def _finish_molecule():
"""
Perform some operations after reading entire PDB chain:
- rebuild (infer) bonds
- rename molecule to reflect a chain ID
- delete protein object if this is not a protein
- append the molecule to the molecule list
"""
if mol == water:
# Skip water, to be added explicitly at the end.
return
if mol.atoms:
###print "READING PDB ", (mol, numconects, chainId)
mol.name = pdbid.lower() + chainId
###idzialprint "SEQ = ", mol.protein.get_sequence_string()
###print "SEC = ", mol.protein.get_secondary_structure_string()
if mol.protein.count_c_alpha_atoms() == 0:
# If there is no C-alpha atoms, consider the chunk
# as a non-protein. But! Split it into individual
# hetero groups.
res_list = mol.protein.get_amino_acids()
assy.part.ensure_toplevel_group()
hetgroup = Group("Heteroatoms", assy, assy.part.topnode)
for res in res_list:
hetmol = Chunk(assy,
res.get_three_letter_code().replace(" ", "") + \
"[" + str(res.get_id()) + "]")
for atom in res.get_atom_list():
newatom = Atom(atom.element.symbol, atom.posn(), hetmol)
# New chunk - infer the bonds anyway (this is not
# correct, should first check connectivity read from
# the PDB file CONECT records).
inferBonds(hetmol)
hetgroup.addchild(hetmol)
mollist.append(hetgroup)
else:
#if numconects == 0:
# msg = orangemsg("PDB file has no bond info; inferring bonds")
# env.history.message(msg)
# # let user see message right away (bond inference can take significant
# # time) [bruce 060620]
# env.history.h_update()
# For protein - infer the bonds anyway.
inferBonds(mol)
mol.protein.set_chain_id(chainId)
mol.protein.set_pdb_id(pdbid)
if mol.atoms:
mollist.append(mol)
else:
env.history.message( redmsg( "Warning: Pdb file contained no atoms"))
env.history.h_update()
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 make_aligned(self,
assy,
name,
aa_idx,
phi, psi,
pos1, pos2,
secondary = SS_COIL,
fake_chain = False,
length = None):
"""
Build and return a chunk that is a h**o-peptide aligned to
a pos2-pos1 vector.
@param aa_idx: amino acid type (index in AMINO_ACIDS list)
@type aa_idx: int
@param name: chunk name
@type name: string
@param phi, psi: peptide bond angles
@type phi, psi: float
@param pos1, pos2: desired peptide positions (beginning and end)
@type pos1, pos2: V
@param secondary: secondary structure class, used for visual representation
The actual peptide chain conformation is based on phi / psi angles.
@type secondary: int
@param fake_chain: if True, create only C-alpha atoms. used for drawing
peptide trace image during interactive peptide placement (used by
PeptideLine_GraphicsMode.py)
@type fake_chain: boolean
@param length: optional peptide length (number of amino acids), if
not specified, pos1 and pos2 are used to figure out the length
@type length: int
@return: A h**o-polypeptide chain.
@rtype: L{Chunk}
"""
if not length:
self.length = self.get_number_of_res(pos1, pos2, phi, psi)
if self.length == 0:
return None
else:
self.length = length
# Create a molecule
mol = Chunk(assy, name)
if not fake_chain:
mol.protein = Protein()
mol.protein.set_chain_id('A')
# Generate dummy atoms positions
self.prev_coords[0][0] = pos1[0] - 1.0
self.prev_coords[0][1] = pos1[1] - 1.0
self.prev_coords[0][2] = pos1[2]
self.prev_coords[1][0] = pos1[0] - 1.0
self.prev_coords[1][1] = pos1[1]
self.prev_coords[1][2] = pos1[2]
self.prev_coords[2][0] = pos1[0]
self.prev_coords[2][1] = pos1[1]
self.prev_coords[2][2] = pos1[2]
name, short_name, symbol, zmatrix, size = AMINO_ACIDS[aa_idx]
# Add a N-terminal hydrogen
self.nterm_hydrogen = None
# Initially, the Peptide Builder was creating peptide structures
# saturated at both ends, i.e. with N-terminal hydrogen and C-terminal
# OH group present. Currently, this code is commented out to allow
# connecting multiple peptide structure be creating bonds between
# the C- and N- terminal ends of two individual structures.
"""
if not fake_chain:
atom = Atom("H", pos1, mol)
atom._is_aromatic = False
atom._is_single = False
self.nterm_hydrogen = atom
mol.protein.add_pdb_atom(atom, "H", 1, name)
atom.pdb_info = {}
atom.pdb_info['atom_name'] = "H"
atom.pdb_info['residue_name'] = short_name
atom.pdb_info['residue_id'] = " 1 "
atom.pdb_info['standard_atom'] = True
"""
self.init_ca = None
# Generate the peptide chain.
for idx in range(int(self.length)):
self._buildResidue(mol, zmatrix, size, idx+1, phi, psi, secondary, None, short_name, fake_chain=fake_chain)
# See the comment above.
"""
# Add a C-terminal OH group
self._buildResidue(mol, CTERM_ZMATRIX, 5, int(self.length), 0.0, 0.0, secondary, None, short_name, fake_chain=fake_chain)
"""
# Compute bonds (slow!)
# This should be replaced by a proper bond assignment.
if not fake_chain:
inferBonds(mol)
# Assign proper bond orders.
i = 1
for atom in mol.atoms.itervalues():
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
# Axis of first selected chunk
ax = V(0.,0.,1.)
mol.rot(Q(mol.getaxis(),ax))
self._orient(mol, pos2, pos1)
if self.init_ca:
mol.move(pos1 - self.init_ca.posn())
mol_dummy = None
return mol
def _readpdb(assy,
filename,
isInsert = False,
showProgressDialog = False,
chainId = None):
"""
Read a Protein DataBank-format file into a single new chunk, which is
returned unless there are no atoms in the file, in which case a warning
is printed and None is returned. (The new chunk (if returned) is in assy,
but is not yet added into any Group or Part in assy -- caller must do that.)
Unless isInsert = True, set assy.filename to match the file we read,
even if we return None.
@param assy: The assembly.
@type assy: L{assembly}
@param filename: The PDB filename to read.
@type filename: string
@param isInsert: If True, the PDB file will be inserted into the current
assembly. If False (default), the PDB is opened as the
assembly.
@param isInsert: boolean
@param showProgressDialog: if True, display a progress dialog while reading
a file.
@type showProgressDialog: boolean
@return: A chunk containing the contents of the PDB file.
@rtype: L{Chunk}
@see: U{B{PDB File Format}<http://www.wwpdb.org/documentation/format23/v2.3.html>}
"""
fi = open(filename,"rU")
lines = fi.readlines()
fi.close()
dir, nodename = os.path.split(filename)
if not isInsert:
assy.filename = filename
ndix = {}
mol = Chunk(assy, nodename)
numconects = 0
atomname_exceptions = {
"HB":"H", #k these are all guesses -- I can't find this documented
# anywhere [bruce 070410]
## "HE":"H", ### REVIEW: I'm not sure about this one --
### leaving it out means it's read as Helium,
# but including it erroneously might prevent reading an actual Helium
# if that was intended.
# Guess for now: include it for ATOM but not HETATM. (So it's
# specialcased below, rather than being included in this table.)
# (Later: can't we use the case of the 'E' to distinguish it from He?)
"HN":"H",
}
# Create and display a Progress dialog while reading the MMP file.
# One issue with this implem is that QProgressDialog always displays
# a "Cancel" button, which is not hooked up. I think this is OK for now,
# but later we should either hook it up or create our own progress
# dialog that doesn't include a "Cancel" button. --mark 2007-12-06
if showProgressDialog:
_progressValue = 0
_progressFinishValue = len(lines)
win = env.mainwindow()
win.progressDialog.setLabelText("Reading file...")
win.progressDialog.setRange(0, _progressFinishValue)
_progressDialogDisplayed = False
_timerStart = time.time()
for card in lines:
key = card[:6].lower().replace(" ", "")
if key in ["atom", "hetatm"]:
## sym = capitalize(card[12:14].replace(" ", "").replace("_", ""))
# bruce 080508 revision (guess at a bugfix for reading NE1-saved
# pdb files):
# get a list of atomnames to try; use the first one we recognize.
# Note that full atom name is in columns 13-16 i.e. card[12:16];
# see http://www.wwpdb.org/documentation/format2.3-0108-us.pdf,
# page 156. The old code only looked at two characters,
# card[12:14] == columns 13-14, and discarded ' ' and '_',
# and capitalized (the first character only). The code as I revised
# it on 070410 also discarded digits, and handled HB, HE, HN
# (guesses) using the atomname_exceptions dict.
name4 = card[12:16].replace(" ", "").replace("_", "")
name3 = card[12:15].replace(" ", "").replace("_", "")
name2 = card[12:14].replace(" ", "").replace("_", "")
def nodigits(name):
for bad in "0123456789":
name = name.replace(bad, "")
return name
atomnames_to_try = [
name4, # as seems best according to documentation
name3,
name2, # like old code
nodigits(name4),
nodigits(name3),
nodigits(name2) # like code as revised on 070410
]
foundit = False
for atomname in atomnames_to_try:
atomname = atomname_exceptions.get(atomname, atomname)
if atomname == "HE" and key == "atom":
atomname = "H" # see comment in atomname_exceptions
sym = capitalize(atomname) # turns either 'he' or 'HE' into 'He'
try:
PeriodicTable.getElement(sym)
except:
# note: this typically fails with AssertionError
# (not e.g. KeyError) [bruce 050322]
continue
else:
foundit = True
break
pass
if not foundit:
msg = "Warning: Pdb file: will use Carbon in place of unknown element %s in: %s" \
% (name4, card)
print msg #bruce 070410 added this print
env.history.message( redmsg( msg ))
##e It would probably be better to create a fake atom, so the
# CONECT records would still work.
#bruce 080508 let's do that:
sym = "C"
# Better still might be to create a fake element,
# so we could write out the pdb file again
# (albeit missing lots of info). [bruce 070410 comment]
# Note: an advisor tells us:
# PDB files sometimes encode atomtypes,
# using C_R instead of C, for example, to represent sp2
# carbons.
# That particular case won't trigger this exception, since we
# only look at 2 characters [eventually, after trying more, as of 080508],
# i.e. C_ in that case. It would be better to realize this means
# sp2 and set the atomtype here (and perhaps then use it when
# inferring bonds, which we do later if the file doesn't have
# any bonds). [bruce 060614/070410 comment]
# Now the element name is in sym.
xyz = map(float, [card[30:38], card[38:46], card[46:54]] )
n = int(card[6:11])
a = Atom(sym, A(xyz), mol)
ndix[n] = a
elif key == "conect":
try:
a1 = ndix[int(card[6:11])]
except:
#bruce 050322 added this level of try/except and its message;
# see code below for at least two kinds of errors this might
# catch, but we don't try to distinguish these here. BTW this
# also happens as a consequence of not finding the element
# symbol, above, since atoms with unknown elements are not
# created.
env.history.message( redmsg( "Warning: Pdb file: can't find first atom in CONECT record: %s" % (card,) ))
else:
for i in range(11, 70, 5):
try:
a2 = ndix[int(card[i:i+5])]
except ValueError:
# bruce 050323 comment:
# we assume this is from int('') or int(' ') etc;
# this is the usual way of ending this loop.
break
except KeyError:
#bruce 050322-23 added history warning for this,
# assuming it comes from ndix[] lookup.
env.history.message( redmsg( "Warning: Pdb file: can't find atom %s in: %s" % (card[i:i+5], card) ))
continue
bond_atoms(a1, a2)
numconects += 1
if showProgressDialog: # Update the progress dialog.
_progressValue += 1
if _progressValue >= _progressFinishValue:
win.progressDialog.setLabelText("Building model...")
elif _progressDialogDisplayed:
win.progressDialog.setValue(_progressValue)
else:
_timerDuration = time.time() - _timerStart
if _timerDuration > 0.25:
# Display progress dialog after 0.25 seconds
win.progressDialog.setValue(_progressValue)
_progressDialogDisplayed = True
if showProgressDialog: # Make the progress dialog go away.
win.progressDialog.setValue(_progressFinishValue)
#bruce 050322 part of fix for bug 433: don't return an empty chunk
if not mol.atoms:
env.history.message( redmsg( "Warning: Pdb file contained no atoms"))
return None
if numconects == 0:
msg = orangemsg("PDB file has no bond info; inferring bonds")
env.history.message(msg)
# let user see message right away (bond inference can take significant
# time) [bruce 060620]
env.history.h_update()
inferBonds(mol)
return mol
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 make_aligned(self,
assy,
name,
aa_idx,
phi,
psi,
pos1,
pos2,
secondary=SS_COIL,
fake_chain=False,
length=None):
"""
Build and return a chunk that is a h**o-peptide aligned to
a pos2-pos1 vector.
@param aa_idx: amino acid type (index in AMINO_ACIDS list)
@type aa_idx: int
@param name: chunk name
@type name: string
@param phi, psi: peptide bond angles
@type phi, psi: float
@param pos1, pos2: desired peptide positions (beginning and end)
@type pos1, pos2: V
@param secondary: secondary structure class, used for visual representation
The actual peptide chain conformation is based on phi / psi angles.
@type secondary: int
@param fake_chain: if True, create only C-alpha atoms. used for drawing
peptide trace image during interactive peptide placement (used by
PeptideLine_GraphicsMode.py)
@type fake_chain: boolean
@param length: optional peptide length (number of amino acids), if
not specified, pos1 and pos2 are used to figure out the length
@type length: int
@return: A h**o-polypeptide chain.
@rtype: L{Chunk}
"""
if not length:
self.length = self.get_number_of_res(pos1, pos2, phi, psi)
if self.length == 0:
return None
else:
self.length = length
# Create a molecule
mol = Chunk(assy, name)
if not fake_chain:
mol.protein = Protein()
mol.protein.set_chain_id('A')
# Generate dummy atoms positions
self.prev_coords[0][0] = pos1[0] - 1.0
self.prev_coords[0][1] = pos1[1] - 1.0
self.prev_coords[0][2] = pos1[2]
self.prev_coords[1][0] = pos1[0] - 1.0
self.prev_coords[1][1] = pos1[1]
self.prev_coords[1][2] = pos1[2]
self.prev_coords[2][0] = pos1[0]
self.prev_coords[2][1] = pos1[1]
self.prev_coords[2][2] = pos1[2]
name, short_name, symbol, zmatrix, size = AMINO_ACIDS[aa_idx]
# Add a N-terminal hydrogen
self.nterm_hydrogen = None
# Initially, the Peptide Builder was creating peptide structures
# saturated at both ends, i.e. with N-terminal hydrogen and C-terminal
# OH group present. Currently, this code is commented out to allow
# connecting multiple peptide structure be creating bonds between
# the C- and N- terminal ends of two individual structures.
"""
if not fake_chain:
atom = Atom("H", pos1, mol)
atom._is_aromatic = False
atom._is_single = False
self.nterm_hydrogen = atom
mol.protein.add_pdb_atom(atom, "H", 1, name)
atom.pdb_info = {}
atom.pdb_info['atom_name'] = "H"
atom.pdb_info['residue_name'] = short_name
atom.pdb_info['residue_id'] = " 1 "
atom.pdb_info['standard_atom'] = True
"""
self.init_ca = None
# Generate the peptide chain.
for idx in range(int(self.length)):
self._buildResidue(mol,
zmatrix,
size,
idx + 1,
phi,
psi,
secondary,
None,
short_name,
fake_chain=fake_chain)
# See the comment above.
"""
# Add a C-terminal OH group
self._buildResidue(mol, CTERM_ZMATRIX, 5, int(self.length), 0.0, 0.0, secondary, None, short_name, fake_chain=fake_chain)
"""
# Compute bonds (slow!)
# This should be replaced by a proper bond assignment.
if not fake_chain:
inferBonds(mol)
# Assign proper bond orders.
i = 1
for atom in mol.atoms.itervalues():
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
# Axis of first selected chunk
ax = V(0., 0., 1.)
mol.rot(Q(mol.getaxis(), ax))
self._orient(mol, pos2, pos1)
if self.init_ca:
mol.move(pos1 - self.init_ca.posn())
mol_dummy = None
return mol