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Simplify implementation of building by NERF

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This commit is contained in:
Kevin Wu
2022-09-07 14:39:50 -07:00
parent 3f88b808d6
commit 0c4e3c8b13
1 changed files with 12 additions and 31 deletions
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43
protdiff/mynerf.py
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@@ -72,40 +72,21 @@ class NERFBuilder:
# The first value of phi at the N terminus is not defined
# The last value of psi and omega at the C terminus are not defined
for i, (phi, psi, omega) in enumerate(
zip(self.phi[1:], self.psi[:-1], self.omega[:-1])
):
# Procedure
for phi, psi, omega in zip(self.phi[1:], self.psi[:-1], self.omega[:-1]):
# Procedure for placing N-CA-C
# Place the next N atom, which requires the C-N bond length/angle, and the psi dihedral
n_coords = place_dihedral(
retval[-3],
retval[-2],
retval[-1],
bond_angle=self.bond_angles[("C", "N")],
bond_length=self.bond_lengths[("C", "N")],
torsion_angle=psi,
)
retval.append(n_coords)
# Place the alpha carbon, which requires the N-CA bond length/angle, and the omega dihedral
ca_coords = place_dihedral(
retval[-3],
retval[-2],
retval[-1],
bond_angle=self.bond_angles[("N", "CA")],
bond_length=self.bond_lengths[("N", "CA")],
torsion_angle=omega,
)
retval.append(ca_coords)
# Place the carbon, which requires the the CA-C bond length/angle, and the phi dihedral
c_coords = place_dihedral(
retval[-3],
retval[-2],
retval[-1],
bond_angle=self.bond_angles[("CA", "C")],
bond_length=self.bond_lengths[("CA", "C")],
torsion_angle=phi,
)
retval.append(c_coords)
for bond, dih in zip(self.bond_lengths.keys(), [psi, omega, phi]):
coords = place_dihedral(
retval[-3],
retval[-2],
retval[-1],
bond_angle=self.bond_angles[bond],
bond_length=self.bond_lengths[bond],
torsion_angle=dih,
)
retval.append(coords)
return np.array(retval)