def torsion_drive(atom1, atom2, atom3, atom4, interval, selection, path, mol_name,):
"""
This function generates input pdbs of dihedral angles selected of intervals specified with interval
:param atom1: name of atom 1 of dihedral
:param atom2: name of atom 2 of dihedral
:param atom3: name of atom 3 of dihedral
:param atom4: name of atom 4 of dihedral
:param interval: int or float (in degrees) of intervals to generate torsion scan for
:param selection: name of selection for molecule
:param path: path to where pdb files should be saved
:param mole_name: name of molecule to append to filenamen
"""
atom1 = selection + " and name " + atom1
atom2 = selection + " and name " + atom2
atom3 = selection + " and name " + atom3
atom4 = selection + " and name " + atom4
for angle in range(0, 360 + int(interval), int(interval)):
try:
os.makedirs('%s/%i' % (path, angle))
except OSError as exc:
if exc.errno == errno.EEXIST and os.path.isdir(path):
pass
else:
raise
cmd.set_dihedral(atom1, atom2, atom3, atom4, angle)
filename = '%s/%i/%s_%i.pdb' % (path, angle, mol_name, angle)
cmd.save(filename, selection, 1)
def test_set_dihedral(self):
cmd.fragment('ala')
angle = 45.0
atoms = ('ID 7', 'ID 2', 'ID 1', 'ID 9')
cmd.set_dihedral(*atoms, angle=angle)
v = cmd.get_dihedral(*atoms)
self.assertAlmostEqual(v, angle, 4)
def test_set_dihedral(self):
cmd.fragment('ala')
angle = 45.0
atoms = ('ID 7', 'ID 2', 'ID 1', 'ID 9')
cmd.set_dihedral(*atoms, angle=angle)
v = cmd.get_dihedral(*atoms)
self.assertAlmostEqual(v, angle, 4)
def set_psi_angle(pymol_object, chainID, aa_number, new_angle):
"""Set Psi dihedral angle of a given residue.
Parameters
----------
pymol_object : String
Name of Pymol object in the session.
chainID : String
ChainID of residue.
aa_number : Integer
Residue number.
new_angle : Float
New psi angle to be set.
Returns
-------
None.
"""
# Atom selection for each atom that participates in the angle
# Ni+1
atom1 = pymol_object + '//' + chainID + '/' + str(aa_number+1) + '/N'
# Ci
atom2 = pymol_object + '//' + chainID + '/' + str(aa_number) + '/C'
# CAi
atom3 = pymol_object + '//' + chainID + '/' + str(aa_number) + '/CA'
# Ni
atom4 = pymol_object + '//' + chainID + '/' + str(aa_number) + '/N'
cmd.set_dihedral(atom1, atom2, atom3, atom4, new_angle)
def set_phipsi(selection, phi=None, psi=None):
'''
DESCRIPTION
Set phi/psi angles for all residues in selection.
SEE ALSO
set_phi, set_psi, set_dihedral, phi_psi, cmd.get_phipsi, DynoPlot
'''
for model, index in cmd.index('byca (' + selection + ')'):
atsele = [
'first ((%s`%d) extend 2 and name C)' % (model, index), # prev C
'first ((%s`%d) extend 1 and name N)' % (model, index), # this N
'(%s`%d)' % (model, index), # this CA
'last ((%s`%d) extend 1 and name C)' % (model, index), # this C
'last ((%s`%d) extend 2 and name N)' % (model, index), # next N
]
try:
if phi is not None:
cmd.set_dihedral(atsele[0], atsele[1], atsele[2], atsele[3],
phi)
if psi is not None:
cmd.set_dihedral(atsele[1], atsele[2], atsele[3], atsele[4],
psi)
except:
print ' Error: cmd.set_dihedral failed'
def set_phipsi(selection, phi=None, psi=None):
'''
DESCRIPTION
Set phi/psi angles for all residues in selection.
SEE ALSO
set_phi, set_psi, set_dihedral, phi_psi, cmd.get_phipsi, DynoPlot
'''
for model, index in cmd.index('byca (' + selection + ')'):
atsele = [
'first ((%s`%d) extend 2 and name C)' % (model, index), # prev C
'first ((%s`%d) extend 1 and name N)' % (model, index), # this N
'(%s`%d)' % (model, index), # this CA
'last ((%s`%d) extend 1 and name C)' % (model, index), # this C
'last ((%s`%d) extend 2 and name N)' % (model, index), # next N
]
try:
if phi is not None:
cmd.set_dihedral(atsele[0], atsele[1], atsele[2], atsele[3], phi)
if psi is not None:
cmd.set_dihedral(atsele[1], atsele[2], atsele[3], atsele[4], psi)
except:
print ' Error: cmd.set_dihedral failed'
def setDihVal(sele, atomNames, dih, val):
cmd.set_dihedral(sele + " and name " + atomNames[0],
sele + " and name " + atomNames[1],
sele + " and name " + atomNames[2],
sele + " and name " + atomNames[3],
val,
quiet=1)
def modify_dihedral(atom1, atom2, atom3, atom4, value):
try:
cmd.set_dihedral(atom1, atom2, atom3, atom4, value)
except:
print "Error in pymol trying modified this dihedral %s %s %s %s %f" % (
atom1, atom2, atom3, atom4, value)
cmd.save("problem.pdb", "all", 0)
exit()
def _set_dihedral(atoms, angle, mode="index"):
if mode == "name":
for i in range(4):
cmd.select('a%d' % i, 'name %s' % atomnames[i])
elif mode == "index":
for i in range(4):
cmd.select('a%d' % i, 'index %d' % atoms[i])
cmd.set_dihedral('a0', 'a1', 'a2', 'a3', angle)
def helicize_beta_peptide(helixtype, selection='all'):
"""
DESCRIPTION
Adjust the torsion angles of a beta-peptide to different helical conformations
USAGE
helicize_beta_peptide helixtype [, selection]
ARGUMENTS
helixtype = the type of the helix (either short or IUPAC name),
or a tuple of 3 floats, representing three torsional angles, or
a list of tuples / short names / IUPAC names.
selection = the selection to operate on. Must be a single peptide chain with
unique residue IDs (default: all)
NOTES"""
if isinstance(helixtype, str):
for perczelname, iupacname, angles, theorylevel in helixtypes:
helixtype = helixtype.replace(iupacname, perczelname).replace(
perczelname, '({}, {}, {})'.format(*angles))
helixtype = helixtype.strip()
if not all([h in '0123456789.,()[] -+efg' for h in helixtype]):
raise ValueError(
'Helixtype parameter contains an invalid character (only numbers, parentheses, brackets, space and commas are accepted)'
)
helixtype = eval(helixtype, {}, {})
assert isinstance(helixtype, collections.Iterable)
if all([isinstance(x, numbers.Real)
for x in helixtype]) and len(helixtype) == 3:
helixtype = [helixtype]
print('Helixtypes: {}'.format(helixtype))
space = {'lis': []}
cmd.iterate(selection, 'lis.append(resv)', space=space)
residues = sorted(set(space['lis']))
for r, ht in zip(sorted(residues), itertools.cycle(helixtype)):
if len(ht) != 3 and not all([isinstance(x, numbers.Real) for x in ht]):
raise ValueError('Invalid helixtype: {}'.format(ht))
calpha = '({}) and (name CA) and (resi {})'.format(selection, r)
cbeta = '({}) and (name CB+CB1) and (resi {})'.format(selection, r)
c = '({}) and (name C) and (resi {})'.format(selection, r)
n = '({}) and (name N) and (resi {})'.format(selection, r)
prevc = '(neighbor ({})) and (name C)'.format(n)
nextn = '(neighbor ({})) and (name N)'.format(c)
prevo = '(neighbor ({})) and (name O)'.format(prevc)
hn = '(neighbor ({})) and (name H+HN)'.format(n)
o = '(neighbor ({})) and (name O)'.format(c)
nexthn = '(neighbor ({})) and (name H+HN)'.format(nextn)
set_beta_helix(prevc, n, cbeta, calpha, c, nextn, ht, selection)
for n_, h_, c_, o_ in [(n, hn, prevc, prevo), (nextn, nexthn, c, o)]:
if cmd.count_atoms(n_) + cmd.count_atoms(h_) + cmd.count_atoms(
c_) + cmd.count_atoms(o_) == 4:
cmd.set_dihedral(h_, n_, c_, o_, 180.)
cmd.orient(selection)
def set_omega(obj, bond, angle, state=1):
"""
Get the dihedral angle omega (O6-C6-C5-C4)
"""
resi_i, resi_j, atom_i, atom_j = bond[0], bond[2], bond[4], bond[5]
atom1 = '%s and resi %s and name O6' % (obj, resi_j)
atom2 = '%s and resi %s and name C6' % (obj, resi_j)
atom3 = '%s and resi %s and name C5' % (obj, resi_j)
atom4 = '%s and resi %s and name C4' % (obj, resi_j)
cmd.set_dihedral(atom1, atom2, atom3, atom4, angle, state=state)
def set_omega(obj, bond, angle, state=1):
"""
Get the dihedral angle omega (O6-C6-C5-C4)
"""
resi_i, resi_j, atom_i, atom_j = bond[0], bond[2], bond[4], bond[5]
atom1 = '%s and resi %s and name O6' % (obj, resi_j)
atom2 = '%s and resi %s and name C6' % (obj, resi_j)
atom3 = '%s and resi %s and name C5' % (obj, resi_j)
atom4 = '%s and resi %s and name C4' % (obj, resi_j)
cmd.set_dihedral(atom1, atom2, atom3, atom4, angle, state=state)
def set_dihedral(modelname, nameandresi1, nameandresi2, nameandresi3,
nameandresi4, value):
"""A safer version of cmd.set_dihedral(): doesn't choke on non-singleton selections"""
selections = [
'({}) and name {} and resi {}'.format(modelname, *nr)
for nr in [nameandresi1, nameandresi2, nameandresi3, nameandresi4]
]
if not all([cmd.count_atoms(s) == 1 for s in selections]):
return False
cmd.set_dihedral(*(selections + [value]))
cmd.unpick()
return True
def set_phipsi(sel, phi, psi):
# Get atoms from selection
atoms = cmd.get_model("byres (" + sel + ")")
# Loop through atoms in selection
for at in atoms.atom: # pylint: disable=E1103
if at.name == "N":
# Check for a null chain id (some PDBs contain this)
unit_select = ""
if not at.chain == "":
unit_select = "chain " + str(at.chain) + " and "
# end if
try:
# Define residue selections
rdef_prev = unit_select + 'resi ' + str(int(at.resi) - 1)
rdef = unit_select + 'resi ' + str(at.resi)
# print "rdef_prev: [%s]" % rdef_prev
# print "rdef : [%s]" % rdef
if at.resn == "PRO":
print "Skipping setting phi for PRO"
else:
old_phi = cmd.get_dihedral(rdef_prev + ' and name C',
rdef + ' and name N',
rdef + ' and name CA',
rdef + ' and name C')
cmd.set_dihedral(rdef_prev + ' and name C',
rdef + ' and name N',
rdef + ' and name CA',
rdef + ' and name C', phi)
print "Changed residue %4s %4s phi: from %6.1f to %6.1f" % (
at.resn, at.resi, old_phi, float(phi))
except:
print "Note skipping set of phi because of error; this is normal for a N-terminal residue"
try:
rdef = unit_select + 'resi ' + str(at.resi)
residue_def_next = unit_select + 'resi ' + str(
int(at.resi) + 1)
# print "rdef : [%s]" % rdef
# print "residue_def_next: [%s]" % residue_def_next
old_psi = cmd.get_dihedral(rdef + ' and name N',
rdef + ' and name CA',
rdef + ' and name C',
residue_def_next + ' and name N')
cmd.set_dihedral(rdef + ' and name N', rdef + ' and name CA',
rdef + ' and name C',
residue_def_next + ' and name N', psi) # pylint: disable=C0301
print "Changed residue %4s %4s psi: from %6.1f to %6.1f" % (
at.resn, at.resi, old_psi, float(psi))
except:
print "Note skipping set of psi; this is normal for a C terminal residue"
def set_psi(obj, bond, angle, state=1):
"""
Set the dihedral angle psi (C1-O'x-C'x-C'x-1)
"""
resi_i, resi_j, atom_i, atom_j = bond[0], bond[2], bond[4], bond[5]
if atom_i > atom_j:
atom_j = atom_i
resi_i, resi_j = resi_j, resi_i
atom1 = '%s and resi %s and name C1' % (obj, resi_i)
atom2 = '%s and resi %s and name O%s' % (obj, resi_j, atom_j)
atom3 = '%s and resi %s and name C%s' % (obj, resi_j, atom_j)
atom4 = '%s and resi %s and name C%s' % (obj, resi_j, (atom_j-1))
cmd.set_dihedral(atom1, atom2, atom3, atom4, angle, state=state)
def set_psi(obj, bond, angle, state=1):
"""
Set the dihedral angle psi (C1-O'x-C'x-C'x-1)
"""
resi_i, resi_j, atom_i, atom_j = bond[0], bond[2], bond[4], bond[5]
if atom_i > atom_j:
atom_j = atom_i
resi_i, resi_j = resi_j, resi_i
atom1 = '%s and resi %s and name C1' % (obj, resi_i)
atom2 = '%s and resi %s and name O%s' % (obj, resi_j, atom_j)
atom3 = '%s and resi %s and name C%s' % (obj, resi_j, atom_j)
atom4 = '%s and resi %s and name C%s' % (obj, resi_j, (atom_j - 1))
cmd.set_dihedral(atom1, atom2, atom3, atom4, angle, state=state)
def set_phipsi(model, index, phi, psi):
atsele = [
'first ((%s`%d) extend 2 and name C)' % (model, index), # prev C
'first ((%s`%d) extend 1 and name N)' % (model, index), # this N
'(%s`%d)' % (model, index), # this CA
'last ((%s`%d) extend 1 and name C)' % (model, index), # this C
'last ((%s`%d) extend 2 and name N)' % (model, index), # next N
]
try:
cmd.set_dihedral(atsele[0], atsele[1], atsele[2], atsele[3], phi)
cmd.set_dihedral(atsele[1], atsele[2], atsele[3], atsele[4], psi)
except:
print ' DynoPlot Error: cmd.set_dihedral failed'
def set_phipsi(model, index, phi, psi, state=-1):
atsele = [
'first ((%s`%d) extend 2 and name C)' % (model, index), # prev C
'first ((%s`%d) extend 1 and name N)' % (model, index), # this N
'(%s`%d)' % (model, index), # this CA
'last ((%s`%d) extend 1 and name C)' % (model, index), # this C
'last ((%s`%d) extend 2 and name N)' % (model, index), # next N
]
try:
cmd.set_dihedral(atsele[0], atsele[1], atsele[2], atsele[3], phi, state)
cmd.set_dihedral(atsele[1], atsele[2], atsele[3], atsele[4], psi, state)
except:
print ' DynoPlot Error: cmd.set_dihedral failed'
def set_beta_helix(prevC, N, CB, CA, C, nextN, helixtype, selection='all'):
"""Set torsion angles of a beta peptide backbone
Inputs:
prevC: selection of the amide carbon in the previous amino acid
N: selection of the amide Nitrogen in this amino acid
CB: selection of the beta carbon
CA: selection of the alpha carbon
C: selection of the amide carbon
nextN: selection of the amide nitrogen of the next amino acid
helixtype: the type of the helix or a tuple of 3 floats: the 3 angles
selection: the main selection in which we operate. Defaults to "*"
"""
try:
helixparam = [
h for h in helixtypes if h[0] == helixtype or h[1] == helixtype
][0]
angles = helixparam[2]
except IndexError:
if isinstance(helixtype, str):
# try to interpret helixtype as a tuple or a list
helixtype = helixtype.strip()
try:
if (helixtype.startswith('(') and helixtype.endswith(')')) or (
helixtype.startswith('[') and helixtype.endswith(']')):
helixtype = helixtype[1:-1]
angles = [float(x.strip()) for x in helixtype.split(',')]
except:
raise ValueError('Unknown helix type: {}'.format(helixtype))
elif (isinstance(helixtype, collections.Sequence)
and all([isinstance(x, numbers.Real) for x in helixtype])):
angles = helixtype
else:
raise ValueError('Unknown helix type: {}'.format(helixtype))
print('Helixtype in set_beta_helix: {} (type: {})'.format(
helixtype, type(helixtype)))
atoms = [
'({}) and ({})'.format(selection, atomidx)
for atomidx in [prevC, N, CB, CA, C, nextN]
]
for i, angle in enumerate(angles):
if any([cmd.count_atoms(atoms[i + j]) != 1 for j in range(4)]):
# if any of the selections contains zero or more than one atoms, do not set the dihedral.
continue
cmd.set_dihedral(*(atoms[i:i + 4] + [angle]))
cmd.delete('pk1')
cmd.delete('pk2')
cmd.delete('pkbond')
cmd.delete('pkmol')
def flip_by_atoms(self, atmA, atmB, atmC, atmD):
from pymol import CmdException, cmd
sele = self.selector()
a, b, c, d = map(lambda a: '{}/{}'.format(sele, a),
[atmA, atmB, atmC, atmD])
try:
dh = cmd.get_dihedral(a, b, c, d)
except CmdException:
print "Error on '{}'.".format(self.selector())
pass
else:
cmd.set_dihedral(a, b, c, d, dh + 180)
cmd.unpick()
def __call__(self):
# Loop through each item on plot to see if updated
for key,value in canvas.shapes.items():
dihedrals = value[5]
# Look for update flag...
if value[2]:
# Set residue's phi,psi to new values
print "Re-setting Phi,Psi: %s,%s" % (value[3],value[4])
cmd.set_dihedral(dihedrals[0],dihedrals[1],dihedrals[2],dihedrals[3],value[3])
cmd.set_dihedral(dihedrals[4],dihedrals[5],dihedrals[6],dihedrals[7],value[4])
value[2] = 0
def unfold_index(name, index):
selection_string_array = [
f'first (({name}`{index}) extend 2 and name C)', # prev C
f'first (({name}`{index}) extend 1 and name N)', # this N
f'({name}`{index})', # this CA
f'last (({name}`{index}) extend 1 and name C)', # this C
f'last (({name}`{index}) extend 2 and name N)'
] # next N
try:
cmd.set_dihedral(selection_string_array[0], selection_string_array[1],
selection_string_array[2], selection_string_array[3],
random.randint(0, 360))
cmd.set_dihedral(selection_string_array[1], selection_string_array[2],
selection_string_array[3], selection_string_array[4],
random.randint(0, 360))
except Exception as e:
pass
def set_phipsi(selection, phi=None, psi=None):
for model, index in cmd.index('byca (' + selection + ')'):
angles = [
'first ((%s`%d) extend 2 and name C)' % (model, index), # prev C
'first ((%s`%d) extend 1 and name N)' % (model, index), # this N
'(%s`%d)' % (model, index), # this CA
'last ((%s`%d) extend 1 and name C)' % (model, index), # this C
'last ((%s`%d) extend 2 and name N)' % (model, index), # next N
]
try:
if phi is not None:
cmd.set_dihedral(angles[0], angles[1], angles[2], angles[3],
phi)
if psi is not None:
cmd.set_dihedral(angles[1], angles[2], angles[3], angles[4],
psi)
except:
print 'Error: cmd.set_dihedral failed'
def set_phipsi(selection, phi=None, psi=None, state=1, quiet=1):
'''
DESCRIPTION
Set phi/psi angles for all residues in selection.
SEE ALSO
phi_psi, cmd.get_phipsi, set_dihedral, DynoPlot
'''
for idx in cmd.index('byca (' + selection + ')'):
x = cmd.index('((%s`%d) extend 2 and name C+N+CA)' % idx)
if len(x) != 5 or x[2] != idx:
print(' Warning: set_phipsi: missing atoms (%s`%d)' % idx)
continue
if phi is not None:
cmd.set_dihedral(x[0], x[1], x[2], x[3], phi, state, quiet)
if psi is not None:
cmd.set_dihedral(x[1], x[2], x[3], x[4], psi, state, quiet)
def set_phipsi(selection, phi=None, psi=None, state=1, quiet=1):
'''
DESCRIPTION
Set phi/psi angles for all residues in selection.
SEE ALSO
phi_psi, cmd.get_phipsi, set_dihedral, DynoPlot
'''
for idx in cmd.index('byca (' + selection + ')'):
x = cmd.index('((%s`%d) extend 2 and name C+N+CA)' % idx)
if len(x) != 5 or x[2] != idx:
print(' Warning: set_phipsi: missing atoms (%s`%d)' % idx)
continue
if phi is not None:
cmd.set_dihedral(x[0], x[1], x[2], x[3], phi, state, quiet)
if psi is not None:
cmd.set_dihedral(x[1], x[2], x[3], x[4], psi, state, quiet)
def set_chi(obj, bond, state=1):
"""
Set the dihedral angles chi (Cx-1-Cx-O'x-H'x) to one of tree predefinied
angles (-60, 60, 180). The perturbed chi angle is selected at random.
This function considers the omega angle as a chi angle.
"""
resi_i, resi_j = bond[0], bond[2]
chises = [1, 2, 3, 4, 5, 6]
np.random.shuffle(chises)
angle = np.random.choice([-60, 60, 180])
resi_i = np.random.choice([resi_i, resi_j])
for chi in chises:
if chi == 1:
try:
cmd.set_dihedral(
'%s and resi %s and name OR' % (obj, resi_i),
'%s and resi %s and name C%S' % (obj, resi_i, chi),
'%s and resi %s and name O%s' % (obj, resi_i, chi),
'%s and resi %s and name H%so' % (obj, resi_i, chi),
angle,
state=state)
break
except:
pass
elif chi <= 5:
try:
cmd.set_dihedral(
'%s and resi %s and name C%s' % (obj, resi_i, chi - 1),
'%s and resi %s and name C%S' % (obj, resi_i, chi),
'%s and resi %s and name O%s' % (obj, resi_i, chi),
'%s and resi %s and name H%so' % (obj, resi_i, chi),
angle,
state=state)
break
except:
pass
else:
try:
set_omega(obj, bond, angle)
break
except:
pass
def set_phipsi(selection, phi=None, psi=None):
for model, index in cmd.index(
'byca (' + selection +
')'): # 'byca' limits selection to one atom per residue
atsele = [
'first ((%s`%d) extend 2 and name C)' % (model, index), # prev C
'first ((%s`%d) extend 1 and name N)' % (model, index), # this N
'(%s`%d)' % (model, index), # this CA
'last ((%s`%d) extend 1 and name C)' % (model, index), # this C
'last ((%s`%d) extend 2 and name N)' % (model, index), # next N
]
try:
if phi is not None:
cmd.set_dihedral(atsele[0], atsele[1], atsele[2], atsele[3],
phi) #sets value for all phi in selection
if psi is not None:
cmd.set_dihedral(atsele[1], atsele[2], atsele[3], atsele[4],
psi) #sets value for all psi
except:
print ' Error: cmd.set_dihedral failed'
def set_phipsi(sel,phi,psi):
# Get atoms from selection
atoms = cmd.get_model("byres ("+sel+")")
# Loop through atoms in selection
for at in atoms.atom: # pylint: disable=E1103
if at.name == "N":
# Check for a null chain id (some PDBs contain this)
unit_select = ""
if not at.chain == "":
unit_select = "chain "+str(at.chain)+" and "
# end if
try:
# Define residue selections
rdef_prev = unit_select+'resi '+str(int(at.resi)-1)
rdef = unit_select+'resi '+str(at.resi)
# print "rdef_prev: [%s]" % rdef_prev
# print "rdef : [%s]" % rdef
if at.resn == "PRO":
print "Skipping setting phi for PRO"
else:
old_phi = cmd.get_dihedral(rdef_prev+' and name C',rdef+' and name N', rdef+' and name CA',rdef+' and name C')
cmd.set_dihedral( rdef_prev+' and name C',rdef+' and name N', rdef+' and name CA',rdef+' and name C',phi)
print "Changed residue %4s %4s phi: from %6.1f to %6.1f" % (at.resn, at.resi, old_phi, float(phi))
except:
print "Note skipping set of phi because of error; this is normal for a N-terminal residue"
try:
rdef = unit_select+'resi '+str(at.resi)
residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
# print "rdef : [%s]" % rdef
# print "residue_def_next: [%s]" % residue_def_next
old_psi = cmd.get_dihedral(rdef +' and name N',rdef+' and name CA',rdef+' and name C', residue_def_next+' and name N')
cmd.set_dihedral( rdef +' and name N',rdef+' and name CA',rdef+' and name C', residue_def_next+' and name N',psi) # pylint: disable=C0301
print "Changed residue %4s %4s psi: from %6.1f to %6.1f" % (at.resn, at.resi, old_psi, float(psi))
except:
print "Note skipping set of psi; this is normal for a C terminal residue"
def torsion_drive(
atom1,
atom2,
atom3,
atom4,
interval,
selection,
path,
mol_name,
):
"""
This function generates input pdbs of dihedral angles selected of intervals specified with interval
:param atom1: name of atom 1 of dihedral
:param atom2: name of atom 2 of dihedral
:param atom3: name of atom 3 of dihedral
:param atom4: name of atom 4 of dihedral
:param interval: int or float (in degrees) of intervals to generate torsion scan for
:param selection: name of selection for molecule
:param path: path to where pdb files should be saved
:param mole_name: name of molecule to append to filenamen
"""
atom1 = selection + " and name " + atom1
atom2 = selection + " and name " + atom2
atom3 = selection + " and name " + atom3
atom4 = selection + " and name " + atom4
for angle in range(0, 360 + int(interval), int(interval)):
try:
os.makedirs('%s/%i' % (path, angle))
except OSError as exc:
if exc.errno == errno.EEXIST and os.path.isdir(path):
pass
else:
raise
cmd.set_dihedral(atom1, atom2, atom3, atom4, angle)
filename = '%s/%i/%s_%i.pdb' % (path, angle, mol_name, angle)
cmd.save(filename, selection, 1)
def set_chi(obj, bond, state=1):
"""
Set the dihedral angles chi (Cx-1-Cx-O'x-H'x) to one of tree predefinied
angles (-60, 60, 180). The perturbed chi angle is selected at random.
This function considers the omega angle as a chi angle.
"""
resi_i, resi_j = bond[0], bond[2]
chises = [1,2,3,4,5,6]
np.random.shuffle(chises)
angle = np.random.choice([-60, 60, 180])
resi_i = np.random.choice([resi_i, resi_j])
for chi in chises:
if chi == 1:
try:
cmd.set_dihedral('%s and resi %s and name OR' % (obj, resi_i),
'%s and resi %s and name C%S' % (obj, resi_i, chi),
'%s and resi %s and name O%s' % (obj, resi_i, chi),
'%s and resi %s and name H%so' % (obj, resi_i, chi), angle, state=state)
break
except:
pass
elif chi <= 5:
try:
cmd.set_dihedral('%s and resi %s and name C%s' % (obj, resi_i, chi-1),
'%s and resi %s and name C%S' % (obj, resi_i, chi),
'%s and resi %s and name O%s' % (obj, resi_i, chi),
'%s and resi %s and name H%so' % (obj, resi_i, chi), angle, state=state)
break
except:
pass
else:
try:
set_omega(obj, bond, angle)
break
except:
pass
def calc_energyprofile(atom1, atom2, atom3, atom4, structurefilename,
forcefield, anglestep, mopacpath):
energyprofilelist = []
pymol.cmd.load(os.path.abspath(os.curdir) + "//" + structurefilename)
for value in range(-180, 180, anglestep):
cmd.set_dihedral("ID " + str(atom1), "ID " + str(atom2),
"ID " + str(atom3), "ID " + str(atom4), value)
tmpstructurefilename = structurefilename.replace(".pdb", "_tmp.pdb")
moptmpstructurefilename = structurefilename.replace(".pdb", "_tmp.mop")
outtmpstructurefilename = structurefilename.replace(".pdb", "_tmp.out")
cmd.save(tmpstructurefilename)
#devnull = open('/dev/null', 'w') #para ocultar stdout
command = "babel -ipdb " + tmpstructurefilename + " -omop " + moptmpstructurefilename + " -xk '" + forcefield + "' 2> /dev/null; " + mopacpath + " " + moptmpstructurefilename
#process = subprocess.Popen(command , shell=True, bufsize=2048, stdout=devnull, stderr=devnull)
os.system(command)
#process.wait()
#devnull.close()
outtmpstructurefile = open(outtmpstructurefilename, "r")
for line in outtmpstructurefile:
if 'FINAL HEAT' in line:
energyprofilelist.append([value, float(line.split()[5])])
outtmpstructurefile.close()
return energyprofilelist
def UpdateSideChainConformations(self):
try:
# temporary sel. var
strSelectSC = ''
# Loop through Flexible side-chains
for residue in self.top.listSideChain:
#print "Setting dihedrals for " + residue
# Were any rotamers accepted for this side-chain
if self.top.dictSideChainNRot.get(residue,''):
#print "List of possible rotamers:" + str(self.top.dictSideChainNRot[residue])
# Residu Name
Res = residue[0:3]
Num = residue[3:len(residue)-1]
Chn = residue[len(residue)-1:len(residue)]
strSelectSC += "(resn " + Res + " & resi " + Num
if Chn != '-':
strSelectSC += " & chain " + Chn
else:
strSelectSC += " & chain ''"
strSelectSC += " & ! name C+O+N " + " & " + self.TargetObj + " & present) or "
# Get Integer value from GA.
IntVal = int(float(self.Line[self.colNo:(self.colNo+10)].strip()) + 0.5)
nFlex = Constants.nFlexBonds[Res]
#print("IntVal", str(IntVal))
#print("nFlex", str(nFlex))
#print strSelectSC
if IntVal > 0: # 0 is the default PDB side-chain conf.
# Get List of Dihedrals to rebuild
for k in range(0,nFlex):
'''
print "for k=" + str(k) + " for residue=" + str(residue)
print self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+0])
print self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+1])
print self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+2])
print self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+3])
print self.top.dictSideChainRotamers[residue]
print self.top.dictSideChainRotamers[residue][(IntVal-1)*nFlex+k]
'''
# Set dihedrals for side-chain
cmd.set_dihedral(self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+0]),
self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+1]),
self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+2]),
self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+3]),
self.top.dictSideChainRotamers[residue][(IntVal-1)*nFlex+k], self.State)
cmd.refresh()
# Get next column starting index
self.colNo = self.colNo + 11
# Side-chain selection string - remove last 4 chars
if strSelectSC != '':
strSelectSC = strSelectSC[:len(strSelectSC)-4]
return strSelectSC
except:
self.CriticalError("Could not update side-chain conformations")
def _set_dihedral(index, angle):
for i in range(4):
cmd.select('a%d' % i, 'id %d' % index[i])
cmd.set_dihedral('a0', 'a1', 'a2', 'a3', angle)
def UpdateSideChainConformations(self):
try:
# temporary sel. var
strSelectSC = ''
# Loop through Flexible side-chains
for residue in self.top.listSideChain:
#print "Setting dihedrals for " + residue
# Were any rotamers accepted for this side-chain
if self.top.dictSideChainNRot.get(residue, ''):
#print "List of possible rotamers:" + str(self.top.dictSideChainNRot[residue])
# Residu Name
Res = residue[0:3]
Num = residue[3:len(residue) - 1]
Chn = residue[len(residue) - 1:len(residue)]
strSelectSC += "(resn " + Res + " & resi " + Num
if Chn != '-':
strSelectSC += " & chain " + Chn
else:
strSelectSC += " & chain ''"
strSelectSC += " & ! name C+O+N " + " & " + self.TargetObj + " & present) or "
# Get Integer value from GA.
IntVal = int(
float(self.Line[self.colNo:(self.colNo +
10)].strip()) + 0.5)
nFlex = Constants.nFlexBonds[Res]
#print("IntVal", str(IntVal))
#print("nFlex", str(nFlex))
#print strSelectSC
if IntVal > 0: # 0 is the default PDB side-chain conf.
# Get List of Dihedrals to rebuild
for k in range(0, nFlex):
'''
print "for k=" + str(k) + " for residue=" + str(residue)
print self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+0])
print self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+1])
print self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+2])
print self.Get_AtomString(Res,Num,Chn,Constants.setDihedrals[Res][4*k+3])
print self.top.dictSideChainRotamers[residue]
print self.top.dictSideChainRotamers[residue][(IntVal-1)*nFlex+k]
'''
# Set dihedrals for side-chain
cmd.set_dihedral(
self.Get_AtomString(
Res, Num, Chn,
Constants.setDihedrals[Res][4 * k + 0]),
self.Get_AtomString(
Res, Num, Chn,
Constants.setDihedrals[Res][4 * k + 1]),
self.Get_AtomString(
Res, Num, Chn,
Constants.setDihedrals[Res][4 * k + 2]),
self.Get_AtomString(
Res, Num, Chn,
Constants.setDihedrals[Res][4 * k + 3]),
self.top.dictSideChainRotamers[residue][
(IntVal - 1) * nFlex + k], self.State)
cmd.refresh()
# Get next column starting index
self.colNo = self.colNo + 11
# Side-chain selection string - remove last 4 chars
if strSelectSC != '':
strSelectSC = strSelectSC[:len(strSelectSC) - 4]
return strSelectSC
except:
self.CriticalError("Could not update side-chain conformations")
def do_library(self):
cmd=self.cmd
pymol=cmd._pymol
if not ((cmd.count_atoms("(%s) and name N"%src_sele)==1) and
(cmd.count_atoms("(%s) and name C"%src_sele)==1) and
(cmd.count_atoms("(%s) and name O"%src_sele)==1)):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable","selector","everythin")
cmd.feedback("disable","editor","actions")
self.prompt = [ 'Loading rotamers...']
self.bump_scores = []
state_best = 0
pymol.stored.name = 'residue'
cmd.iterate("first (%s)"%src_sele,'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight",src_sele)
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele,animate=-1)
self.lib_mode = self.mode
if self.lib_mode=="current":
pymol.stored.resn=""
cmd.iterate("(%s & name CA)"%src_sele,"stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn,pymol.stored.resn)
if (self.c_cap!='none') or (self.n_cap!='none') or (self.hyd != 'auto'):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name,src_sele,1,1)
if self.c_cap=='open':
cmd.remove("%s and name OXT"%frag_name)
if self.lib_mode!='current':
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == 'posi') and (frag_type[0:3]!='NT_'):
if not ( cmd.count_atoms(
"elem C & !(%s) & (bto. (name N & (%s))) &! resn ACE"%
(src_sele,src_sele))):
# use N-terminal fragment
frag_type ="NT_"+frag_type
if (self.c_cap == 'nega') and (frag_type[0:3]!='CT_'):
if not ( cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele))):
# use C-terminal fragment
frag_type ="CT_"+frag_type
if rot_type[0:3] in [ 'NT_', 'CT_' ]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(frag_type.lower(), frag_name, origin=0)
# trim off hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# copy identifying information
cmd.alter("?%s & name CA" % src_sele, "stored.identifiers = (segi, chain, resi, ss, color)", space=self.space)
cmd.alter("?%s" % frag_name, "(segi, chain, resi, ss) = stored.identifiers[:4]", space=self.space)
# move the fragment
if ((cmd.count_atoms("(%s & name CB)"%frag_name)==1) and
(cmd.count_atoms("(%s & name CB)"%src_sele)==1)):
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name CB)"%frag_name,
"(%s & name CB)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
else:
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
# fix the carbonyl position...
cmd.iterate_state(1,"(%s & name O)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name O)"%frag_name,"(x,y,z)=stored.list")
if cmd.count_atoms("(%s & name OXT)"%src_sele):
cmd.iterate_state(1,"(%s & name OXT)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name OXT)"%frag_name,"(x,y,z)=stored.list")
elif cmd.count_atoms("(%s & name OXT)"%frag_name): # place OXT if no template exists
angle = cmd.get_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name O)"%frag_name)
cmd.protect("(%s & name O)"%frag_name)
cmd.set_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name OXT)"%frag_name,180.0+angle)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%frag_name)==1:
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%src_sele)==1:
cmd.iterate_state(1,"(hydro and bound_to (name N & (%s)))"%src_sele,
"stored.list=[x,y,z]")
cmd.alter_state(1,"(hydro and bound_to (name N & (%s)))"%frag_name,
"(x,y,z)=stored.list")
elif cmd.select(tmp_sele1,"(name C & bound_to (%s and elem N))"%src_sele)==1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
tmp_sele1)
cmd.set_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
"(%s & name H)"%frag_name,180.0+angle)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in [ 'amin', 'nmet' ]:
if not cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele)):
if cmd.count_atoms("name C & (%s)"%(frag_name))==1:
if self.c_cap == 'amin':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nhh')
elif self.c_cap == 'nmet':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nme')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & bound_to (name C & (%s))"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# add n-cap (if appropriate)
if self.n_cap in [ 'acet' ]:
if not cmd.count_atoms("elem C & !(%s) & (bto. (name N & (%s))) & !resn ACE "%
(src_sele,src_sele)):
if cmd.count_atoms("name N & (%s)"%(frag_name))==1:
if self.n_cap == 'acet':
editor.attach_amino_acid("name N & (%s)"%(frag_name), 'ace')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & (%s)"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
cartoon = (cmd.count_atoms("(%s & name CA & rep cartoon)"%src_sele)>0)
sticks = (cmd.count_atoms("(%s & name CA & rep sticks)"%src_sele)>0)
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == 'dep':
try:
result = cmd.phi_psi("%s"%src_sele)
if len(result)==1:
(phi,psi) = list(result.values())[0]
(phi,psi) = (int(10*round(phi/10)),int(10*(round(psi/10))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(20*round(phi/20)),int(20*(round(psi/20))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(60*round(phi/60)),int(60*(round(psi/60))))
key = (rot_type,phi,psi)
lib = self.dep_library.get(key,None)
except:
pass
if lib is None:
key = rot_type
lib = self.ind_library.get(key,None)
if (lib is not None) and self.dep == 'dep':
print(' Mutagenesis: no phi/psi, using backbone-independent rotamers.')
if lib is not None:
state = 1
for a in lib:
cmd.create(obj_name,frag_name,1,state)
if state == 1:
cmd.select(mut_sele,"(byres (%s like %s))"%(obj_name,src_sele))
if rot_type=='PRO':
cmd.unbond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
for b in a.keys():
if b!='FREQ':
cmd.set_dihedral("(%s & n;%s)"%(mut_sele,b[0]),
"(%s & n;%s)"%(mut_sele,b[1]),
"(%s & n;%s)"%(mut_sele,b[2]),
"(%s & n;%s)"%(mut_sele,b[3]),
a[b],state=state)
else:
cmd.set_title(obj_name,state,"%1.1f%%"%(a[b]*100))
if rot_type=='PRO':
cmd.bond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
state = state + 1
cmd.delete(frag_name)
print(" Mutagenesis: %d rotamers loaded."%len(lib))
if self.bump_check:
cmd.delete(bump_name)
cmd.create(bump_name,
"(((byobj %s) within 6 of (%s and not name N+C+CA+O+H+HA)) and (not (%s)))|(%s)"%
(src_sele,mut_sele,src_sele,mut_sele),singletons=1)
cmd.color("gray50",bump_name+" and elem C")
cmd.set("seq_view",0,bump_name,quiet=1)
cmd.hide("everything",bump_name)
if ((cmd.select(tmp_sele1, "(name N & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "(name C & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
if ((cmd.select(tmp_sele1,"(name C & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"(name N & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name N+C+CA+O+H+HA))"%
(bump_name,bump_name,mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo",bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode",1,bump_name)
state = 1
score_best = 1e6
for a in lib:
score = cmd.sculpt_iterate(bump_name, state, 1)
self.bump_scores.append(score)
if score < score_best:
state_best = state
score_best = score
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name,frag_name,1,1)
print(" Mutagenesis: no rotamers found in library.")
cmd.set("seq_view",0,obj_name,quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("("+obj_name+")")
cmd.show(self.rep,obj_name)
cmd.show('lines',obj_name) #neighbor always show lines
if cartoon:
cmd.show("cartoon",obj_name)
if sticks:
cmd.show("sticks",obj_name)
cmd.set('auto_zoom',auto_zoom,quiet=1)
cmd.delete(frag_name)
cmd.frame(state_best)
cmd.unpick()
cmd.feedback("pop")
# pymol -qc mutate.py pdb selection new_residue
# example: pymol -qc mutate.py 0.pdb C/1/ ALA 0_mutated.pdb
from pymol import cmd
import sys
pdb, selection, mutant, output_name = sys.argv[-4:]
print("file:", pdb)
print("selection:", selection)
print("mutating to:", mutant)
print("output name:", output_name)
cmd.load(pdb, "file")
resi_num = selection.split("/")[1]
#prefix = "chain B & resi " + resi_num + " & name "
prefix = "chain A & resi " + resi_num + " & name "
orig_dihedral = cmd.get_dihedral(prefix + "C", prefix + "CA", prefix + "CB", prefix + "CG")
cmd.wizard("mutagenesis")
cmd.refresh_wizard()
cmd.get_wizard().do_select(selection)
cmd.get_wizard().set_mode(mutant)
cmd.get_wizard().apply()
cmd.set_wizard()
cmd.set_dihedral(prefix + "C", prefix + "CA", prefix + "CB", prefix + "1HB", orig_dihedral)
cmd.save(output_name, "file")
def do_library(self):
cmd=self.cmd
pymol=cmd._pymol
if not ((cmd.count_atoms("(%s) and name N"%src_sele)==1) and
(cmd.count_atoms("(%s) and name C"%src_sele)==1) and
(cmd.count_atoms("(%s) and name O"%src_sele)==1)):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable","selector","everythin")
cmd.feedback("disable","editor","actions")
self.prompt = [ 'Loading rotamers...']
self.bump_scores = []
state_best = 0
pymol.stored.name = 'residue'
cmd.iterate("first (%s)"%src_sele,'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight",src_sele)
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele,animate=-1)
self.lib_mode = self.mode
if self.lib_mode=="current":
pymol.stored.resn=""
cmd.iterate("(%s & name CA)"%src_sele,"stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn,pymol.stored.resn)
if (self.c_cap!='none') or (self.n_cap!='none') or (self.hyd != 'auto'):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name,src_sele,1,1)
if self.c_cap=='open':
cmd.remove("%s and name OXT"%frag_name)
if self.lib_mode!='current':
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == 'posi') and (frag_type[0:3]!='NT_'):
if not ( cmd.count_atoms(
"elem C & !(%s) & (bto. (name N & (%s))) &! resn ACE"%
(src_sele,src_sele))):
# use N-terminal fragment
frag_type ="NT_"+frag_type
if (self.c_cap == 'nega') and (frag_type[0:3]!='CT_'):
if not ( cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele))):
# use C-terminal fragment
frag_type ="CT_"+frag_type
if rot_type[0:3] in [ 'NT_', 'CT_' ]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(frag_type.lower(), frag_name, origin=0)
# trim off hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# copy identifying information
cmd.alter("?%s & name CA" % src_sele, "stored.identifiers = (segi, chain, resi, ss, color)", space=self.space)
cmd.alter("?%s" % frag_name, "(segi, chain, resi, ss) = stored.identifiers[:4]", space=self.space)
# move the fragment
if ((cmd.count_atoms("(%s & name CB)"%frag_name)==1) and
(cmd.count_atoms("(%s & name CB)"%src_sele)==1)):
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name CB)"%frag_name,
"(%s & name CB)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
else:
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
# fix the carbonyl position...
cmd.iterate_state(1,"(%s & name O)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name O)"%frag_name,"(x,y,z)=stored.list")
if cmd.count_atoms("(%s & name OXT)"%src_sele):
cmd.iterate_state(1,"(%s & name OXT)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name OXT)"%frag_name,"(x,y,z)=stored.list")
elif cmd.count_atoms("(%s & name OXT)"%frag_name): # place OXT if no template exists
angle = cmd.get_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name O)"%frag_name)
cmd.protect("(%s & name O)"%frag_name)
cmd.set_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name OXT)"%frag_name,180.0+angle)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%frag_name)==1:
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%src_sele)==1:
cmd.iterate_state(1,"(hydro and bound_to (name N & (%s)))"%src_sele,
"stored.list=[x,y,z]")
cmd.alter_state(1,"(hydro and bound_to (name N & (%s)))"%frag_name,
"(x,y,z)=stored.list")
elif cmd.select(tmp_sele1,"(name C & bound_to (%s and elem N))"%src_sele)==1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
tmp_sele1)
cmd.set_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
"(%s & name H)"%frag_name,180.0+angle)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in [ 'amin', 'nmet' ]:
if not cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele)):
if cmd.count_atoms("name C & (%s)"%(frag_name))==1:
if self.c_cap == 'amin':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nhh')
elif self.c_cap == 'nmet':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nme')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & bound_to (name C & (%s))"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# add n-cap (if appropriate)
if self.n_cap in [ 'acet' ]:
if not cmd.count_atoms("elem C & !(%s) & (bto. (name N & (%s))) & !resn ACE "%
(src_sele,src_sele)):
if cmd.count_atoms("name N & (%s)"%(frag_name))==1:
if self.n_cap == 'acet':
editor.attach_amino_acid("name N & (%s)"%(frag_name), 'ace')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & (%s)"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
cartoon = (cmd.count_atoms("(%s & name CA & rep cartoon)"%src_sele)>0)
sticks = (cmd.count_atoms("(%s & name CA & rep sticks)"%src_sele)>0)
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == 'dep':
try:
result = cmd.phi_psi("%s"%src_sele)
if len(result)==1:
(phi,psi) = list(result.values())[0]
(phi,psi) = (int(10*round(phi/10)),int(10*(round(psi/10))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(20*round(phi/20)),int(20*(round(psi/20))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(60*round(phi/60)),int(60*(round(psi/60))))
key = (rot_type,phi,psi)
lib = self.dep_library.get(key,None)
except:
pass
if lib == None:
key = rot_type
lib = self.ind_library.get(key,None)
if (lib!= None) and self.dep == 'dep':
print(' Mutagenesis: no phi/psi, using backbone-independent rotamers.')
if lib != None:
state = 1
for a in lib:
cmd.create(obj_name,frag_name,1,state)
if state == 1:
cmd.select(mut_sele,"(byres (%s like %s))"%(obj_name,src_sele))
if rot_type=='PRO':
cmd.unbond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
for b in a.keys():
if b!='FREQ':
cmd.set_dihedral("(%s & n;%s)"%(mut_sele,b[0]),
"(%s & n;%s)"%(mut_sele,b[1]),
"(%s & n;%s)"%(mut_sele,b[2]),
"(%s & n;%s)"%(mut_sele,b[3]),
a[b],state=state)
else:
cmd.set_title(obj_name,state,"%1.1f%%"%(a[b]*100))
if rot_type=='PRO':
cmd.bond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
state = state + 1
cmd.delete(frag_name)
print(" Mutagenesis: %d rotamers loaded."%len(lib))
if self.bump_check:
cmd.delete(bump_name)
cmd.create(bump_name,
"(((byobj %s) within 6 of (%s and not name N+C+CA+O+H+HA)) and (not (%s)))|(%s)"%
(src_sele,mut_sele,src_sele,mut_sele),singletons=1)
cmd.color("gray50",bump_name+" and elem C")
cmd.set("seq_view",0,bump_name,quiet=1)
cmd.hide("everything",bump_name)
if ((cmd.select(tmp_sele1, "(name N & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "(name C & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
if ((cmd.select(tmp_sele1,"(name C & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"(name N & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name N+C+CA+O+H+HA))"%
(bump_name,bump_name,mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo",bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode",1,bump_name)
state = 1
score_best = 1e6
for a in lib:
score = cmd.sculpt_iterate(bump_name, state, 1)
self.bump_scores.append(score)
if score < score_best:
state_best = state
score_best = score
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name,frag_name,1,1)
print(" Mutagenesis: no rotamers found in library.")
cmd.set("seq_view",0,obj_name,quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("("+obj_name+")")
cmd.show(self.rep,obj_name)
cmd.show('lines',obj_name) #neighbor always show lines
if cartoon:
cmd.show("cartoon",obj_name)
if sticks:
cmd.show("sticks",obj_name)
cmd.set('auto_zoom',auto_zoom,quiet=1)
cmd.delete(frag_name)
cmd.frame(state_best)
cmd.unpick()
cmd.feedback("pop")
def attach_amino_acid(selection,amino_acid,phi,psi):
if not selection in cmd.get_names("selections"):
if amino_acid in cmd.get_names("objects"):
print " Error: an object with than name already exists"
raise QuietException
cmd.fragment(amino_acid)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(hydro and %s)"%amino_acid)
if cmd.count_atoms("((%s) and name c)"%amino_acid,quiet=1):
cmd.edit("((%s) and name c)"%amino_acid)
else:
cmd.fragment(amino_acid,tmp_editor)
if cmd.count_atoms("((%s) and elem n)"%selection,quiet=1):
cmd.select(tmp_ed_save,"(%s)"%selection)
cmd.iterate("(%s)"%selection,"stored.resv=resv")
stored.resi = str(stored.resv-1)
cmd.alter(tmp_editor,"resi=stored.resi")
cmd.fuse("(%s and name C)"%(tmp_editor),"(pk1)",2)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(pkmol and hydro)")
cmd.set_dihedral("(name ca and neighbor pk2)",
"(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
cmd.set_geometry("pk2",3,3) # make nitrogen planer
cmd.select(tpk1,"pk2")
cmd.select(tpk2,"pk1")
if amino_acid[0:3]!='pro':
cmd.set_dihedral( # PHI
"(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
"(name ca and neighbor "+tpk1+")", # CA
tpk1, # N
tpk2, # C
phi)
cmd.set_dihedral( # PSI (n-1)
tpk1, # N
tpk2, # C
"(name ca and neighbor "+tpk2+")", # CA
"(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
psi)
cmd.delete(tpk1)
cmd.delete(tpk2)
sele = ("(name N and (byres neighbor %s) and not (byres %s))"%
(tmp_ed_save,tmp_ed_save))
if cmd.count_atoms(sele,quiet=1):
cmd.edit(sele)
cmd.delete(tmp_ed_save)
elif cmd.count_atoms("((%s) and elem c)"%selection,quiet=1):
cmd.select(tmp_ed_save,"(%s)"%selection)
cmd.iterate("(%s)"%selection,"stored.resv=resv")
stored.resi = str(stored.resv+1)
cmd.alter(tmp_editor,"resi=stored.resi")
cmd.fuse("(%s and name N)"%(tmp_editor),"(pk1)",2)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(pkmol and hydro)")
cmd.set_dihedral("(name ca and neighbor pk2)",
"(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
cmd.set_geometry("pk1",3,3) # make nitrogen planar
cmd.select(tpk1,"pk1")
cmd.select(tpk2,"pk2")
if amino_acid[0:3]!='pro':
cmd.set_dihedral( # PHI
tpk2, # C
tpk1, # N
"(name ca and neighbor "+tpk1+")", # CA
"(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
phi)
cmd.set_dihedral( # PSI (n-1)
"(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
"(name ca and neighbor "+tpk2+")", # CA
tpk2, # C
tpk1, # N
psi)
cmd.delete(tpk1)
cmd.delete(tpk2)
sele = ("(name C and (byres neighbor %s) and not (byres %s))"%
(tmp_ed_save,tmp_ed_save))
if cmd.count_atoms(sele,quiet=1):
cmd.edit(sele)
cmd.delete(tmp_ed_save)
elif cmd.count_atoms("((%s) and elem h)"%selection,quiet=1):
print " Error: please pick a nitrogen or carbonyl carbon to grow from."
cmd.delete(tmp_editor)
raise QuietException
cmd.delete(tmp_editor)
def mutate(selection, new_resn, inplace=0, sculpt=0, hydrogens='auto', mode=0, quiet=1):
'''
DESCRIPTION
Mutate a single residue. Does call the mutagenesis wizard non-interactively
and tries to select the best rotamer. Can do some sculpting in the end to
the best rotamer.
USAGE
mutate selection, new_resn [, inplace [, sculpt [, hydrogens]]]
ARGUMENTS
selection = string: atom selection of single residue
new_resn = string: new residue name (3-letter or 1-letter)
inplace = 0 or 1: work on copy of input object if 0 {default: 0}
sculpt = 0: no sculpting {default}
sculpt = 1: do sculpting on best rotamer
sculpt = 2: do sculpting with neighbors
hydrogens = string: keep, auto or none {default: auto}
mode = 0: select rotamer with best clash score {default}
mode = 1: take chi angles from original residue
mode = 2: first rotamer
EXAMPLE
fetch 2x19, async=0
select x, A/CYS`122/
zoom x
mutate x, LYS
'''
from pymol.wizard import mutagenesis
from . import three_letter
inplace, sculpt = int(inplace), int(sculpt)
mode = int(mode)
quiet = int(quiet)
org = cmd.get_object_list(selection)[0]
tmp = cmd.get_unused_name()
new_resn = new_resn.upper()
new_resn = three_letter.get(new_resn, new_resn)
if inplace:
cpy = org
else:
cpy = cmd.get_unused_name(org + '_cpy')
cmd.create(cpy, org, -1, 1, zoom=0)
scr = []
cmd.iterate('first (%s)' % selection, 'scr[:] = (segi,chain,resi,resn)', space={'scr': scr})
res = '/%s/%s/%s/%s' % tuple([cpy] + scr[:3])
if mode == 1:
old_resn = scr[3]
chi_atoms = {
'ALA': [],
'ARG': ['C','CA','CB','CG','CD','NE','CZ'],
'ASN': ['C','CA','CB','CG','OD1'],
'ASP': ['C','CA','CB','CG','OD1'],
'CYS': ['C','CA','CB','SG'],
'GLN': ['C','CA','CB','CG','CD','OE1'],
'GLU': ['C','CA','CB','CG','CD','OE1'],
'GLY': [],
'HIS': ['C','CA','CB','CG','ND1'],
'ILE': ['C','CA','CB','CG1','CD1'],
'LEU': ['C','CA','CB','CG','CD1'],
'LYS': ['C','CA','CB','CG','CD','CE','NZ'],
'MET': ['C','CA','CB','CG','SD','CE'],
'MSE': ['C','CA','CB','CG','SE','CE'],
'PHE': ['C','CA','CB','CG','CD1'],
'PRO': [],
'SER': ['C','CA','CB','OG'],
'THR': ['C','CA','CB','OG1'],
'TRP': ['C','CA','CB','CG','CD2'],
'TYR': ['C','CA','CB','CG','CD1'],
'VAL': ['C','CA','CB','CG2'],
}
atoms = [res + '/' + name for name in chi_atoms.get(old_resn, [])]
old_chi = []
for args in zip(atoms, atoms[1:], atoms[2:], atoms[3:]):
try:
old_chi.append(cmd.get_dihedral(*args))
except:
break
cmd.remove('%s and not name CA+C+N+O+OXT' % (res))
# start the wizard to count the number of rotamers for this residue
cmd.wizard("mutagenesis")
cmd.get_wizard().set_mode(new_resn)
cmd.get_wizard().set_hyd(hydrogens)
cmd.get_wizard().do_select("("+res+")")
def get_best_state_bump():
best_state = (1, 1e9)
cmd.create(tmp, '%s and not name CA+C+N+O or (%s within 8.0 of (%s and name CB))' % \
(mutagenesis.obj_name, cpy, mutagenesis.obj_name), zoom=0, singletons=1)
cmd.bond('name CB and %s in %s' % (tmp, mutagenesis.obj_name),
'name CA and %s in %s' % (tmp, res))
cmd.sculpt_activate(tmp)
for i in range(1, cmd.count_states(tmp)+1):
score = cmd.sculpt_iterate(tmp, state=i)
if not quiet:
print('Frame %d Score %.2f' % (i, score))
if score < best_state[1]:
best_state = (i, score)
cmd.delete(tmp)
if not quiet:
print(' Best: Frame %d Score %.2f' % best_state)
return best_state
if cmd.count_states(mutagenesis.obj_name) < 2 or mode > 0:
best_state = (1, -1.0)
else:
best_state = get_best_state_bump()
cmd.frame(best_state[0])
cmd.get_wizard().apply()
cmd.wizard()
if mode == 1:
atoms = [res + '/' + name for name in chi_atoms.get(new_resn, [])]
for args in zip(atoms, atoms[1:], atoms[2:], atoms[3:], old_chi):
cmd.set_dihedral(*args)
cmd.unpick()
if sculpt > 0:
sculpt_relax(res, 0, sculpt == 2, cpy)
return cpy
def generate(dihedrals,
directory="temp",
setup_path="default",
verbose="False"):
# dihedrals = [[atom a, atom b, atom c, atom d]]
# Log generation
log = Log()
log.write(
"\n\n########################################\n########### G E N E R A T E ############\n########################################\n\n"
)
#verbose
if verbose.lower() in ['true', '1', 't', 'y', 'yes']: verbose = True
else: verbose = False
# dihedrals: auto?
if dihedrals.lower() in ['auto']:
dihedrals = 'auto' #To DO: generate dihedrals automatically
# get setup.ini
setup = Setup(log, setup_path)
if setup.isLoaded() == True:
angle_step = 360 / setup.angle_count
dihedrals = dihedrals.strip(' []').split(',')
for i in range(0, len(dihedrals)):
dihedrals[i] = dihedrals[i].strip(' []')
if len(dihedrals) % 4 != 0 and len(dihedrals) != 1:
log.write(
"Error: Problem in dihedral selection. 4 selections are needed for each dihedral. [%s] "
% dihedrals)
return False
dihedral_count = int(len(dihedrals) / 4)
combination_count = int(setup.angle_count**dihedral_count)
log.write("Number of dihedrals: %s" % dihedral_count)
log.write("For each dihedral: %s steps of %s degree" %
(setup.angle_count, angle_step))
log.write("That represents %s combinations" % combination_count)
result = backup_generate(directory) # create backup
if result: log.write("Making archives: %s" % result, verbose)
else: log.write("Making directory: %s" % directory, verbose)
if combination_count == 0:
path = "%s/%s_0.pdb" % (directory, cmd.get_object_list()[0])
try:
cmd.set("retain_order", 1)
cmd.save(path)
except:
log.write(
"Error: Can't save %s first conformer. One conformer will be missing!"
% path, verbose)
else:
# Generate all the combinations
combination_list = [{} for k in range(0, combination_count)]
for i in range(0, combination_count
): # iterate all the combinations of dihedrals
dihedrals_curr_cbn = [{} for k in range(dihedral_count)]
count = i
for j in range(
0, dihedral_count
): # modify the dihedral according to the combination
dihedrals_curr_cbn[j] = int(count % setup.angle_count)
count = int(count / setup.angle_count)
log.write("Combination %s : %s " % (i, dihedrals_curr_cbn),
verbose)
combination_list[i] = dihedrals_curr_cbn
# Too many combinations?
if combination_count > setup.combination_limit:
todestroy_count = combination_count - setup.combination_limit
log.write(
"The amount of possibility is %s. The limit is set at %s. %s combinations will be deleted to go down to the limit using %s algorithm."
% (combination_count, setup.combination_limit,
todestroy_count, setup.combination_remove_algorithm))
if setup.combination_remove_algorithm == "random":
for i in range(
0, todestroy_count
): # loop as many time as the amount to randomly destroy
del combination_list[random.randint(
0, len(combination_list))]
log.write(
"%s combinations. Limit is %s. Reduction of combinations done."
% (len(combination_list), setup.combination_limit),
verbose)
# Generate the files
for i in range(
len(combination_list)): # going through each combination
for j in range(
len(combination_list[i])
): # going through each dihedral of the combination
try:
cmd.set_dihedral(dihedrals[j * 4],
dihedrals[j * 4 + 1],
dihedrals[j * 4 + 2],
dihedrals[j * 4 + 3],
combination_list[i][j] * angle_step)
except:
log.write(
"Error: Can't set the dihedrals. cmd.set_dihedrals failed."
)
log.write(
"Writing Combination %s : %s " % (i, combination_list[i]),
verbose)
path = "%s/%s_%s.pdb" % (directory, cmd.get_object_list()[0],
str(i))
try:
cmd.set("retain_order", 1)
cmd.save(path)
except:
log.write(
"Error: Can't save %s. One conformer will be missing!"
% path)
for j in range(0, dihedral_count):
cmd.undo()
log.write(
"----------------------------\n---- Normal Termination ----\n----------------------------\n"
)
log.finalize()
return True
else:
log.write(
"Error: Failed to load setup.ini in [%s]. Fix it to continue." %
setup_path)
return False
def _set_dihedral(atomnames,angle):
for i in range(4):
cmd.select('a%d'%i, 'name %s'%atomnames[i])
cmd.set_dihedral('a0','a1','a2','a3',angle)
for valor in paramod[npam]:
matrizval[nsal].append(valor)
nsal = nsal + 1
matrizval.sort() #importante para el programa
#3. Genera Archivos de Salidas
infilenamediv=infilename.split(".")
for nsal in range(0,nrosalidas):
salida = [] #lista que contiene las lineas para un archivo de salida especifico
npam = 0
extname = infilenamediv[0]
for line in atomIDs:
linediv=line.split(",")
val = float(matrizval[int(nsal)][int(npam)])
cmd.set_dihedral(linediv[0],linediv[1],linediv[2],linediv[3], val)
#extname = extname + "_D" + linediv[0].strip("ID ")+"-"+linediv[1].strip("ID ")+"-"+linediv[2].strip("ID ")+"-"+linediv[3].strip("ID ") + "_" + str(int(val)) #nombre de salida con valores de parametros
extname = extname + "_D" + str(npam) + "_" + str(int(val)) #nombre de salida con valores de parametros
npam = npam + 1
cmd.save(extname+".pdb")
print "Se creo el archivo " + extname+".pdb"
else:
print "No se encuentran parametros para modificar"
# Get out!
pymol.cmd.quit()
def mutate(selection, new_resn, inplace=0, sculpt=0, hydrogens='auto', mode=0, quiet=1):
'''
DESCRIPTION
Mutate a single residue. Does call the mutagenesis wizard non-interactively
and tries to select the best rotamer. Can do some sculpting in the end to
the best rotamer.
USAGE
mutate selection, new_resn [, inplace [, sculpt [, hydrogens]]]
ARGUMENTS
selection = string: atom selection of single residue
new_resn = string: new residue name (3-letter or 1-letter)
inplace = 0 or 1: work on copy of input object if 0 {default: 0}
sculpt = 0: no sculpting {default}
sculpt = 1: do sculpting on best rotamer
sculpt = 2: do sculpting with neighbors
hydrogens = string: keep, auto or none {default: auto}
mode = 0: select rotamer with best clash score {default}
mode = 1: take chi angles from original residue
mode = 2: first rotamer
EXAMPLE
fetch 2x19, async=0
select x, A/CYS`122/
zoom x
mutate x, LYS
'''
from pymol.wizard import mutagenesis
from . import three_letter
inplace, sculpt = int(inplace), int(sculpt)
mode = int(mode)
quiet = int(quiet)
org = cmd.get_object_list(selection)[0]
tmp = cmd.get_unused_name()
new_resn = new_resn.upper()
new_resn = three_letter.get(new_resn, new_resn)
if inplace:
cpy = org
else:
cpy = cmd.get_unused_name(org + '_cpy')
cmd.create(cpy, org, -1, 1, zoom=0)
scr = []
cmd.iterate('first (%s)' % selection, 'scr[:] = (segi,chain,resi,resn)', space={'scr': scr})
res = '/%s/%s/%s/%s' % tuple([cpy] + scr[:3])
if mode == 1:
old_resn = scr[3]
chi_atoms = {
'ALA': [],
'ARG': ['C','CA','CB','CG','CD','NE','CZ'],
'ASN': ['C','CA','CB','CG','OD1'],
'ASP': ['C','CA','CB','CG','OD1'],
'CYS': ['C','CA','CB','SG'],
'GLN': ['C','CA','CB','CG','CD','OE1'],
'GLU': ['C','CA','CB','CG','CD','OE1'],
'GLY': [],
'HIS': ['C','CA','CB','CG','ND1'],
'ILE': ['C','CA','CB','CG1','CD1'],
'LEU': ['C','CA','CB','CG','CD1'],
'LYS': ['C','CA','CB','CG','CD','CE','NZ'],
'MET': ['C','CA','CB','CG','SD','CE'],
'MSE': ['C','CA','CB','CG','SE','CE'],
'PHE': ['C','CA','CB','CG','CD1'],
'PRO': [],
'SER': ['C','CA','CB','OG'],
'THR': ['C','CA','CB','OG1'],
'TRP': ['C','CA','CB','CG','CD2'],
'TYR': ['C','CA','CB','CG','CD1'],
'VAL': ['C','CA','CB','CG2'],
}
atoms = [res + '/' + name for name in chi_atoms.get(old_resn, [])]
old_chi = []
for args in zip(atoms, atoms[1:], atoms[2:], atoms[3:]):
try:
old_chi.append(cmd.get_dihedral(*args))
except:
break
cmd.remove('%s and not name CA+C+N+O+OXT' % (res))
# start the wizard to count the number of rotamers for this residue
cmd.wizard("mutagenesis")
cmd.get_wizard().set_mode(new_resn)
cmd.get_wizard().set_hyd(hydrogens)
cmd.get_wizard().do_select("("+res+")")
def get_best_state_bump():
best_state = (1, 1e9)
cmd.create(tmp, '%s and not name CA+C+N+O or (%s within 8.0 of (%s and name CB))' % \
(mutagenesis.obj_name, cpy, mutagenesis.obj_name), zoom=0, singletons=1)
cmd.bond('name CB and %s in %s' % (tmp, mutagenesis.obj_name),
'name CA and %s in %s' % (tmp, res))
cmd.sculpt_activate(tmp)
for i in range(1, cmd.count_states(tmp)+1):
score = cmd.sculpt_iterate(tmp, state=i)
if not quiet:
print('Frame %d Score %.2f' % (i, score))
if score < best_state[1]:
best_state = (i, score)
cmd.delete(tmp)
if not quiet:
print(' Best: Frame %d Score %.2f' % best_state)
return best_state
if cmd.count_states(mutagenesis.obj_name) < 2 or mode > 0:
best_state = (1, -1.0)
else:
best_state = get_best_state_bump()
cmd.frame(best_state[0])
cmd.get_wizard().apply()
cmd.wizard()
if mode == 1:
atoms = [res + '/' + name for name in chi_atoms.get(new_resn, [])]
for args in zip(atoms, atoms[1:], atoms[2:], atoms[3:], old_chi):
cmd.set_dihedral(*args)
cmd.unpick()
if sculpt > 0:
sculpt_relax(res, 0, sculpt == 2, cpy)
return cpy
def do_library(self):
cmd = self.cmd
pymol = cmd._pymol
if not (
(cmd.count_atoms("(%s) and name n" % src_sele) == 1)
and (cmd.count_atoms("(%s) and name c" % src_sele) == 1)
and (cmd.count_atoms("(%s) and name o" % src_sele) == 1)
):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable", "selector", "everythin")
cmd.feedback("disable", "editor", "actions")
self.prompt = ["Loading rotamers..."]
pymol.stored.name = "residue"
cmd.iterate("first (%s)" % src_sele, 'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight", src_sele)
auto_zoom = cmd.get_setting_text("auto_zoom")
cmd.set("auto_zoom", "0", quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele, animate=-1)
self.lib_mode = self.mode
if self.lib_mode == "current":
pymol.stored.resn = ""
cmd.iterate("(%s and n;ca)" % src_sele, "stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn, pymol.stored.resn)
if (self.c_cap != "none") or (self.n_cap != "none") or (self.hyd != "auto"):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name, src_sele, 1, 1)
if self.c_cap == "open":
cmd.remove("%s and name OXT" % frag_name)
if self.lib_mode != "current":
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == "posi") and (frag_type[0:3] != "NT_"):
if not (cmd.count_atoms("elem c & !(%s) & (bto. (n;n & (%s))) &! r. ace" % (src_sele, src_sele))):
# use N-terminal fragment
frag_type = "NT_" + frag_type
if (self.c_cap == "nega") and (frag_type[0:3] != "CT_"):
if not (cmd.count_atoms("elem n & !(%s) & (bto. (n;c & (%s))) & !r. nme+nhh" % (src_sele, src_sele))):
# use C-terminal fragment
frag_type = "CT_" + frag_type
if rot_type[0:3] in ["NT_", "CT_"]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(string.lower(frag_type), frag_name)
# trim off hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
# copy identifying information
cmd.iterate("(%s and n;ca)" % src_sele, "stored.chain=chain")
cmd.alter("(%s)" % frag_name, "chain=stored.chain")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.resi=resi")
cmd.alter("(%s)" % frag_name, "resi=stored.resi")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.segi=segi")
cmd.alter("(%s)" % frag_name, "segi=stored.segi")
cmd.iterate("(%s and n;ca)" % src_sele, "stored.ss=ss")
cmd.alter("(%s)" % frag_name, "ss=stored.ss")
# move the fragment
if (cmd.count_atoms("(%s and n;cb)" % frag_name) == 1) and (
cmd.count_atoms("(%s and n;cb)" % src_sele) == 1
):
cmd.pair_fit(
"(%s and n;ca)" % frag_name,
"(%s and n;ca)" % src_sele,
"(%s and n;cb)" % frag_name,
"(%s and n;cb)" % src_sele,
"(%s and n;c)" % frag_name,
"(%s and n;c)" % src_sele,
"(%s and n;n)" % frag_name,
"(%s and n;n)" % src_sele,
)
else:
cmd.pair_fit(
"(%s and n;ca)" % frag_name,
"(%s and n;ca)" % src_sele,
"(%s and n;c)" % frag_name,
"(%s and n;c)" % src_sele,
"(%s and n;n)" % frag_name,
"(%s and n;n)" % src_sele,
)
# fix the carbonyl position...
cmd.iterate_state(1, "(%s and n;o)" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(%s and n;o)" % frag_name, "(x,y,z)=stored.list")
if cmd.count_atoms("(%s and n;oxt)" % src_sele):
cmd.iterate_state(1, "(%s and n;oxt)" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(%s and n;oxt)" % frag_name, "(x,y,z)=stored.list")
elif cmd.count_atoms("(%s and n;oxt)" % frag_name): # place OXT if no template exists
angle = cmd.get_dihedral(
"(%s and n;n)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;c)" % frag_name,
"(%s and n;o)" % frag_name,
)
cmd.protect("(%s and n;o)" % frag_name)
cmd.set_dihedral(
"(%s and n;n)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;c)" % frag_name,
"(%s and n;oxt)" % frag_name,
180.0 + angle,
)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(elem h and bound_to (n;n and (%s)))" % frag_name) == 1:
if cmd.count_atoms("(elem h and bound_to (n;n and (%s)))" % src_sele) == 1:
cmd.iterate_state(1, "(elem h and bound_to (n;n and (%s)))" % src_sele, "stored.list=[x,y,z]")
cmd.alter_state(1, "(elem h and bound_to (n;n and (%s)))" % frag_name, "(x,y,z)=stored.list")
elif cmd.select(tmp_sele1, "(n;c and bound_to (%s and e;n))" % src_sele) == 1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral(
"(%s and n;c)" % frag_name, "(%s and n;ca)" % frag_name, "(%s and n;n)" % frag_name, tmp_sele1
)
cmd.set_dihedral(
"(%s and n;c)" % frag_name,
"(%s and n;ca)" % frag_name,
"(%s and n;n)" % frag_name,
"(%s and n;h)" % frag_name,
180.0 + angle,
)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in ["amin", "nmet"]:
if not cmd.count_atoms("elem n & !(%s) & (bto. (n;c & (%s))) & !r. nme+nhh" % (src_sele, src_sele)):
if cmd.count_atoms("n;c & (%s)" % (frag_name)) == 1:
if self.c_cap == "amin":
editor.attach_amino_acid("n;c & (%s)" % (frag_name), "nhh")
elif self.c_cap == "nmet":
editor.attach_amino_acid("n;c & (%s)" % (frag_name), "nme")
if cmd.count_atoms("hydro & bound_to (n;n & bound_to (n;c & (%s)))" % frag_name):
cmd.h_fix("n;n & bound_to (n;c & (%s))" % frag_name)
# trim hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
# add n-cap (if appropriate)
if self.n_cap in ["acet"]:
if not cmd.count_atoms("elem c & !(%s) & (bto. (n;n & (%s))) & !r. ace " % (src_sele, src_sele)):
if cmd.count_atoms("n;n & (%s)" % (frag_name)) == 1:
if self.n_cap == "acet":
editor.attach_amino_acid("n;n & (%s)" % (frag_name), "ace")
if cmd.count_atoms("hydro & bound_to (n;n & bound_to (n;c & (%s)))" % frag_name):
cmd.h_fix("n;n & (%s)" % frag_name)
# trim hydrogens
if self.hyd == "none":
cmd.remove("(" + frag_name + " and hydro)")
elif self.hyd == "auto":
if cmd.count_atoms("(" + src_sele + ") and hydro") == 0:
cmd.remove("(" + frag_name + " and hydro)")
cartoon = cmd.count_atoms("(%s and n;ca and rep cartoon)" % src_sele) > 0
sticks = cmd.count_atoms("(%s and n;ca and rep sticks)" % src_sele) > 0
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == "dep":
try:
result = cmd.phi_psi("%s" % src_sele)
if len(result) == 1:
(phi, psi) = result[result.keys()[0]]
(phi, psi) = (int(10 * round(phi / 10)), int(10 * (round(psi / 10))))
key = (rot_type, phi, psi)
if not self.dep_library.has_key(key):
(phi, psi) = (int(20 * round(phi / 20)), int(20 * (round(psi / 20))))
key = (rot_type, phi, psi)
if not self.dep_library.has_key(key):
(phi, psi) = (int(60 * round(phi / 60)), int(60 * (round(psi / 60))))
key = (rot_type, phi, psi)
lib = self.dep_library.get(key, None)
except:
pass
if lib == None:
key = rot_type
lib = self.ind_library.get(key, None)
if (lib != None) and self.dep == "dep":
print " Mutagenesis: no phi/psi, using backbone-independent rotamers."
if lib != None:
state = 1
for a in lib:
cmd.create(obj_name, frag_name, 1, state)
if state == 1:
cmd.select(mut_sele, "(byres (%s like %s))" % (obj_name, src_sele))
if rot_type == "PRO":
cmd.unbond("(%s & name N)" % mut_sele, "(%s & name CD)" % mut_sele)
for b in a.keys():
if b != "FREQ":
cmd.set_dihedral(
"(%s & n;%s)" % (mut_sele, b[0]),
"(%s & n;%s)" % (mut_sele, b[1]),
"(%s & n;%s)" % (mut_sele, b[2]),
"(%s & n;%s)" % (mut_sele, b[3]),
a[b],
state=state,
)
else:
cmd.set_title(obj_name, state, "%1.1f%%" % (a[b] * 100))
if rot_type == "PRO":
cmd.bond("(%s & name N)" % mut_sele, "(%s & name CD)" % mut_sele)
state = state + 1
cmd.delete(frag_name)
print " Mutagenesis: %d rotamers loaded." % len(lib)
if self.bump_check:
cmd.delete(bump_name)
cmd.create(
bump_name,
"(((byobj %s) within 6 of (%s and not name n+c+ca+o+h+ha)) and (not (%s)))|(%s)"
% (src_sele, mut_sele, src_sele, mut_sele),
singletons=1,
)
cmd.color("gray50", bump_name + " and elem c")
cmd.set("seq_view", 0, bump_name, quiet=1)
cmd.hide("everything", bump_name)
if (cmd.select(tmp_sele1, "(n;N and (%s in (neighbor %s)))" % (bump_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "(n;C and (%s in %s))" % (bump_name, mut_sele)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
if (cmd.select(tmp_sele1, "(n;C and (%s in (neighbor %s)))" % (bump_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "(n;N and (%s in %s))" % (bump_name, mut_sele)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name n+c+ca+o+h+ha))" % (bump_name, bump_name, mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo", bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode", 1, bump_name)
state = 1
for a in lib:
cmd.sculpt_iterate(bump_name, state=state)
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name, frag_name, 1, 1)
print " Mutagenesis: no rotamers found in library."
cmd.set("seq_view", 0, obj_name, quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("(" + obj_name + ")")
cmd.show(self.rep, obj_name)
cmd.show("lines", obj_name) # neighbor always show lines
if cartoon:
cmd.show("cartoon", obj_name)
if sticks:
cmd.show("sticks", obj_name)
cmd.set("auto_zoom", auto_zoom, quiet=1)
cmd.delete(frag_name)
cmd.frame(0)
cmd.unpick()
cmd.feedback("pop")
cmd.load(in_protein, "MyProtein")
# Get original chain names
Chains = cmd.get_chains()
# Fix dihedral angles of residues near C-termini
for chn in Chains:
# Fix Psi dihedral angle of LYS-31 to alpha-helix
res0 = 31
atom2 = "/MyProtein//" + chn + "/" + str(res0) + "/N"
atom3 = "/MyProtein//" + chn + "/" + str(res0) + "/CA"
atom4 = "/MyProtein//" + chn + "/" + str(res0) + "/C"
atom5 = "/MyProtein//" + chn + "/" + str(res0 + 1) + "/N"
cmd.set_dihedral(atom2, atom3, atom4, atom5, -45)
# Set Phi dihedral angle of ARG-32 to alpha-helix
res0 = 32
atom1 = "/MyProtein//" + chn + "/" + str(res0 - 1) + "/C"
atom2 = "/MyProtein//" + chn + "/" + str(res0) + "/N"
atom3 = "/MyProtein//" + chn + "/" + str(res0) + "/CA"
atom4 = "/MyProtein//" + chn + "/" + str(res0) + "/C"
cmd.set_dihedral(atom1, atom2, atom3, atom4, -60)
# Add missing residues to C-termini on ARG-376
# NOTE: Amidate C-termini by default. For the last residue, we need a N to set Psi
# So, this is why we cap peptides from the beginning
cmd.select("MyAA", "/MyProtein//" + chn + "/THR`32/C")
def attach_amino_acid(selection,amino_acid,phi,psi):
if not selection in cmd.get_names("selections"):
if amino_acid in cmd.get_names("objects"):
print " Error: an object with than name already exists"
raise QuietException
cmd.fragment(amino_acid)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(hydro and %s)"%amino_acid)
if cmd.count_atoms("((%s) and name c)"%amino_acid,quiet=1):
cmd.edit("((%s) and name c)"%amino_acid)
else:
cmd.fragment(amino_acid,tmp_editor)
if cmd.count_atoms("((%s) and elem n)"%selection,quiet=1):
cmd.select(tmp_ed_save,"(%s)"%selection)
cmd.iterate("(%s)"%selection,"stored.resv=resv")
stored.resi = str(stored.resv-1)
cmd.alter(tmp_editor,"resi=stored.resi")
cmd.fuse("(%s and name C)"%(tmp_editor),"(pk1)",2)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(pkmol and hydro)")
cmd.set_dihedral("(name ca and neighbor pk2)",
"(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
cmd.set_geometry("pk2",3,3) # make nitrogen planer
# if ss:
cmd.select(tpk1,"pk2")
cmd.select(tpk2,"pk1")
if amino_acid[0:3]!='pro':
cmd.set_dihedral( # PHI
"(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
"(name ca and neighbor "+tpk1+")", # CA
tpk1, # N
tpk2, # C
phi)
cmd.set_dihedral( # PSI (n-1)
tpk1, # N
tpk2, # C
"(name ca and neighbor "+tpk2+")", # CA
"(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
psi)
cmd.delete(tpk1)
cmd.delete(tpk2)
sele = ("(name N and (byres neighbor %s) and not (byres %s))"%
(tmp_ed_save,tmp_ed_save))
if cmd.count_atoms(sele,quiet=1):
cmd.edit(sele)
cmd.delete(tmp_ed_save)
elif cmd.count_atoms("((%s) and elem c)"%selection,quiet=1):
cmd.select(tmp_ed_save,"(%s)"%selection)
cmd.iterate("(%s)"%selection,"stored.resv=resv")
stored.resi = str(stored.resv+1)
cmd.alter(tmp_editor,"resi=stored.resi")
cmd.fuse("(%s and name N)"%(tmp_editor),"(pk1)",2)
if cmd.get_setting_legacy("auto_remove_hydrogens"):
cmd.remove("(pkmol and hydro)")
cmd.set_dihedral("(name ca and neighbor pk2)",
"(pk2)","(pk1)","(name ca,ch3 and neighbor pk1)",180.0)
cmd.set_geometry("pk1",3,3) # make nitrogen planer
# if ss:
cmd.select(tpk1,"pk1")
cmd.select(tpk2,"pk2")
if amino_acid[0:3]!='pro':
cmd.set_dihedral( # PHI
tpk2, # C
tpk1, # N
"(name ca and neighbor "+tpk1+")", # CA
"(name c and neighbor (name ca and neighbor "+tpk1+"))", # C
phi)
cmd.set_dihedral( # PSI (n-1)
"(name n and neighbor (name ca and neighbor "+tpk2+"))", # C
"(name ca and neighbor "+tpk2+")", # CA
tpk2, # C
tpk1, # N
psi)
cmd.delete(tpk1)
cmd.delete(tpk2)
sele = ("(name C and (byres neighbor %s) and not (byres %s))"%
(tmp_ed_save,tmp_ed_save))
if cmd.count_atoms(sele,quiet=1):
cmd.edit(sele)
cmd.delete(tmp_ed_save)
elif cmd.count_atoms("((%s) and elem h)"%selection,quiet=1):
print " Error: please pick a nitrogen or carbonyl carbon to grow from."
cmd.delete(tmp_editor)
raise QuietException
cmd.delete(tmp_editor)
nsal = 0
for p in range(0, nrosalidas / len(paramod[npam])):
for valor in paramod[npam]:
matrizval[nsal].append(valor)
nsal = nsal + 1
matrizval.sort() #importante para el programa
#3. Genera Archivos de Salidas
infilenamediv = infilename.split(".")
for nsal in range(0, nrosalidas):
salida = [
] #lista que contiene las lineas para un archivo de salida especifico
npam = 0
extname = infilenamediv[0]
for line in atomIDs:
linediv = line.split(",")
val = float(matrizval[int(nsal)][int(npam)])
cmd.set_dihedral(linediv[0], linediv[1], linediv[2], linediv[3],
val)
extname = extname + "_D" + str(npam) + "_" + str(
int(val)) #nombre de salida con valores de parametros
npam = npam + 1
cmd.set('pdb_conect_all')
cmd.save(extname + ".pdb")
print "Se creo el archivo " + extname + ".pdb"
else:
print "No se encuentran parametros para modificar"
# Get out!
pymol.cmd.quit()
