def localSculpt(obj, site):
res = str(site)
cmd.protect('(not %s/) or name CA+C+N+O+OXT' % (res))
print "Activating Sculpting."
cmd.sculpt_activate(obj[:-4])
cmd.sculpt_iterate(obj[:-4], cycles=5000)
cmd.sculpt_deactivate(obj[:-4])
cmd.deprotect()
def test_protect(self):
cmd.pseudoatom('m1', pos=[0., 0., 0.])
cmd.pseudoatom('m1', pos=[1., 0., 0.])
cmd.protect('m1`1')
cmd.translate([0., 1., 0.])
self.assertEqual([0., 0., 0.], cmd.get_atom_coords('m1`1'))
self.assertEqual([1., 1., 0.], cmd.get_atom_coords('m1`2'))
cmd.deprotect()
cmd.translate([0., 0., 1.])
self.assertEqual([0., 0., 1.], cmd.get_atom_coords('m1`1'))
self.assertEqual([1., 1., 1.], cmd.get_atom_coords('m1`2'))
def test_protect(self):
cmd.pseudoatom('m1', pos=[0.,0.,0.])
cmd.pseudoatom('m1', pos=[1.,0.,0.])
cmd.protect('m1`1')
cmd.translate([0.,1.,0.])
self.assertEqual([0.,0.,0.], cmd.get_atom_coords('m1`1'))
self.assertEqual([1.,1.,0.], cmd.get_atom_coords('m1`2'))
cmd.deprotect()
cmd.translate([0.,0.,1.])
self.assertEqual([0.,0.,1.], cmd.get_atom_coords('m1`1'))
self.assertEqual([1.,1.,1.], cmd.get_atom_coords('m1`2'))
def protectme(event):
try:
if len(maskent.get()) < 1:
showinfo("Error", 'Please enter the name of an object.')
interior.mainloop()
else:
cmd.protect(maskent.get())
except:
showinfo("Error", 'That object is not present')
interior.mainloop()
def sculpt_relax(selection,
backbone=1,
neighbors=0,
model=None,
cycles=100,
state=0,
quiet=1):
'''
DESCRIPTION
Relax the given selection.
SO FAR ONLY SUPPORTS SELECTIONS WITHIN THE SAME MODEL!
Do 100 iterations, 75 of them with all terms but low VDW weights,
and 25 with only local geometry terms. With default VDW weights and
atom clashes, the structure gets distorted very easily!
USAGE
sculpt_relax selection [, backbone [, neighbors [, model [, cycles ]]]]
'''
from pymol import selector
backbone, neighbors = int(backbone), int(neighbors)
cycles, state, quiet = int(cycles), int(state), int(quiet)
sele = selector.process(selection)
org = cmd.get_object_list(sele)[0]
if model is None:
model = org
elif model != org:
sele = sele.replace('(%s)' % org, '(%s)' % model)
cmd.protect()
cmd.deprotect(sele)
if not backbone:
cmd.protect('name CA+C+N+O+OXT')
cmd.sculpt_activate(model, state)
cmd.set('sculpt_vdw_weight', 0.25, model) # Low VDW forces
cmd.set('sculpt_field_mask', 0x1FF, model) # Default
if neighbors:
cmd.sculpt_iterate(model, state, int(cycles * 0.25))
cmd.deprotect('byres (%s within 6.0 of (%s))' % (model, sele))
if not backbone:
cmd.protect('name CA+C+N+O+OXT')
cmd.sculpt_iterate(model, state, cycles=int(cycles * 0.50))
else:
cmd.sculpt_iterate(model, state, int(cycles * 0.75))
cmd.set('sculpt_field_mask', 0x01F, model) # Local Geometry Only
cmd.sculpt_iterate(model, state, int(cycles * 0.25))
cmd.unset('sculpt_vdw_weight', model)
cmd.unset('sculpt_field_mask', model)
cmd.sculpt_deactivate(model)
cmd.deprotect()
def local_sculpt(obj, variant_three, site):
# Original version of local side chain optimization
#res = str(site)
#cmd.protect('(not %s/) or name CA+C+N+O+OXT' % (res))
#print "Activating Sculpting."
#cmd.sculpt_activate(obj[:-4])
#cmd.sculpt_iterate(obj[:-4], cycles=50)
#cmd.sculpt_deactivate(obj[:-4])
#cmd.deprotect()
# New version of local side chain optimization.
#cmd.select("%s%s_exp" % (variant_one, site), "(byres (\"%s/\" expand 1.8))" % site)
#cmd.select("%s%s_exp_sc" % (variant_one, site), "%s%s and (not name C+CA+N+O+HA+HT)" % (variant_one, site))
#cmd.protect("not %s%s_exp_sc" % (variant_one, site))
variant_one = get_one(variant_three)
cmd.select("%s%s" % (variant_one, site), "%s/" % site)
cmd.select("bb", "name C+CA+N+O+H+HA+HT")
cmd.select("%s%s_sc" % (variant_one, site), "%s%s and not bb" % (variant_one, site))
cmd.protect("not %s%s_sc" % (variant_one, site))
cmd.sculpt_activate(obj[:-4])
cmd.sculpt_iterate(obj[:-4], cycles=3000)
cmd.sculpt_deactivate(obj[:-4])
cmd.deprotect()
def sculpt_relax(selection, backbone=1, neighbors=0, model=None, cycles=100,
state=0, quiet=1):
'''
DESCRIPTION
Relax the given selection.
SO FAR ONLY SUPPORTS SELECTIONS WITHIN THE SAME MODEL!
Do 100 iterations, 75 of them with all terms but low VDW weights,
and 25 with only local geometry terms. With default VDW weights and
atom clashes, the structure gets distorted very easily!
USAGE
sculpt_relax selection [, backbone [, neighbors [, model [, cycles ]]]]
'''
from pymol import selector
backbone, neighbors = int(backbone), int(neighbors)
cycles, state, quiet = int(cycles), int(state), int(quiet)
sele = selector.process(selection)
org = cmd.get_object_list(sele)[0]
if model is None:
model = org
elif model != org:
sele = sele.replace('(%s)' % org, '(%s)' % model)
cmd.protect()
cmd.deprotect(sele)
if not backbone:
cmd.protect('name CA+C+N+O+OXT')
cmd.sculpt_activate(model, state)
cmd.set('sculpt_vdw_weight', 0.25, model) # Low VDW forces
cmd.set('sculpt_field_mask', 0x1FF, model) # Default
if neighbors:
cmd.sculpt_iterate(model, state, int(cycles * 0.25))
cmd.deprotect('byres (%s within 6.0 of (%s))' % (model, sele))
if not backbone:
cmd.protect('name CA+C+N+O+OXT')
cmd.sculpt_iterate(model, state, cycles=int(cycles * 0.50))
else:
cmd.sculpt_iterate(model, state, int(cycles * 0.75))
cmd.set('sculpt_field_mask', 0x01F, model) # Local Geometry Only
cmd.sculpt_iterate(model, state, int(cycles * 0.25))
cmd.unset('sculpt_vdw_weight', model)
cmd.unset('sculpt_field_mask', model)
cmd.sculpt_deactivate(model)
cmd.deprotect()
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")
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 peptide_rebuild(name, selection='all', cycles=1000, state=1, quiet=1):
'''
DESCRIPTION
Rebuild the peptide from selection. All atoms which are present in
selection will be kept fixed, while atoms missing in selection are
placed by sculpting.
USAGE
peptide_rebuild name [, selection [, cycles [, state ]]]
SEE ALSO
stub2ala, add_missing_atoms, peptide_rebuild_modeller
'''
from chempy import fragments, feedback, models
cycles, state, quiet = int(cycles), int(state), int(quiet)
# suppress feedback for model merging
feedback['actions'] = False
# work with named selection
namedsele = cmd.get_unused_name('_')
cmd.select(namedsele, selection, 0)
identifiers = []
cmd.iterate(namedsele + ' and polymer and guide and alt +A',
'identifiers.append([segi,chain,resi,resv,resn])', space=locals())
model = models.Indexed()
for (segi,chain,resi,resv,resn) in identifiers:
try:
fname = resn.lower() if resn != 'MSE' else 'met'
frag = fragments.get(fname)
except IOError:
print(' Warning: unknown residue: ' + resn)
continue
for a in frag.atom:
a.segi = segi
a.chain = chain
a.resi = resi
a.resi_number = resv
a.resn = resn
model.merge(frag)
if not quiet:
print(' Loading model...')
cmd.load_model(model, name, 1, zoom=0)
if cmd.get_setting_boolean('auto_remove_hydrogens'):
cmd.remove(name + ' and hydro')
cmd.protect(name + ' in ' + namedsele)
cmd.sculpt_activate(name)
cmd.update(name, namedsele, 1, state)
cmd.delete(namedsele)
if not quiet:
print(' Sculpting...')
cmd.set('sculpt_field_mask', 0x003, name) # bonds and angles only
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x09F, name) # local + torsions
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x0FF, name) # ... + vdw
cmd.sculpt_iterate(name, 1, int(cycles / 2))
cmd.sculpt_deactivate(name)
cmd.deprotect(name)
cmd.unset('sculpt_field_mask', name)
if not quiet:
print(' Connecting peptide...')
pairs = cmd.find_pairs(name + ' and name C', name + ' and name N', 1, 1, 2.0)
for pair in pairs:
cmd.bond(*pair)
cmd.h_fix(name)
if not quiet:
print(' peptide_rebuild: done')
def peptide_rebuild(name, selection='all', cycles=1000, state=1, quiet=1):
'''
DESCRIPTION
Rebuild the peptide from selection. All atoms which are present in
selection will be kept fixed, while atoms missing in selection are
placed by sculpting.
USAGE
peptide_rebuild name [, selection [, cycles [, state ]]]
SEE ALSO
stub2ala, add_missing_atoms, peptide_rebuild_modeller
'''
from chempy import fragments, feedback, models
cycles, state, quiet = int(cycles), int(state), int(quiet)
# suppress feedback for model merging
feedback['actions'] = False
# work with named selection
namedsele = cmd.get_unused_name('_')
cmd.select(namedsele, selection, 0)
identifiers = []
cmd.iterate(namedsele + ' and polymer and guide and alt +A',
'identifiers.append([segi,chain,resi,resv,resn])', space=locals())
model = models.Indexed()
for (segi,chain,resi,resv,resn) in identifiers:
try:
fname = resn.lower() if resn != 'MSE' else 'met'
frag = fragments.get(fname)
except IOError:
print(' Warning: unknown residue:', resn)
continue
for a in frag.atom:
a.segi = segi
a.chain = chain
a.resi = resi
a.resi_number = resv
a.resn = resn
model.merge(frag)
if not quiet:
print(' Loading model...')
cmd.load_model(model, name, 1, zoom=0)
if cmd.get_setting_boolean('auto_remove_hydrogens'):
cmd.remove(name + ' and hydro')
cmd.protect(name + ' in ' + namedsele)
cmd.sculpt_activate(name)
cmd.update(name, namedsele, 1, state)
cmd.delete(namedsele)
if not quiet:
print(' Sculpting...')
cmd.set('sculpt_field_mask', 0x003, name) # bonds and angles only
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x09F, name) # local + torsions
cmd.sculpt_iterate(name, 1, int(cycles / 4))
cmd.set('sculpt_field_mask', 0x0FF, name) # ... + vdw
cmd.sculpt_iterate(name, 1, int(cycles / 2))
cmd.sculpt_deactivate(name)
cmd.deprotect(name)
cmd.unset('sculpt_field_mask', name)
if not quiet:
print(' Connecting peptide...')
pairs = cmd.find_pairs(name + ' and name C', name + ' and name N', 1, 1, 2.0)
for pair in pairs:
cmd.bond(*pair)
cmd.h_fix(name)
if not quiet:
print(' peptide_rebuild: done')
cmd.unpick()
# Set dihedral angles fo new residues to alpha-helix
for res0 in range(32, 35):
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"
atom5 = "/MyProtein//" + chn + "/" + str(res0 + 1) + "/N"
# # Set (Phi,Psi) dihedral angles per residue, respectively
cmd.set_dihedral(atom1, atom2, atom3, atom4, -60)
cmd.set_dihedral(atom2, atom3, atom4, atom5, -45)
# Remove steric clashes between sidechains
## Select only sidechain of THR-32 to ASN-35
# cmd.select("sidechains", "resi 32:35 and ! bb.")
cmd.select("backbone_range", "resi 32:35 and bb.")
## Protect rest of the protein from modifications by sculpting
# cmd.protect('(not sidechains)')
cmd.protect('(backbone_range)')
## Carry out Sculpting for 7000 cycles
cmd.sculpt_activate('MyProtein')
cmd.sculpt_iterate('MyProtein', cycles=7000)
cmd.sculpt_deactivate('MyProtein')
cmd.deprotect()
# Save sculpted structure into output file
cmd.save(out_protein, "MyProtein")
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")
cmd.get_wizard().set_hyd("none")
for chain in Chains:
# Select residue to mutate in chain
cmd.select("to_mutate", "/MyProtein//" + chain + "/" + to_mutate)
# Allow Wizard to identify selected residue
cmd.get_wizard().do_select('''to_mutate''')
# Generate mutation
cmd.get_wizard().apply()
# Restart selection for next mutation
cmd.select("to_mutate", 'none')
# Close Wizard
cmd.set_wizard()
cmd.delete("to_mutate")
res = int(to_mutate.split("`")[1])
around_res = str(res - 1) + ":" + str(res + 1)
cmd.select("sidechains", "resi " + around_res + "and ! bb.")
## Protect rest of the protein from modifications by sculpting
cmd.protect('(not sidechains)')
## Carry out Sculpting for 5000 cycles
cmd.sculpt_activate('MyProtein')
cmd.sculpt_iterate('MyProtein', cycles=5000)
cmd.sculpt_deactivate('MyProtein')
cmd.deprotect()
# Save mutated protein
cmd.save(out_protein, "MyProtein")
def set_dihedral_angles_update(pymol_object, chainID, Aa_list,
phi_psi_list, protect_selection,
moving_atom, target_atom, start_num=1):
"""Set several dihedral angles to a set of amino acids.
Function that will change the dihedral angles for each amino acid in
Aa_list for the ones in the phi_psi_list. Amino acids selected in
protect_selection will not move. After changing the angles the new
structure is saved.
This method is an updated version of "set_dihedral_angles". Instead of
changing the angles of the structures and then setting them back to
the original values, this method creates a copy of the pymol object
and then changes its angles. Thus, this does not modify the initial
structure.
This method also returns a list with information regarding the amino acid
modified, the angle used, the distance between moving atom and target atom
and the pdb file created. This is useful to create a log of the
modifications made.
Parameters
----------
pymol_object : String
Name of Pymol object in the session.
chainID : String
ChainID of residue.
Aa_list : List
List of amino acid numbers (int).
phi_psi_list : List
List of tuples containing phi and psi angles.
protect_selection : String
Slection string from pymol_object which will remain static.
Example: '//X/44-316/*'
moving_atom : String
Atom selection for atom 1 used for distance mesurement, ussualy from
chain being modified.
target_atom : String
Atom selection for atom 2 used for distance mesurement.
start_num : Int, optional
Number used to start the pdb files counter. The default is 1.
Returns
-------
pdb_files : List
List of tuples containing information about the output pdb file,
distance between target-moving atoms, aminoacid modified and new phi
and psi angles: (pdb_name,distance, aa_number, (new_phi, new_psi)).
"""
# track of PDB file numbers
pdb_num = start_num
# pdb_file_list = [] #PDB file name list as output
pdb_files = []
for aa_number in Aa_list:
for dihedral_angles in phi_psi_list:
# Create a copy of object to be modified
cmd.copy('obj_copy', pymol_object)
# Protect residues
cmd.protect('obj_copy'+protect_selection)
new_phi, new_psi = dihedral_angles
set_phi_psi_angles('obj_copy', chainID, aa_number,
phi=new_phi, psi=new_psi)
# get distance
distance = cmd.get_distance('obj_copy' + moving_atom, target_atom)
# save new structure with pdb_num as name
pdb_name = '{}_{}.pdb'.format(pymol_object, pdb_num)
cmd.save(pdb_name, 'obj_copy')
pdb_files.append((pdb_name, distance, aa_number, (new_phi, new_psi)))
pdb_num += 1
# Remove the object copy
cmd.delete('obj_copy')
print('Finished!')
return pdb_files