def build_struct(self, name, params, position, mol=None, createPrinted=False):
"""
Build a peptide from a sequence entered through the Property Manager dialog.
"""
if len(self.peptide_cache) == 0:
return None
# Create a molecule
mol = Chunk(self.win.assy,name)
# Generate dummy atoms positions
self.prev_coords[0][0] = position[0] - 1.499
self.prev_coords[0][1] = position[1] + 1.539
self.prev_coords[0][2] = position[2]
self.prev_coords[1][0] = position[0] - 1.499
self.prev_coords[1][1] = position[1]
self.prev_coords[1][2] = position[2]
self.prev_coords[2][0] = position[0]
self.prev_coords[2][1] = position[1]
self.prev_coords[2][2] = position[2]
# Add a N-terminal hydrogen
atom = Atom("H", position, mol)
atom._is_aromatic = False
atom._is_single = False
self.nterm_hydrogen = atom
# Generate the peptide chain.
self.length = 1
for index, phi, psi in self.peptide_cache:
name, short_name, symbol, zmatrix, size = AMINO_ACIDS[index]
self._buildResiduum(mol, zmatrix, size, phi, psi, None, symbol)
# Add a C-terminal OH group
self._buildResiduum(mol, CTERM_ZMATRIX, 5, 0.0, 0.0, None, symbol)
# Compute bonds (slow!)
# This should be replaced by a proper bond assignment.
inferBonds(mol)
mol._protein_helix = []
mol._protein_sheet = []
# Assign proper bond orders.
i = 1
for atom in mol.atoms.itervalues():
if self.ss_idx == 1:
mol._protein_helix.append(i)
elif self.ss_idx == 2:
mol._protein_sheet.append(i)
if atom.bonds:
for bond in atom.bonds:
if bond.atom1.getAtomTypeName()=="sp2" and \
bond.atom2.getAtomTypeName()=="sp2":
if (bond.atom1._is_aromatic and
bond.atom2._is_aromatic):
bond.set_v6(V_AROMATIC)
elif ((bond.atom1._is_aromatic == False and
bond.atom1._is_aromatic == False) and
not (bond.atom1._is_single and
bond.atom2._is_single)):
bond.set_v6(V_DOUBLE)
i += 1
# Remove temporary attributes.
for atom in mol.atoms.itervalues():
del atom._is_aromatic
del atom._is_single
return mol
def _buildResiduum(self, mol, zmatrix, n_atoms, phi, psi, init_pos, symbol):
"""
Builds cartesian coordinates for an amino acid from the internal
coordinates table.
mol is a chunk to which the amino acid will be added.
zmatrix is an internal coordinates array corresponding to a given amino acid.
n_atoms is a number of atoms to be build + 3 dummy atoms.
phi is a peptide bond PHI angle.
psi is a peptide bond PSI angle.
init_pos are optional postions of previous CA, C and O atoms.
symbol is a current amino acid symbol (used for proline case)
Note: currently, it doesn't rebuild bonds, so inferBonds has to be called after.
Unfortunately, the proper bond order can not be correctly recognized this way.
"""
if mol == None:
return
if not init_pos: # assign three previous atom positions
for i in range (0,3):
self.coords[i][0] = self.prev_coords[i][0]
self.coords[i][1] = self.prev_coords[i][1]
self.coords[i][2] = self.prev_coords[i][2]
else: # if no prev_coords are given, compute the first three atom positions
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[1]
self.coords[0][0] = 0.0;
self.coords[0][1] = 0.0;
self.coords[0][2] = 0.0;
self.coords[1][0] = r;
self.coords[1][1] = 0.0;
self.coords[1][2] = 0.0;
ccos = cos(DEG2RAD*a)
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[2]
if atom_c == 1:
self.coords[2][0] = self.coords[0][0] + r*ccos
else:
self.coords[2][0] = self.coords[0][0] - r*ccos
self.coords[2][1] = r * sin(DEG2RAD*a)
self.coords[2][2] = 0.0
for i in range (0, 3):
self.prev_coords[i][0] = self.coords[i][0] + init_pos[0]
self.prev_coords[i][1] = self.coords[i][1] + init_pos[1]
self.prev_coords[i][2] = self.coords[i][2] + init_pos[2]
for n in range (3, n_atoms):
# Generate all coordinates using three previous atoms
# as a frame of reference,
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[n]
cosa = cos(DEG2RAD * a)
xb = self.coords[atom_b][0] - self.coords[atom_c][0]
yb = self.coords[atom_b][1] - self.coords[atom_c][1]
zb = self.coords[atom_b][2] - self.coords[atom_c][2]
rbc = 1.0 / sqrt(xb*xb + yb*yb + zb*zb)
if abs(cosa) >= 0.999:
# Linear bond case
# Skip angles, just extend along the bond.
rbc = r * rbc * cosa
self.coords[n][0] = self.coords[atom_c][0] + xb*rbc
self.coords[n][1] = self.coords[atom_c][1] + yb*rbc
self.coords[n][2] = self.coords[atom_c][2] + zb*rbc
else:
xa = self.coords[atom_a][0] - self.coords[atom_c][0]
ya = self.coords[atom_a][1] - self.coords[atom_c][1]
za = self.coords[atom_a][2] - self.coords[atom_c][2]
xyb = sqrt(xb*xb + yb*yb)
inv = False
if xyb < 0.001:
xpa = za
za = -xa
xa = xpa
xpb = zb
zb = -xb
xb = xpb
xyb = sqrt(xb*xb + yb*yb)
inv = True
costh = xb / xyb
sinth = yb / xyb
xpa = xa * costh + ya * sinth
ypa = ya * costh - xa * sinth
sinph = zb * rbc
cosph = sqrt(abs(1.0- sinph * sinph))
xqa = xpa * cosph + za * sinph
zqa = za * cosph - xpa * sinph
yza = sqrt(ypa * ypa + zqa * zqa)
if yza < 1e-8:
coskh = 1.0
sinkh = 0.0
else:
coskh = ypa / yza
sinkh = zqa / yza
# Apply the peptide bond conformation
if symbol != "P":
if name == "N " and not init_pos:
t = self.prev_psi + 0.0
if name == "O ":
t = psi + 180.0
if name == "HA " or name == "HA2":
t = 120.0 + phi
if name == "CB " or name == "HA3":
t = 240.0 + phi
if name == "C ":
t = phi
else:
# proline
if name == "N " and not init_pos:
t = self.prev_psi + 0.0
if name == "O ":
t = psi + 180.0
if name == "CA ":
t = phi - 120.0
if name == "CD ":
t = phi + 60.0
sina = sin(DEG2RAD * a)
sind = -sin(DEG2RAD * t)
cosd = cos(DEG2RAD * t)
# Apply the bond length.
xd = r * cosa
yd = r * sina * cosd
zd = r * sina * sind
# Compute the atom position using bond and torsional angles.
ypd = yd * coskh - zd * sinkh
zpd = zd * coskh + yd * sinkh
xpd = xd * cosph - zpd * sinph
zqd = zpd * cosph + xd * sinph
xqd = xpd * costh - ypd * sinth
yqd = ypd * costh + xpd * sinth
if inv:
tmp = -zqd
zqd = xqd
xqd = tmp
self.coords[n][0] = xqd + self.coords[atom_c][0]
self.coords[n][1] = yqd + self.coords[atom_c][1]
self.coords[n][2] = zqd + self.coords[atom_c][2]
if self.nterm_hydrogen:
# It is a hack for the first hydrogen atom
# to make sure the bond length is correct.
self.nterm_hydrogen.setposn(
self.nterm_hydrogen.posn() + 0.325 * norm(V(xqd, yqd, zqd)))
self.nterm_hydrogen = None
ax = self.coords[n][0]
ay = self.coords[n][1]
az = self.coords[n][2]
# Store previous coordinates for the next building step
if not init_pos:
if name=="N ":
self.prev_coords[0][0] = self.coords[n][0]
self.prev_coords[0][1] = self.coords[n][1]
self.prev_coords[0][2] = self.coords[n][2]
if name=="CA ":
self.prev_coords[1][0] = self.coords[n][0]
self.prev_coords[1][1] = self.coords[n][1]
self.prev_coords[1][2] = self.coords[n][2]
if name=="C ":
self.prev_coords[2][0] = self.coords[n][0]
self.prev_coords[2][1] = self.coords[n][1]
self.prev_coords[2][2] = self.coords[n][2]
# Add a new atom to the molecule
atom = Atom(
atom_name,
V(self.coords[n][0], self.coords[n][1], self.coords[n][2]),
mol)
# Create temporary attributes for proper bond assignment.
atom._is_aromatic = False
atom._is_single = False
if atom_type == "sp2a":
atom_type = "sp2"
atom._is_aromatic = True
if atom_type == "sp2s":
atom_type = "sp2"
atom._is_single = True
atom.set_atomtype_but_dont_revise_singlets(atom_type)
if name == "CA ":
# Set c-alpha flag for protein main chain visualization.
atom._protein_ca = True
else:
atom._protein_ca = False
if name == "CB ":
# Set c-alpha flag for protein main chain visualization.
atom._protein_cb = True
else:
atom._protein_cb = False
if name == "N ":
# Set c-alpha flag for protein main chain visualization.
atom._protein_n = True
else:
atom._protein_n = False
if name == "C ":
# Set c-alpha flag for protein main chain visualization.
atom._protein_c = True
else:
atom._protein_c = False
if name == "O ":
# Set c-alpha flag for protein main chain visualization.
atom._protein_o = True
else:
atom._protein_o = False
# debug - output in PDB format
# print "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f" % ( n, name, "ALA", ' ', res_num, coords[n][0], coords[n][1], coords[n][2])
self.prev_psi = psi # Remember previous psi angle.
self.length += 1 # Increase the amino acid counter.
return
def _buildResidue(self, mol, zmatrix, n_atoms, idx, phi, psi, secondary, init_pos, residue_name, fake_chain=False):
"""
Builds cartesian coordinates for an amino acid from the internal
coordinates table.
@param mol: a chunk to which the amino acid will be added.
@type mol: Chunk
@param zmatrix: is an internal coordinates array corresponding to a
given amino acid.
@type zmatrix: list
@param n_atoms: size of z-matrix (a number of atoms to be build + 3
dummy atoms)
@type n_atoms: int
@param idx: is a residue index (1..length).
@type idx: integer
@param phi, psi: peptide bond phi and psi angles
@type phi, psi: float
@param init_pos: optional postions of previous CA, C and O atoms.
@type init_pos: V
@param symbol: current amino acid symbol (used to derermine proline case)
@type symbol: string
"""
# note: currently, it doesn't rebuild bonds, so inferBonds has to be
# called after this method. Unfortunately, the proper bond order can
# not be correctly recognized this way. Therefore, temporary atom flags
# _is_aromatic and _is_single are used.
#this code was re-factored by EricM and internal-to-cartesian
# conversion method was moved to geometry.InternalCoordinatesToCartesian
if mol is None:
return
if not init_pos: # assign three previous atom positions
coords = self.prev_coords
else:
# if no prev_coords are given, compute the first three atom positions
coords = zeros([3,3], Float)
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[1]
coords[0][0] = 0.0;
coords[0][1] = 0.0;
coords[0][2] = 0.0;
coords[1][0] = r;
coords[1][1] = 0.0;
coords[1][2] = 0.0;
ccos = cos(DEG2RAD*a)
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[2]
if atom_c == 1:
coords[2][0] = coords[0][0] + r*ccos
else:
coords[2][0] = coords[0][0] - r*ccos
coords[2][1] = r * sin(DEG2RAD*a)
coords[2][2] = 0.0
for i in range (0, 3):
self.prev_coords[i][0] = coords[i][0] + init_pos[0]
self.prev_coords[i][1] = coords[i][1] + init_pos[1]
self.prev_coords[i][2] = coords[i][2] + init_pos[2]
translator = InternalCoordinatesToCartesian(n_atoms, coords)
for n in range (3, n_atoms):
# Generate all coordinates using three previous atoms
# as a frame of reference,
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[n]
# Apply the peptide bond conformation
if residue_name != "PRO":
if name == "N " and not init_pos:
t = self.prev_psi + 0.0
if name == "O ":
t = psi + 180.0
if name == "HA " or name == "HA2":
t = 120.0 + phi
if name == "CB " or name == "HA3":
t = 240.0 + phi
if name == "C ":
t = phi
else:
# proline
if name == "N " and not init_pos:
t = self.prev_psi + 0.0
if name == "O ":
t = psi + 180.0
if name == "CA ":
t = phi - 120.0
if name == "CD ":
t = phi + 60.0
translator.addInternal(n+1, atom_c+1, atom_b+1, atom_a+1, r, a, t)
xyz = translator.getCartesian(n+1)
if self.nterm_hydrogen:
# This is a hack for the first hydrogen atom
# to make sure the bond length is correct.
self.nterm_hydrogen.setposn(
self.nterm_hydrogen.posn() + \
0.325 * norm(xyz))
self.nterm_hydrogen = None
# Store previous coordinates for the next building step
if not init_pos:
if name=="N ":
self.prev_coords[0][0] = xyz[0]
self.prev_coords[0][1] = xyz[1]
self.prev_coords[0][2] = xyz[2]
if name=="CA ":
self.prev_coords[1][0] = xyz[0]
self.prev_coords[1][1] = xyz[1]
self.prev_coords[1][2] = xyz[2]
if name=="C ":
self.prev_coords[2][0] = xyz[0]
self.prev_coords[2][1] = xyz[1]
self.prev_coords[2][2] = xyz[2]
# Add a new atom to the molecule
if not fake_chain or \
name == "CA ":
atom = Atom(
atom_name,
xyz,
mol)
if not self.init_ca and \
name == "CA ":
self.init_ca = atom
if mol.protein:
aa = mol.protein.add_pdb_atom(atom,
name.replace(' ',''),
idx,
AA_3_TO_1[residue_name])
atom.pdb_info = {}
atom.pdb_info['atom_name'] = name.replace(' ','')
atom.pdb_info['residue_name'] = residue_name
residue_id = "%3d " % idx
atom.pdb_info['residue_id'] = residue_id
atom.pdb_info['standard_atom'] = True
atom.pdb_info['chain_id'] = True
if aa:
aa.set_secondary_structure(secondary)
# Create temporary attributes for proper bond assignment.
atom._is_aromatic = False
atom._is_single = False
if atom_type == "sp2a":
atom_type = "sp2"
atom._is_aromatic = True
if atom_type == "sp2s":
atom_type = "sp2"
atom._is_single = True
atom.set_atomtype_but_dont_revise_singlets(atom_type)
### debug - output in PDB format
### print "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f" % ( n, name, "ALA", ' ', res_num, xyz[0], xyz[1], xyz[2])
self.prev_psi = psi # Remember previous psi angle.
return
def build_struct(self,
name,
params,
position,
mol=None,
createPrinted=False):
"""
Build a peptide from a sequence entered through the Property Manager dialog.
"""
if len(self.peptide_cache) == 0:
return None
# Create a molecule
mol = Chunk(self.win.assy, name)
# Generate dummy atoms positions
self.prev_coords[0][0] = position[0] - 1.499
self.prev_coords[0][1] = position[1] + 1.539
self.prev_coords[0][2] = position[2]
self.prev_coords[1][0] = position[0] - 1.499
self.prev_coords[1][1] = position[1]
self.prev_coords[1][2] = position[2]
self.prev_coords[2][0] = position[0]
self.prev_coords[2][1] = position[1]
self.prev_coords[2][2] = position[2]
# Add a N-terminal hydrogen
atom = Atom("H", position, mol)
atom._is_aromatic = False
atom._is_single = False
self.nterm_hydrogen = atom
# Generate the peptide chain.
self.length = 1
for index, phi, psi in self.peptide_cache:
name, short_name, symbol, zmatrix, size = AMINO_ACIDS[index]
self._buildResiduum(mol, zmatrix, size, phi, psi, None, symbol)
# Add a C-terminal OH group
self._buildResiduum(mol, CTERM_ZMATRIX, 5, 0.0, 0.0, None, symbol)
# Compute bonds (slow!)
# This should be replaced by a proper bond assignment.
inferBonds(mol)
mol._protein_helix = []
mol._protein_sheet = []
# Assign proper bond orders.
i = 1
for atom in mol.atoms.itervalues():
if self.ss_idx == 1:
mol._protein_helix.append(i)
elif self.ss_idx == 2:
mol._protein_sheet.append(i)
if atom.bonds:
for bond in atom.bonds:
if bond.atom1.getAtomTypeName()=="sp2" and \
bond.atom2.getAtomTypeName()=="sp2":
if (bond.atom1._is_aromatic
and bond.atom2._is_aromatic):
bond.set_v6(V_AROMATIC)
elif ((bond.atom1._is_aromatic == False
and bond.atom1._is_aromatic == False)
and not (bond.atom1._is_single
and bond.atom2._is_single)):
bond.set_v6(V_DOUBLE)
i += 1
# Remove temporary attributes.
for atom in mol.atoms.itervalues():
del atom._is_aromatic
del atom._is_single
return mol
def _buildResiduum(self, mol, zmatrix, n_atoms, phi, psi, init_pos,
symbol):
"""
Builds cartesian coordinates for an amino acid from the internal
coordinates table.
mol is a chunk to which the amino acid will be added.
zmatrix is an internal coordinates array corresponding to a given amino acid.
n_atoms is a number of atoms to be build + 3 dummy atoms.
phi is a peptide bond PHI angle.
psi is a peptide bond PSI angle.
init_pos are optional postions of previous CA, C and O atoms.
symbol is a current amino acid symbol (used for proline case)
Note: currently, it doesn't rebuild bonds, so inferBonds has to be called after.
Unfortunately, the proper bond order can not be correctly recognized this way.
"""
if mol == None:
return
if not init_pos: # assign three previous atom positions
for i in range(0, 3):
self.coords[i][0] = self.prev_coords[i][0]
self.coords[i][1] = self.prev_coords[i][1]
self.coords[i][2] = self.prev_coords[i][2]
else: # if no prev_coords are given, compute the first three atom positions
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[1]
self.coords[0][0] = 0.0
self.coords[0][1] = 0.0
self.coords[0][2] = 0.0
self.coords[1][0] = r
self.coords[1][1] = 0.0
self.coords[1][2] = 0.0
ccos = cos(DEG2RAD * a)
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[2]
if atom_c == 1:
self.coords[2][0] = self.coords[0][0] + r * ccos
else:
self.coords[2][0] = self.coords[0][0] - r * ccos
self.coords[2][1] = r * sin(DEG2RAD * a)
self.coords[2][2] = 0.0
for i in range(0, 3):
self.prev_coords[i][0] = self.coords[i][0] + init_pos[0]
self.prev_coords[i][1] = self.coords[i][1] + init_pos[1]
self.prev_coords[i][2] = self.coords[i][2] + init_pos[2]
for n in range(3, n_atoms):
# Generate all coordinates using three previous atoms
# as a frame of reference,
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[n]
cosa = cos(DEG2RAD * a)
xb = self.coords[atom_b][0] - self.coords[atom_c][0]
yb = self.coords[atom_b][1] - self.coords[atom_c][1]
zb = self.coords[atom_b][2] - self.coords[atom_c][2]
rbc = 1.0 / sqrt(xb * xb + yb * yb + zb * zb)
if abs(cosa) >= 0.999:
# Linear bond case
# Skip angles, just extend along the bond.
rbc = r * rbc * cosa
self.coords[n][0] = self.coords[atom_c][0] + xb * rbc
self.coords[n][1] = self.coords[atom_c][1] + yb * rbc
self.coords[n][2] = self.coords[atom_c][2] + zb * rbc
else:
xa = self.coords[atom_a][0] - self.coords[atom_c][0]
ya = self.coords[atom_a][1] - self.coords[atom_c][1]
za = self.coords[atom_a][2] - self.coords[atom_c][2]
xyb = sqrt(xb * xb + yb * yb)
inv = False
if xyb < 0.001:
xpa = za
za = -xa
xa = xpa
xpb = zb
zb = -xb
xb = xpb
xyb = sqrt(xb * xb + yb * yb)
inv = True
costh = xb / xyb
sinth = yb / xyb
xpa = xa * costh + ya * sinth
ypa = ya * costh - xa * sinth
sinph = zb * rbc
cosph = sqrt(abs(1.0 - sinph * sinph))
xqa = xpa * cosph + za * sinph
zqa = za * cosph - xpa * sinph
yza = sqrt(ypa * ypa + zqa * zqa)
if yza < 1e-8:
coskh = 1.0
sinkh = 0.0
else:
coskh = ypa / yza
sinkh = zqa / yza
# Apply the peptide bond conformation
if symbol != "P":
if name == "N " and not init_pos:
t = self.prev_psi + 0.0
if name == "O ":
t = psi + 180.0
if name == "HA " or name == "HA2":
t = 120.0 + phi
if name == "CB " or name == "HA3":
t = 240.0 + phi
if name == "C ":
t = phi
else:
# proline
if name == "N " and not init_pos:
t = self.prev_psi + 0.0
if name == "O ":
t = psi + 180.0
if name == "CA ":
t = phi - 120.0
if name == "CD ":
t = phi + 60.0
sina = sin(DEG2RAD * a)
sind = -sin(DEG2RAD * t)
cosd = cos(DEG2RAD * t)
# Apply the bond length.
xd = r * cosa
yd = r * sina * cosd
zd = r * sina * sind
# Compute the atom position using bond and torsional angles.
ypd = yd * coskh - zd * sinkh
zpd = zd * coskh + yd * sinkh
xpd = xd * cosph - zpd * sinph
zqd = zpd * cosph + xd * sinph
xqd = xpd * costh - ypd * sinth
yqd = ypd * costh + xpd * sinth
if inv:
tmp = -zqd
zqd = xqd
xqd = tmp
self.coords[n][0] = xqd + self.coords[atom_c][0]
self.coords[n][1] = yqd + self.coords[atom_c][1]
self.coords[n][2] = zqd + self.coords[atom_c][2]
if self.nterm_hydrogen:
# It is a hack for the first hydrogen atom
# to make sure the bond length is correct.
self.nterm_hydrogen.setposn(self.nterm_hydrogen.posn() +
0.325 * norm(V(xqd, yqd, zqd)))
self.nterm_hydrogen = None
ax = self.coords[n][0]
ay = self.coords[n][1]
az = self.coords[n][2]
# Store previous coordinates for the next building step
if not init_pos:
if name == "N ":
self.prev_coords[0][0] = self.coords[n][0]
self.prev_coords[0][1] = self.coords[n][1]
self.prev_coords[0][2] = self.coords[n][2]
if name == "CA ":
self.prev_coords[1][0] = self.coords[n][0]
self.prev_coords[1][1] = self.coords[n][1]
self.prev_coords[1][2] = self.coords[n][2]
if name == "C ":
self.prev_coords[2][0] = self.coords[n][0]
self.prev_coords[2][1] = self.coords[n][1]
self.prev_coords[2][2] = self.coords[n][2]
# Add a new atom to the molecule
atom = Atom(
atom_name,
V(self.coords[n][0], self.coords[n][1], self.coords[n][2]),
mol)
# Create temporary attributes for proper bond assignment.
atom._is_aromatic = False
atom._is_single = False
if atom_type == "sp2a":
atom_type = "sp2"
atom._is_aromatic = True
if atom_type == "sp2s":
atom_type = "sp2"
atom._is_single = True
atom.set_atomtype_but_dont_revise_singlets(atom_type)
if name == "CA ":
# Set c-alpha flag for protein main chain visualization.
atom._protein_ca = True
else:
atom._protein_ca = False
if name == "CB ":
# Set c-alpha flag for protein main chain visualization.
atom._protein_cb = True
else:
atom._protein_cb = False
if name == "N ":
# Set c-alpha flag for protein main chain visualization.
atom._protein_n = True
else:
atom._protein_n = False
if name == "C ":
# Set c-alpha flag for protein main chain visualization.
atom._protein_c = True
else:
atom._protein_c = False
if name == "O ":
# Set c-alpha flag for protein main chain visualization.
atom._protein_o = True
else:
atom._protein_o = False
# debug - output in PDB format
# print "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f" % ( n, name, "ALA", ' ', res_num, coords[n][0], coords[n][1], coords[n][2])
self.prev_psi = psi # Remember previous psi angle.
self.length += 1 # Increase the amino acid counter.
return
def _buildResidue(self,
mol,
zmatrix,
n_atoms,
idx,
phi,
psi,
secondary,
init_pos,
residue_name,
fake_chain=False):
"""
Builds cartesian coordinates for an amino acid from the internal
coordinates table.
@param mol: a chunk to which the amino acid will be added.
@type mol: Chunk
@param zmatrix: is an internal coordinates array corresponding to a
given amino acid.
@type zmatrix: list
@param n_atoms: size of z-matrix (a number of atoms to be build + 3
dummy atoms)
@type n_atoms: int
@param idx: is a residue index (1..length).
@type idx: integer
@param phi, psi: peptide bond phi and psi angles
@type phi, psi: float
@param init_pos: optional postions of previous CA, C and O atoms.
@type init_pos: V
@param symbol: current amino acid symbol (used to derermine proline case)
@type symbol: string
"""
# note: currently, it doesn't rebuild bonds, so inferBonds has to be
# called after this method. Unfortunately, the proper bond order can
# not be correctly recognized this way. Therefore, temporary atom flags
# _is_aromatic and _is_single are used.
#this code was re-factored by EricM and internal-to-cartesian
# conversion method was moved to geometry.InternalCoordinatesToCartesian
if mol is None:
return
if not init_pos: # assign three previous atom positions
coords = self.prev_coords
else:
# if no prev_coords are given, compute the first three atom positions
coords = zeros([3, 3], Float)
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[1]
coords[0][0] = 0.0
coords[0][1] = 0.0
coords[0][2] = 0.0
coords[1][0] = r
coords[1][1] = 0.0
coords[1][2] = 0.0
ccos = cos(DEG2RAD * a)
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[2]
if atom_c == 1:
coords[2][0] = coords[0][0] + r * ccos
else:
coords[2][0] = coords[0][0] - r * ccos
coords[2][1] = r * sin(DEG2RAD * a)
coords[2][2] = 0.0
for i in range(0, 3):
self.prev_coords[i][0] = coords[i][0] + init_pos[0]
self.prev_coords[i][1] = coords[i][1] + init_pos[1]
self.prev_coords[i][2] = coords[i][2] + init_pos[2]
translator = InternalCoordinatesToCartesian(n_atoms, coords)
for n in range(3, n_atoms):
# Generate all coordinates using three previous atoms
# as a frame of reference,
num, name, atom_name, atom_type, \
atom_c, atom_b, atom_a, r, a, t = zmatrix[n]
# Apply the peptide bond conformation
if residue_name != "PRO":
if name == "N " and not init_pos:
t = self.prev_psi + 0.0
if name == "O ":
t = psi + 180.0
if name == "HA " or name == "HA2":
t = 120.0 + phi
if name == "CB " or name == "HA3":
t = 240.0 + phi
if name == "C ":
t = phi
else:
# proline
if name == "N " and not init_pos:
t = self.prev_psi + 0.0
if name == "O ":
t = psi + 180.0
if name == "CA ":
t = phi - 120.0
if name == "CD ":
t = phi + 60.0
translator.addInternal(n + 1, atom_c + 1, atom_b + 1, atom_a + 1,
r, a, t)
xyz = translator.getCartesian(n + 1)
if self.nterm_hydrogen:
# This is a hack for the first hydrogen atom
# to make sure the bond length is correct.
self.nterm_hydrogen.setposn(
self.nterm_hydrogen.posn() + \
0.325 * norm(xyz))
self.nterm_hydrogen = None
# Store previous coordinates for the next building step
if not init_pos:
if name == "N ":
self.prev_coords[0][0] = xyz[0]
self.prev_coords[0][1] = xyz[1]
self.prev_coords[0][2] = xyz[2]
if name == "CA ":
self.prev_coords[1][0] = xyz[0]
self.prev_coords[1][1] = xyz[1]
self.prev_coords[1][2] = xyz[2]
if name == "C ":
self.prev_coords[2][0] = xyz[0]
self.prev_coords[2][1] = xyz[1]
self.prev_coords[2][2] = xyz[2]
# Add a new atom to the molecule
if not fake_chain or \
name == "CA ":
atom = Atom(atom_name, xyz, mol)
if not self.init_ca and \
name == "CA ":
self.init_ca = atom
if mol.protein:
aa = mol.protein.add_pdb_atom(atom, name.replace(' ', ''),
idx, AA_3_TO_1[residue_name])
atom.pdb_info = {}
atom.pdb_info['atom_name'] = name.replace(' ', '')
atom.pdb_info['residue_name'] = residue_name
residue_id = "%3d " % idx
atom.pdb_info['residue_id'] = residue_id
atom.pdb_info['standard_atom'] = True
atom.pdb_info['chain_id'] = True
if aa:
aa.set_secondary_structure(secondary)
# Create temporary attributes for proper bond assignment.
atom._is_aromatic = False
atom._is_single = False
if atom_type == "sp2a":
atom_type = "sp2"
atom._is_aromatic = True
if atom_type == "sp2s":
atom_type = "sp2"
atom._is_single = True
atom.set_atomtype_but_dont_revise_singlets(atom_type)
### debug - output in PDB format
### print "ATOM %5d %-3s %3s %c%4d %8.3f%8.3f%8.3f" % ( n, name, "ALA", ' ', res_num, xyz[0], xyz[1], xyz[2])
self.prev_psi = psi # Remember previous psi angle.
return