def __init__(self, pdbfile):
""" Wrapper class for Bio.PDB which makes it convenient to
read phi/psi/omega/chi torsion angles from a PDB-file.
Arguments:
pdbfile -- The PDB file you wish to read.
"""
try:
self._parser = PDBParser(QUIET=True)
except:
# Workaround for missing QUIET keyword
# in certain versions of Biopython.
self._parser = PDBParser()
self._pdbfile = pdbfile
self._structure = self._parser.get_structure("pdb", self._pdbfile)
self._chain = self._get_first_chain(self._structure)
self._sequence = self._get_sequence_from_chain(self._chain)
def __init__(self, pdbfile):
""" Wrapper class for Bio.PDB which makes it convenient to
read phi/psi/omega/chi torsion angles from a PDB-file.
Arguments:
pdbfile -- The PDB file you wish to read.
"""
try:
self._parser = PDBParser(QUIET=True)
except:
# Workaround for missing QUIET keyword
# in certain versions of Biopython.
self._parser = PDBParser()
self._pdbfile = pdbfile
self._structure = self._parser.get_structure("pdb", self._pdbfile)
self._chain = self._get_first_chain(self._structure)
self._sequence = self._get_sequence_from_chain(self._chain)
class PDB:
""" Usually instantiated from something like:
pdbfile = fragbuilder.PDB("1UBQ.pdb")
"""
def __init__(self, pdbfile):
""" Wrapper class for Bio.PDB which makes it convenient to
read phi/psi/omega/chi torsion angles from a PDB-file.
Arguments:
pdbfile -- The PDB file you wish to read.
"""
try:
self._parser = PDBParser(QUIET=True)
except:
# Workaround for missing QUIET keyword
# in certain versions of Biopython.
self._parser = PDBParser()
self._pdbfile = pdbfile
self._structure = self._parser.get_structure("pdb", self._pdbfile)
self._chain = self._get_first_chain(self._structure)
self._sequence = self._get_sequence_from_chain(self._chain)
def get_length(self):
""" Returns the length of the protein.
"""
length = 0
for residue in self._chain:
if is_aa(residue):
length += 1
return length
def get_residue_numbers(self):
""" Returns a list with indexes of all amino acids in the chain.
Can be used for iterating over residues, e.g.:
>>> for i in pdbfile.get_residue_numbers():
... print i, pdbfile.get_residue_bb_angles(i)
"""
length = self.get_length()
return range(1, length + 1)
def get_chi_angles(self, resnum):
""" Returns a list of chi angles for a residue.
Arguments:
resnum -- The number of the residue.
NOTE: Also corrects for incorrect naming of CG1/CG2 in
valine residues and CD1/CD2 in leucine residues.
Will display an error if .pdb file is incorrect.
"""
angles_rad = self._get_chi(self._chain[resnum])
angles_deg = [angle * RAD_TO_DEG for angle in angles_rad]
return angles_deg
def get_bb_angles(self, resnum):
""" Returns a list of [phi, psi, omega] angles for a residue.
Arguments:
resnum -- The number of the residue.
"""
length = self.get_length()
angles_deg = []
if resnum == 1:
res_1 = self._chain[resnum]
res_2 = self._chain[resnum + 1]
N1 = res_1['N'].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C'].get_vector()
N2 = res_2['N'].get_vector()
phi = None
psi = calc_dihedral(N1, CA1, C1, N2) * RAD_TO_DEG
omega = None
angles_deg = [phi, psi, omega]
elif resnum == length:
res_0 = self._chain[resnum - 1]
res_1 = self._chain[resnum]
CA0 = res_0['CA'].get_vector()
C0 = res_0['C'].get_vector()
N1 = res_1['N'].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C'].get_vector()
phi = calc_dihedral(C0, N1, CA1, C1) * RAD_TO_DEG
psi = None
omega = calc_dihedral(CA0, C0, N1, CA1) * RAD_TO_DEG
angles_deg = [phi, psi, omega]
else:
res_0 = self._chain[resnum - 1]
res_1 = self._chain[resnum]
res_2 = self._chain[resnum + 1]
CA0 = res_0['CA'].get_vector()
C0 = res_0['C'].get_vector()
N1 = res_1['N'].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C'].get_vector()
N2 = res_2['N'].get_vector()
phi = calc_dihedral(C0, N1, CA1, C1) * RAD_TO_DEG
psi = calc_dihedral(N1, CA1, C1, N2) * RAD_TO_DEG
omega = calc_dihedral(CA0, C0, N1, CA1) * RAD_TO_DEG
angles_deg = [phi, psi, omega]
return angles_deg
def _get_chi(self, residue):
""" Returns a list of chi angles for a residue """
if residue.get_resname() == 'ALA':
return []
if residue.get_resname() == 'GLY':
return []
if residue.get_resname() == 'ARG':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['NE'].get_vector()
sc_atom7 = residue['CZ'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom6, sc_atom7)
return [chi1, chi2, chi3, chi4]
if residue.get_resname() == 'ASN':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['OD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'ASP':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['OD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'CYS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['SG'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'GLU':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['OE1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'GLN':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['OE1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'HIS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD2'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'ILE':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG1'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'LEU':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
sc_atom5_b = residue['CD2'].get_vector()
# Check for correct naming of CD1/CD2
check_angle = calc_dihedral(sc_atom5, sc_atom4, sc_atom3,
sc_atom5_b)
# If the naming of the CD1 and CD2 atoms is correct,
# the check_angle will be around -120 deg. If the names
# are swapped, the angle will be around 120 deg.
if check_angle > 0:
sc_atom5 = sc_atom5_b
print "WARNING: Correcting for incorrect naming of CD1 and CD2 in residue LEU%i." % residue.get_id(
)[1]
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'LYS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['CE'].get_vector()
sc_atom7 = residue['NZ'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom6, sc_atom7)
return [chi1, chi2, chi3, chi4]
if residue.get_resname() == 'MET':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['SD'].get_vector()
sc_atom6 = residue['CE'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'PHE':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'PRO':
# sc_atom1 = residue['N'].get_vector()
# sc_atom2 = residue['CA'].get_vector()
# sc_atom3 = residue['CB'].get_vector()
# sc_atom4 = residue['CG'].get_vector()
# sc_atom5 = residue['CD'].get_vector()
# chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
# chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
# chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom1)
# chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom1, sc_atom2)
# return [chi1, chi2, chi3, chi4]
return []
if residue.get_resname() == 'SER':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['OG'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'THR':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['OG1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'TRP':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'TYR':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'VAL':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG1'].get_vector()
sc_atom4_b = residue['CG2'].get_vector()
# Check for correct naming of CG1/CG2
check_angle = calc_dihedral(sc_atom4, sc_atom3, sc_atom2,
sc_atom4_b)
# If the naming of the CG1 and CG2 atoms is correct,
# the check_angle will be around -120 deg. If the names
# are swapped, the angle will be around 120 deg.
if check_angle > 0:
sc_atom4 = sc_atom4_b
print "WARNING: Correcting for incorrect naming of CG1 and CG2 in residue VAL%i." % residue.get_id(
)[1]
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
else:
return "FAILLLL"
def _get_first_chain(self, structure):
""" Returns the first chain in a Bio.PDB structure object """
for model in structure:
for chain in model:
return chain
def get_sequence(self):
""" Returns the amino acid sequence from the PDB structure. """
return self._sequence
def get_resname(self, resnum):
""" Returns the three letter code for a residue in the PDB file.
E.g. "VAL", "ALA", etc.
Arguments:
resnum -- The number of the residue
"""
letter = self._sequence[resnum - 1]
return one_to_three(letter)
def _get_sequence_from_chain(self, chain):
""" Extracts the amino acid sequence from a Bio.PDB chain object """
sequence = ""
for residue in chain:
if is_aa(residue):
sequence += three_to_one(residue.get_resname())
else:
break
return sequence
class PDB:
""" Usually instantiated from something like:
pdbfile = fragbuilder.PDB("1UBQ.pdb")
"""
def __init__(self, pdbfile):
""" Wrapper class for Bio.PDB which makes it convenient to
read phi/psi/omega/chi torsion angles from a PDB-file.
Arguments:
pdbfile -- The PDB file you wish to read.
"""
try:
self._parser = PDBParser(QUIET=True)
except:
# Workaround for missing QUIET keyword
# in certain versions of Biopython.
self._parser = PDBParser()
self._pdbfile = pdbfile
self._structure = self._parser.get_structure("pdb", self._pdbfile)
self._chain = self._get_first_chain(self._structure)
self._sequence = self._get_sequence_from_chain(self._chain)
def get_length(self):
""" Returns the length of the protein.
"""
length = 0
for residue in self._chain:
if is_aa(residue):
length += 1
return length
def get_residue_numbers(self):
""" Returns a list with indexes of all amino acids in the chain.
Can be used for iterating over residues, e.g.:
>>> for i in pdbfile.get_residue_numbers():
... print i, pdbfile.get_residue_bb_angles(i)
"""
length = self.get_length()
return range(1, length + 1)
def get_chi_angles(self, resnum):
""" Returns a list of chi angles for a residue.
Arguments:
resnum -- The number of the residue.
NOTE: Also corrects for incorrect naming of CG1/CG2 in
valine residues and CD1/CD2 in leucine residues.
Will display an error if .pdb file is incorrect.
"""
angles_rad = self._get_chi(self._chain[resnum])
angles_deg = [angle * RAD_TO_DEG for angle in angles_rad]
return angles_deg
def get_bb_angles(self, resnum):
""" Returns a list of [phi, psi, omega] angles for a residue.
Arguments:
resnum -- The number of the residue.
"""
length = self.get_length()
angles_deg = []
if resnum == 1:
res_1 = self._chain[resnum]
res_2 = self._chain[resnum + 1]
N1 = res_1['N' ].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C' ].get_vector()
N2 = res_2['N' ].get_vector()
phi = None
psi = calc_dihedral(N1, CA1, C1, N2) * RAD_TO_DEG
omega = None
angles_deg = [phi, psi, omega]
elif resnum == length:
res_0 = self._chain[resnum - 1]
res_1 = self._chain[resnum]
CA0 = res_0['CA'].get_vector()
C0 = res_0['C' ].get_vector()
N1 = res_1['N' ].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C' ].get_vector()
phi = calc_dihedral(C0, N1, CA1, C1) * RAD_TO_DEG
psi = None
omega = calc_dihedral(CA0, C0, N1, CA1) * RAD_TO_DEG
angles_deg = [phi, psi, omega]
else:
res_0 = self._chain[resnum - 1]
res_1 = self._chain[resnum]
res_2 = self._chain[resnum + 1]
CA0 = res_0['CA'].get_vector()
C0 = res_0['C' ].get_vector()
N1 = res_1['N' ].get_vector()
CA1 = res_1['CA'].get_vector()
C1 = res_1['C' ].get_vector()
N2 = res_2['N' ].get_vector()
phi = calc_dihedral(C0, N1, CA1, C1) * RAD_TO_DEG
psi = calc_dihedral(N1, CA1, C1, N2) * RAD_TO_DEG
omega = calc_dihedral(CA0, C0, N1, CA1) * RAD_TO_DEG
angles_deg = [phi, psi, omega]
return angles_deg
def _get_chi(self, residue):
""" Returns a list of chi angles for a residue """
if residue.get_resname() == 'ALA':
return []
if residue.get_resname() == 'GLY':
return []
if residue.get_resname() == 'ARG':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['NE'].get_vector()
sc_atom7 = residue['CZ'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom6, sc_atom7)
return [chi1, chi2, chi3, chi4]
if residue.get_resname() == 'ASN':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['OD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'ASP':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['OD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'CYS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['SG'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'GLU':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['OE1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'GLN':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['OE1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'HIS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD2'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'ILE':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG1'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'LEU':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
sc_atom5_b = residue['CD2'].get_vector()
# Check for correct naming of CD1/CD2
check_angle = calc_dihedral(sc_atom5, sc_atom4, sc_atom3, sc_atom5_b)
# If the naming of the CD1 and CD2 atoms is correct,
# the check_angle will be around -120 deg. If the names
# are swapped, the angle will be around 120 deg.
if check_angle > 0:
sc_atom5 = sc_atom5_b
print "WARNING: Correcting for incorrect naming of CD1 and CD2 in residue LEU%i." % residue.get_id()[1]
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'LYS':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD'].get_vector()
sc_atom6 = residue['CE'].get_vector()
sc_atom7 = residue['NZ'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom6, sc_atom7)
return [chi1, chi2, chi3, chi4]
if residue.get_resname() == 'MET':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['SD'].get_vector()
sc_atom6 = residue['CE'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom6)
return [chi1, chi2, chi3]
if residue.get_resname() == 'PHE':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'PRO':
# sc_atom1 = residue['N'].get_vector()
# sc_atom2 = residue['CA'].get_vector()
# sc_atom3 = residue['CB'].get_vector()
# sc_atom4 = residue['CG'].get_vector()
# sc_atom5 = residue['CD'].get_vector()
# chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
# chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
# chi3 = calc_dihedral(sc_atom3, sc_atom4, sc_atom5, sc_atom1)
# chi4 = calc_dihedral(sc_atom4, sc_atom5, sc_atom1, sc_atom2)
# return [chi1, chi2, chi3, chi4]
return []
if residue.get_resname() == 'SER':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['OG'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'THR':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['OG1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
if residue.get_resname() == 'TRP':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'TYR':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG'].get_vector()
sc_atom5 = residue['CD1'].get_vector()
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
chi2 = calc_dihedral(sc_atom2, sc_atom3, sc_atom4, sc_atom5)
return [chi1, chi2]
if residue.get_resname() == 'VAL':
sc_atom1 = residue['N'].get_vector()
sc_atom2 = residue['CA'].get_vector()
sc_atom3 = residue['CB'].get_vector()
sc_atom4 = residue['CG1'].get_vector()
sc_atom4_b = residue['CG2'].get_vector()
# Check for correct naming of CG1/CG2
check_angle = calc_dihedral(sc_atom4, sc_atom3, sc_atom2, sc_atom4_b)
# If the naming of the CG1 and CG2 atoms is correct,
# the check_angle will be around -120 deg. If the names
# are swapped, the angle will be around 120 deg.
if check_angle > 0:
sc_atom4 = sc_atom4_b
print "WARNING: Correcting for incorrect naming of CG1 and CG2 in residue VAL%i." % residue.get_id()[1]
chi1 = calc_dihedral(sc_atom1, sc_atom2, sc_atom3, sc_atom4)
return [chi1]
else:
return "FAILLLL"
def _get_first_chain(self, structure):
""" Returns the first chain in a Bio.PDB structure object """
for model in structure:
for chain in model:
return chain
def get_sequence(self):
""" Returns the amino acid sequence from the PDB structure. """
return self._sequence
def get_resname(self, resnum):
""" Returns the three letter code for a residue in the PDB file.
E.g. "VAL", "ALA", etc.
Arguments:
resnum -- The number of the residue
"""
letter = self._sequence[resnum - 1]
return one_to_three(letter)
def _get_sequence_from_chain(self, chain):
""" Extracts the amino acid sequence from a Bio.PDB chain object """
sequence = ""
for residue in chain:
if is_aa(residue):
sequence += three_to_one(residue.get_resname())
else:
break
return sequence
