def get_pdb_transform(pdb, center_res, top_res):
"""
Returns a transformation matrix that centers pdb to
center_res on the z-axis and moves top_res above center_res
on the y-axis
"""
soup = pdbatoms.Soup(pdb)
atoms = soup.atoms()
soup_center = pdbatoms.get_center(atoms)
translation = v3.translation(-soup_center)
soup.transform(translation)
result = translation
center_atom = find_ca_of_resname(soup.atoms(), center_res)
view = v3.vector(0, 0, 1)
axis = v3.cross(view, center_atom.pos)
angle = v3.vec_dihedral(view, axis, center_atom.pos)
rotation = v3.rotation(axis, angle)
soup.transform(rotation)
result = v3.combine(rotation, result)
top_atom = find_ca_of_resname(soup.atoms(), top_res)
top_dir = v3.vector(0, 1, 0)
axis = view.copy()
angle = v3.vec_dihedral(top_dir, axis, top_atom.pos)
rotation2 = v3.rotation(axis, angle)
result = v3.combine(rotation2, result)
del soup
return result
def __init__(self, grid_spacing, width, center):
self.width = float(width)
half_width = self.width / 2.0
self.center = v3.vector(center)
self.spacing = float(grid_spacing)
self.inv_spacing = 1.0 / self.spacing
self.n = 1
cover = 0
self.low = v3.vector()
while cover < half_width:
self.n += 1
half_n_point = int(self.n / 2)
self.low[0] = self.center[0] - half_n_point * self.spacing
self.low[1] = self.center[1] - half_n_point * self.spacing
self.low[2] = self.center[2] - half_n_point * self.spacing
width_1 = abs(self.center[0] - self.low[0])
high_x = self.low[0] + self.n * self.spacing
width_2 = abs(high_x - self.center[0])
cover = min(width_1, width_2)
self.actual_width = self.n * self.spacing
self.total_volume = self.actual_width**3
self.total_point = self.n**3
self.array = array.array('b')
for i in xrange(self.total_point):
self.array.append(0)
self.n_sq = self.n**2
self.x = [self.low[0] + i * self.spacing for i in xrange(self.n)]
self.y = [self.low[1] + j * self.spacing for j in xrange(self.n)]
self.z = [self.low[2] + k * self.spacing for k in xrange(self.n)]
def get_pdb_transform(pdb, center_res, top_res): """ Returns a transformation matrix that centers pdb to center_res on the z-axis and moves top_res above center_res on the y-axis """ soup = pdbatoms.Soup(pdb) atoms = soup.atoms() soup_center = pdbatoms.get_center(atoms) translation = v3.translation(-soup_center) soup.transform(translation) result = translation center_atom = find_ca_of_resname(soup.atoms(), center_res) view = v3.vector(0, 0, 1) axis = v3.cross(view, center_atom.pos) angle = v3.vec_dihedral(view, axis, center_atom.pos) rotation = v3.rotation(axis, angle) soup.transform(rotation) result = v3.combine(rotation, result) top_atom = find_ca_of_resname(soup.atoms(), top_res) top_dir = v3.vector(0, 1, 0) axis = view.copy() angle = v3.vec_dihedral(top_dir, axis, top_atom.pos) rotation2 = v3.rotation(axis, angle) result = v3.combine(rotation2, result) del soup return result
def __init__(self, grid_spacing, width, center):
self.width = float(width)
half_width = self.width / 2.0
self.center = v3.vector(center)
self.spacing = float(grid_spacing)
self.inv_spacing = 1.0 / self.spacing
self.n = 1
cover = 0
self.low = v3.vector()
while cover < half_width:
self.n += 1
half_n_point = int(self.n / 2)
self.low[0] = self.center[0] - half_n_point*self.spacing
self.low[1] = self.center[1] - half_n_point*self.spacing
self.low[2] = self.center[2] - half_n_point*self.spacing
width_1 = abs(self.center[0] - self.low[0])
high_x = self.low[0] + self.n*self.spacing
width_2 = abs(high_x - self.center[0])
cover = min(width_1, width_2)
self.actual_width = self.n*self.spacing
self.total_volume = self.actual_width**3
self.total_point = self.n**3
self.array = array.array('b')
for i in xrange(self.total_point):
self.array.append(0)
self.n_sq = self.n**2
self.x = [self.low[0] + i*self.spacing for i in xrange(self.n)]
self.y = [self.low[1] + j*self.spacing for j in xrange(self.n)]
self.z = [self.low[2] + k*self.spacing for k in xrange(self.n)]
def exclude_sphere(self, pos, r):
low = v3.vector(pos[0] - r, pos[1] - r, pos[2] - r)
low_i, low_j, low_k = self.indices(low)
high = v3.vector(pos[0] + r, pos[1] + r, pos[2] + r)
high_i, high_j, high_k = self.indices(high)
r_sq = r*r
for i in self.int_range(low_i, high_i):
for j in self.int_range(low_j, high_j):
for k in self.int_range(low_k, high_k):
l = i*self.n_sq + j*self.n + k
if self.array[l] == 0:
if self.is_grid_point_near_sphere(i, j, k, pos, r_sq):
self.array[l] = 1
def exclude_sphere(self, pos, r):
low = v3.vector(pos[0] - r, pos[1] - r, pos[2] - r)
low_i, low_j, low_k = self.indices(low)
high = v3.vector(pos[0] + r, pos[1] + r, pos[2] + r)
high_i, high_j, high_k = self.indices(high)
r_sq = r * r
for i in self.int_range(low_i, high_i):
for j in self.int_range(low_j, high_j):
for k in self.int_range(low_k, high_k):
l = i * self.n_sq + j * self.n + k
if self.array[l] == 0:
if self.is_grid_point_near_sphere(i, j, k, pos, r_sq):
self.array[l] = 1
def __init__(self): self.is_hetatm = False self.pos = v3.vector() self.vel = v3.vector() self.mass = 0.0 self.type = "" self.element = "" self.chain_id = " " self.res_type = "" self.res_num = "" self.res_insert = "" self.bfactor = 0.0 self.occupancy = 0.0 self.num = 0
def __init__(self):
self.is_hetatm = False
self.pos = v3.vector()
self.vel = v3.vector()
self.mass = 0.0
self.type = ""
self.element = ""
self.chain_id = " "
self.res_type = ""
self.res_num = ""
self.res_insert = ""
self.bfactor = 0.0
self.occupancy = 0.0
self.num = 0
def get_center(atoms):
"""
Returns the geometric center position vector of atoms.
"""
center = v3.vector()
for atom in atoms:
center += atom.pos
result = v3.scale(center, 1.0/float(len(atoms)))
return result
def average_vel(atoms):
"""
Returns the mass-averaged velocity of atoms.
"""
momentum = v3.vector()
mass = 0.0
for a in atoms:
momentum += v3.scale(a.vel, a.mass)
mass += a.mass
return v3.scale(momentum, 1.0 / mass)
def average_vel(atoms):
"""
Returns the mass-averaged velocity of atoms.
"""
momentum = v3.vector()
mass = 0.0
for a in atoms:
momentum += v3.scale(a.vel, a.mass)
mass += a.mass
return v3.scale(momentum, 1.0/mass)
def __init__(self, pos=None, atom_type="", res_num=None): """ Normally initialized as an empty container, and filled up progressively as fields are read by parsers. """ self.is_hetatm = False self.pos = v3.vector() if pos is None else pos self.vel = v3.vector() self.mass = 0.0 self.charge = 0.0 self.type = "" self.element = "" self.chain_id = " " self.res_type = "" self.res_num = "" self.res_insert = "" self.bfactor = 0.0 self.occupancy = 0.0 self.num = 0 self.alt_conform = " "
def generate_sphere_points(n):
"""
Returns list of coordinates on a sphere using the Golden-
Section Spiral algorithm.
"""
points = []
inc = math.pi * (3 - math.sqrt(5))
offset = 2 / float(n)
for k in range(int(n)):
y = k * offset - 1 + (offset / 2)
r = math.sqrt(1 - y * y)
phi = k * inc
points.append(v3.vector(math.cos(phi) * r, y, math.sin(phi) * r))
return points
def generate_sphere_points(n):
"""
Returns list of coordinates on a sphere using the Golden-
Section Spiral algorithm.
"""
points = []
inc = math.pi * (3 - math.sqrt(5))
offset = 2 / float(n)
for k in range(int(n)):
y = k * offset - 1 + (offset / 2)
r = math.sqrt(1 - y*y)
phi = k * inc
points.append(v3.vector(math.cos(phi)*r, y, math.sin(phi)*r))
return points
def add_rotational_velocity(atoms, rot_vel, axis, anchor):
"""
Adds the rot_vel to the vel vector of atoms with respect
to the rotation around axis and attached to anchor.
"""
for atom in atoms:
r_perp = v3.perpendicular(atom.pos - anchor, axis)
v_tang_dir = v3.cross(axis, r_perp)
v_tang_dir_len = v3.mag(v_tang_dir)
if v3.is_similar_mag(v_tang_dir_len, 0):
v_tang = v3.vector()
else:
v_new_len = rot_vel * v3.mag(r_perp)
v_tang = v3.scale(v_tang_dir, v_new_len/v_tang_dir_len)
atom.vel += v_tang
def add_rotational_velocity(atoms, rot_vel, axis, anchor):
"""
Adds the rot_vel to the vel vector of atoms with respect
to the rotation around axis and attached to anchor.
"""
for atom in atoms:
r_perp = v3.perpendicular(atom.pos - anchor, axis)
v_tang_dir = v3.cross(axis, r_perp)
v_tang_dir_len = v3.mag(v_tang_dir)
if v3.is_similar_mag(v_tang_dir_len, 0):
v_tang = v3.vector()
else:
v_new_len = rot_vel * v3.mag(r_perp)
v_tang = v3.scale(v_tang_dir, v_new_len / v_tang_dir_len)
atom.vel += v_tang
def soup_from_psf(psf):
"""
Returns a Soup from a .psf file
"""
soup = pdbatoms.Soup()
curr_res_num = None
is_header = True
for line in open(psf):
if is_header:
if "NATOM" in line:
n_atom = int(line.split()[0])
is_header = False
continue
words = line.split()
atom_num = int(words[0])
chain_id = words[1]
res_num = int(words[2])
res_type = words[3]
atom_type = words[4]
charge = float(words[6])
mass = float(words[7])
if chain_id.startswith('WT') or chain_id.startswith('ION'):
is_hetatm = True
chain_id = " "
else:
is_hetatm = False
chain_id = chain_id[0]
if curr_res_num != res_num:
res = pdbatoms.Residue(res_type, chain_id, res_num)
soup.append_residue(res)
curr_res_num = res_num
atom = pdbatoms.Atom()
atom.vel = v3.vector()
atom.chain_id = chain_id
atom.is_hetatm = is_hetatm
atom.num = atom_num
atom.res_num = res_num
atom.res_type = res_type
atom.type = atom_type
atom.mass = mass
atom.charge = charge
atom.element = data.guess_element(res_type, atom_type)
soup.insert_atom(-1, atom)
if len(soup.atoms()) == n_atom:
break
convert_to_pdb_atom_names(soup)
return soup
def soup_from_topology(topology):
"""
Returns a Soup from a topology dictionary.
"""
soup = pdbatoms.Soup()
chain_id = ''
n_res = topology['NRES']
n_atom = topology['NATOM']
for i_res in range(n_res):
res_type = topology['RESIDUE_LABEL'][i_res].strip()
if res_type == "WAT":
res_type = "HOH"
res = pdbatoms.Residue(res_type, chain_id, i_res+1)
soup.append_residue(res)
res = soup.residue(i_res)
i_atom_start = topology['RESIDUE_POINTER'][i_res] - 1
if i_res == n_res-1:
i_atom_end = n_atom
else:
i_atom_end = topology['RESIDUE_POINTER'][i_res+1] - 1
for i_atom in range(i_atom_start, i_atom_end):
atom = pdbatoms.Atom()
atom.vel = v3.vector()
atom.num = i_atom+1
atom.res_num = i_res+1
atom.res_type = res_type
atom.type = topology['ATOM_NAME'][i_atom].strip()
atom.mass = topology['MASS'][i_atom]
atom.charge = topology['CHARGE'][i_atom]/sqrt_of_k
atom.element = data.guess_element(
atom.res_type, atom.type)
soup.insert_atom(-1, atom)
convert_to_pdb_atom_names(soup)
if topology['IFBOX'] > 0:
# create dummy dimension to ensure box dimension recognized
soup.box_dimension_str = "1.000000 1.0000000 1.000000"
return soup
def soup_from_topology(topology):
"""
Returns a Soup from a topology dictionary.
"""
soup = pdbatoms.Soup()
chain_id = ''
n_res = topology['NRES']
n_atom = topology['NATOM']
for i_res in range(n_res):
res_type = topology['RESIDUE_LABEL'][i_res].strip()
if res_type == "WAT":
res_type = "HOH"
res = pdbatoms.Residue(res_type, chain_id, i_res + 1)
soup.append_residue(res)
res = soup.residue(i_res)
i_atom_start = topology['RESIDUE_POINTER'][i_res] - 1
if i_res == n_res - 1:
i_atom_end = n_atom
else:
i_atom_end = topology['RESIDUE_POINTER'][i_res + 1] - 1
for i_atom in range(i_atom_start, i_atom_end):
atom = pdbatoms.Atom()
atom.vel = v3.vector()
atom.num = i_atom + 1
atom.res_num = i_res + 1
atom.res_type = res_type
atom.type = topology['ATOM_NAME'][i_atom].strip()
atom.mass = topology['MASS'][i_atom]
atom.charge = topology['CHARGE'][i_atom] / sqrt_of_k
atom.element = data.guess_element(atom.res_type, atom.type)
soup.insert_atom(-1, atom)
convert_to_pdb_atom_names(soup)
if topology['IFBOX'] > 0:
# create dummy dimension to ensure box dimension recognized
soup.box_dimension_str = "1.000000 1.0000000 1.000000"
return soup
def get_center(atoms):
center = v3.vector()
for atom in atoms:
center += atom.pos
return center / float(len(atoms))
def pos(self, i, j, k):
return v3.vector(self.x[i], self.y[j], self.z[k])
def get_center(atoms):
center = v3.vector()
for atom in atoms:
center += atom.pos
return center/float(len(atoms))
def pos(self, i, j, k): return v3.vector(self.x[i], self.y[j], self.z[k])
