def builder(residues, bonds, mol_name):
"""Using the list generated by read_input connects monosacharides in
a single oligosaccharide"""
cmd.set('suspend_updates', 'on')
cmd.feedback('disable', 'executive', 'actions')
every_object = cmd.get_object_list('all')
if mol_name in every_object:
cmd.delete(mol_name)
every_object.remove(mol_name)
if every_object:
sel = 'not (' + ' or '.join(every_object) + ') and'
else:
sel = ''
for i in range(0, len(residues)):
res_name = residues[i]
cmd.load(os.path.join(path, 'db_glycans', '%s.pdb' % res_name))
cmd.set_name(res_name,
i) #rename object (necessary to avoid repeating names)
cmd.alter(i, 'resi = %s' % i) #name residues for further referencing
cmd.sort(i)
for i in range(0, len(bonds)):
resi_i, resi_j, atom_i, atom_j = bonds[i][0], bonds[i][2], bonds[i][
4], bonds[i][5]
if atom_i > atom_j:
cmd.remove('%s (resi %s and name O%s+H%so)' %
(sel, resi_j, atom_j, atom_j))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_i, atom_i))
cmd.fuse('%s (resi %s and name O%s)' % (sel, resi_i, atom_i),
'%s (resi %s and name C%s)' % (sel, resi_j, atom_j),
mode=2)
else:
cmd.remove('%s (resi %s and name O%s+H%so)' %
(sel, resi_i, atom_i, atom_i))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_j, atom_j))
cmd.fuse('%s (resi %s and name C%s)' % (sel, resi_i, atom_i),
'%s (resi %s and name O%s)' % (sel, resi_j, atom_j),
mode=2)
cmd.delete('%s' % i)
cmd.copy(mol_name, '%s' % resi_j)
cmd.delete('%s' % resi_j)
for i in range(0, len(bonds)):
set_phi(mol_name, bonds[i], -60)
set_psi(mol_name, bonds[i], 120)
cmd.delete('pk1')
cmd.delete('pk2')
cmd.delete('pkbond')
cmd.delete('pkmol')
if babel:
fast_min(mol_name, 5000)
minimize(mol_name)
else:
fast_min(mol_name, 5000)
cmd.feedback('enable', 'executive', 'actions')
cmd.set('suspend_updates', 'off')
def apply(self):
'''
Permanently applies the mutation upon the selected residue
Overrides method from Wizard class
'''
cmd = self.cmd
if self._status == Status.NO_SELECTION:
return
#Remove all atoms that are not in the sugar/phosphate group
#Needed for non-canonical bases
cmd.select("_tmp_sele_invert", "(none)")
for a in self._sugar_phos_atoms:
cmd.select("_tmp_sele_invert",
"_tmp_sele_invert | (%s & name %s)" % (SRC_SELE, a))
cmd.select("_tmp_sele_invert",
"%s and not _tmp_sele_invert" % SRC_SELE)
cmd.remove("_tmp_sele_invert")
try:
new_name = cmd.get_object_list(SRC_SELE)[0]
except IndexError:
print(" Mutagenesis: object not found.")
return
frag_name_three = self._mode_labels[self.mode]
frag_name_one = self._base3_to_1[frag_name_three.lower()]
# FUSE
cmd.fuse(
"%s & name %s" % (FRAG_NAME, self._frag_N_atom_name),
"/%s/%s/%s/%s & name %s" %
(new_name, self._stored.identifiers[0],
self._stored.identifiers[1], self._stored.identifiers[2],
self._src_Cp_atom_name), 1)
#Check to see if DNA
dnaPrefix = ''
if cmd.count_atoms("%s & name O2'" % SRC_SELE) == 0:
dnaPrefix = 'D'
cmd.alter(
"/%s/%s/%s/%s" %
(new_name, self._stored.identifiers[0],
self._stored.identifiers[1], self._stored.identifiers[2]),
"(resn) = '%s%s'" % (dnaPrefix, frag_name_one.upper()),
space=self._space)
cmd.unpick()
self.clear()
def apply(self):
'''
Permanently applies the mutation upon the selected residue
Overrides method from Wizard class
'''
cmd = self.cmd
if self._status == Status.NO_SELECTION:
return
#Remove all atoms that are not in the sugar/phosphate group
#Needed for non-canonical bases
cmd.select("_tmp_sele_invert", "(none)")
for a in self._sugar_phos_atoms:
cmd.select("_tmp_sele_invert",
"_tmp_sele_invert | (%s & name %s)" % (SRC_SELE, a))
cmd.select("_tmp_sele_invert",
"%s and not _tmp_sele_invert" % SRC_SELE)
cmd.remove("_tmp_sele_invert")
try:
new_name = cmd.get_object_list(SRC_SELE)[0]
except IndexError:
print(" Mutagenesis: object not found.")
return
frag_name_three = self._mode_labels[self.mode]
frag_name_one = self._base3_to_1[frag_name_three.lower()]
# FUSE
cmd.fuse(
"%s & name %s" % (FRAG_NAME, self._frag_N_atom_name),
"/%s/%s/%s/%s & name %s" %
(new_name, self._stored.identifiers[0],
self._stored.identifiers[1], self._stored.identifiers[2],
self._src_Cp_atom_name), 1)
#Check to see if DNA
dnaPrefix = ''
if cmd.count_atoms("%s & name O2'" % SRC_SELE) == 0:
dnaPrefix = 'D'
cmd.alter(
"/%s/%s/%s/%s" %
(new_name, self._stored.identifiers[0],
self._stored.identifiers[1], self._stored.identifiers[2]),
"(resn) = '%s%s'" % (dnaPrefix, frag_name_one.upper()),
space=self._space)
cmd.unpick()
self.clear()
def builder(residues, bonds, mol_name):
"""Using the list generated by read_input connects monosacharides in
a single oligosaccharide"""
cmd.set('suspend_updates', 'on')
cmd.feedback('disable', 'executive', 'actions')
every_object = cmd.get_object_list('all')
if mol_name in every_object:
cmd.delete(mol_name)
every_object.remove(mol_name)
if every_object:
sel = 'not (' + ' or '.join(every_object) + ') and'
else:
sel = ''
for i in range(0, len(residues)):
res_name = residues[i]
cmd.load(os.path.join(path, 'db_glycans', '%s.pdb' % res_name))
cmd.set_name(res_name, i) #rename object (necessary to avoid repeating names)
cmd.alter(i, 'resi = %s' % i) #name residues for further referencing
cmd.sort(i)
for i in range(0, len(bonds)):
resi_i, resi_j, atom_i, atom_j = bonds[i][0], bonds[i][2], bonds[i][4], bonds[i][5]
if atom_i > atom_j:
cmd.remove('%s (resi %s and name O%s+H%so)' % (sel, resi_j, atom_j, atom_j))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_i, atom_i))
cmd.fuse('%s (resi %s and name O%s)' % (sel, resi_i, atom_i), '%s (resi %s and name C%s)' % (sel, resi_j, atom_j), mode=2)
else:
cmd.remove('%s (resi %s and name O%s+H%so)' % (sel, resi_i, atom_i, atom_i))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_j, atom_j))
cmd.fuse('%s (resi %s and name C%s)' % (sel, resi_i, atom_i), '%s (resi %s and name O%s)' % (sel, resi_j, atom_j), mode=2)
cmd.delete('%s' % i)
cmd.copy(mol_name, '%s' % resi_j)
cmd.delete('%s' % resi_j)
for i in range(0, len(bonds)):
set_phi(mol_name, bonds[i], -60)
set_psi(mol_name, bonds[i], 120)
cmd.delete('pk1')
cmd.delete('pk2')
cmd.delete('pkbond')
cmd.delete('pkmol')
if babel:
fast_min(mol_name, 5000)
minimize(mol_name)
else:
fast_min(mol_name, 5000)
cmd.feedback('enable', 'executive', 'actions')
cmd.set('suspend_updates', 'off')
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 add_missing_atoms(selection='all', cycles=200, quiet=1):
'''
DESCRIPTION
Mutate those residues to themselves which have missing atoms
SEE ALSO
stub2ala
'''
from collections import defaultdict
from chempy import fragments
cycles, quiet = int(cycles), int(quiet)
reference = {
'ALA': set(['CB']),
'ARG': set(['CB', 'CG', 'NE', 'CZ', 'NH1', 'NH2', 'CD']),
'ASN': set(['CB', 'CG', 'OD1', 'ND2']),
'ASP': set(['CB', 'CG', 'OD1', 'OD2']),
'CYS': set(['CB', 'SG']),
'GLN': set(['CB', 'CG', 'CD', 'NE2', 'OE1']),
'GLU': set(['CB', 'CG', 'OE2', 'CD', 'OE1']),
'GLY': set([]),
'HIS': set(['CE1', 'CB', 'CG', 'CD2', 'ND1', 'NE2']),
'ILE': set(['CB', 'CD1', 'CG1', 'CG2']),
'LEU': set(['CB', 'CG', 'CD1', 'CD2']),
'LYS': set(['CB', 'CG', 'NZ', 'CE', 'CD']),
'MET': set(['CB', 'CG', 'CE', 'SD']),
'PHE': set(['CE1', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
'PRO': set(['CB', 'CG', 'CD']),
'SER': set(['OG', 'CB']),
'THR': set(['CB', 'OG1', 'CG2']),
'TRP': set(['CZ2', 'CB', 'CG', 'CH2', 'CE3', 'CD1', 'CD2', 'CZ3', 'NE1', 'CE2']),
'TYR': set(['CE1', 'OH', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
'VAL': set(['CB', 'CG1', 'CG2']),
}
namedsele = cmd.get_unused_name('_')
cmd.select(namedsele, selection, 0)
namelists = defaultdict(list)
cmd.iterate('(%s) and polymer' % namedsele,
'namelists[model,segi,chain,resn,resi,resv].append(name)',
space=locals())
sele_dict = defaultdict(list)
tmp_name = cmd.get_unused_name('_')
for key, namelist in namelists.items():
resn = key[3]
if resn not in reference:
if not quiet:
print(' Unknown residue: + ' + resn)
continue
if not reference[resn].issubset(namelist):
try:
frag = fragments.get(resn.lower())
for a in frag.atom:
a.segi = key[1]
a.chain = key[2]
a.resi = key[4]
a.resi_number = key[5]
cmd.load_model(frag, tmp_name, 1, zoom=0)
skey = '/%s/%s/%s/%s`%s' % key[:5]
cmd.remove(skey + ' and not name N+C+O+OXT+CA')
cmd.align(tmp_name, skey + ' and name N+C+CA', cycles=0)
cmd.remove(tmp_name + ' and (name N+C+O+CA or hydro)')
cmd.fuse('name CB and ' + tmp_name, 'name CA and ' + skey, move=0)
if resn == 'PRO':
cmd.bond(skey + '/N', skey + '/CD')
cmd.unpick()
cmd.delete(tmp_name)
sele_dict[key[0]].append(skey)
if not quiet:
print(' Mutated ' + skey)
except:
print(' Mutating ' + skey + ' failed')
for model in sele_dict:
cmd.sort(model)
sculpt_relax(' '.join(sele_dict[model]), 0, 0, model, cycles)
cmd.delete(namedsele)
def add_missing_atoms(selection='all', cycles=200, quiet=1):
'''
DESCRIPTION
Mutate those residues to themselves which have missing atoms
SEE ALSO
stub2ala
'''
from collections import defaultdict
from chempy import fragments
cycles, quiet = int(cycles), int(quiet)
reference = {
'ALA': set(['CB']),
'ARG': set(['CB', 'CG', 'NE', 'CZ', 'NH1', 'NH2', 'CD']),
'ASN': set(['CB', 'CG', 'OD1', 'ND2']),
'ASP': set(['CB', 'CG', 'OD1', 'OD2']),
'CYS': set(['CB', 'SG']),
'GLN': set(['CB', 'CG', 'CD', 'NE2', 'OE1']),
'GLU': set(['CB', 'CG', 'OE2', 'CD', 'OE1']),
'GLY': set([]),
'HIS': set(['CE1', 'CB', 'CG', 'CD2', 'ND1', 'NE2']),
'ILE': set(['CB', 'CD1', 'CG1', 'CG2']),
'LEU': set(['CB', 'CG', 'CD1', 'CD2']),
'LYS': set(['CB', 'CG', 'NZ', 'CE', 'CD']),
'MET': set(['CB', 'CG', 'CE', 'SD']),
'PHE': set(['CE1', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
'PRO': set(['CB', 'CG', 'CD']),
'SER': set(['OG', 'CB']),
'THR': set(['CB', 'OG1', 'CG2']),
'TRP': set(['CZ2', 'CB', 'CG', 'CH2', 'CE3', 'CD1', 'CD2', 'CZ3', 'NE1', 'CE2']),
'TYR': set(['CE1', 'OH', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
'VAL': set(['CB', 'CG1', 'CG2']),
}
namedsele = cmd.get_unused_name('_')
cmd.select(namedsele, selection, 0)
namelists = defaultdict(list)
cmd.iterate('(%s) and polymer' % namedsele,
'namelists[model,segi,chain,resn,resi,resv].append(name)',
space=locals())
sele_dict = defaultdict(list)
tmp_name = cmd.get_unused_name('_')
for key, namelist in namelists.items():
resn = key[3]
if resn not in reference:
if not quiet:
print(' Unknown residue:', resn)
continue
if not reference[resn].issubset(namelist):
try:
frag = fragments.get(resn.lower())
for a in frag.atom:
a.segi = key[1]
a.chain = key[2]
a.resi = key[4]
a.resi_number = key[5]
cmd.load_model(frag, tmp_name, 1, zoom=0)
skey = '/%s/%s/%s/%s`%s' % key[:5]
cmd.remove(skey + ' and not name N+C+O+OXT+CA')
cmd.align(tmp_name, skey + ' and name N+C+CA', cycles=0)
cmd.remove(tmp_name + ' and (name N+C+O+CA or hydro)')
cmd.fuse('name CB and ' + tmp_name, 'name CA and ' + skey, move=0)
if resn == 'PRO':
cmd.bond(skey + '/N', skey + '/CD')
cmd.unpick()
cmd.delete(tmp_name)
sele_dict[key[0]].append(skey)
if not quiet:
print(' Mutated ', skey)
except:
print(' Mutating', skey, 'failed')
for model in sele_dict:
cmd.sort(model)
sculpt_relax(' '.join(sele_dict[model]), 0, 0, model, cycles)
cmd.delete(namedsele)
def test_fuse(self):
cmd.fragment('ala')
cmd.fragment('gly')
cmd.fuse("gly and elem N", "ala and elem O")
self.assertEqual(17, cmd.count_atoms('ala'))
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)
ligand_name = file.split('_')[0]
loaded_ligs.append(ligand_name)
cmd.load('ligs/' + file, ligand_name)
#select the ligand atomes of the original ligand to align with
target_atom1 = 'RA95_target and name C3'
target_atom2 = 'RA95_target and name C4'
target_atom3 = 'RA95_target and name C5'
#select the ligand atomes of the new ligand to align with and align the selected atoms of old and new ligand
for ligand in loaded_ligs:
mobile_atom1 = ligand + ' and name CL1'
mobile_atom2 = ligand + ' and name CL'
mobile_atom3 = ligand + ' and name CL2'
cmd.pair_fit(mobile_atom1, target_atom1, mobile_atom2, target_atom2,
mobile_atom3, target_atom3)
#remove old ligand
cmd.remove('RA95_target and resn PEN')
#build bond between Lys83 and the new ligand and generate pdb file
for ligand in loaded_ligs:
cmd.copy('RA95_' + ligand, 'RA95_target')
cmd.fuse(ligand + ' and name CL',
'RA95_' + ligand + ' and resn LYX and name NZ', '3')
cmd.bond('RA95_' + ligand + ' and resn LYX and name NZ',
'RA95_' + ligand + ' and name CL')
cmd.alter('RA95_' + ligand + ' and resn ' + ligand, 'segi="B"')
cmd.sort('RA95_' + ligand)
cmd.save('RA95_' + ligand + '.pdb', 'RA95_' + ligand, '0')
def test_fuse(self):
cmd.fragment('ala')
cmd.fragment('gly')
cmd.fuse("gly and elem N", "ala and elem O")
self.assertEqual(17, cmd.count_atoms('ala'))