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lgscore
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‎lightdock/scoring/lgscore/__init__.py

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‎lightdock/scoring/lgscore/data/__init__.py

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‎lightdock/scoring/lgscore/data/amber.py

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‎lightdock/scoring/lgscore/data/solvation.py

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import numpy as np
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default_energy = 0.0
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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},
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'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},
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'GLY': {'C': 0.019177, 'CA': 0.019177, 'O': -0.03128, 'N': -0.0391,},
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'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},
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'CYS': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'O': -0.03128, 'N': -0.0391, 'SG': 0.02576},
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'CYX': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'O': -0.03128, 'N': -0.0391, 'SG': 0.00506},
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'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},
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'SER': {'C': 0.019177, 'OG': -0.04255, 'CB': 0.019177, 'CA': 0.019177, 'O': -0.03128, 'N': -0.0391,},
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'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},
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'PRO': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'O': -0.03128, 'CD': 0.019177, 'N': -0.0391},
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'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},
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'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},
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'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},
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'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},
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'VAL': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'O': -0.03128, 'N': -0.0391, 'CG1': 0.019177, 'CG2': 0.019177},
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'THR': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'OG1': -0.04255, 'O': -0.03128, 'N': -0.0391, 'CG2': 0.019177},
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'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},
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'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},
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'ALA': {'CB': 0.019177, 'CA': 0.019177, 'C': 0.019177, 'O': -0.03128, 'N': -0.0391},
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'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},
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'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},
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'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},
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'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},
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'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,},
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'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},
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'APE': {'C': 0.019177, 'CB': 0.019177, 'CA': 0.019177, 'CG': 0.019177, 'O': -0.03128, 'CD': 0.019177, 'N': -0.0391}}
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def get_solvation(protein):
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"""Get the solvation score for a given molecule"""
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energy_per_atom = []
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for atom in protein.atoms:
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if not atom.is_hydrogen():
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residue_name = atom.residue_name
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atom_name = atom.name
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# Special cases
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if atom_name == "OXT":
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residue_name = "ASP"
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atom_name = "OD1"
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if residue_name == 'HSD':
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residue_name = 'HID'
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if residue_name == 'HSP':
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residue_name = 'HIP'
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if residue_name == 'HSE':
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residue_name = 'HIE'
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if residue_name == 'HID':
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residue_name = 'HIP'
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try:
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energy_per_atom.append(energies[residue_name][atom_name])
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except KeyError:
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energy_per_atom.append(default_energy)
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else:
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energy_per_atom.append(default_energy)
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return np.array(energy_per_atom)

‎lightdock/scoring/lgscore/data/vdw.py

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"""Van der Waals charges and parameters"""
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vdw_energy = {'IP': 0.00277, 'HS': 0.0157, 'HP': 0.0157, 'Na': 0.00277, 'N*': 0.17, 'Li': 0.0183, 'HO': 0.0,
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'Rb': 0.00017, 'HC': 0.0157, 'HA': 0.015, 'O3': 0.21, 'CQ': 0.086, 'C*': 0.086, 'NA': 0.17, 'NB': 0.17,
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'NC': 0.17, 'O2': 0.21, 'I': 0.4, 'Br': 0.32, 'H': 0.0157, 'HW': 0.0, 'C0': 0.459789, 'K': 0.000328,
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'CK': 0.086, 'Cs': 8.06e-05, 'C': 0.086, 'Cl': 0.1, 'CN': 0.086, 'CM': 0.086, 'F': 0.061, 'CC': 0.086,
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'CB': 0.086, 'CA': 0.086, 'Zn': 0.0125, 'O': 0.21, 'N': 0.17, 'P': 0.2, 'S': 0.25, 'CR': 0.086,
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'N2': 0.17, 'N3': 0.17, 'CW': 0.086, 'CV': 0.086, 'CT': 0.1094, 'MG': 0.8947, 'OH': 0.2104, 'H2': 0.0157,
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'H3': 0.0157, 'H1': 0.0157, 'H4': 0.015, 'H5': 0.015, 'SH': 0.25, 'OW': 0.152, 'OS': 0.17}
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vdw_radii = {'IP': 1.868, 'HS': 0.6, 'HP': 1.1, 'Na': 1.868, 'N*': 1.824, 'Li': 1.137, 'HO': 0.0001, 'Rb': 2.956,
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'HC': 1.487, 'HA': 1.459, 'O3': 1.6612, 'CQ': 1.908, 'C*': 1.908, 'NA': 1.824, 'NB': 1.824, 'NC': 1.824,
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'O2': 1.6612, 'I': 2.35, 'Br': 2.22, 'H': 0.6, 'HW': 0.0001, 'C0': 1.7131, 'K': 2.658, 'CK': 1.908,
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'Cs': 3.395, 'C': 1.908, 'Cl': 2.47, 'CN': 1.908, 'CM': 1.908, 'F': 1.75, 'CC': 1.908, 'CB': 1.908,
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'CA': 1.908, 'Zn': 1.1, 'O': 1.6612, 'N': 1.824, 'P': 2.1, 'S': 2.0, 'CR': 1.908, 'N2': 1.824, 'N3': 1.875,
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'CW': 1.908, 'CV': 1.908, 'CT': 1.908, 'MG': 0.7926, 'OH': 1.721, 'H2': 1.287, 'H3': 1.187, 'H1': 1.387,
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'H4': 1.409, 'H5': 1.359, 'SH': 2.0, 'OW': 1.7683, 'OS': 1.6837}

‎lightdock/scoring/lgscore/driver.py

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"""Implementation of the lgscore scoring function.
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C-implementation of the lgscore scoring function and using the freesasa library:
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https://github.com/mittinatten/freesasa
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"""
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import numpy as np
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import freesasa
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from freesasa import Structure
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from lightdock.scoring.functions import ScoringFunction, ModelAdapter
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from lightdock.structure.model import DockingModel
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import lightdock.scoring.lgscore.energy.c.clgscore as clgscore
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import lightdock.scoring.lgscore.energy.parameters as parameters
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import lightdock.scoring.lgscore.data.amber as amber
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import lightdock.scoring.lgscore.data.vdw as vdw
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import lightdock.scoring.lgscore.data.solvation as solvation
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from lightdock.util.logger import LoggingManager
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log = LoggingManager.get_logger('lgscore')
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freesasa.setVerbosity(freesasa.silent)
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class LgScoreModel(DockingModel):
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"""Prepares the structure necessary for the C-implementation of the lgscore scoring function"""
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def __init__(self, objects, coordinates, restraints, charges,
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vdw_energy, vdw_radii, des_energy, sasa, desolvation, hydrogens,
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reference_points=None, n_modes=None):
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super(LgScoreModel, self).__init__(objects, coordinates, restraints, reference_points)
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self.charges = charges
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self.vdw_energy = vdw_energy
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self.vdw_radii = vdw_radii
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self.des_energy = des_energy
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self.sasa = sasa
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self.desolvation = desolvation
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self.hydrogens = hydrogens
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self.n_modes = n_modes
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def clone(self):
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"""Creates a copy of the current model"""
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return LgScoreModel(self.objects, self.coordinates.copy(), self.restraints,
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self.charges, self.vdw_energy, self.vdw_radii,
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self.des_energy, self.sasa, self.desolvation, self.hydrogens,
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reference_points=self.reference_points.copy())
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class LgScoreAdapter(ModelAdapter):
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"""Adapts a given Complex to a DockingModel object suitable for this
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scoring function.
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"""
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def _get_docking_model(self, molecule, restraints):
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atoms = molecule.atoms
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parsed_restraints = {}
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# Assign properties to atoms
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for atom_index, atom in enumerate(atoms):
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res_id = "%s.%s.%s" % (atom.chain_id, atom.residue_name, str(atom.residue_number))
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if restraints and res_id in restraints:
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try:
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parsed_restraints[res_id].append(atom_index)
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except:
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parsed_restraints[res_id] = [atom_index]
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res_name = atom.residue_name
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atom_name = atom.name
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if res_name == "HIS":
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res_name = 'HID'
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if atom_name in amber.translate:
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atom_name = amber.translate[atom.name]
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atom_id = "%s-%s" % (res_name, atom_name)
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atom.amber_type = amber.amber_types[atom_id]
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atom.charge = amber.charges[atom_id]
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atom.mass = amber.masses[atom.amber_type]
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atom.vdw_energy = vdw.vdw_energy[atom.amber_type]
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atom.vdw_radius = vdw.vdw_radii[atom.amber_type]
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# Prepare common model information
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elec_charges = np.array([atom.charge for atom in atoms])
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vdw_energies = np.array([atom.vdw_energy for atom in atoms])
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vdw_radii = np.array([atom.vdw_radius for atom in atoms])
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coordinates = molecule.copy_coordinates()
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des_energy = solvation.get_solvation(molecule)
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# Calculate desolvation reference energy
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log.info('Calculating reference SASA...')
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structure = Structure()
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for i, atom in enumerate(atoms):
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if not atom.is_hydrogen():
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structure.addAtom(atom.name, atom.residue_name, atom.residue_number, atom.chain_id,
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atom.x, atom.y, atom.z)
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sasa_result = freesasa.calc(structure)
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sasa = []
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j = 0
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for i, atom in enumerate(atoms):
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if not atom.is_hydrogen():
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sasa.append(sasa_result.atomArea(j))
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j += 1
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else:
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sasa.append(-1.0)
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sasa = np.array(sasa)
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hydrogens = np.array([0 if atom.is_hydrogen() else 1 for atom in atoms])
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log.info('Done.')
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desolvation = np.sum(sasa * des_energy)
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reference_points = ModelAdapter.load_reference_points(molecule)
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try:
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return LgScoreModel(atoms, coordinates, parsed_restraints, elec_charges, vdw_energies, vdw_radii, des_energy,
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sasa, desolvation, hydrogens, reference_points=reference_points, n_modes=molecule.n_modes.copy())
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except AttributeError:
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return LgScoreModel(atoms, coordinates, parsed_restraints, elec_charges, vdw_energies, vdw_radii, des_energy,
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sasa, desolvation, hydrogens, reference_points=reference_points)
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class LgScore(ScoringFunction):
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def __init__(self, weight=1.0):
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super(LgScore, self).__init__(weight)
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self.scoring_vdw_weight = parameters.scoring_vdw_weight
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def __call__(self, receptor, receptor_coordinates, ligand, ligand_coordinates):
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"""Computes the lgscore scoring energy using receptor and ligand which are
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instances of DockingModel.
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"""
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elec, vdw, solv, interface_receptor, interface_ligand = clgscore.calculate_energy(receptor_coordinates, ligand_coordinates,
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receptor.charges, ligand.charges,
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receptor.vdw_energy, ligand.vdw_energy,
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receptor.vdw_radii, ligand.vdw_radii,
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receptor.hydrogens, ligand.hydrogens,
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receptor.sasa, ligand.sasa,
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receptor.des_energy, ligand.des_energy,
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3.9)
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solvation = solv - (receptor.desolvation + ligand.desolvation)
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energy = (elec + parameters.scoring_vdw_weight * vdw + solvation)*-1.
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perc_receptor_restraints = ScoringFunction.restraints_satisfied(receptor.restraints, set(interface_receptor))
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perc_ligand_restraints = ScoringFunction.restraints_satisfied(ligand.restraints, set(interface_ligand))
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return energy + perc_receptor_restraints * energy + perc_ligand_restraints * energy
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# Needed to dynamically load the scoring functions from command line
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DefinedScoringFunction = LgScore
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DefinedModelAdapter = LgScoreAdapter

‎lightdock/scoring/lgscore/energy/__init__.py

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‎lightdock/scoring/lgscore/energy/c/__init__.py

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