C., ; Mittal, J. (2021). Improved coarse-grained model for studying sequence dependent phase separation of disordered proteins. Protein Science, 30(7), 1371–1379. https://doi.org/10.1002/pro.4094

..math::

lambda_{ij} = muy lambda_0_ij - delta

muy=1, delta= 0.08 is the optimal set for the set of 42 proteins they studied. lambda_{ij} = lambda0_{ij} - 0.08 = 0.5*(lambda_i+lambda_j) - 0.08 = 0.5(lambda_i -0.08 + lambda_j-0.08)

In both version, KR and Urry, we can tune directly lambda parameter in Urry by 0.08 so we can use only one equation for two model (choose parameter when passing model parameter)

hps.parameters.model_parameters.parameters: dictionary contains model parameters.

hps.parameters.model_parameters.parameters = {'hps_kr': {'A': {'charge': -1.0, 'hps': -0.054, 'mass': 329.2, 'radii': 0.844}, 'ALA': {'charge': 0.0, 'hps': 0.73, 'mass': 71.08, 'radii': 0.504}, 'ALY': {'charge': 0.0, 'hps': 0.7567, 'mass': 170.2, 'radii': 0.681}, 'ARG': {'charge': 1.0, 'hps': 0.0, 'mass': 156.2, 'radii': 0.656}, 'ASN': {'charge': 0.0, 'hps': 0.432, 'mass': 114.1, 'radii': 0.568}, 'ASP': {'charge': -1.0, 'hps': 0.378, 'mass': 115.1, 'radii': 0.558}, 'C': {'charge': -1.0, 'hps': -0.027, 'mass': 305.2, 'radii': 0.822}, 'CYS': {'charge': 0.0, 'hps': 0.595, 'mass': 103.1, 'radii': 0.548}, 'G': {'charge': -1.0, 'hps': -0.189, 'mass': 345.2, 'radii': 0.851}, 'GLN': {'charge': 0.0, 'hps': 0.514, 'mass': 128.1, 'radii': 0.602}, 'GLU': {'charge': -1.0, 'hps': 0.459, 'mass': 129.1, 'radii': 0.592}, 'GLY': {'charge': 0.0, 'hps': 0.649, 'mass': 57.05, 'radii': 0.45}, 'HIS': {'charge': 0.5, 'hps': 0.514, 'mass': 137.1, 'radii': 0.608}, 'ILE': {'charge': 0.0, 'hps': 0.973, 'mass': 113.2, 'radii': 0.618}, 'LEU': {'charge': 0.0, 'hps': 0.973, 'mass': 113.2, 'radii': 0.618}, 'LYS': {'charge': 1.0, 'hps': 0.514, 'mass': 128.2, 'radii': 0.636}, 'MET': {'charge': 0.0, 'hps': 0.838, 'mass': 131.2, 'radii': 0.618}, 'PHE': {'charge': 0.0, 'hps': 1.0, 'mass': 147.2, 'radii': 0.636}, 'PRO': {'charge': 0.0, 'hps': 1.0, 'mass': 97.12, 'radii': 0.556}, 'PTR': {'charge': -2.0, 'hps': 0.189, 'mass': 241.15, 'radii': 0.738}, 'SEP': {'charge': -2.0, 'hps': 0.162, 'mass': 165.03, 'radii': 0.636}, 'SER': {'charge': 0.0, 'hps': 0.595, 'mass': 87.08, 'radii': 0.518}, 'THR': {'charge': 0.0, 'hps': 0.676, 'mass': 101.1, 'radii': 0.562}, 'TPO': {'charge': -2.0, 'hps': 0.0081, 'mass': 179.05, 'radii': 0.662}, 'TRP': {'charge': 0.0, 'hps': 0.946, 'mass': 186.2, 'radii': 0.678}, 'TYR': {'charge': 0.0, 'hps': 0.865, 'mass': 163.2, 'radii': 0.646}, 'U': {'charge': -1.0, 'hps': -0.027, 'mass': 306.2, 'radii': 0.817}, 'VAL': {'charge': 0.0, 'hps': 0.892, 'mass': 99.07, 'radii': 0.586}, 'bond_force_constant': 8368.0, 'bond_length_nucleic': 0.5, 'bond_length_protein': 0.38, 'bonded_exclusions_index': 1}, 'hps_ss': {'ALA': {'charge': 0.0, 'eps_di': -2.59, 'hps': 0.522942, 'mass': 71.08, 'radii': 0.504}, 'ARG': {'charge': 1.0, 'eps_di': -1.37, 'hps': 0.478824, 'mass': 156.2, 'radii': 0.656}, 'ASN': {'charge': 0.0, 'eps_di': -0.42, 'hps': 0.508236, 'mass': 114.1, 'radii': 0.568}, 'ASP': {'charge': -1.0, 'eps_di': -0.8, 'hps': 0.214119, 'mass': 115.1, 'radii': 0.558}, 'CYS': {'charge': 0.0, 'eps_di': -0.15, 'hps': 0.56706, 'mass': 103.1, 'radii': 0.548}, 'GLN': {'charge': 0.0, 'eps_di': -1.25, 'hps': 0.478824, 'mass': 128.1, 'radii': 0.602}, 'GLU': {'charge': -1.0, 'eps_di': -1.8, 'hps': -0.08, 'mass': 129.1, 'radii': 0.592}, 'GLY': {'charge': 0.0, 'eps_di': 0.65, 'hps': 0.49353, 'mass': 57.05, 'radii': 0.45}, 'HIS': {'charge': 0.0, 'eps_di': 0.8, 'hps': 0.684707, 'mass': 137.1, 'radii': 0.608}, 'ILE': {'charge': 0.0, 'eps_di': -1.39, 'hps': 0.625883, 'mass': 113.2, 'radii': 0.618}, 'LEU': {'charge': 0.0, 'eps_di': -2.05, 'hps': 0.640589, 'mass': 113.2, 'radii': 0.618}, 'LYS': {'charge': 1.0, 'eps_di': -0.95, 'hps': 0.302354, 'mass': 128.2, 'radii': 0.636}, 'MET': {'charge': 0.0, 'eps_di': -1.6, 'hps': 0.596471, 'mass': 131.2, 'radii': 0.618}, 'PHE': {'charge': 0.0, 'eps_di': -0.68, 'hps': 0.74353, 'mass': 147.2, 'radii': 0.636}, 'PRO': {'charge': 0.0, 'eps_di': 3.7, 'hps': 0.678824, 'mass': 97.12, 'radii': 0.556}, 'SER': {'charge': 0.0, 'eps_di': -0.69, 'hps': 0.508236, 'mass': 87.08, 'radii': 0.518}, 'THR': {'charge': 0.0, 'eps_di': -0.3, 'hps': 0.508236, 'mass': 101.1, 'radii': 0.562}, 'TRP': {'charge': 0.0, 'eps_di': -1.15, 'hps': 0.92, 'mass': 186.2, 'radii': 0.678}, 'TYR': {'charge': 0.0, 'eps_di': -0.68, 'hps': 0.817059, 'mass': 163.2, 'radii': 0.646}, 'VAL': {'charge': 0.0, 'eps_di': -0.75, 'hps': 0.584707, 'mass': 99.07, 'radii': 0.586}, 'bond_force_constant': 8368.0, 'bond_length_nucleic': 0.5, 'bond_length_protein': 0.382, 'bonded_exclusions_index': 3}, 'hps_urry': {'ALA': {'charge': 0.0, 'hps': 0.522942, 'mass': 71.08, 'radii': 0.504}, 'ARG': {'charge': 1.0, 'hps': 0.478824, 'mass': 156.2, 'radii': 0.656}, 'ASN': {'charge': 0.0, 'hps': 0.508236, 'mass': 114.1, 'radii': 0.568}, 'ASP': {'charge': -1.0, 'hps': 0.214119, 'mass': 115.1, 'radii': 0.558}, 'CYS': {'charge': 0.0, 'hps': 0.56706, 'mass': 103.1, 'radii': 0.548}, 'GLN': {'charge': 0.0, 'hps': 0.478824, 'mass': 128.1, 'radii': 0.602}, 'GLU': {'charge': -1.0, 'hps': -0.08, 'mass': 129.1, 'radii': 0.592}, 'GLY': {'charge': 0.0, 'hps': 0.49353, 'mass': 57.05, 'radii': 0.45}, 'HIS': {'charge': 0.0, 'hps': 0.684707, 'mass': 137.1, 'radii': 0.608}, 'ILE': {'charge': 0.0, 'hps': 0.625883, 'mass': 113.2, 'radii': 0.618}, 'LEU': {'charge': 0.0, 'hps': 0.640589, 'mass': 113.2, 'radii': 0.618}, 'LYS': {'charge': 1.0, 'hps': 0.302354, 'mass': 128.2, 'radii': 0.636}, 'MET': {'charge': 0.0, 'hps': 0.596471, 'mass': 131.2, 'radii': 0.618}, 'PHE': {'charge': 0.0, 'hps': 0.74353, 'mass': 147.2, 'radii': 0.636}, 'PRO': {'charge': 0.0, 'hps': 0.678824, 'mass': 97.12, 'radii': 0.556}, 'SER': {'charge': 0.0, 'hps': 0.508236, 'mass': 87.08, 'radii': 0.518}, 'THR': {'charge': 0.0, 'hps': 0.508236, 'mass': 101.1, 'radii': 0.562}, 'TRP': {'charge': 0.0, 'hps': 0.92, 'mass': 186.2, 'radii': 0.678}, 'TYR': {'charge': 0.0, 'hps': 0.817059, 'mass': 163.2, 'radii': 0.646}, 'VAL': {'charge': 0.0, 'hps': 0.584707, 'mass': 99.07, 'radii': 0.586}, 'bond_force_constant': 8368.0, 'bond_length_nucleic': 0.5, 'bond_length_protein': 0.382, 'bonded_exclusions_index': 1}, 'mpipi': {'ALA': {'charge': 0.0, 'id': 5, 'mass': 71.08}, 'ARG': {'charge': 0.75, 'id': 4, 'mass': 156.2}, 'ASN': {'charge': 0.0, 'id': 16, 'mass': 114.1}, 'ASP': {'charge': -0.75, 'id': 6, 'mass': 115.1}, 'CYS': {'charge': 0.0, 'id': 18, 'mass': 103.1}, 'GLN': {'charge': 0.0, 'id': 11, 'mass': 128.1}, 'GLU': {'charge': -0.75, 'id': 7, 'mass': 129.1}, 'GLY': {'charge': 0.0, 'id': 1, 'mass': 57.05}, 'HIS': {'charge': 0.375, 'id': 15, 'mass': 137.1}, 'ILE': {'charge': 0.0, 'id': 19, 'mass': 113.2}, 'LEU': {'charge': 0.0, 'id': 10, 'mass': 113.2}, 'LYS': {'charge': 0.75, 'id': 2, 'mass': 128.2}, 'MET': {'charge': 0.0, 'id': 0, 'mass': 131.2}, 'PHE': {'charge': 0.0, 'id': 13, 'mass': 147.2}, 'PRO': {'charge': 0.0, 'id': 17, 'mass': 97.12}, 'SER': {'charge': 0.0, 'id': 14, 'mass': 87.08}, 'THR': {'charge': 0.0, 'id': 3, 'mass': 101.1}, 'TRP': {'charge': 0.0, 'id': 12, 'mass': 186.2}, 'TYR': {'charge': 0.0, 'id': 8, 'mass': 163.2}, 'VAL': {'charge': 0.0, 'id': 9, 'mass': 99.07}, 'bond_force_constant': 8030.0, 'bond_length_nucleic': 0.5, 'bond_length_protein': 0.381, 'bonded_exclusions_index': 1, 'eps_ij': array([[1.655360e-01, 2.845830e-01, 1.367580e-01, 1.471140e-01, 7.176190e-01, 1.862800e-01, 3.061520e-01, 3.245820e-01, 9.597050e-01, 9.443700e-02, 1.057760e-01, 5.021050e-01, 1.233991e+00, 9.020830e-01, 2.116350e-01, 8.514060e-01, 4.882980e-01, 2.473580e-01, 2.277640e-01, 8.359200e-02], [2.845830e-01, 4.036300e-01, 2.558060e-01, 2.661610e-01, 8.366660e-01, 3.053270e-01, 4.251990e-01, 4.436300e-01, 1.078752e+00, 2.134840e-01, 2.248230e-01, 6.211520e-01, 1.353039e+00, 1.021130e+00, 3.306820e-01, 9.704540e-01, 6.073450e-01, 3.664050e-01, 3.468120e-01, 2.026390e-01], [1.367580e-01, 2.558060e-01, 7.998600e-02, 1.183360e-01, 5.101890e-01, 1.575020e-01, 2.063000e-03, 2.201000e-03, 4.297010e-01, 6.566000e-02, 7.699800e-02, 4.733280e-01, 4.384660e-01, 4.823150e-01, 1.828580e-01, 3.655560e-01, 4.595200e-01, 2.185810e-01, 1.989870e-01, 5.481500e-02], [1.471140e-01, 2.661610e-01, 1.183360e-01, 1.286910e-01, 6.991970e-01, 1.678580e-01, 2.877290e-01, 3.061600e-01, 9.412830e-01, 7.601500e-02, 8.735400e-02, 4.836830e-01, 1.215565e+00, 8.836610e-01, 1.932130e-01, 8.329840e-01, 4.698760e-01, 2.289360e-01, 2.093420e-01, 6.517000e-02], [7.176190e-01, 8.366660e-01, 5.101890e-01, 6.991970e-01, 3.762090e-01, 7.383630e-01, 6.368000e-03, 6.502000e-03, 2.543119e+00, 6.465200e-01, 6.578590e-01, 1.054188e+00, 2.893893e+00, 2.280037e+00, 7.637180e-01, 5.198080e-01, 1.040381e+00, 7.994410e-01, 7.798470e-01, 6.356750e-01], [1.862800e-01, 3.053270e-01, 1.575020e-01, 1.678580e-01, 7.383630e-01, 2.070240e-01, 3.268960e-01, 3.453260e-01, 9.804490e-01, 1.151810e-01, 1.265200e-01, 5.228490e-01, 1.254736e+00, 9.228270e-01, 2.323790e-01, 8.721510e-01, 5.090460e-01, 2.681020e-01, 2.485090e-01, 1.043360e-01], [3.061520e-01, 4.251990e-01, 2.063000e-03, 2.877290e-01, 6.368000e-03, 3.268960e-01, 3.309380e-01, 3.445900e-01, 1.100321e+00, 2.350490e-01, 2.463870e-01, 6.427210e-01, 1.374603e+00, 1.042699e+00, 3.522470e-01, 7.355000e-03, 6.289140e-01, 3.879740e-01, 3.683800e-01, 2.242080e-01], [3.245820e-01, 4.436300e-01, 2.201000e-03, 3.061600e-01, 6.502000e-03, 3.453260e-01, 3.445900e-01, 3.582420e-01, 1.118751e+00, 2.534790e-01, 2.648180e-01, 6.611510e-01, 1.393034e+00, 1.061129e+00, 3.706770e-01, 7.494000e-03, 6.473440e-01, 4.064040e-01, 3.868110e-01, 2.426390e-01], [9.597050e-01, 1.078752e+00, 4.297010e-01, 9.412830e-01, 2.543119e+00, 9.804490e-01, 1.100321e+00, 1.118751e+00, 1.753874e+00, 8.886060e-01, 8.999450e-01, 1.296274e+00, 2.028156e+00, 1.696252e+00, 1.005804e+00, 1.645576e+00, 1.282467e+00, 1.041527e+00, 1.021934e+00, 8.777610e-01], [9.443700e-02, 2.134840e-01, 6.566000e-02, 7.601500e-02, 6.465200e-01, 1.151810e-01, 2.350490e-01, 2.534790e-01, 8.886060e-01, 2.333800e-02, 3.467700e-02, 4.310060e-01, 1.162888e+00, 8.309840e-01, 1.405360e-01, 7.803080e-01, 4.171990e-01, 1.762590e-01, 1.566660e-01, 1.249300e-02], [1.057760e-01, 2.248230e-01, 7.699800e-02, 8.735400e-02, 6.578590e-01, 1.265200e-01, 2.463870e-01, 2.648180e-01, 8.999450e-01, 3.467700e-02, 4.601600e-02, 4.423450e-01, 1.174227e+00, 8.423230e-01, 1.518750e-01, 7.916460e-01, 4.285380e-01, 1.875980e-01, 1.680040e-01, 2.383200e-02], [5.021050e-01, 6.211520e-01, 4.733280e-01, 4.836830e-01, 1.054188e+00, 5.228490e-01, 6.427210e-01, 6.611510e-01, 1.296274e+00, 4.310060e-01, 4.423450e-01, 8.386740e-01, 1.570556e+00, 1.238652e+00, 5.482040e-01, 1.187976e+00, 8.248670e-01, 5.839270e-01, 5.643340e-01, 4.201610e-01], [1.233991e+00, 1.353039e+00, 4.384660e-01, 1.215565e+00, 2.893893e+00, 1.254736e+00, 1.374603e+00, 1.393034e+00, 2.028156e+00, 1.162888e+00, 1.174227e+00, 1.570556e+00, 2.302443e+00, 1.970538e+00, 1.280086e+00, 1.919858e+00, 1.556753e+00, 1.315814e+00, 1.296220e+00, 1.152048e+00], [9.020830e-01, 1.021130e+00, 4.823150e-01, 8.836610e-01, 2.280037e+00, 9.228270e-01, 1.042699e+00, 1.061129e+00, 1.696252e+00, 8.309840e-01, 8.423230e-01, 1.238652e+00, 1.970538e+00, 1.638630e+00, 9.481820e-01, 1.587954e+00, 1.224845e+00, 9.839050e-01, 9.643120e-01, 8.201390e-01], [2.116350e-01, 3.306820e-01, 1.828580e-01, 1.932130e-01, 7.637180e-01, 2.323790e-01, 3.522470e-01, 3.706770e-01, 1.005804e+00, 1.405360e-01, 1.518750e-01, 5.482040e-01, 1.280086e+00, 9.481820e-01, 2.577340e-01, 8.975060e-01, 5.343970e-01, 2.934570e-01, 2.738640e-01, 1.296910e-01], [8.514060e-01, 9.704540e-01, 3.655560e-01, 8.329840e-01, 5.198080e-01, 8.721510e-01, 7.355000e-03, 7.494000e-03, 1.645576e+00, 7.803080e-01, 7.916460e-01, 1.187976e+00, 1.919858e+00, 1.587954e+00, 8.975060e-01, 1.138720e-01, 1.174168e+00, 9.332290e-01, 9.136350e-01, 7.694630e-01], [4.882980e-01, 6.073450e-01, 4.595200e-01, 4.698760e-01, 1.040381e+00, 5.090460e-01, 6.289140e-01, 6.473440e-01, 1.282467e+00, 4.171990e-01, 4.285380e-01, 8.248670e-01, 1.556753e+00, 1.224845e+00, 5.343970e-01, 1.174168e+00, 8.110640e-01, 5.701240e-01, 5.505310e-01, 4.063580e-01], [2.473580e-01, 3.664050e-01, 2.185810e-01, 2.289360e-01, 7.994410e-01, 2.681020e-01, 3.879740e-01, 4.064040e-01, 1.041527e+00, 1.762590e-01, 1.875980e-01, 5.839270e-01, 1.315814e+00, 9.839050e-01, 2.934570e-01, 9.332290e-01, 5.701240e-01, 3.291850e-01, 3.095910e-01, 1.654190e-01], [2.277640e-01, 3.468120e-01, 1.989870e-01, 2.093420e-01, 7.798470e-01, 2.485090e-01, 3.683800e-01, 3.868110e-01, 1.021934e+00, 1.566660e-01, 1.680040e-01, 5.643340e-01, 1.296220e+00, 9.643120e-01, 2.738640e-01, 9.136350e-01, 5.505310e-01, 3.095910e-01, 2.899970e-01, 1.458250e-01], [8.359200e-02, 2.026390e-01, 5.481500e-02, 6.517000e-02, 6.356750e-01, 1.043360e-01, 2.242080e-01, 2.426390e-01, 8.777610e-01, 1.249300e-02, 2.383200e-02, 4.201610e-01, 1.152048e+00, 8.201390e-01, 1.296910e-01, 7.694630e-01, 4.063580e-01, 1.654190e-01, 1.458250e-01, 1.653000e-03]]), 'mu_ij': array([[ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 4.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2., 2.], [ 2., 2., 2., 2., 2., 2., 2., 2., 2., 4., 2., 2., 2., 2., 2., 2., 2., 2., 2., 11.]]), 'nu_ij': array([[1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.], [1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1., 1.]]), 'rc_ij': array([[1.940385, 1.672854, 1.970335, 1.853468, 1.993189, 1.760551, 1.842438, 1.895453, 1.977011, 1.896171, 1.945033, 1.909556, 2.026719, 1.961463, 1.781682, 1.917752, 1.856406, 1.840339, 1.828288, 1.948918], [1.672854, 1.408533, 1.701401, 1.585327, 1.729916, 1.49404 , 1.577776, 1.630912, 1.71395 , 1.623718, 1.673679, 1.64589 , 1.763771, 1.698366, 1.515757, 1.654623, 1.592705, 1.574997, 1.562617, 1.674099], [1.970335, 1.701401, 2.001402, 1.88382 , 2.021458, 1.790006, 1.871096, 1.924073, 2.005225, 1.930062, 1.977767, 1.937908, 2.054906, 1.989684, 1.810854, 1.945981, 1.884764, 1.869318, 1.857346, 1.985399], [1.853468, 1.585327, 1.88382 , 1.766718, 1.905605, 1.673384, 1.75496 , 1.807962, 1.889419, 1.81109 , 1.859427, 1.821986, 1.939133, 1.873875, 1.694402, 1.830159, 1.76883 , 1.752959, 1.740963, 1.864385], [1.993189, 1.729916, 2.021458, 1.905605, 2.051715, 1.814728, 1.898958, 1.952126, 2.035872, 1.94334 , 1.993382, 1.967484, 2.085765, 2.020273, 1.836572, 1.976511, 1.914308, 1.895955, 1.883483, 1.993474], [1.760551, 1.49404 , 1.790006, 1.673384, 1.814728, 1.581022, 1.663531, 1.716595, 1.798612, 1.714402, 1.763755, 1.730964, 1.848366, 1.783057, 1.602356, 1.73933 , 1.677803, 1.661215, 1.64906 , 1.766179], [1.842438, 1.577776, 1.871096, 1.75496 , 1.898958, 1.663531, 1.747057, 1.800175, 1.882942, 1.793621, 1.843527, 1.815012, 1.932732, 1.867367, 1.68519 , 1.823628, 1.761839, 1.744364, 1.732021, 1.844096], [1.895453, 1.630912, 1.924073, 1.807962, 1.952126, 1.716595, 1.800175, 1.853301, 1.936109, 1.846512, 1.896437, 1.868164, 1.985908, 1.92054 , 1.738266, 1.8768 , 1.814997, 1.797457, 1.785109, 1.896998], [1.977011, 1.71395 , 2.005225, 1.889419, 2.035872, 1.798612, 1.882942, 1.936109, 2.02009 , 1.927065, 1.977116, 1.951575, 2.070015, 2.004477, 1.820484, 1.960707, 1.898395, 1.879889, 1.867395, 1.977165], [1.896171, 1.623718, 1.930062, 1.81109 , 1.94334 , 1.714402, 1.793621, 1.846512, 1.927065, 1.8798 , 1.91728 , 1.859919, 1.976735, 1.911535, 1.734499, 1.867831, 1.806782, 1.792299, 1.780701, 2.015403], [1.945033, 1.673679, 1.977767, 1.859427, 1.993382, 1.763755, 1.843527, 1.896437, 1.977116, 1.91728 , 1.960222, 1.909947, 2.026781, 1.961581, 1.784091, 1.917883, 1.856809, 1.842064, 1.830374, 1.982317], [1.909556, 1.64589 , 1.937908, 1.821986, 1.967484, 1.730964, 1.815012, 1.868164, 1.951575, 1.859919, 1.909947, 1.883355, 2.001422, 1.935983, 1.752766, 1.89223 , 1.830178, 1.812104, 1.799656, 1.910146], [2.026719, 1.763771, 2.054906, 1.939133, 2.085765, 1.848366, 1.932732, 1.985908, 2.070015, 1.976735, 2.026781, 2.001422, 2.119964, 2.054395, 1.870242, 2.010627, 1.948249, 1.929652, 1.91716 , 2.02681 ], [1.961463, 1.698366, 1.989684, 1.873875, 2.020273, 1.783057, 1.867367, 1.92054 , 2.004477, 1.911535, 1.961581, 1.935983, 2.054395, 1.988865, 1.80492 , 1.945102, 1.882808, 1.864322, 1.851836, 1.961636], [1.781682, 1.515757, 1.810854, 1.694402, 1.836572, 1.602356, 1.68519 , 1.738266, 1.820484, 1.734499, 1.784091, 1.752766, 1.870242, 1.80492 , 1.623801, 1.76119 , 1.699598, 1.682795, 1.670544, 1.78576 ], [1.917752, 1.654623, 1.945981, 1.830159, 1.976511, 1.73933 , 1.823628, 1.8768 , 1.960707, 1.867831, 1.917883, 1.89223 , 2.010627, 1.945102, 1.76119 , 1.901335, 1.839054, 1.820595, 1.808106, 1.917944], [1.856406, 1.592705, 1.884764, 1.76883 , 1.914308, 1.677803, 1.761839, 1.814997, 1.898395, 1.806782, 1.856809, 1.830178, 1.948249, 1.882808, 1.699598, 1.839054, 1.777005, 1.758925, 1.746493, 1.856996], [1.840339, 1.574997, 1.869318, 1.752959, 1.895955, 1.661215, 1.744364, 1.797457, 1.879889, 1.792299, 1.842064, 1.812104, 1.929652, 1.864322, 1.682795, 1.820595, 1.758925, 1.741847, 1.729545, 1.843158], [1.828288, 1.562617, 1.857346, 1.740963, 1.883483, 1.64906 , 1.732021, 1.785109, 1.867395, 1.780701, 1.830374, 1.799656, 1.91716 , 1.851836, 1.670544, 1.808106, 1.746493, 1.729545, 1.717309, 1.83176 ], [1.948918, 1.674099, 1.985399, 1.864385, 1.993474, 1.766179, 1.844096, 1.896998, 1.977165, 2.015403, 1.982317, 1.910146, 2.02681 , 1.961636, 1.78576 , 1.917944, 1.856996, 1.843158, 1.83176 , 2.076504]]), 'sigma_ij': array([[0.646795, 0.557618, 0.656778, 0.617823, 0.664396, 0.58685 , 0.614146, 0.631818, 0.659004, 0.632057, 0.648344, 0.636519, 0.675573, 0.653821, 0.593894, 0.639251, 0.618802, 0.613446, 0.609429, 0.649639], [0.557618, 0.469511, 0.567134, 0.528442, 0.576639, 0.498013, 0.525925, 0.543637, 0.571317, 0.541239, 0.557893, 0.54863 , 0.587924, 0.566122, 0.505252, 0.551541, 0.530902, 0.524999, 0.520872, 0.558033], [0.656778, 0.567134, 0.667134, 0.62794 , 0.673819, 0.596669, 0.623699, 0.641358, 0.668408, 0.643354, 0.659256, 0.645969, 0.684969, 0.663228, 0.603618, 0.64866 , 0.628255, 0.623106, 0.619115, 0.6618 ], [0.617823, 0.528442, 0.62794 , 0.588906, 0.635202, 0.557795, 0.584987, 0.602654, 0.629806, 0.603697, 0.619809, 0.607329, 0.646378, 0.624625, 0.564801, 0.610053, 0.58961 , 0.58432 , 0.580321, 0.621462], [0.664396, 0.576639, 0.673819, 0.635202, 0.683905, 0.604909, 0.632986, 0.650709, 0.678624, 0.64778 , 0.664461, 0.655828, 0.695255, 0.673424, 0.612191, 0.658837, 0.638103, 0.631985, 0.627828, 0.664491], [0.58685 , 0.498013, 0.596669, 0.557795, 0.604909, 0.527007, 0.55451 , 0.572198, 0.599537, 0.571467, 0.587918, 0.576988, 0.616122, 0.594352, 0.534119, 0.579777, 0.559268, 0.553738, 0.549687, 0.588726], [0.614146, 0.525925, 0.623699, 0.584987, 0.632986, 0.55451 , 0.582352, 0.600058, 0.627647, 0.597874, 0.614509, 0.605004, 0.644244, 0.622456, 0.56173 , 0.607876, 0.58728 , 0.581455, 0.57734 , 0.614699], [0.631818, 0.543637, 0.641358, 0.602654, 0.650709, 0.572198, 0.600058, 0.617767, 0.64537 , 0.615504, 0.632146, 0.622721, 0.661969, 0.64018 , 0.579422, 0.6256 , 0.604999, 0.599152, 0.595036, 0.632333], [0.659004, 0.571317, 0.668408, 0.629806, 0.678624, 0.599537, 0.627647, 0.64537 , 0.673363, 0.642355, 0.659039, 0.650525, 0.690005, 0.668159, 0.606828, 0.653569, 0.632798, 0.62663 , 0.622465, 0.659055], [0.632057, 0.541239, 0.643354, 0.603697, 0.64778 , 0.571467, 0.597874, 0.615504, 0.642355, 0.6266 , 0.639093, 0.619973, 0.658912, 0.637178, 0.578166, 0.62261 , 0.602261, 0.597433, 0.593567, 0.671801], [0.648344, 0.557893, 0.659256, 0.619809, 0.664461, 0.587918, 0.614509, 0.632146, 0.659039, 0.639093, 0.653407, 0.636649, 0.675594, 0.65386 , 0.594697, 0.639294, 0.618936, 0.614021, 0.610125, 0.660772], [0.636519, 0.54863 , 0.645969, 0.607329, 0.655828, 0.576988, 0.605004, 0.622721, 0.650525, 0.619973, 0.636649, 0.627785, 0.667141, 0.645328, 0.584255, 0.630743, 0.610059, 0.604035, 0.599885, 0.636715], [0.675573, 0.587924, 0.684969, 0.646378, 0.695255, 0.616122, 0.644244, 0.661969, 0.690005, 0.658912, 0.675594, 0.667141, 0.706655, 0.684798, 0.623414, 0.670209, 0.649416, 0.643217, 0.639053, 0.675603], [0.653821, 0.566122, 0.663228, 0.624625, 0.673424, 0.594352, 0.622456, 0.64018 , 0.668159, 0.637178, 0.65386 , 0.645328, 0.684798, 0.662955, 0.60164 , 0.648367, 0.627603, 0.621441, 0.617279, 0.653879], [0.593894, 0.505252, 0.603618, 0.564801, 0.612191, 0.534119, 0.56173 , 0.579422, 0.606828, 0.578166, 0.594697, 0.584255, 0.623414, 0.60164 , 0.541267, 0.587063, 0.566533, 0.560932, 0.556848, 0.595253], [0.639251, 0.551541, 0.64866 , 0.610053, 0.658837, 0.579777, 0.607876, 0.6256 , 0.653569, 0.62261 , 0.639294, 0.630743, 0.670209, 0.648367, 0.587063, 0.633778, 0.613018, 0.606865, 0.602702, 0.639315], [0.618802, 0.530902, 0.628255, 0.58961 , 0.638103, 0.559268, 0.58728 , 0.604999, 0.632798, 0.602261, 0.618936, 0.610059, 0.649416, 0.627603, 0.566533, 0.613018, 0.592335, 0.586308, 0.582164, 0.618999], [0.613446, 0.524999, 0.623106, 0.58432 , 0.631985, 0.553738, 0.581455, 0.599152, 0.62663 , 0.597433, 0.614021, 0.604035, 0.643217, 0.621441, 0.560932, 0.606865, 0.586308, 0.580616, 0.576515, 0.614386], [0.609429, 0.520872, 0.619115, 0.580321, 0.627828, 0.549687, 0.57734 , 0.595036, 0.622465, 0.593567, 0.610125, 0.599885, 0.639053, 0.617279, 0.556848, 0.602702, 0.582164, 0.576515, 0.572436, 0.610587], [0.649639, 0.558033, 0.6618 , 0.621462, 0.664491, 0.588726, 0.614699, 0.632333, 0.659055, 0.671801, 0.660772, 0.636715, 0.675603, 0.653879, 0.595253, 0.639315, 0.618999, 0.614386, 0.610587, 0.692168]])}}: HPS_SS = HPS-Urry with angle and torsion potential. eps_di is parameter control the dihedral potential. Here we implemented the (i,i+4) assignment and 1-1001-1 mixing rule. torsion angle made by residue (i, i+3) residue (i-1) and (i+4) are preceding and succeeding residues 1-1001-1 means:

weight of residues (i-1), (i), (i+3) and (i+4) are 1 weight of residues (i+1), (i+2) are 0

Module contents

Module defines model parameters. At the moment, two main models are supported:

hps-kr

*hps-urry.

Other model parameter can be easily defined here such as M2 from Lindorff-larsen

Tesei, G., Schulze, T. K., Crehuet, R., & Lindorff-larsen, K. (2021). Accurate model of liquid-liquid phase behaviour of intrinsically-disordered proteins from data-driven optimization of single-chain properties. BioRxiv, 1–9.