def do_state(self,state):
cmd=self.cmd
if cmd.get("sculpting")=="on":
names = cmd.get_names("all_objects")
if (bump_name in names) and (obj_name in names):
cmd.update(bump_name,obj_name)
if self.bump_scores:
state = cmd.get_state()
print(' Rotamer %d/%d, strain=%.2f' % (state,
cmd.count_states(obj_name), self.bump_scores[state - 1]))
def do_state(self,state):
cmd=self.cmd
if cmd.get("sculpting")=="on":
names = cmd.get_names("all_objects")
if (bump_name in names) and (obj_name in names):
cmd.update(bump_name,obj_name)
if self.bump_scores:
state = cmd.get_state()
print(' Rotamer %d/%d, strain=%.2f' % (state,
cmd.count_states(obj_name), self.bump_scores[state - 1]))
def do_state(self,state):
cmd=self.cmd
if cmd.get("sculpting")=="on":
names = cmd.get_names("all_objects")
if (bump_name in names) and (obj_name in names):
cmd.update(bump_name,obj_name)
if self.bump_scores:
print(' Rotamer %d/%d, strain=%.2f' % (state,
cmd.count_states(obj_name), self.bump_scores[state - 1]))
# update hbonds (polar contacts)
cmd.delete(tmp_hbonds)
cmd.distance(tmp_hbonds,
"?{}".format(obj_name),
"(byobj ?{}) and not ?{}".format(src_sele, src_sele),
mode=2, state1=state, state2=1)
def join_states(name, selection='all', discrete=-1, zoom=0, quiet=1):
'''
DESCRIPTION
The reverse of split_states
ARGUMENTS
name = string: name of object to create or modify
selection = string: atoms to include in the new object
discrete = -2: match atoms by sequence alignment
discrete = -1: Assume identical input objects (matching all atom
identifiers) but also check for missing atoms and only include atoms
that are present in all input objects {default}
discrete = 0: Assume identical input objects
discrete = 1: Input object may be (totally) different
'''
discrete, quiet = int(discrete), int(quiet)
if discrete == -2:
_assert_package_import()
from .selecting import wait_for
aln_obj = cmd.get_unused_name('_')
models = cmd.get_object_list('(' + selection + ')')
for i in range(len(models)):
if discrete == -1 and i > 0:
cmd.remove('(%s) and not (alt A+ and (%s) in (%s))' %
(name, name, models[i]))
cmd.create(name, '(%s) in (%s)' % (models[i], name), 1, i + 1, 0,
0, quiet)
elif discrete == -2 and i > 0:
cmd.align(models[i], name, cycles=0, transform=0, object=aln_obj)
wait_for(aln_obj)
cmd.remove('(%s) and not (%s)' % (name, aln_obj))
cmd.create(name, name, 1, i + 1, 0, 0, quiet)
cmd.update(name, '(%s) and (%s)' % (models[i], aln_obj), i + 1, 1,
0, quiet)
cmd.delete(aln_obj)
else:
cmd.create(name, models[i], 1, i + 1, discrete == 1, 0, quiet)
if int(zoom):
cmd.zoom(name, state=0)
def join_states(name, selection="all", discrete=-1, zoom=0, quiet=1):
"""
DESCRIPTION
The reverse of split_states
ARGUMENTS
name = string: name of object to create or modify
selection = string: atoms to include in the new object
discrete = -2: match atoms by sequence alignment
discrete = -1: Assume identical input objects (matching all atom
identifiers) but also check for missing atoms and only include atoms
that are present in all input objects {default}
discrete = 0: Assume identical input objects
discrete = 1: Input object may be (totally) different
"""
discrete, quiet = int(discrete), int(quiet)
if discrete == -2:
from .selecting import wait_for
aln_obj = cmd.get_unused_name("_")
models = cmd.get_object_list("(" + selection + ")")
for i in range(len(models)):
if discrete == -1 and i > 0:
cmd.remove("(%s) and not (alt A+ and (%s) in (%s))" % (name, name, models[i]))
cmd.create(name, "(%s) in (%s)" % (models[i], name), 1, i + 1, 0, 0, quiet)
elif discrete == -2 and i > 0:
cmd.align(models[i], name, cycles=0, transform=0, object=aln_obj)
wait_for(aln_obj)
cmd.remove("(%s) and not (%s)" % (name, aln_obj))
cmd.create(name, name, 1, i + 1, 0, 0, quiet)
cmd.update(name, "(%s) and (%s)" % (models[i], aln_obj), i + 1, 1, 0, quiet)
cmd.delete(aln_obj)
else:
cmd.create(name, models[i], 1, i + 1, discrete == 1, 0, quiet)
if int(zoom):
cmd.zoom(name, state=0)
def test_update(self):
# 3 states
cmd.fragment('gly', 'm1')
cmd.create('m1', 'm1', 1, 2)
cmd.create('m1', 'm1', 1, 3)
# second object, 90 degree rotates
cmd.copy('m2', 'm1')
cmd.rotate('x', 90, '(m2)', state=0)
# reference coordsets
cs = cmd.get_coordset
cs1 = cs('m1', 1)
cs2 = cs('m2', 1)
# m2/3 will change (pre-check)
self.assertArrayEqual(cs2, cs('m2', 3))
self.assertArrayNotEqual(cs1, cs('m2', 3))
# update explicit state
cmd.update('m2', 'm1', 3, 2)
# m2/3 has changed
self.assertArrayEqual(cs1, cs('m2', 3))
self.assertArrayNotEqual(cs2, cs('m2', 3))
# these haven't changed
self.assertArrayEqual(cs2, cs('m2', 1))
self.assertArrayEqual(cs2, cs('m2', 2))
# reset m2/3
cmd.load_coordset(cs2, 'm2', 3)
self.assertArrayEqual(cs2, cs('m2', 3))
# update all states
cmd.update('m2', 'm1', 0, 0)
self.assertArrayEqual(cs1, cs('m2', 1))
self.assertArrayEqual(cs1, cs('m2', 2))
self.assertArrayEqual(cs1, cs('m2', 3))
def test_update(self):
# 3 states
cmd.fragment('gly', 'm1')
cmd.create('m1', 'm1', 1, 2)
cmd.create('m1', 'm1', 1, 3)
# second object, 90 degree rotates
cmd.copy('m2', 'm1')
cmd.rotate('x', 90, '(m2)', state=0)
# reference coordsets
cs = cmd.get_coordset
cs1 = cs('m1', 1)
cs2 = cs('m2', 1)
# m2/3 will change (pre-check)
self.assertArrayEqual(cs2, cs('m2', 3))
self.assertArrayNotEqual(cs1, cs('m2', 3))
# update explicit state
cmd.update('m2', 'm1', 3, 2)
# m2/3 has changed
self.assertArrayEqual(cs1, cs('m2', 3))
self.assertArrayNotEqual(cs2, cs('m2', 3))
# these haven't changed
self.assertArrayEqual(cs2, cs('m2', 1))
self.assertArrayEqual(cs2, cs('m2', 2))
# reset m2/3
cmd.load_coordset(cs2, 'm2', 3)
self.assertArrayEqual(cs2, cs('m2', 3))
# update all states
cmd.update('m2', 'm1', 0, 0)
self.assertArrayEqual(cs1, cs('m2', 1))
self.assertArrayEqual(cs1, cs('m2', 2))
self.assertArrayEqual(cs1, cs('m2', 3))
def do_state(self, state):
cmd = self.cmd
if cmd.get("sculpting") == "on":
names = cmd.get_names("all_objects")
if (bump_name in names) and (obj_name in names):
cmd.update(bump_name, obj_name)
def apply(self):
cmd = self.cmd
pymol = cmd._pymol
if self.status == 1:
# find the name of the object which contains the selection
new_name = None
obj_list = cmd.get_names("objects")
for a in obj_list:
if cmd.get_type(a) == "object:molecule":
if cmd.count_atoms("(%s and %s)" % (a, src_sele)):
new_name = a
break
src_frame = cmd.get_state()
if new_name == None:
print " Mutagenesis: object not found."
else:
auto_zoom = cmd.get_setting_text("auto_zoom")
cmd.set("auto_zoom", "0", quiet=1)
if self.lib_mode != "current":
# create copy w/o residue
cmd.create(tmp_obj1, "(%s and not %s)" % (new_name, src_sele))
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)" % (tmp_obj1, src_sele))
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)" % (tmp_obj1, src_sele))
# save copy for bonded atom reference
cmd.create(tmp_obj3, new_name)
# transfer the selection to copy
cmd.select(src_sele, "(%s in %s)" % (tmp_obj3, src_sele))
# create copy with mutant in correct frame
cmd.create(tmp_obj2, obj_name, src_frame, 1)
cmd.set_title(tmp_obj2, 1, "")
cmd.delete(new_name)
# create the merged molecule
cmd.create(new_name, "(%s or %s)" % (tmp_obj1, tmp_obj2), 1) # only one state in merged object...
# now connect them
cmd.select(mut_sele, "(byres (%s like %s))" % (new_name, src_sele))
# bond N+0 to C-1
if (cmd.select(tmp_sele1, "(name C and (%s in (neighbor %s)))" % (new_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "((%s in %s) and n;N)" % (mut_sele, tmp_obj2)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
cmd.set_geometry(tmp_sele1, 3, 3) # make amide planer
cmd.set_geometry(tmp_sele2, 3, 3) # make amide planer
# bond C+0 to N+1
if (cmd.select(tmp_sele1, "(name N and (%s in (neighbor %s)))" % (new_name, src_sele)) == 1) and (
cmd.select(tmp_sele2, "((%s in %s) and n;C)" % (mut_sele, tmp_obj2)) == 1
):
cmd.bond(tmp_sele1, tmp_sele2)
cmd.set_geometry(tmp_sele1, 3, 3) # make amide planer
cmd.set_geometry(tmp_sele2, 3, 3) # make amide planer
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
# fix N-H hydrogen position (if any exists)
cmd.h_fix("(name N and bound_to (%s in %s and n;H))" % (new_name, tmp_obj2))
# now transfer selection back to the modified object
cmd.delete(tmp_obj1)
cmd.delete(tmp_obj2)
cmd.delete(tmp_obj3)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
else:
# create copy with conformation in correct state
cmd.create(tmp_obj2, obj_name, src_frame, 1)
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)" % (new_name, src_sele))
cmd.remove("(%s) and name OXT" % src_sele)
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)" % (new_name, src_sele))
# save existing conformation on undo stack
# cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele))
cmd.push_undo("(" + src_sele + ")")
# modify the conformation
cmd.update(new_name, tmp_obj2)
# cmd.unpick()
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
cmd.set("auto_zoom", auto_zoom, quiet=1)
def apply(self):
cmd=self.cmd
if self.status==1:
# find the name of the object which contains the selection
src_frame = cmd.get_state()
try:
new_name = cmd.get_object_list(src_sele)[0]
except IndexError:
print(" Mutagenesis: object not found.")
return
if True:
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
if self.lib_mode!="current":
# create copy with mutant in correct frame
state = cmd.get_object_state(new_name)
cmd.create(tmp_obj2, obj_name, src_frame, state)
cmd.set_title(tmp_obj2, state, '')
cmd.color(self.stored.identifiers[4], "?%s & elem C" % tmp_obj2)
cmd.alter(tmp_obj2, 'ID = -1')
# select backbone connection atoms
cmd.select(tmp_sele1, 'neighbor ?%s' % (src_sele), 0)
# remove residue and neighboring c-cap/n-cap (if any)
cmd.remove("?%s | byres (?%s & "
"(name N & resn NME+NHH | name C & resn ACE))" % (src_sele, tmp_sele1))
# create the merged molecule
cmd.create(new_name, "?%s | ?%s" % (new_name, tmp_obj2), state, state)
# now connect them
cmd.select(tmp_sele2, '/%s/%s/%s/%s' % ((new_name,) + self.stored.identifiers[:3]))
cmd.bond('?%s & name C' % (tmp_sele1), '?%s & name N' % (tmp_sele2), quiet=1)
cmd.bond('?%s & name N' % (tmp_sele1), '?%s & name C' % (tmp_sele2), quiet=1)
cmd.set_geometry('(?%s | ?%s) & name C+N' % (tmp_sele1, tmp_sele2), 3, 3) # make amide planer
# fix N-H hydrogen position (if any exists)
cmd.h_fix('?%s & name N' % (tmp_sele2))
# delete temporary objects/selections
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
else:
# create copy with conformation in correct state
cmd.create(tmp_obj2,obj_name,src_frame,1)
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn NME+NHH)"%
(new_name,src_sele))
cmd.remove("(%s) and name OXT"%src_sele)
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ACE)"%
(new_name,src_sele))
# save existing conformation on undo stack
# cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele))
cmd.push_undo("("+src_sele+")")
# modify the conformation
cmd.update(new_name,tmp_obj2)
# cmd.unpick()
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
cmd.set('auto_zoom',auto_zoom,quiet=1)
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')
def do_state(self,state):
cmd=self.cmd
if cmd.get("sculpting")=="on":
names = cmd.get_names("all_objects")
if (bump_name in names) and (obj_name in names):
cmd.update(bump_name,obj_name)
def apply(self):
cmd=self.cmd
pymol=cmd._pymol
if self.status==1:
# find the name of the object which contains the selection
new_name = None
obj_list = cmd.get_names('objects')
for a in obj_list:
if cmd.get_type(a)=="object:molecule":
if cmd.count_atoms("(%s and %s)"%(a,src_sele)):
new_name = a
break
src_frame = cmd.get_state()
if new_name==None:
print " Mutagenesis: object not found."
else:
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
if self.lib_mode!="current":
# create copy w/o residue
cmd.create(tmp_obj1,"(%s and not %s)"%(new_name,src_sele))
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)"%
(tmp_obj1,src_sele))
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)"%
(tmp_obj1,src_sele))
# save copy for bonded atom reference
cmd.create(tmp_obj3,new_name)
# transfer the selection to copy
cmd.select(src_sele,"(%s in %s)"%(tmp_obj3,src_sele))
# create copy with mutant in correct frame
cmd.create(tmp_obj2,obj_name,src_frame,1)
cmd.set_title(tmp_obj2,1,'')
cmd.delete(new_name)
# create the merged molecule
cmd.create(new_name,"(%s or %s)"%(tmp_obj1,tmp_obj2),1) # only one state in merged object...
# now connect them
cmd.select(mut_sele,"(byres (%s like %s))"%(new_name,src_sele))
# bond N+0 to C-1
if ((cmd.select(tmp_sele1, "(name C and (%s in (neighbor %s)))"%
(new_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "((%s in %s) and n;N)"%
(mut_sele,tmp_obj2)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.set_geometry(tmp_sele1,3,3) # make amide planer
cmd.set_geometry(tmp_sele2,3,3) # make amide planer
# bond C+0 to N+1
if ((cmd.select(tmp_sele1, "(name N and (%s in (neighbor %s)))"%
(new_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"((%s in %s) and n;C)"%
(mut_sele,tmp_obj2)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.set_geometry(tmp_sele1,3,3) # make amide planer
cmd.set_geometry(tmp_sele2,3,3) # make amide planer
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
# fix N-H hydrogen position (if any exists)
cmd.h_fix("(name N and bound_to (%s in %s and n;H))"%(new_name,tmp_obj2))
# now transfer selection back to the modified object
cmd.delete(tmp_obj1)
cmd.delete(tmp_obj2)
cmd.delete(tmp_obj3)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
else:
# create copy with conformation in correct state
cmd.create(tmp_obj2,obj_name,src_frame,1)
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn nme,nhh)"%
(new_name,src_sele))
cmd.remove("(%s) and name OXT"%src_sele)
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ace)"%
(new_name,src_sele))
# save existing conformation on undo stack
# cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele))
cmd.push_undo("("+src_sele+")")
# modify the conformation
cmd.update(new_name,tmp_obj2)
# cmd.unpick()
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
cmd.set('auto_zoom',auto_zoom,quiet=1)
def apply(self):
cmd=self.cmd
if self.status==1:
# find the name of the object which contains the selection
src_frame = cmd.get_state()
try:
new_name = cmd.get_object_list(src_sele)[0]
except IndexError:
print(" Mutagenesis: object not found.")
return
if True:
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
if self.lib_mode!="current":
# create copy with mutant in correct frame
state = cmd.get_object_state(new_name)
cmd.create(tmp_obj2, obj_name, src_frame, state)
cmd.set_title(tmp_obj2, state, '')
cmd.color(self.stored.identifiers[4], "?%s & elem C" % tmp_obj2)
cmd.alter(tmp_obj2, 'ID = -1')
# select backbone connection atoms
cmd.select(tmp_sele1, 'neighbor ?%s' % (src_sele), 0)
# remove residue and neighboring c-cap/n-cap (if any)
cmd.remove("?%s | byres (?%s & "
"(name N & resn NME+NHH | name C & resn ACE))" % (src_sele, tmp_sele1))
# create the merged molecule
cmd.create(new_name, "?%s | ?%s" % (new_name, tmp_obj2), state, state)
# now connect them
cmd.select(tmp_sele2, '/%s/%s/%s/%s' % ((new_name,) + self.stored.identifiers[:3]))
cmd.bond('?%s & name C' % (tmp_sele1), '?%s & name N' % (tmp_sele2), quiet=1)
cmd.bond('?%s & name N' % (tmp_sele1), '?%s & name C' % (tmp_sele2), quiet=1)
cmd.set_geometry('(?%s | ?%s) & name C+N' % (tmp_sele1, tmp_sele2), 3, 3) # make amide planer
# fix N-H hydrogen position (if any exists)
cmd.h_fix('?%s & name N' % (tmp_sele2))
# delete temporary objects/selections
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
else:
# create copy with conformation in correct state
cmd.create(tmp_obj2,obj_name,src_frame,1)
# remove existing c-cap in copy (if any)
cmd.remove("byres (name N and (%s in (neighbor %s)) and resn NME+NHH)"%
(new_name,src_sele))
cmd.remove("(%s) and name OXT"%src_sele)
# remove existing n-cap in copy (if any)
cmd.remove("byres (name C and (%s in (neighbor %s)) and resn ACE)"%
(new_name,src_sele))
# save existing conformation on undo stack
# cmd.edit("((%s in %s) and name ca)"%(new_name,src_sele))
cmd.push_undo("("+src_sele+")")
# modify the conformation
cmd.update(new_name,tmp_obj2)
# cmd.unpick()
cmd.delete(tmp_obj2)
self.clear()
# and return to frame 1
cmd.frame(1)
cmd.refresh_wizard()
cmd.set('auto_zoom',auto_zoom,quiet=1)
# This script gets a copy of the coordinates in Python,
# rotates the object about the Z axis, and then
# updates the coordinates in the original object.
from pymol import cmd
model = cmd.get_model("pept")
for a in model.atom:
a.coord=[ -a.coord[1], a.coord[0], a.coord[2]]
cmd.load_model(model,"tmp")
cmd.update("pept","tmp")
cmd.delete("tmp")
