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Adds Functionality to Logger

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This commit is contained in:
Vitor Hideyoshi
2023-04-27 05:14:07 -03:00
parent 2d488bd749
commit 9c822c6848
5 changed files with 177 additions and 87 deletions
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121
diceplayer/shared/environment/system.py
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@@ -42,6 +42,29 @@ class System:
raise TypeError("Error: nmols is not an integer")
self.nmols.append(nmols)
def update_molecule(self, position: np.ndarray, fh: TextIO) -> None:
"""Updates the position of the molecule in the Output file
Args:
position (np.ndarray): numpy position vector
fh (TextIO): Output file
"""
position_in_ang = (position * BOHR2ANG).tolist()
self.add_type(self.nmols[0], deepcopy(self.molecule[0]))
for atom in self.molecule[-1].atom:
atom.rx = position_in_ang.pop(0)
atom.ry = position_in_ang.pop(0)
atom.rz = position_in_ang.pop(0)
rmsd, self.molecule[0] = self.rmsd_fit(-1, 0)
self.molecule.pop(-1)
fh.write("\nProjected new conformation of reference molecule with RMSD fit\n")
fh.write("RMSD = {:>8.5f} Angstrom\n".format(rmsd))
def rmsd_fit(self, p_index: int, r_index: int) -> Tuple[float, Molecule]:
projecting_mol = self.molecule[p_index]
@@ -176,65 +199,43 @@ class System:
# self.molecule.pop(-1)
#
# return min_dist, nearestmol
def update_molecule(self, position: np.ndarray, fh: TextIO) -> None:
"""Updates the position of the molecule in the Output file
Args:
position (np.ndarray): numpy position vector
fh (TextIO): Output file
"""
position_in_ang = (position * BOHR2ANG).tolist()
self.add_type(self.nmols[0], deepcopy(self.molecule[0]))
for atom in self.molecule[-1].atom:
atom.rx = position_in_ang.pop(0)
atom.ry = position_in_ang.pop(0)
atom.rz = position_in_ang.pop(0)
rmsd, self.molecule[0] = self.rmsd_fit(-1, 0)
self.molecule.pop(-1)
fh.write("\nProjected new conformation of reference molecule with RMSD fit\n")
fh.write("RMSD = {:>8.5f} Angstrom\n".format(rmsd))
def print_geom(self, cycle: int, fh: TextIO) -> None:
"""
Print the geometry of the molecule in the Output file
Args:
cycle (int): Number of the cycle
fh (TextIO): Output file
"""
fh.write("Cycle # {}\n".format(cycle))
fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
for atom in self.molecule[0].atom:
symbol = atomsymb[atom.na]
fh.write(
"{:<2s} {:>10.6f} {:>10.6f} {:>10.6f}\n".format(
symbol, atom.rx, atom.ry, atom.rz
)
)
def printChargesAndDipole(self, cycle: int, fh: TextIO) -> None:
"""
Print the charges and dipole of the molecule in the Output file
Args:
cycle (int): Number of the cycle
fh (TextIO): Output file
"""
fh.write("Cycle # {}\n".format(cycle))
fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
chargesAndDipole = self.molecule[0].charges_and_dipole()
fh.write(
"{:>10.6f} {:>10.6f} {:>10.6f} {:>10.6f} {:>10.6f}\n".format(
chargesAndDipole[0], chargesAndDipole[1], chargesAndDipole[2], chargesAndDipole[3], chargesAndDipole[4]
)
)
# def print_geom(self, cycle: int, fh: TextIO) -> None:
# """
# Print the geometry of the molecule in the Output file
#
# Args:
# cycle (int): Number of the cycle
# fh (TextIO): Output file
# """
#
# fh.write("Cycle # {}\n".format(cycle))
# fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
# for atom in self.molecule[0].atom:
# symbol = atomsymb[atom.na]
# fh.write(
# "{:<2s} {:>10.6f} {:>10.6f} {:>10.6f}\n".format(
# symbol, atom.rx, atom.ry, atom.rz
# )
# )
#
# def printChargesAndDipole(self, cycle: int, fh: TextIO) -> None:
# """
# Print the charges and dipole of the molecule in the Output file
#
# Args:
# cycle (int): Number of the cycle
# fh (TextIO): Output file
# """
#
# fh.write("Cycle # {}\n".format(cycle))
# fh.write("Number of site: {}\n".format(len(self.molecule[0].atom)))
#
# chargesAndDipole = self.molecule[0].charges_and_dipole()
#
# fh.write(
# "{:>10.6f} {:>10.6f} {:>10.6f} {:>10.6f} {:>10.6f}\n".format(
# chargesAndDipole[0], chargesAndDipole[1], chargesAndDipole[2], chargesAndDipole[3], chargesAndDipole[4]
# )
# )