def make_equilibrium_pdb(trajectory, pdb, start=None, end=None):
"""
Calculates the equilibrium structure between start and end
frames. Default: last half of trajectory.
"""
if start is None:
start = trajectory.n_frame // 2
if end is None:
end = trajectory.n_frame
if start < 0 or start >= trajectory.n_frame:
raise IndexError("Start frame out of range")
if end < 0 or end > trajectory.n_frame+1:
raise IndexError("End frame out of range")
# sum_soup stores cumulative values
sum_soup = trajectory.soup.copy()
for a in sum_soup.atoms():
v3.set_vector(a.pos, 0, 0, 0)
n_frame = 0
for i in range(start, end):
trajectory.load_frame(i)
n_frame += 1
for sum_atom, atom in zip(
sum_soup.atoms(), trajectory.soup.atoms()):
sum_atom.pos += atom.pos
for a in sum_soup.atoms():
x = a.pos.x / float(n_frame)
y = a.pos.y / float(n_frame)
z = a.pos.z / float(n_frame)
v3.set_vector(a.pos, x, y, z)
trajectory.soup.write_pdb(pdb)
def make_equilibrium_pdb(trajectory, pdb, start=None, end=None):
"""
Calculates the equilibrium structure between start and end
frames. Default: last half of trajectory.
"""
if start is None:
start = trajectory.n_frame // 2
if end is None:
end = trajectory.n_frame
if start < 0 or start >= trajectory.n_frame:
raise IndexError("Start frame out of range")
if end < 0 or end > trajectory.n_frame + 1:
raise IndexError("End frame out of range")
# sum_soup stores cumulative values
sum_soup = trajectory.soup.copy()
for a in sum_soup.atoms():
v3.set_vector(a.pos, 0, 0, 0)
n_frame = 0
for i in range(start, end):
trajectory.load_frame(i)
n_frame += 1
for sum_atom, atom in zip(sum_soup.atoms(), trajectory.soup.atoms()):
sum_atom.pos += atom.pos
for a in sum_soup.atoms():
x = a.pos.x / float(n_frame)
y = a.pos.y / float(n_frame)
z = a.pos.z / float(n_frame)
v3.set_vector(a.pos, x, y, z)
trajectory.soup.write_pdb(pdb)
def AtomFromPdbLine(line):
"""
Returns an Atom object from an atom line in a pdb file.
"""
atom = Atom()
if line.startswith('HETATM'):
atom.is_hetatm = True
else:
atom.is_hetatm = False
atom.num = int(line[6:11])
atom.type = line[12:16].strip(" ")
atom.alt_conform = line[16]
atom.res_type = line[17:21].strip()
atom.element = data.guess_element(atom.res_type, atom.type)
atom.chain_id = line[21]
atom.res_num = int(line[22:26])
atom.res_insert = line[26]
if atom.res_insert == " ":
atom.res_insert = ""
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
v3.set_vector(atom.pos, x, y, z)
try:
atom.occupancy = float(line[54:60])
except:
atom.occupancy = 100.0
try:
atom.bfactor = float(line[60:66])
except:
atom.bfactor = 0.0
return atom
def apply(self, soup):
residue = soup.residue(self.i_res)
atoms = residue.atoms()
n_chi = get_n_chi(residue)
if self.mean_chis is None:
self.mean_chis = [calculate_chi(residue, i) for i in range(n_chi)]
rot_vels = [get_rot_vel_chi(residue, i) for i in range(n_chi)]
for atom in atoms:
v3.set_vector(atom.vel, 0.0, 0.0, 0.0)
for i_chi in reversed(range(n_chi)):
chi = calculate_chi(residue, i_chi)
delta_chi = v3.normalize_angle(chi - self.mean_chis[i_chi])
target_rot_vel = get_random_chi_rot_vel(residue, i_chi,
self.heating_temperature)
if abs(delta_chi) > self.max_delta_chi:
if delta_chi > self.max_delta_chi:
target_rot_vel = -target_rot_vel
else:
if rot_vels[i_chi] < 0.0:
target_rot_vel *= -target_rot_vel
add_rot_vel_to_chi(residue, i_chi, target_rot_vel)
anderson_velocity_scale(atoms, self.heating_temperature,
3 * len(atoms))
def apply(self, soup):
residue = soup.residue(self.i_res)
atoms = residue.atoms()
n_chi = get_n_chi(residue)
if self.mean_chis is None:
self.mean_chis = [calculate_chi(residue, i) for i in range(n_chi)]
rot_vels = [get_rot_vel_chi(residue, i) for i in range(n_chi)]
for atom in atoms:
v3.set_vector(atom.vel, 0.0, 0.0, 0.0)
for i_chi in reversed(range(n_chi)):
chi = calculate_chi(residue, i_chi)
delta_chi = v3.normalize_angle(chi - self.mean_chis[i_chi])
target_rot_vel = get_random_chi_rot_vel(
residue, i_chi, self.heating_temperature)
if abs(delta_chi) > self.max_delta_chi:
if delta_chi > self.max_delta_chi:
target_rot_vel = -target_rot_vel
else:
if rot_vels[i_chi] < 0.0:
target_rot_vel *= -target_rot_vel
add_rot_vel_to_chi(residue, i_chi, target_rot_vel)
anderson_velocity_scale(atoms, self.heating_temperature, 3*len(atoms))
def load_frame(self, i_frame):
box, positions, velocities, forces = self.trr_reader[i_frame]
for i, atom in enumerate(self.atoms):
v3.set_vector(atom.pos, positions[i][0] * 10, positions[i][1] * 10,
positions[i][2] * 10)
v3.set_vector(atom.vel, velocities[i][0] * 10,
velocities[i][1] * 10, velocities[i][2] * 10)
self.i_frame = self.trr_reader.i_frame
def gas_randomize(atoms, temperature):
"""
Randomly assigns a velocity to atoms based on a Maxwellian
distribution at temperature.
"""
for atom in atoms:
v3.set_vector(atom.vel, maxwell_velocity(temperature, atom.mass),
maxwell_velocity(temperature, atom.mass),
maxwell_velocity(temperature, atom.mass))
def gas_randomize(atoms, temperature):
"""
Randomly assigns a velocity to atoms based on a Maxwellian
distribution at temperature.
"""
for atom in atoms:
v3.set_vector(
atom.vel,
maxwell_velocity(temperature, atom.mass),
maxwell_velocity(temperature, atom.mass),
maxwell_velocity(temperature, atom.mass))
def load_frame(self, i_frame):
x, y, z = self.coor_dcd_reader[i_frame]
atoms = self.soup.atoms()
for i in range(len(atoms)):
v3.set_vector(atoms[i].pos, x[i], y[i], z[i])
if self.vel_dcd_reader is not None:
x, y, z = self.vel_dcd_reader[i_frame]
for i in range(len(atoms)):
v3.set_vector(atoms[i].vel, x[i], y[i], z[i])
self.i_frame = self.coor_dcd_reader.i_frame
def load_frame(self, i):
# Load coordinates of soup with coordinates from self.trj_reader
crds = self.trj_reader[i]
vels = self.vel_trj_reader[i] if self.vel_trj_reader else None
atoms = self.soup.atoms()
for i in range(self.n_atom):
atom = atoms[i]
k = 3 * i
v3.set_vector(atom.pos, crds[k], crds[k + 1], crds[k + 2])
if vels:
v3.set_vector(atom.vel, vels[k], vels[k + 1], vels[k + 2])
self.i_frame = self.trj_reader.i_frame
def load_frame(self, i_frame):
# Load coordinates of soup with coordinates from self.trj_reader
crds = self.trj_reader[i_frame]
vels = self.vel_trj_reader[i_frame] if self.vel_trj_reader else None
atoms = self.soup.atoms()
for i in range(self.n_atom):
atom = atoms[i]
k = 3*i
v3.set_vector(atom.pos, crds[k], crds[k+1], crds[k+2])
if vels:
v3.set_vector(atom.vel, vels[k], vels[k+1], vels[k+2])
self.i_frame = self.trj_reader.i_frame
def write_soup_to_crds_and_vels(in_soup, basename):
"""
From soup, writes out the coordinate/velocities, used for pulsing
"""
soup = in_soup.copy()
convert_to_namd_atom_names(soup)
coor = basename + '.coor'
soup.write_pdb(coor)
for atom in soup.atoms():
v3.set_vector(atom.pos, atom.vel[0], atom.vel[1], atom.vel[2])
vel = basename + '.vel'
soup.write_pdb(vel)
return coor, vel
def load_frame(self, i_frame):
box, positions, velocities, forces = self.trr_reader[i_frame]
for i, atom in enumerate(self.atoms):
v3.set_vector(
atom.pos,
positions[i][0]*10,
positions[i][1]*10,
positions[i][2]*10)
v3.set_vector(
atom.vel,
velocities[i][0]*10,
velocities[i][1]*10,
velocities[i][2]*10)
self.i_frame = self.trr_reader.i_frame
def soup_from_restart_files(psf, in_coor, in_vel='', skip_solvent=False):
"""
Reads a Soup from restart files.
"""
soup = soup_from_psf(psf)
coord_soup = pdbatoms.Soup(in_coor)
for atom, coord_atom in zip(soup.atoms(), coord_soup.atoms()):
p = coord_atom.pos
v3.set_vector(atom.pos, p[0], p[1], p[2])
if in_vel:
vel_soup = pdbatoms.Soup(in_vel)
for atom, vel_atom in zip(soup.atoms(), vel_soup.atoms()):
v = vel_atom.pos
v3.set_vector(atom.vel, v[0], v[1], v[2])
return soup
def anderson_velocity_scale(atoms, temperature, n_degree_of_freedom):
"""
Scales the velocity of atoms such that average energy
is consistent with the temperature.
"""
# This is the classic Anderson approach to temperature
# regulation. Whilst deterministic, can be easily trapped in
# local minima.
target_energy = mean_energy(temperature, n_degree_of_freedom)
kin = kinetic_energy(atoms)
if v3.is_similar_mag(kin, 0):
gas_randomize(atoms, temperature)
else:
scaling_factor = math.sqrt(target_energy / kin)
for atom in atoms:
v3.set_vector(atom.vel, v3.scale(atom.vel, scaling_factor))
def anderson_velocity_scale(atoms, temperature, n_degree_of_freedom):
"""
Scales the velocity of atoms such that average energy
is consistent with the temperature.
"""
# This is the classic Anderson approach to temperature
# regulation. Whilst deterministic, can be easily trapped in
# local minima.
target_energy = mean_energy(temperature, n_degree_of_freedom)
kin = kinetic_energy(atoms)
if v3.is_similar_mag(kin, 0):
gas_randomize(atoms, temperature)
else:
scaling_factor = math.sqrt(target_energy / kin)
for atom in atoms:
v3.set_vector(atom.vel, v3.scale(atom.vel, scaling_factor))
def load_crd_or_rst_into_soup(soup, crd_or_rst):
"""
Loads the coordinates and velocities of .crd or .rst into the soup.
"""
f = open(crd_or_rst, "r")
f.readline() # skip first line
n_atom = int(f.readline().split()[0])
# calculate size of file based on field sizes
n_crd = n_atom * 3
n_line = n_crd / 6
if n_crd % 6 > 0:
n_line += 1
# read all the numbers in the coordinate section
line_list = [f.readline()[:-1] for i in range(0, n_line)]
s = "".join(line_list)
vals = [float(s[i:i + 12]) for i in xrange(0, len(s), 12)]
if len(vals) != n_crd:
raise ValueError, "Improper number of coordinates in rst file."
# load numbers into soup object
for i, atom in enumerate(sorted(soup.atoms(), pdbatoms.cmp_atom)):
v3.set_vector(atom.pos, vals[i * 3], vals[i * 3 + 1], vals[i * 3 + 2])
# if .rst file, then there will be velocity values
if crd_or_rst.endswith('.rst'):
line_list = [f.readline()[:-1] for i in range(0, n_line)]
s = "".join(line_list)
vals = [float(s[i:i + 12]) for i in xrange(0, len(s), 12)]
if len(vals) != n_crd:
raise ValueError, "Improper number of coordinates in rst file."
# now convert amber velocities to angs/ps and load into soup
convert_vel_to_angs_per_ps = 20.455
for i, atom in enumerate(sorted(soup.atoms(), pdbatoms.cmp_atom)):
v3.set_vector(atom.vel, vals[i * 3], vals[i * 3 + 1],
vals[i * 3 + 2])
atom.vel = v3.scale(atom.vel, convert_vel_to_angs_per_ps)
f.close()
def load_crd_or_rst_into_soup(soup, crd_or_rst):
"""
Loads the coordinates and velocities of .crd or .rst into the soup.
"""
f = open(crd_or_rst, "r")
f.readline() # skip first line
n_atom = int(f.readline().split()[0])
# calculate size of file based on field sizes
n_crd = n_atom * 3
n_line = n_crd / 6
if n_crd % 6 > 0:
n_line += 1
# read all the numbers in the coordinate section
line_list = [f.readline()[:-1] for i in range(0, n_line)]
s = "".join(line_list)
vals = [float(s[i:i+12]) for i in xrange(0, len(s), 12)]
if len(vals) != n_crd:
raise ValueError, "Improper number of coordinates in rst file."
# load numbers into soup object
for i, atom in enumerate(sorted(soup.atoms(), pdbatoms.cmp_atom)):
v3.set_vector(atom.pos, vals[i*3], vals[i*3+1], vals[i*3+2])
# if .rst file, then there will be velocity values
if crd_or_rst.endswith('.rst'):
line_list = [f.readline()[:-1] for i in range(0, n_line)]
s = "".join(line_list)
vals = [float(s[i:i+12]) for i in xrange(0, len(s), 12)]
if len(vals) != n_crd:
raise ValueError, "Improper number of coordinates in rst file."
# now convert amber velocities to angs/ps and load into soup
convert_vel_to_angs_per_ps = 20.455
for i, atom in enumerate(sorted(soup.atoms(), pdbatoms.cmp_atom)):
v3.set_vector(atom.vel, vals[i*3], vals[i*3+1], vals[i*3+2])
atom.vel = v3.scale(atom.vel, convert_vel_to_angs_per_ps)
f.close()
def AtomFromGroLine(line):
"""
Returns an Atom object from a .gro atom line.
"""
atom = pdbatoms.Atom()
atom.res_num = int(line[0:5])
atom.res_type = line[5:8].strip()
atom.type = line[10:15].strip(" ")
atom.element = data.guess_element(atom.res_type, line[12:15])
atom.num = int(line[15:20])
# 10 x multiplier converts from nm to angstroms
x = 10.0 * float(line[20:28])
y = 10.0 * float(line[28:36])
z = 10.0 * float(line[36:44])
v3.set_vector(atom.pos, x, y, z)
if len(line) > 62:
# 10 x multiplier converts from nm to angstroms
x = 10.0 * float(line[44:52])
y = 10.0 * float(line[52:60])
z = 10.0 * float(line[60:68])
v3.set_vector(atom.vel, x, y, z)
return atom
def AtomFromGroLine(line):
"""
Returns an Atom object from a .gro atom line.
"""
atom = pdbatoms.Atom()
atom.res_num = int(line[0:5])
atom.res_type = line[5:8].strip()
atom.type = line[10:15].strip(" ")
atom.element = data.guess_element(
atom.res_type, line[12:15])
atom.num = int(line[15:20])
# 10 x multiplier converts from nm to angstroms
x = 10.0*float(line[20:28])
y = 10.0*float(line[28:36])
z = 10.0*float(line[36:44])
v3.set_vector(atom.pos, x, y, z)
if len(line) > 62:
# 10 x multiplier converts from nm to angstroms
x = 10.0*float(line[44:52])
y = 10.0*float(line[52:60])
z = 10.0*float(line[60:68])
v3.set_vector(atom.vel, x, y, z)
return atom
def AtomFromPdbLine(line):
"""Returns an Atom object from an atom line in a pdb file."""
atom = Atom()
if line.startswith('HETATM'):
atom.is_hetatm = True
else:
atom.is_hetatm = False
atom.num = int(line[6:11])
atom.type = line[12:16].strip(" ")
element = ''
for c in line[12:15]:
if not c.isdigit() and c != " ":
element += c
if element[:2] in two_char_elements:
atom.element = element[:2]
else:
atom.element = element[0]
atom.res_type = line[17:20]
atom.chain_id = line[21]
atom.res_num = int(line[22:26])
atom.res_insert = line[26]
if atom.res_insert == " ":
atom.res_insert = ""
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
v3.set_vector(atom.pos, x, y, z)
try:
atom.occupancy = float(line[54:60])
except:
atom.occupancy = 100.0
try:
atom.bfactor = float(line[60:66])
except:
atom.bfactor = 0.0
return atom
def AtomFromPdbLine(line):
"""Returns an Atom object from an atom line in a pdb file."""
atom = Atom()
if line.startswith('HETATM'):
atom.is_hetatm = True
else:
atom.is_hetatm = False
atom.num = int(line[6:11])
atom.type = line[12:16].strip(" ")
element = ''
for c in line[12:15]:
if not c.isdigit() and c != " ":
element += c
if element[:2] in two_char_elements:
atom.element = element[:2]
else:
atom.element = element[0]
atom.res_type = line[17:20]
atom.chain_id = line[21]
atom.res_num = int(line[22:26])
atom.res_insert = line[26]
if atom.res_insert == " ":
atom.res_insert = ""
x = float(line[30:38])
y = float(line[38:46])
z = float(line[46:54])
v3.set_vector(atom.pos, x, y, z)
try:
atom.occupancy = float(line[54:60])
except:
atom.occupancy = 100.0
try:
atom.bfactor = float(line[60:66])
except:
atom.bfactor = 0.0
return atom
def transform(self, matrix): """ Transforms the pos vector by a v3.transform matrix. """ new_pos = v3.transform(matrix, self.pos) v3.set_vector(self.pos, new_pos)
def transform(self, matrix):
new_pos = v3.transform(matrix, self.pos)
v3.set_vector(self.pos, new_pos)
def transform(self, matrix): new_pos = v3.transform(matrix, self.pos) v3.set_vector(self.pos, new_pos)