def testPairFit(self):
cmd.fragment('trp')
cmd.fragment('his')
# 1 atom
sele = ('trp and guide', 'his and guide')
pos = list(map(cmd.get_atom_coords, sele))
vec = cpv.sub(*pos)
mat_ref = [
1.0, 0.0, 0.0, -vec[0],
0.0, 1.0, 0.0, -vec[1],
0.0, 0.0, 1.0, -vec[2],
0.0, 0.0, 0.0, 1.0]
rms = cmd.pair_fit(*sele)
self.assertEqual(rms, 0.0)
mat = cmd.get_object_matrix('trp')
self.assertArrayEqual(mat, mat_ref, 1e-4)
# 2 atoms
sele += ('trp & name CB', 'his & name CB')
rms = cmd.pair_fit(*sele)
self.assertAlmostEqual(rms, 0.0082, delta=1e-4)
# 4 atoms
sele += ('trp & name CG', 'his & name CG',
'trp & name CD1', 'his & name CD2')
rms = cmd.pair_fit(*sele)
self.assertAlmostEqual(rms, 0.0713, delta=1e-4)
def pairfitCys(Cysmolecule, molecule, chain, residue):
RN = "/" + Cysmolecule + "//" + "/" + "/N"
PN = "/" + molecule + "//" + chain + "/" + residue + "/N"
RCA = "/" + Cysmolecule + "//" + "/" + "/CA"
PCA = "/" + molecule + "//" + chain + "/" + residue + "/CA"
RC = "/" + Cysmolecule + "//" + "/" + "/C"
PC = "/" + molecule + "//" + chain + "/" + residue + "/C"
RCB = "/" + Cysmolecule + "//" + "/" + "/CB"
PCB = "/" + molecule + "//" + chain + "/" + residue + "/CB"
cmd.select("CBatom", PCB)
CBatomNr = cmd.count_atoms("CBatom")
# If PRO or GLY, then only fit N, CA, C atoms
if CBatomNr == 0:
cmd.pair_fit(RN, PN, RCA, PCA, RC, PC)
else:
# cmd.pair_fit(RN,PN,RCA,PCA,RC,PC,RCB,PCB)
cmd.pair_fit(RN, PN, RCA, PCA, RC, PC)
cmd.delete("CBatom")
def pairfitCys(Cysmolecule, molecule, chain, residue):
RN = "/" + Cysmolecule + "//" + "/" + "/N"
PN = "/" + molecule + "//" + chain + "/" + residue + "/N"
RCA = "/" + Cysmolecule + "//" + "/" + "/CA"
PCA = "/" + molecule + "//" + chain + "/" + residue + "/CA"
RC = "/" + Cysmolecule + "//" + "/" + "/C"
PC = "/" + molecule + "//" + chain + "/" + residue + "/C"
RCB = "/" + Cysmolecule + "//" + "/" + "/CB"
PCB = "/" + molecule + "//" + chain + "/" + residue + "/CB"
cmd.select("CBatom", PCB)
CBatomNr = cmd.count_atoms("CBatom")
### If PRO or GLY, then only fit N, CA, C atoms
if CBatomNr == 0:
cmd.pair_fit(RN, PN, RCA, PCA, RC, PC)
else:
#cmd.pair_fit(RN,PN,RCA,PCA,RC,PC,RCB,PCB)
cmd.pair_fit(RN, PN, RCA, PCA, RC, PC)
cmd.delete("CBatom")
def show_motif(value):
cmd.delete("*")
domain1 = align_pairs[value][0]
domain2 = align_pairs[value][1]
residues1 = align_pairs[value][2]
residues2 = align_pairs[value][3]
cmd.load("PDBFiles/%s.pdb" % domain1)
cmd.load("PDBFiles/%s.pdb" % domain2)
cmd.bg_color("white")
cmd.hide("all")
cmd.show("cartoon", "all")
cmd.select("motif1", "none")
cmd.select("motif1",
"motif1 or (%s and n. CA and resi %s)" % (domain1, residues1))
cmd.select("motif2", "none")
cmd.select("motif2",
"motif2 or (%s and n. CA and resi %s)" % (domain2, residues2))
cmd.select("none")
cmd.color("gray80", domain1)
cmd.color("gray60", domain2)
cmd.color("cyan", "motif1")
cmd.color("magenta", "motif2")
#cmd.seqview("on")
try:
cmd.pair_fit("motif1", "motif2", object="alignment")
cmd.center(domain1)
#cmd.png("PNGsRenumb/%s_%s_PF.png"%(domain1, domain2), dpi = 300)
except CmdException:
pass
try:
cmd.cealign("motif1", "motif2", object="alignment")
cmd.center(domain1)
#cmd.png("PNGsRenumb/%s_%s_CE.png"%(domain1, domain2), dpi = 300)
except CmdException:
pass
def fit(self):
# build up the pair-wise list of selections
cmd.delete(dist_prefix + "*")
lst = self.get_sele_list()
c = 0
args = []
while 1:
if not len(lst): break
a = lst.pop()
if not len(lst): break
b = lst.pop()
args.append(a)
args.append(b)
# do the fit
if len(args):
cmd.push_undo(args[0])
dist = cmd.pair_fit(*args)
self.message = "RMS over %d pairs = %5.3f" % (self.n_pair, dist)
cmd.refresh_wizard()
self.update_dashes()
def fit(self):
# build up the pair-wise list of selections
cmd.delete(dist_prefix+"*")
lst = self.get_sele_list()
c = 0
args = []
while 1:
if not len(lst): break
a = lst.pop()
if not len(lst): break
b = lst.pop()
args.append(a)
args.append(b)
# do the fit
if len(args):
cmd.push_undo(args[0])
dist = cmd.pair_fit(*args)
self.message = "RMS over %d pairs = %5.3f"%(self.n_pair,dist)
cmd.refresh_wizard()
self.update_dashes()
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")
def showCorr(self, ar):
try:
cmd.reinitialize()
self.multiListBox1.focus()
cmd.load(self.ref_Entry.get(), object="obj1")
self.index = ar[0]
self.selection_row = self.multiListBox1.get(self.index)
self.selection_data = self.selection_row[0]
self.rank = self.selection_data[0]
self.zincId = self.selection_data[1]
# Empty box2
self.multiListBox2.delete(0, END)
file_type = ".mol2"
result_Filename = self.rank + "_" + self.zincId + file_type
log.info("Filename:'%s'" % result_Filename)
i = 0
j = 0
k = 0
line = ()
# timestamp_Folder=os.path.join(result_Folder,timestamp_Done)
file_Mol = os.path.join(self.timestamp_Folder, result_Filename)
print file_Mol
self.ref = ()
self.tar = ()
try:
fh = open(file_Mol, "r") # handle possible exceptions
cmd.load(file_Mol, object="obj2")
except IOError:
tkMessageBox.showinfo("No data found", "The result molecules were not written to the output")
for block in iter(lambda: fh.readline(), ""):
if i == 1:
if j == 1:
if not block == "\n":
k = k + 1
line = block.split()
self.ref = self.ref + (line[1],)
self.tar = self.tar + (line[3],)
self.multiListBox2.insert(END, *line)
else:
i = 0
j = 0
if "LiSiCA RESULTS" in block:
i = 1
if i == 1:
if "--------------" in block:
j = 1
log.info("Displayed the atom correspondence of the selected atom")
if self.dimension.get() == 2:
cmd.set("grid_mode", value=1)
cmd.set("grid_slot", value=1, selection="obj1")
cmd.set("grid_slot", value=2, selection="obj2")
cmd.align("obj1", "obj2")
elif self.dimension.get() == 3:
self.lig1_atoms = "obj1////"
self.lig2_atoms = "obj2////"
for item in self.ref:
self.lig1_atoms = self.lig1_atoms + item + "+"
for item in self.tar:
self.lig2_atoms = self.lig2_atoms + item + "+"
self.lig1_atoms = self.lig1_atoms[:-1]
self.lig2_atoms = self.lig2_atoms[:-1]
cmd.pair_fit(self.lig1_atoms, self.lig2_atoms)
else:
log.error("Dimension value is wrong")
cmd.orient()
except:
pass
def _do_mutation(self):
'''
After selection, propose what the fragment will look like where
applied.
Exception: _do_mutation should be wrapped in a try-exception block
when called
'''
cmd = self.cmd
cmd.delete(FRAG_NAME)
cmd.refresh_wizard()
if any(
cmd.count_atoms("(%s) & name %s" % (SRC_SELE, name)) != 1
for name in ("C1'", "C2'", "C3'", "C4'", "O4'")):
self.clear()
raise pymol.wizarding.WizardError(
'Improper selection of nucleic acid.')
frag_type_lower = self._mode_labels[self.mode].lower()
cmd.fragment(frag_type_lower, FRAG_NAME, origin=0)
self._update_reps()
cmd.color("white", "%s & elem C" % FRAG_NAME)
cmd.iterate(
"first (%s)" % SRC_SELE,
'stored.name = model+"/"+segi+"/"+chain+"/"+resn+"`"+resi',
space=self._space)
self.res_text = self._space['stored'].name
cmd.alter(
"?%s & name C1'" % SRC_SELE,
"stored.identifiers = (segi, chain, resi, ss, color)",
space=self._space)
self._status = Status.MUTAGENIZING
self.get_prompt()
cmd.iterate(
"(%s & name C1')" % SRC_SELE,
"stored.resn = resn",
space=self._space)
src_type_lower = self._space['stored'].resn.lower()
self._src_O_atom_name, self._src_Cp_atom_name, self._src_N_atom_name, \
self._src_C_atom_name = self._get_chi_dihedral_atoms(src_type_lower)
self._frag_O_atom_name, self._frag_Cp_atom_name, self._frag_N_atom_name, \
self._frag_C_atom_name = self._get_chi_dihedral_atoms(frag_type_lower)
cmd.pair_fit("(%s & name %s)" % (FRAG_NAME, self._frag_O_atom_name),
"(%s & name %s)" % (SRC_SELE, self._src_O_atom_name),
"(%s & name %s)" % (FRAG_NAME, self._frag_Cp_atom_name),
"(%s & name %s)" % (SRC_SELE, self._src_Cp_atom_name),
"(%s & name %s)" % (FRAG_NAME, self._frag_N_atom_name),
"(%s & name %s)" % (SRC_SELE, self._src_N_atom_name))
self._transfer_dihedral()
for a in self._sugar_phos_atoms:
cmd.remove("(%s & name %s)" % (FRAG_NAME, a))
if self._auto_center == "ON":
cmd.center(FRAG_NAME, animate=1)
def _do_mutation(self):
'''
After selection, propose what the fragment will look like where
applied.
Exception: _do_mutation should be wrapped in a try-exception block
when called
'''
cmd = self.cmd
cmd.delete(FRAG_NAME)
cmd.refresh_wizard()
if any(
cmd.count_atoms("(%s) & name %s" % (SRC_SELE, name)) != 1
for name in ("C1'", "C2'", "C3'", "C4'", "O4'")):
self.clear()
raise pymol.wizarding.WizardError(
'Improper selection of nucleic acid.')
frag_type_lower = self._mode_labels[self.mode].lower()
cmd.fragment(frag_type_lower, FRAG_NAME, origin=0)
self._update_reps()
cmd.color("white", "%s & elem C" % FRAG_NAME)
cmd.iterate(
"first (%s)" % SRC_SELE,
'stored.name = model+"/"+segi+"/"+chain+"/"+resn+"`"+resi',
space=self._space)
self.res_text = self._space['stored'].name
cmd.alter(
"?%s & name C1'" % SRC_SELE,
"stored.identifiers = (segi, chain, resi, ss, color)",
space=self._space)
self._status = Status.MUTAGENIZING
self.get_prompt()
cmd.iterate(
"(%s & name C1')" % SRC_SELE,
"stored.resn = resn",
space=self._space)
src_type_lower = self._space['stored'].resn.lower()
self._src_O_atom_name, self._src_Cp_atom_name, self._src_N_atom_name, \
self._src_C_atom_name = self._get_chi_dihedral_atoms(src_type_lower)
self._frag_O_atom_name, self._frag_Cp_atom_name, self._frag_N_atom_name, \
self._frag_C_atom_name = self._get_chi_dihedral_atoms(frag_type_lower)
cmd.pair_fit("(%s & name %s)" % (FRAG_NAME, self._frag_O_atom_name),
"(%s & name %s)" % (SRC_SELE, self._src_O_atom_name),
"(%s & name %s)" % (FRAG_NAME, self._frag_Cp_atom_name),
"(%s & name %s)" % (SRC_SELE, self._src_Cp_atom_name),
"(%s & name %s)" % (FRAG_NAME, self._frag_N_atom_name),
"(%s & name %s)" % (SRC_SELE, self._src_N_atom_name))
self._transfer_dihedral()
for a in self._sugar_phos_atoms:
cmd.remove("(%s & name %s)" % (FRAG_NAME, a))
if self._auto_center == "ON":
cmd.center(FRAG_NAME, animate=1)
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")
pymol.finish_launching()
if '-h' in args:
print("help")
else:
if ('-r' in args) and ('-i' in args) and ('-o' in args) and (
'-n' in args) and (len(args) == 9):
prot_a = args[args.index('-r') + 1]
prot_b = args[args.index('-i') + 1]
outfile = args[args.index('-o') + 1]
pos = int(args[args.index('-n') + 1])
cmd.load(protein)
cmd.load(loop)
a_name = os.path.basename(prot_a).split('.')[0]
b_name = os.path.basename(prot_b).split('.')[0]
cmd.select("a_s1", "/%s///%d/N" % (a_name, pos))
cmd.select("a_s2", "/%s///%d/CA" % (a_name, pos))
cmd.select("a_s3", "/%s///%d/C" % (a_name, pos))
cmd.select("a_s4", "/%s///%d/CB" % (a_name, pos))
cmd.select("a_s1", "/%s///%d/N" % (b_name, pos))
cmd.select("a_s2", "/%s///%d/CA" % (b_name, pos))
cmd.select("a_s3", "/%s///%d/C" % (b_name, pos))
cmd.select("a_s4", "/%s///%d/CB" % (b_name, pos))
out_loop = cmd.select("out_prot", "/%s////" % (b_name))
cmd.pair_fit("b_s1", "a_s1", "b_s2", "a_s2", "b_s3", "a_s3", "b_s4",
"a_s4")
cmd.save(outfile, "out_prot")
else:
print("help")
cmd.select("p_s3", "/%s//%s/%d/C" % (p_name, chain, ini - 2))
cmd.select("p_s4", "/%s//%s/%d/N" % (p_name, chain, ini - 1))
cmd.select("p_s5", "/%s//%s/%d/CA" % (p_name, chain, ini - 1))
cmd.select("p_s6", "/%s//%s/%d/C" % (p_name, chain, ini - 1))
cmd.select("p_e1", "/%s//%s/%d/N" % (p_name, chain, end + 1))
cmd.select("p_e2", "/%s//%s/%d/CA" % (p_name, chain, end + 1))
cmd.select("p_e3", "/%s//%s/%d/C" % (p_name, chain, end + 1))
cmd.select("p_e4", "/%s//%s/%d/N" % (p_name, chain, end + 2))
cmd.select("p_e5", "/%s//%s/%d/CA" % (p_name, chain, end + 2))
cmd.select("p_e6", "/%s//%s/%d/C" % (p_name, chain, end + 2))
cmd.select("l_s1", "/%s///%d/N" % (l_name, ini - 2))
cmd.select("l_s2", "/%s///%d/CA" % (l_name, ini - 2))
cmd.select("l_s3", "/%s///%d/C" % (l_name, ini - 2))
cmd.select("l_s4", "/%s///%d/N" % (l_name, ini - 1))
cmd.select("l_s5", "/%s///%d/CA" % (l_name, ini - 1))
cmd.select("l_s6", "/%s///%d/C" % (l_name, ini - 1))
cmd.select("l_e1", "/%s///%d/N" % (l_name, end + 1))
cmd.select("l_e2", "/%s///%d/CA" % (l_name, end + 1))
cmd.select("l_e3", "/%s///%d/C" % (l_name, end + 1))
cmd.select("l_e4", "/%s///%d/N" % (l_name, end + 2))
cmd.select("l_e5", "/%s///%d/CA" % (l_name, end + 2))
cmd.select("l_e6", "/%s///%d/C" % (l_name, end + 2))
out_loop = cmd.select("out_loop", "/%s////" % (l_name))
cmd.pair_fit("l_s1", "p_s1", "l_s2", "p_s2", "l_s3", "p_s3", "l_s4",
"p_s4", "l_s5", "p_s5", "l_s6", "p_s6", "l_e1", "p_e1",
"l_e2", "p_e2", "l_e3", "p_e3", "l_e4", "p_e4", "l_e5",
"p_e5", "l_e6", "p_e6")
cmd.save(outfile, "out_loop")
else:
print("help")
def scanFactor( nucleosome, probe, cutoff=2, clashKeep=1, writeModels=False ):
"""
USAGE
scanFactor nucleosome object,
probe object,
probe DNA chain ID,
distance in Ångstrom below which atoms are considered clashing,
keep models with fewer than the specified number of residue clashes
"""
results=[]
if writeModels:
dirName = None
dirName = ("%s_%s_models" % (nucleosome, probe) )
if not os.path.exists(dirName):
os.mkdir("%s" % (dirName) )
if not cmd.select("polymer.nucleic and %s" % (nucleosome) ) :
print("\nThe nucleosome object \'%s\' must contain contain DNA – are you sure this is a nucleosome model?\n" % (nucleosome) )
return
if not cmd.select("polymer.nucleic and %s" % (probe) ) :
print("\nThe probe object \'%s\' must contain at least two DNA bases for superposition, the first two of which should correspond\nto the position of the central two bases of the factor's recognition sequence when bound to DNA\n" % (probe) )
return
# Determine probe DNA chain ID
cmd.select("probeDNA","polymer.nucleic and %s" % (probe) )
probeDNAChain = cmd.get_model("probeDNA").atom[0].chain
# Renumber probe DNA chain to start from 1
firstBase = []
firstBase = int(cmd.get_model("%s and chain %s" % (probe, probeDNAChain)).atom[0].resi)
secondBase = firstBase+1
offset = firstBase-1
print ("Renumbering %s chain %s to start at residue 1\n" % (probe, probeDNAChain) )
cmd.alter("%s and chain %s" % (probe, probeDNAChain), "resi=str(int(resi)-%d)" % (offset) )
# Remove hydrogens
print ("\nRemoving hydrogens\n")
cmd.remove("hydrogens")
# Determine nucleosomal DNA chain IDs
chains = []
chains = cmd.get_chains("polymer.nucleic and %s" % (nucleosome) )
# Loop over nuclesomal DNA
for chain in chains:
firstBase = int(cmd.get_model("%s and chain %s" % (nucleosome, chain)).atom[0].resi)
chainLength = (len(cmd.get_model("polymer and %s and chain %s" % (nucleosome, chain)).get_residues()))
for i in range(firstBase, (firstBase + chainLength) ):
j=(i+1)
# Handle lack of 5' phosphates (such as on the first base)
if not cmd.select("%s and chain %s and resi %d and name P" % (nucleosome, chain, i) ) :
cmd.select("moving", "%s and chain %s and resi 2 and backbone and not (n. P or n. OP1 or n. OP2)" % (probe, probeDNAChain) )
cmd.select("target", "%s and chain %s and resi %d and backbone and not (n. P or n. OP1 or n. OP2)" % (nucleosome, chain, j) )
# Handle overhanging superposition for final base
elif i == (firstBase + chainLength - 1):
cmd.select("moving", "%s and chain %s and resi 1 and backbone" % (probe, probeDNAChain) )
cmd.select("target", "%s and chain %s and resi %d and backbone" % (nucleosome, chain, i) )
else:
cmd.select("moving", "%s and chain %s and resi 1-2 and backbone" % (probe, probeDNAChain) )
cmd.select("target", "%s and chain %s and resi %d-%d and backbone" % (nucleosome, chain, i, j) )
#numAtomMoving=(cmd.count_atoms("moving"))
#print ("Number of moving atoms: %d" % (numAtomMoving) )
#numAtomTarget=(cmd.count_atoms("target"))
#print ("Number of target atoms: %d" % (numAtomTarget) )
alignResult=[]
alignResult = cmd.pair_fit("moving", "target")
if alignResult:
# alignResult = cmd.super("moving", "target")
# print ("RMSD after refinement %.4f with %d atoms in alignhment after %d refinement cycles" % (alignResult[0],alignResult[1],alignResult[2]) )
# print(" ".join('%s' % x for x in alignResult))
clashes=("clashes")
# Calculate clashes excluding DNA portion of probe
cmd.select("%s" % (clashes), "(%s and not chain %s) within %f of %s" % (probe, probeDNAChain, float(cutoff), nucleosome) )
scoreAtoms = (cmd.count_atoms("%s" % (clashes) ))
cmd.select("%s" % (clashes), "clashes byres clashes")
scoreRes = (cmd.count_atoms("%s" % (clashes) + " and name CA"))
# Write out models (nuclesome + current superimposed probe) for Rosetta scoring
if writeModels :
modelName = None
modelName = ("%s_probe_%s_%d-%d" % (nucleosome, chain, i, j) )
editing.copy_to("%s" % (modelName), "(%s or %s)" % (nucleosome, probe) )
cmd.save("%s/%s.pdb" % (dirName,modelName), "(%s)" % (modelName) )
cmd.delete("%s" % (modelName) )
# Retain models with no. residue clashes less than or equal to 'clashKeep'
if scoreRes < (int(clashKeep)+1):
editing.copy_to("probe_%s_%d-%d" % (chain, i, j), "%s" % (probe) )
cmd.group("ClashKeep %s)" % (clashKeep),"nonclashing + probe_%s_%d-%d" % (chain, i, j) )
cmd.order("probe_*", "yes")
print ("DNA chain %s bases %d - %d : %s clashes with %d non-hydrogen atoms in %d residues" % (chain, i, j, probe, scoreAtoms, scoreRes) )
clashes=("%s,%d,%d,%d,%d" % (chain, i, j, scoreAtoms, scoreRes) )
results.append((clashes))
# Catch superpostion failures
else:
print ("DNA chain %s bases %d - %d : %s superpositon failed and clashes were not calculated – check for missing atoms, alternate conformations, or unsual bases at these positions" % (chain, i, j, probe) )
clashes=("%s,%d,%d,-,-" % (chain, i, j) )
results.append((clashes))
with open('%s_scanFactor.csv' % (nucleosome), 'w') as output:
output.write("DNAchain,start,end,atomClashes,residueClashes\n")
for i in results:
output.write("%s\n" % i)
print ("\nOutput saved to %s_scanFactor.csv\n" % (nucleosome) )
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.split_states(target, prefix="Molecule_Name_")
#cmd.split_states(target)
cmd.delete(target)
counter = 0
#target_atom1=''
#target_atom2=''
#target_atom3=''
#target_atom4=''
for object in cmd.get_object_list('(all)'):
cmd.alter(object, 'resn="' + three_letter_code + '"')
counter += 1
if counter == 1:
target_object = object
target_atom1 = target_object + ' and name ' + atoms_to_align[0]
target_atom2 = target_object + ' and name ' + atoms_to_align[1]
target_atom3 = target_object + ' and name ' + atoms_to_align[2]
if counter > 1:
mobile_atom1 = object + ' and name ' + atoms_to_align[0]
mobile_atom2 = object + ' and name ' + atoms_to_align[1]
mobile_atom3 = object + ' and name ' + atoms_to_align[2]
print(target_atom1)
print(mobile_atom1)
cmd.pair_fit(mobile_atom1, target_atom1, mobile_atom2, target_atom2,
mobile_atom3, target_atom3)
for element in delete_atoms:
print("got here")
cmd.remove('{object} and name {element}'.format(object=object,
element=element))
cmd.join_states(three_letter_code + '.rotlib', '*')
7
def scanDamage(nucleosome, uvddb, cutoff=2, clashKeep=1, writeModels=False):
"""
USAGE
scanDamage nucleosome object (DNA in chains I and J),
UVDDB probe object (containing appropriately positioned 2 bp ssDNA in chain Z as residues 1-2 for superpositioning),
distance in Ångstrom closer than which atoms are considered clashing,
keep models with fewer than the specified number of clashes,
write all models (for scoring externally for instance)
"""
chains = ['I', 'J']
results = []
if writeModels:
dirName = None
dirName = ("%s_%s_models" % (nucleosome, uvddb))
if not os.path.exists(dirName):
os.mkdir("%s" % (dirName))
for chain in chains:
chainLength = (len(
cmd.get_model("polymer and %s and chain %s" %
(nucleosome, chain)).get_residues()))
for i in range(0, chainLength + 1):
# for i in range(130, 146):
j = (i + 1)
if chain == 'I':
comnplementaryChain = 'J'
elif chain == 'J':
matchedChain = 'I'
# Handle lack of 5' phosphate on first nucleotide
if i == 0:
cmd.select(
"moving",
"%s and chain Z and resi 2 and backbone and not (n. P or n. OP1 or n. OP2)"
% (uvddb))
cmd.select(
"target",
"%s and chain %s and resi %d and backbone and not (n. P or n. OP1 or n. OP2)"
% (nucleosome, chain, j))
elif i == 1:
cmd.select(
"moving",
"%s and chain Z and resi 1-2 and backbone and not (n. P or n. OP1 or n. OP2)"
% (uvddb))
cmd.select(
"target",
"%s and chain %s and resi %d-%d and backbone and not (n. P or n. OP1 or n. OP2)"
% (nucleosome, chain, i, j))
# Handle final base
elif i == chainLength:
cmd.select("moving",
"%s and chain Z and resi 1 and backbone" % (uvddb))
cmd.select(
"target", "%s and chain %s and resi %d and backbone" %
(nucleosome, chain, i))
else:
cmd.select(
"moving",
"%s and chain Z and resi 1-2 and backbone" % (uvddb))
cmd.select(
"target", "%s and chain %s and resi %d-%d and backbone" %
(nucleosome, chain, i, j))
#numAtomMoving=(cmd.count_atoms("moving"))
#print ("\nNumber of moving atoms: %d" % (numAtomMoving) )
#numAtomTarget=(cmd.count_atoms("target"))
#print ("Number of target atoms: %d" % (numAtomTarget) )
alignResult = []
alignResult = cmd.pair_fit("moving", "target")
# alignResult = cmd.super("moving", "target")
# print ("RMSD after refinement %.4f with %d atoms in alignhment after %d refinement cycles" % (alignResult[0],alignResult[1],alignResult[2]) )
# print(" ".join('%s' % x for x in alignResult))
clashes = ("clashes")
# Calculate clashes excluding DNA portion (chain Z resi 1-2) of UV-DDB probe
cmd.select(
"%s" % (clashes), "(%s and not chain Z) within %d of %s" %
(uvddb, float(cutoff), nucleosome))
scoreAtoms = (cmd.count_atoms("%s" % (clashes)))
cmd.select("%s" % (clashes), "clashes byres clashes")
scoreRes = (cmd.count_atoms("%s" % (clashes) + " and name CA"))
# Write out models (nucleosome + current superimposed UV-DDB probe) for Rosetta scoring
if writeModels:
modelName = None
modelName = ("%s_uvddb_%s_%d-%d" % (nucleosome, chain, i, j))
editing.copy_to("%s" % (modelName),
"(%s or %s)" % (nucleosome, uvddb))
cmd.save("%s/%s.pdb" % (dirName, modelName),
"(%s)" % (modelName))
cmd.delete("%s" % (modelName))
# Retain models with no. residue clashes less than or equal to 'clashKeep'
if scoreRes < (int(clashKeep) + 1):
editing.copy_to("uvddb_%s_%d-%d" % (chain, i, j),
"%s" % (uvddb))
cmd.group("ClashKeep %s)" % (clashKeep),
"nonclashing + uvddb_%s_%d-%d" % (chain, i, j))
cmd.order("uvddb_*", "yes")
print(
"DNA chain %s bases %d - %d : UV-DDB clashes atoms %d residues %d "
% (chain, i, j, scoreAtoms, scoreRes))
clashes = ("%s,%d,%d,%d,%d" % (chain, i, j, scoreAtoms, scoreRes))
results.append((clashes))
with open('%s_scanDamage.csv' % (nucleosome), 'w') as output:
output.write("DNAchain,start,end,atomClashes,residueClashes\n")
for i in results:
output.write("%s\n" % i)
print("\nOutput saved to %s_scanDamage.csv\n" % (nucleosome))