|
| 1 | +import numpy as np |
| 2 | + |
| 3 | +default_energy = 0.0 |
| 4 | + |
| 5 | +energies = {'ILE': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'O': -0.03128, 'N': -0.0391, 'CD1': 0.019177, 'CG1': 0.019177, 'CG2': 0.019177}, |
| 6 | + 'GLN': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'O': -0.03128, 'CD': 0.019177, 'N': -0.0391, 'NE2': -0.0391, 'OE1': -0.03128}, |
| 7 | + 'GLY': {'C': 0.019177, 'CA': 0.019177, 'O': -0.03128, 'N': -0.0391,}, |
| 8 | + 'GLU': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'O': -0.03128, 'CD': 0.019177, 'OE2': -0.06877, 'N': -0.0391, 'OE1': -0.06877}, |
| 9 | + 'CYS': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'O': -0.03128, 'N': -0.0391, 'SG': 0.02576}, |
| 10 | + 'CYX': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'O': -0.03128, 'N': -0.0391, 'SG': 0.00506}, |
| 11 | + 'ASP': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'O': -0.03128, 'N': -0.0391, 'OD1': -0.06877, 'OD2': -0.06877}, |
| 12 | + 'SER': {'C': 0.019177, 'OG': -0.04255, 'CB': 0.019177, 'CA': 0.019177, 'O': -0.03128, 'N': -0.0391,}, |
| 13 | + 'LYS': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'CE': 0.019177, 'CD': 0.019177, 'NZ': -0.12604, 'O': -0.03128, 'N': -0.0391}, |
| 14 | + 'PRO': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'O': -0.03128, 'CD': 0.019177, 'N': -0.0391}, |
| 15 | + 'HIS': {'C': 0.019177, 'CE1': 0.110176, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.110176, 'O': -0.03128, 'N': -0.0391, 'CD2': 0.110176, 'ND1': -0.0391, 'NE2': -0.0391}, |
| 16 | + 'HID': {'C': 0.019177, 'CE1': 0.110176, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.110176, 'O': -0.03128, 'N': -0.0391, 'CD2': 0.110176, 'ND1': -0.06279, 'NE2': -0.0391}, |
| 17 | + 'HIE': {'C': 0.019177, 'CE1': 0.110176, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.110176, 'O': -0.03128, 'N': -0.0391, 'CD2': 0.110176, 'ND1': -0.0391, 'NE2': -0.06279}, |
| 18 | + 'ASN': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'O': -0.03128, 'N': -0.0391, 'OD1': -0.03128, 'ND2': -0.0391}, |
| 19 | + 'VAL': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'O': -0.03128, 'N': -0.0391, 'CG1': 0.019177, 'CG2': 0.019177}, |
| 20 | + 'THR': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'OG1': -0.04255, 'O': -0.03128, 'N': -0.0391, 'CG2': 0.019177}, |
| 21 | + 'TRP': {'C': 0.019177, 'CZ2': 0.110176, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.110176, 'CH2': 0.110176, 'O': -0.03128, 'N': -0.0391, 'CE2': 0.110176, 'CE3': 0.110176, 'CD1': 0.110176, 'CD2': 0.110176, 'CZ3': 0.110176, 'NE1': -0.0391}, |
| 22 | + 'PHE': {'C': 0.019177, 'CE1': 0.110176, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.110176, 'O': -0.03128, 'N': -0.0391, 'CZ': 0.110176, 'CD1': 0.110176, 'CD2': 0.110176, 'CE2': 0.110176}, |
| 23 | + 'ALA': {'CB': 0.019177, 'CA': 0.019177, 'C': 0.019177, 'O': -0.03128, 'N': -0.0391}, |
| 24 | + 'MET': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'CE': 0.019177, 'N': -0.0391, 'O': -0.03128, 'SD': 0.00506}, |
| 25 | + 'AHP': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'CE': 0.019177, 'CD': 0.019177, 'CZ': 0.019177, 'O': -0.03128, 'N': -0.0391}, |
| 26 | + 'LEU': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'O': -0.03128, 'N': -0.0391, 'CD1': 0.019177, 'CD2': 0.019177}, |
| 27 | + 'ARG': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'NE': -0.0391, 'O': -0.03128, 'CD': 0.019177, 'CZ': 0.019177, 'NH1': -0.06279, 'NH2': -0.06279, 'N': -0.0391}, |
| 28 | + 'AHX': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'CE': 0.019177, 'CD': 0.019177, 'O': -0.03128, 'N': -0.0391,}, |
| 29 | + 'TYR': {'C': 0.019177, 'CE1': 0.110176, 'OH': -0.04255, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.110176, 'O': -0.03128, 'N': -0.0391, 'CZ': 0.110176, 'CD1': 0.110176, 'CD2': 0.110176, 'CE2': 0.110176}, |
| 30 | + 'APE': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'O': -0.03128, 'CD': 0.019177, 'N': -0.0391}} |
| 31 | + |
| 32 | + |
| 33 | +def get_solvation(protein): |
| 34 | + """Get the solvation score for a given molecule""" |
| 35 | + energy_per_atom = [] |
| 36 | + for atom in protein.atoms: |
| 37 | + if not atom.is_hydrogen(): |
| 38 | + residue_name = atom.residue_name |
| 39 | + atom_name = atom.name |
| 40 | + |
| 41 | + # Special cases |
| 42 | + if atom_name == "OXT": |
| 43 | + residue_name = "ASP" |
| 44 | + atom_name = "OD1" |
| 45 | + if residue_name == 'HSD': |
| 46 | + residue_name = 'HID' |
| 47 | + if residue_name == 'HSP': |
| 48 | + residue_name = 'HIP' |
| 49 | + if residue_name == 'HSE': |
| 50 | + residue_name = 'HIE' |
| 51 | + if residue_name == 'HID': |
| 52 | + residue_name = 'HIP' |
| 53 | + try: |
| 54 | + energy_per_atom.append(energies[residue_name][atom_name]) |
| 55 | + except KeyError: |
| 56 | + energy_per_atom.append(default_energy) |
| 57 | + else: |
| 58 | + energy_per_atom.append(default_energy) |
| 59 | + |
| 60 | + return np.array(energy_per_atom) |
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