def insertin(assy, filename):
_init()
dir, nodename = os.path.split(filename)
mol = Chunk(assy, nodename)
mol.showOverlayText = True
file = open(filename)
lines = file.readlines()
atoms = {}
transform = InternalCoordinatesToCartesian(len(lines), None)
for line in lines:
columns = line.strip().split()
index = int(columns[0])
name = columns[1]
type = columns[2]
na = int(columns[4])
nb = int(columns[5])
nc = int(columns[6])
r = float(columns[7])
theta = float(columns[8])
phi = float(columns[9])
transform.addInternal(index, na, nb, nc, r, theta, phi)
xyz = transform.getCartesian(index)
if (index > 3):
if (AMBER_AtomTypes.has_key(type)):
sym = AMBER_AtomTypes[type]
else:
print "unknown AMBER atom type, substituting Carbon: %s" % type
sym = "C"
a = Atom(sym, A(xyz), mol)
atoms[index] = a
a.setOverlayText(type)
if (na > 3):
a2 = atoms[na]
bond_atoms(a, a2)
assy.addmol(mol)
def insertin(assy, filename):
_init()
dir, nodename = os.path.split(filename)
mol = Chunk(assy, nodename)
mol.showOverlayText = True
file = open(filename)
lines = file.readlines()
atoms = {}
transform = InternalCoordinatesToCartesian(len(lines), None)
for line in lines:
columns = line.strip().split()
index = int(columns[0])
name = columns[1]
type = columns[2]
na = int(columns[4])
nb = int(columns[5])
nc = int(columns[6])
r = float(columns[7])
theta = float(columns[8])
phi = float(columns[9])
transform.addInternal(index, na, nb, nc, r, theta, phi)
xyz = transform.getCartesian(index)
if (index > 3):
if (AMBER_AtomTypes.has_key(type)):
sym = AMBER_AtomTypes[type]
else:
print "unknown AMBER atom type, substituting Carbon: %s" % type
sym = "C"
a = Atom(sym, A(xyz), mol)
atoms[index] = a
a.setOverlayText(type)
if (na > 3):
a2 = atoms[na]
bond_atoms(a, a2)
assy.addmol(mol)
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 _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