def draw_bonds(self, selection):
warn = False
selection_objects = cmd.get_object_list(selection)
for obj in selection_objects:
elastics_obj = obj+"_elastics"
# Create dummy object to draw elastic bonds in
cmd.copy(elastics_obj, obj)
for a, b, data in self.graph.edges(data=True):
# draw non-elastic bonds
if data['type'] in ['bonds', 'constr']:
try:
a += 1
b += 1
try:
cmd.add_bond(obj, a, b)
except AttributeError:
cmd.bond(f"({obj} and ID {a})", f"({obj} and ID {b})")
except KeyError:
warn = True
# Draw elastic network
if data['type'] == 'harmonic':
try:
a += 1
b += 1
try:
cmd.add_bond(elastics_obj, a, b)
except AttributeError:
cmd.bond(f"({elastics_obj} and ID {a})", f"({elastics_obj} and ID {b})")
except KeyError:
warn = True
cmd.color("orange", elastics_obj)
# warn about missing atoms if needed.
if warn:
print('WARNING: some atoms present in the tpr file were not found in the loaded '
'structure.\n Bonds containing those atoms were not drawn.')
def bond_zns(sel):
cmd.unbond(sel + " and resn ZNS", sel + " and not resn ZNS")
# for c, i in getres("resn ZNS"):
# cmd.bond(sel+" and chain %s and resi %i and name ZN1"%(c, i),
# sel+" and chain %s and resi %i and name S*"%(c, i))
for c, i in getres("name ZN1"):
cmd.bond(
sel + " and chain %s and resi %i and name ZN1" % (c, i),
sel + " and chain %s and resi %i and name S*, N2, N4" % (c, i),
)
allsg = cmd.get_model(sel + " and (resn CYS and (name CB))").atom
allsf = cmd.get_model(sel + " and (resn ZHC and (name S*, C1, C4))").atom
while allsg:
closest = [9e9, None, None]
for sga in allsg:
for sfa in allsf:
sg = Vec(sga.coord)
sf = Vec(sfa.coord)
if (sg - sf).length() < closest[0]:
closest = [(sg - sf).length(), sga, sfa]
sga, sfa = closest[1:]
allsg.remove(sga)
allsf.remove(sfa)
if closest[0] > 10.0:
break
cmd.bond(
sel + " and resi %s and chain %s and name %s" % (sga.resi, sga.chain, sga.name),
sel + " and resi %s and chain %s and name %s" % (sfa.resi, sfa.chain, sfa.name),
)
def load_links():
file_links = open_it()
for line in open(file_links, "r"):
edge = line.split()
for i in range(0, len(edge)):
edge[i] = "resi " + edge[i]
cmd.bond(edge[0], edge[1])
def bond_zns(sel):
cmd.unbond(sel + " and resn ZNS", sel + " and not resn ZNS")
# for c,i in getres("resn ZNS"):
# cmd.bond(sel+" and chain %s and resi %i and name ZN1"%(c,i),
# sel+" and chain %s and resi %i and name S*"%(c,i))
for c, i in getres("name ZN1"):
cmd.bond(sel + " and chain %s and resi %i and name ZN1" % (c, i),
sel + " and chain %s and resi %i and name S*,N2,N4" % (c, i))
allsg = cmd.get_model(sel + " and (resn CYS and (name CB))").atom
allsf = cmd.get_model(sel + " and (resn ZHC and (name S*,C1,C4))").atom
while allsg:
closest = [9e9, None, None]
for sga in allsg:
for sfa in allsf:
sg = Vec(sga.coord)
sf = Vec(sfa.coord)
if (sg - sf).length() < closest[0]:
closest = [(sg - sf).length(), sga, sfa]
sga, sfa = closest[1:]
allsg.remove(sga)
allsf.remove(sfa)
if closest[0] > 10.0: break
cmd.bond(
sel + " and resi %s and chain %s and name %s" %
(sga.resi, sga.chain, sga.name),
sel + " and resi %s and chain %s and name %s" %
(sfa.resi, sfa.chain, sfa.name))
def bond_connections_from_array(interactiongraph, residuemap, cutoff=0.0):
# Make strength be proportional to girth of bonds
graph = numpy.sqrt(numpy.absolute(interactiongraph))
# Simple min-max scaling parameters
minimum = numpy.min(graph)
maximum = numpy.max(graph)
residues = list(residuemap.keys())
shown = []
for i in range(graph.shape[0]):
for j in range(i, graph.shape[1]):
# Only draw bonds if interaction strength over cutoff threshold
if graph[i][j] > cutoff:
resa = residues[i]
resb = residues[j]
shown.append(resa)
shown.append(resb)
a = "chain {} and resi {} and name CA".format(
resa.split(':')[0],
resa.split(':')[1][1:])
b = "chain {} and resi {} and name CA".format(
resb.split(':')[0],
resb.split(':')[1][1:])
cmd.bond(a, b)
strength = 1.0 if maximum == minimum else 0.1 + (0.9 * (
(graph[i][j] - minimum) / (maximum - minimum)))
cmd.set_bond("stick_radius", strength, a, b)
return shown
def draw_dist_pairs(drs_inp, molecule, draw_type="line"):
f_drsinp = open(drs_inp, "r")
obj = "network"
cmd.create(obj, molecule)
cmd.hide("everything", obj)
for i, line in enumerate(f_drsinp):
print "Pair No.: ", i
if line.split()[1] != "LIST" and line.split()[1] != "STOP":
chainid1, resid1, resname1, atomname1 = line.split(
)[0], line.split()[1], line.split()[2], line.split()[3]
chainid2, resid2, resname2, atomname2 = line.split(
)[4], line.split()[5], line.split()[6], line.split()[7]
print chainid1, resid1, resname1, atomname1, chainid2, resid2, resname2, atomname2
if draw_type == "line":
cmd.bond("%s and chain %s and resi %s and name %s"%(obj,chainid1,resid1,atomname1),\
"%s and chain %s and resi %s and name %s"%(obj,chainid2,resid2,atomname2) )
cmd.show(
"lines", "%s and chain %s and resi %s and name %s" %
(obj, chainid1, resid1, atomname1))
cmd.show(
"lines", "%s and chain %s and resi %s and name %s" %
(obj, chainid2, resid2, atomname2))
elif draw_type == "dist":
cmd.distance("dist%s"%i, "chain %s and resi %s and name %s"%(chainid1,str(resid1),atomname1),\
"chain %s and resi %s and name %s"%(chainid2,str(resid2),atomname2) )
print "chain %s and resi %s and name %s" % (chainid1, resid1,
atomname1)
elif line.split()[1] == "STOP":
print "Reached last line"
break
def showcst(fname):
for l in open(fname).readlines():
kind, a1, r1, a2, r2 = l.split()[:5]
a1 = "(resi %s and name %s)" % (r1, a1)
a2 = "(resi %s and name %s)" % (r2, a2)
cmd.bond(a1, a2)
cmd.show("lines", a1)
cmd.show("lines", a2)
def bondzn():
for o in cmd.get_object_list():
for c, r in getres(o + " and elem ZN"):
print "add zn bonds for", o, "resi", r, "chain", c
cmd.bond(
"(%s and resi %s and chain %s)" % (o, r, c),
"(%s and elem N) within 2.5 of (%s and resi %s and chain %s)" %
(o, o, r, c))
def showcst(fname):
for l in open(fname).readlines():
kind, a1, r1, a2, r2 = l.split()[:5]
a1 = "(resi %s and name %s)" % (r1, a1)
a2 = "(resi %s and name %s)" % (r2, a2)
cmd.bond(a1, a2)
cmd.show("lines", a1)
cmd.show("lines", a2)
def bondzn():
for o in cmd.get_object_list():
print "add zn bonds for", o
for r, c in getres(o + " and elem ZN"):
cmd.bond(
"(%s and resi %s and chain %s)" % (o, r, c),
"(%s and resn HIS and elem N) within 2.5 of (%s and resi %s and chain %s)" % (o, o, r, c),
)
break
def chop(self, sele):
try:
model = cmd.get_model(sele)
except:
return
chain2resId2atomNames = {}
for atom in model.atom:
resnum = int(atom.resi)
pdbname = atom.name
chain = atom.chain
if not chain in chain2resId2atomNames:
chain2resId2atomNames[chain] = {resnum: set([pdbname])}
else:
if resnum in chain2resId2atomNames[chain]:
chain2resId2atomNames[chain][resnum].add(pdbname)
else:
chain2resId2atomNames[chain][resnum] = set([pdbname])
for chain in chain2resId2atomNames:
resId2atomNames = chain2resId2atomNames[chain]
resIds2addN = set([])
resIds2addC = set([])
for resnum in resId2atomNames:
if resId2atomNames[resnum] != set([
"CA", "C", "O"
]) and resId2atomNames[resnum] != set(["CA", "N"]):
resIds2addC.add(resnum + 1)
resIds2addN.add(resnum - 1)
resIds2addN -= set(resId2atomNames.keys())
resIds2addC -= set(resId2atomNames.keys())
stateNo = cmd.get_state()
for resnum in resIds2addC:
cmd.create(
sele, " %" + sele + " or ( ( resi " + str(resnum) +
" and chain " + chain + " ) and ( name CA or name N) ) ",
stateNo)
cmd.bond(
"%" + sele + " and name N and resi " + str(resnum),
"%" + sele + " and name C and resi " + str(resnum - 1), 1)
for resnum in resIds2addN:
cmd.create(
sele, " %" + sele + " or ( ( resi " + str(resnum) +
" and chain " + chain +
" ) and ( name CA or name C or name O) ) ", stateNo)
cmd.bond(
"%" + sele + " and name C and resi " + str(resnum),
"%" + sele + " and name N and resi " + str(resnum + 1), 1)
cmd.show("sticks", sele)
def test_bond(self):
cmd.pseudoatom('m1', pos=(0, 0, 0))
cmd.pseudoatom('m1', pos=(1, 0, 0))
cmd.pseudoatom('m1', pos=(1, 1, 0))
cmd.bond('m1`1', 'm1`2')
count = cmd.count_atoms('(m1`1) extend 1')
self.assertEqual(count, 2)
cmd.unbond('m1`1', 'm1`2')
count = cmd.count_atoms('(m1`1) extend 1')
self.assertEqual(count, 1)
def test_bond(self):
cmd.pseudoatom('m1', pos=(0,0,0))
cmd.pseudoatom('m1', pos=(1,0,0))
cmd.pseudoatom('m1', pos=(1,1,0))
cmd.bond('m1`1', 'm1`2')
count = cmd.count_atoms('(m1`1) extend 1')
self.assertEqual(count, 2)
cmd.unbond('m1`1', 'm1`2')
count = cmd.count_atoms('(m1`1) extend 1')
self.assertEqual(count, 1)
def load_net():
file_coors= open_it()
net=network(file_coors)
for ii in range(net.num_nodes):
cmd.pseudoatom('net',pos=net.node[ii].coors,resi=ii,chain='A')
selec='resi '+str(ii)
cmd.alter(selec,'resn='+'"'+net.node[ii].label+'"')
cmd.label(selec,'"'+net.node[ii].label+'"')
cmd.alter(selec,'b='+str(net.node[ii].weight))
cmd.alter(selec,'q='+str(net.node[ii].cluster))
for ii in range(net.num_nodes):
for jj in net.node[ii].link.keys():
cmd.bond('resi '+str(ii),'resi '+str(jj))
cmd.spectrum('b','blue_red')
def bond_connections(clusters, interactions):
cutoff=10
## show_list=["A:240","A:182","A:184","A:204","A:201","A:216"]
# shell1=["A:240"]
## shell1=["A:204","A:240"]
# shell2=["A:182","A:184","A:204","A:201","A:216"]
# shell3=["A:151","A:155","A:156","A:199","A:205","A:208","A:214","A:238","A:242"]
# shell4=["A:154","A:158","A:163","A:166","A:167","A:170","A:180","A:185","A:196","A:203","A:207","A:211","A:212","A:219","A:68"]
# shell5=["A:135","A:136","A:149","A:160","A:162","A:164","A:171","A:173","A:174","A:178","A:192","A:197","A:200","A:206","A:222","A:230","A:235","A:236","A:237","A:26","A:29","A:66","A:69"]
# shell6=["A:134","A:138","A:139","A:143","A:146","A:152","A:157","A:159","A:169","A:183","A:187","A:19","A:195","A:220","A:223","A:227","A:23","A:232","A:24","A:244","A:46","A:87","A:89","A:90","A:91"]
#
# show_list_wt=shell1 + shell2 + shell3 + shell4 + shell5 + shell6
# show_list_S=shell1
# show_list=shell1
# #show_list=show_list_wt
# #show_list.append(shell1)
# #show_list.append(shell2)
# #print(show_list)
for cluster in clusters:
#print(cluster)
for i in range(len(cluster)):
for j in range(i, len(cluster)):
resa = cluster[i]
resb = cluster[j]
# Only draw bonds if interaction strength at all present
if resa in interactions:
if resb in interactions[resa]:
resa_=re.sub(r':\w',':',resa)
resb_=re.sub(r':\w',':',resb)
a = "chain {} and resi {} and name CA".format(
resa_.split(':')[0], resa_.split(':')[1])
b = "chain {} and resi {} and name CA".format(
resb_.split(':')[0], resb_.split(':')[1])
# if interactions[resa][resb] > cutoff and (resa in show_list or resb in show_list):
if interactions[resa][resb] > cutoff: #and (resa in show_list or resb in show_list):
#if resa not in show_list:
# print(resa)
#if resb not in show_list:
# print(resb)
# print(resa + " " + resb)
print(a + " " + b + " " + str(interactions[resa][resb]))
cmd.bond(a, b)
cmd.set_bond("line_width",
(interactions[resa][resb]/3),
a, b)
cmd.set_bond("line_color",get_color(resa,resb),a,b)
def garnish(file=None, selection='all', gmx=None):
"""
DESCRIPTION
Allow a coarse grained structure to be visualized in pymol like an atomistic structure
by drawing bonds and elastic network.
Without a top/tpr file, this function only adds bonds between the backbone beads
so they can be nicely visualized using line or stick representation.
Adding a top/tpr file provides topology information that can be used
to draw side chain and elastic bonds.
USAGE
garnish [file [, selection [, gmx]]]
ARGUMENTS
file = a tpr or topology file to extract bond information from (default: None)
selection = any selection to act upon (default: all)
gmx = gmx executable path (default: inferred by `which gmx`)
"""
# Retain order so pymol does not sort the atoms, giving a different result when saving the file
cmd.set("retain_order", 1)
if file:
# parse the file
sys_dict = parse(file, gmx)
# create System object and draw all the bonds
system = System(sys_dict)
system.draw_bonds(selection)
system.transfer_attributes(selection)
else:
bb_beads = get_chain_bb(selection)
# For each object and chain, draw bonds between BB beads
for obj, chains in bb_beads.items():
for _, bbs in chains.items():
# create bond tuples for "adjacent" backbone beads
bonds = [(bbs[i], bbs[i + 1]) for i in range(len(bbs) - 1)]
for a, b in bonds:
try:
cmd.add_bond(obj, a, b)
except AttributeError:
cmd.bond(f"{obj} and ID {a}", f"{obj} and ID {b}")
# Fix the view nicely
cmd.hide("everything", selection)
cmd.show_as("sticks", selection)
cmd.show_as("lines", '*_elastics')
def get_best_state_bump():
best_state = (1, 1e9)
cmd.create(tmp, '%s and not name CA+C+N+O or (%s within 8.0 of (%s and name CB))' % \
(mutagenesis.obj_name, cpy, mutagenesis.obj_name), zoom=0, singletons=1)
cmd.bond('name CB and %s in %s' % (tmp, mutagenesis.obj_name),
'name CA and %s in %s' % (tmp, res))
cmd.sculpt_activate(tmp)
for i in range(1, cmd.count_states(tmp)+1):
score = cmd.sculpt_iterate(tmp, state=i)
if not quiet:
print('Frame %d Score %.2f' % (i, score))
if score < best_state[1]:
best_state = (i, score)
cmd.delete(tmp)
if not quiet:
print(' Best: Frame %d Score %.2f' % best_state)
return best_state
def get_best_state_bump():
best_state = (1, 1e9)
cmd.create(tmp, '%s and not name CA+C+N+O or (%s within 8.0 of (%s and name CB))' % \
(mutagenesis.obj_name, cpy, mutagenesis.obj_name), zoom=0, singletons=1)
cmd.bond('name CB and %s in %s' % (tmp, mutagenesis.obj_name),
'name CA and %s in %s' % (tmp, res))
cmd.sculpt_activate(tmp)
for i in range(1, cmd.count_states(tmp)+1):
score = cmd.sculpt_iterate(tmp, state=i)
if not quiet:
print('Frame %d Score %.2f' % (i, score))
if score < best_state[1]:
best_state = (i, score)
cmd.delete(tmp)
if not quiet:
print(' Best: Frame %d Score %.2f' % best_state)
return best_state
def bond_connections(clusters, interactions):
# Quickfix - find min and max
# this filtering should be done before supplying to this function
# That is, the "interactions" data should be already formatted
# as a float in a way that makes it look nice with bond
# stick_radius
minimum = None
maximum = None
for cluster in clusters:
for i in range(len(cluster)):
for j in range(i, len(cluster)):
resa = cluster[i]
resb = cluster[j]
if resa in interactions:
if resb in interactions[resa]:
strength = interactions[resa][resb][0]
if minimum is None:
minimum = strength
else:
minimum = strength if minimum > strength else minimum
if maximum is None:
maximum = strength
else:
maximum = strength if maximum < strength else maximum
for cluster in clusters:
for i in range(len(cluster)):
for j in range(i, len(cluster)):
resa = cluster[i]
resb = cluster[j]
# Only draw bonds if interaction strength at all present
if resa in interactions:
if resb in interactions[resa]:
a = "chain {} and resi {} and name CA".format(
resa.split(':')[0],
resa.split(':')[1][1:])
b = "chain {} and resi {} and name CA".format(
resb.split(':')[0],
resb.split(':')[1][1:])
cmd.bond(a, b)
strength = 1.0 if maximum == minimum else 0.1 + (
0.9 * ((interactions[resa][resb][0] - minimum) /
(maximum - minimum)))
cmd.set_bond("stick_radius", strength, a, b)
def test_extinction_coefficient():
cmd.reinitialize()
eps_reduced = 2 * 5500 + 3 * 1490
eps_ss_1 = eps_reduced + 1 * 125
eps_ss_2 = eps_reduced + 2 * 125
cmd.fab("AWWYYYCCCC", "m1")
eps, A_280 = psico.querying.extinction_coefficient("m1")
assert eps == eps_reduced
assert A_280 == approx(eps_reduced / 1345.58908)
cmd.remove("hydro")
eps, A_280 = psico.querying.extinction_coefficient("m1")
assert eps == eps_reduced
assert A_280 == approx(eps_reduced / 1347.60496)
cmd.bond("7/SG", "8/SG")
eps, A_280 = psico.querying.extinction_coefficient("m1")
assert eps == eps_ss_1
assert A_280 == approx(eps_ss_1 / 1345.58908)
cmd.bond("9/SG", "10/SG")
eps, A_280 = psico.querying.extinction_coefficient("m1")
assert eps == eps_ss_2
assert A_280 == approx(eps_ss_2 / 1343.5732)
def draw_dist_pairs(drs_inp, molecule, draw_type="line"):
f_drsinp = open(drs_inp, "r")
obj = "network"
cmd.create(obj, molecule)
cmd.hide("everything", obj)
for i, line in enumerate(f_drsinp):
print "Pair No.: ", i
if line.split()[1] != "LIST" and line.split()[1] != "STOP":
chainid1, resid1, resname1, atomname1 = line.split()[0], line.split()[1], line.split()[2],line.split()[3]
chainid2, resid2, resname2, atomname2 = line.split()[4], line.split()[5], line.split()[6],line.split()[7]
print chainid1, resid1, resname1, atomname1, chainid2, resid2, resname2, atomname2
if draw_type == "line":
cmd.bond("%s and chain %s and resi %s and name %s"%(obj,chainid1,resid1,atomname1),\
"%s and chain %s and resi %s and name %s"%(obj,chainid2,resid2,atomname2) )
cmd.show("lines", "%s and chain %s and resi %s and name %s"%(obj, chainid1,resid1,atomname1))
cmd.show("lines", "%s and chain %s and resi %s and name %s"%(obj, chainid2,resid2,atomname2))
elif draw_type == "dist":
cmd.distance("dist%s"%i, "chain %s and resi %s and name %s"%(chainid1,str(resid1),atomname1),\
"chain %s and resi %s and name %s"%(chainid2,str(resid2),atomname2) )
print "chain %s and resi %s and name %s"%(chainid1,resid1,atomname1)
elif line.split()[1] == "STOP":
print "Reached last line"
break
def load_network(points, edges):
with open(points, 'r') as infile:
for line in infile.readlines():
field = line.strip().split()
xyz = map(float, field)
xyz = [10 * x for x in xyz]
cmd.pseudoatom("test", elem='O', pos=xyz)
with open(edges, 'r') as infile:
for line in infile.readlines():
field = line.strip().split()
if float(field[-1]) > 0.1:
plop = cmd.bond('index %s' % field[0], 'index %s' % field[1])
cmd.set_bond('line_color', float(field[-1]), 'i. 1')
cmd.show("sphere", "test")
cmd.set('line_width', 5.0)
return 0
ligand_name = file.split('_')[0]
loaded_ligs.append(ligand_name)
cmd.load('ligs/' + file, ligand_name)
#select the ligand atomes of the original ligand to align with
target_atom1 = 'RA95_target and name C3'
target_atom2 = 'RA95_target and name C4'
target_atom3 = 'RA95_target and name C5'
#select the ligand atomes of the new ligand to align with and align the selected atoms of old and new ligand
for ligand in loaded_ligs:
mobile_atom1 = ligand + ' and name CL1'
mobile_atom2 = ligand + ' and name CL'
mobile_atom3 = ligand + ' and name CL2'
cmd.pair_fit(mobile_atom1, target_atom1, mobile_atom2, target_atom2,
mobile_atom3, target_atom3)
#remove old ligand
cmd.remove('RA95_target and resn PEN')
#build bond between Lys83 and the new ligand and generate pdb file
for ligand in loaded_ligs:
cmd.copy('RA95_' + ligand, 'RA95_target')
cmd.fuse(ligand + ' and name CL',
'RA95_' + ligand + ' and resn LYX and name NZ', '3')
cmd.bond('RA95_' + ligand + ' and resn LYX and name NZ',
'RA95_' + ligand + ' and name CL')
cmd.alter('RA95_' + ligand + ' and resn ' + ligand, 'segi="B"')
cmd.sort('RA95_' + ligand)
cmd.save('RA95_' + ligand + '.pdb', 'RA95_' + ligand, '0')
def format_bonds(
selection='all',
bonds=4,
):
'''
DESCRIPTION
Formats bonds in aromatic or charged residues
EXAMPLE
frag PHE
format_bonds
USAGE
format_bonds [ selection [, bonds ]]
ARGUMENTS
selection: <str> input selection {default: 'all'}
bonds: <int> toogles format of bonds
1: single bonds (deactivates valence display)
2: regular double bonds (activates valence display)
>=3: delocalized (activates valence display)
'''
# Selection
try:
# group selection with bracketing and select complete residues
selection = '(byres (' + str(selection) + '))'
# checks functional selection
cmd.count_atoms(selection)
except:
print "invalid selection"
return False
# PARAMETERS
try:
bonds = int(bonds)
except:
pass
if (not (bonds in [1, 2])):
bonds = 4
if bonds == 1:
cmd.set('valence', 0)
print "Valence display disabled!"
return bonds
else:
cmd.set('valence', 1)
print "Valence display enabled!"
# proceed
##### SELECTION BY OBJECT AND CHAIN #####
# variable for the selections
# get the names of the proteins in the selection
objects = cmd.get_object_list(selection)
# include chains
# subselect chains
names = []
for p in objects:
for chain in cmd.get_chains('model ' + p) or ['']:
names.append("(model %s and chain '%s')" % (p, chain))
##### SELECTION LISTS #####
# get TRP
stored.temp = []
for p in names:
cmd.iterate((
'(%s) and (resn TRP+NIW) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p
)
# the integer is to ensure unique keys
TRP_tuple = (1,) + tuple(stored.temp)
# get PHETYR
stored.temp = []
for p in names:
cmd.iterate((
'(%s) and (resn PHE+TYR+PTR+NIY+PNIY) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p
)
PHETYR_tuple = (2,) + tuple(stored.temp)
# get HIS
stored.temp = []
for p in names:
cmd.iterate((
'(%s) and (resn HIS) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p
)
HIS_tuple = (3,) + tuple(stored.temp)
# get NITRO
stored.temp = []
for p in names:
cmd.iterate((
'(%s) and (resn NIY+PNIY+NIW) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p
)
NITRO_tuple = (4,) + tuple(stored.temp)
# get GLU
stored.temp = []
for p in names:
cmd.iterate((
'(%s) and (resn GLU) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p
)
GLU_tuple = (5,) + tuple(stored.temp)
# get ASP
stored.temp = []
for p in names:
cmd.iterate((
'(%s) and (resn ASP) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p
)
ASP_tuple = (6,) + tuple(stored.temp)
# get CTERM
stored.temp = []
for p in names:
cmd.iterate(
'(byres (last %s)) and (not (hetatm)) '
'and (name OXT)' % (p),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p
)
CTERM_tuple = (7,) + tuple(stored.temp)
# get ARG
stored.temp = []
for p in names:
cmd.iterate((
'(%s) and (resn ARG) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p
)
ARG_tuple = (8,) + tuple(stored.temp)
##### SELECTION TUPLES DONE #####
##### ATOM LISTS #####
TRP_bonds_all = [
['CG', 'CD1'],
['CD1', 'NE1'],
['NE1', 'CE2'],
['CE2', 'CD2'],
['CD2', 'CG'],
['CD2', 'CE3'],
['CE3', 'CZ3'],
['CZ3', 'CH2'],
['CH2', 'CZ2'],
['CZ2', 'CE2']
]
TRP_bonds_double = [
['CG', 'CD1'],
['CE2', 'CD2'],
['CE3', 'CZ3'],
['CH2', 'CZ2']
]
PHETYR_bonds_all = [
['CG', 'CD1'],
['CD1', 'CE1'],
['CE1', 'CZ'],
['CZ', 'CE2'],
['CE2', 'CD2'],
['CD2', 'CG']
]
PHETYR_bonds_double = [
['CG', 'CD1'],
['CE1', 'CZ'],
['CE2', 'CD2']
]
HIS_bonds_all = [
['CG', 'CD2'],
['CD2', 'NE2'],
['NE2', 'CE1'],
['CE1', 'ND1'],
['ND1', 'CG'],
]
HIS_bonds_double = [
['CG', 'CD2'],
['CE1', 'ND1']
]
NITRO_bonds_all = [
['NN', 'O1'],
['NN', 'O2']
]
NITRO_bonds_double = [
['NN', 'O1']
]
GLU_bonds_all = [
['CD', 'OE1'],
['CD', 'OE2']
]
GLU_bonds_double = [
['CD', 'OE1']
]
ASP_bonds_all = [
['CG', 'OD1'],
['CG', 'OD2']
]
ASP_bonds_double = [
['CG', 'OD1']
]
CTERM_bonds_all = [
['C', 'O'],
['C', 'OXT']
]
CTERM_bonds_double = [
['C', 'O']
]
ARG_bonds_all = [
['CZ', 'NH1'],
['CZ', 'NH2']
]
ARG_bonds_double=[
['CZ','NH1']
]
##### FORMATING #####
# dictionary: entries:atoms
format_dict = {
TRP_tuple: [TRP_bonds_all, TRP_bonds_double],
PHETYR_tuple: [PHETYR_bonds_all, PHETYR_bonds_double],
HIS_tuple: [HIS_bonds_all, HIS_bonds_double],
NITRO_tuple: [NITRO_bonds_all, NITRO_bonds_double],
GLU_tuple: [GLU_bonds_all, GLU_bonds_double],
ASP_tuple: [ASP_bonds_all, ASP_bonds_double],
CTERM_tuple: [CTERM_bonds_all, CTERM_bonds_double],
ARG_tuple: [ARG_bonds_all, ARG_bonds_double]
}
if bonds != 2:
lines = 4
print "Formating as delocalized bonds"
else:
lines = 1
print "Formating as double bonds"
# for all tuples (i.e format_dict.keys())
for p in format_dict.keys():
# go through list except ID at pos 1
for q in p[1:]:
# format bonds
for r in format_dict[p][0]:
cmd.unbond('%s and name %s' % (q, r[0]), '%s and name %s' % (q, r[1]))
cmd.bond('%s and name %s' % (q, r[0]), '%s and name %s' % (q, r[1]), lines)
if lines == 1:
# add double bonds
for r in format_dict[p][1]:
cmd.unbond('%s and name %s' % (q, r[0]), '%s and name %s' % (q, r[1]))
cmd.bond('%s and name %s' % (q, r[0]), '%s and name %s' % (q, r[1]), 2)
return bonds
def create_object_with_flipkin_coords(mpobj, which_flips='NQ'):
'''Duplicate the mpobj molecule and apply the flipNQ/H group coordinates.
PARAMETERS
mpobj An MPObject instance
which_flips Either 'NQ' or 'H' to specify which flipkin to use
'''
flipkin_name = 'flipkin{}'.format(which_flips)
flipkin = mpobj.kin[flipkin_name]
flip_group = 'flip{}'.format(which_flips)
reduced_obj = mpobj.pdb['reduce']
flipped_obj = mpobj.pdb[flipkin_name]
cmd.create(flipped_obj, reduced_obj)
for vl in flipkin.vectorlists():
# Skip if not coordinates
if vl[0].vectorlist_name == 'x':
msg = 'skipping non-coords vectorlist {}'
logger.debug(msg.format(vl[0].vectorlist_name))
continue
# Skip everything except the'flipNQ' (or 'flipH') group
if vl[0].group[0] != flip_group:
msg = 'skipping non-{} vectorlist'.format(flip_group)
logger.debug(msg)
continue
logger.debug('begin flipping vectorlist')
for v in vl:
if not (v.atom[0] and v.atom[1]):
msg = 'vector {} was missing atoms: {}'.format(v, v.atom)
logger.warning(msg)
continue
macro = v.macro(1)
sel = v.sel(1)
logger.debug('atom to be flipped: {}\n sel: {}'.format(macro, sel))
source_coords = v.coords[1]
target_sel = '{} and {}'.format(flipped_obj, sel)
msg = 'flipping atom {} to {}'.format(target_sel, source_coords)
logger.debug(msg)
ret = cmd.load_coords([source_coords], target_sel)
if ret == -1:
success = 0
a = v.atom[1]
if a['resn'] == 'HIS':
his_h = {
'HD1': {
'old_h': 'HE2',
'old_n': 'NE2',
'new_h': 'HD1',
'new_n': 'ND1',
},
'HE2': {
'old_h': 'HD1',
'old_n': 'ND1',
'new_h': 'HE2',
'new_n': 'NE2',
}
}
if a['name'] in his_h.keys():
# Reduce has switched which N is protonated. Let's move
# the old H atom and rename it.
resi_sel = '{} and chain {} and resi {}'.format(
flipped_obj, a['chain'], a['resi'])
h = his_h[a['name']]
old_h = '{} and name {}'.format(resi_sel, h['old_h'])
old_n = '{} and name {}'.format(resi_sel, h['old_n'])
new_h = '{} and name {}'.format(resi_sel, h['new_h'])
new_n = '{} and name {}'.format(resi_sel, h['new_n'])
# Break the old bond
cmd.unbond(old_h, old_n)
# Rename the atom
cmd.alter(old_h, 'name="{}"'.format(a['name']))
# Make the new bond
cmd.bond(new_h, new_n)
# Retry loading coordinates
ret = cmd.load_coords([source_coords], target_sel)
if not ret == -1:
success = 1
if not success:
msg = 'failed to load coords for {}!'.format(macro)
logger.warning(msg)
logger.debug('end flipping vectorlist')
# Basic Python Script using PyMol API to bond all the alpha carbons in a protein chain.
# Scripted to visualize knots and slipknots in a protein chain.
__author__ = 'Shashank'
from pymol import cmd, stored
# An array list used to store all the residue numbers which will be fetched.
residues = []
# iterate command used to fetch all the alpha carbon residue numbers from the given PDB
cmd.iterate('(n. CA)', 'residues.append(resi)')
n = residues.__len__()
i = 0
# Bond command in the API is used to connect all the consecutive CA atoms in the chain
while i<n-1:
cmd.bond(residues[i]+'/CA',residues[i+1]+'/CA')
print "Bonding "+residues[i]+" And "+residues[i+1]
i = i+1
# Coloring the bonds using the Spectrum command
# cmd.load("1ALK_A_test.pdb")
# cmd.set("line_color","white")
def fix_bonds(selection):
stored.residues = []
cmd.iterate(selection + ' and n. ca',
'stored.residues.append((resi,resn))')
last_residue = stored.residues[-1][0]
print(last_residue)
for r1 in range(len(stored.residues)):
residue1 = selection + " and r. " + stored.residues[r1][
1] + " and i. " + stored.residues[r1][0]
sele1 = residue1 + " and n. ca+c+c+o+n"
sele2 = residue1 + " and !n. ca+c+c+o+n+cb"
print("unbond ", sele1, ",", sele2)
cmd.unbond(sele1, sele2)
for r2 in range(r1 + 1, len(stored.residues)):
residue2 = selection + " and r. " + stored.residues[r2][
1] + " and i. " + stored.residues[r2][0]
if int(stored.residues[r1][0]) != int(stored.residues[r2][0]):
sele1 = residue1
sele2 = residue2
print("unbond ", sele1, ",", sele2)
cmd.unbond(sele1, sele2)
if int(stored.residues[r2][0]) == (int(stored.residues[r1][0]) +
1):
sele1 = residue1 + " and n. c"
sele2 = residue2 + " and n. n"
print("bond ", sele1, ",", sele2)
cmd.bond(sele1, sele2)
# FIX RESIDUE SIDE CHAIN
if stored.residues[r1][1] == "PRO":
sele1 = residue1 + " and n. n"
sele2 = residue1 + " and n. cd"
print("bond ", sele1, ",", sele2)
cmd.bond(sele1, sele2)
elif stored.residues[r1][1] == "THR":
sele1 = residue1 + " and !n. ca+og1+cg2+cb"
sele2 = residue1 + " and n. cb"
print("unbond ", sele1, ",", sele2)
cmd.unbond(sele1, sele2)
elif stored.residues[r1][1] == "ILE" or stored.residues[r1][1] == "VAL":
for resitype in ["ILE", "VAL"]:
sele1 = residue1 + " and !n. ca+cg1+cg2+cb"
sele2 = residue1 + " and n. cb"
print("unbond ", sele1, ",", sele2)
cmd.unbond(sele1, sele2)
elif stored.residues[r1][1] == "SER":
sele1 = residue1 + " and !n. ca+og+cb"
sele2 = residue1 + " and n. cb"
print("unbond ", sele1, ",", sele2)
cmd.unbond(sele1, sele2)
elif stored.residues[r1][1] == "CYS":
sele1 = residue1 + " and !n. ca+sg+cb"
sele2 = residue1 + " and n. cb"
print("unbond ", sele1, ",", sele2)
cmd.unbond(sele1, sele2)
else:
sele1 = residue1 + " and !n. ca+cg+cb"
sele2 = residue1 + " and n. cb"
print("unbond ", sele1, ",", sele2)
cmd.unbond(sele1, sele2)
# FIX CENTROID LEVEL
sele1 = residue1 + " and n. cen"
sele2 = residue1 + " and n. cb"
print("bond ", sele1, ",", sele2)
cmd.bond(sele1, sele2)
# FIX C-TERMINAL
if stored.residues[r1][0] == last_residue:
sele1 = residue1 + " and n. c"
sele2 = residue1 + " and n. oxt"
print("bond ", sele1, ",", sele2)
cmd.bond(sele1, sele2)
stored.cys = []
cmd.iterate(selection + ' and r. CYS and n. cb',
'stored.cys.append((resi,resn))')
if len(stored.cys) >= 2:
for r1 in range(len(stored.cys)):
for r2 in range(r1 + 1, len(stored.cys)):
if stored.cys[r1][0] != stored.cys[r2][0]:
sele1 = selection + " and i. " + stored.cys[r1][
0] + " and n. cb"
sele2 = selection + " and i. " + stored.cys[r2][
0] + " and n. cb"
dist = cmd.distance("tmpdist", sele1, sele2)
if dist < 4.0:
print(dist, sele1, ",", sele2)
sele1 = selection + " and i. " + stored.cys[r1][
0] + " and n. sg"
sele2 = selection + " and i. " + stored.cys[r2][
0] + " and n. sg"
print("bond ", sele1, ",", sele2)
cmd.bond(sele1, sele2)
cmd.delete("tmpdist")
cmd.pseudoatom("1-tess",
pos=[-2.168, 63.157, 26.015],
segi="lig",
resn="LIG",
resi=0,
chain=0,
name="O11")
cmd.select("c_pro", "/1-tess/pro///c*")
cmd.color("tv_green", "c_pro")
cmd.select("n_pro", "/1-tess/pro///n*")
cmd.color("tv_blue", "n_pro")
cmd.select("o_pro", "/1-tess/pro///o*")
cmd.color("tv_red", "o_pro")
cmd.select("s_pro", "/1-tess/pro///s*")
cmd.color("tv_yellow", "s_pro")
cmd.bond("/1-tess/lig/0/0/C1", "/1-tess/lig/0/0/C2")
cmd.bond("/1-tess/lig/0/0/C1", "/1-tess/lig/0/0/C3")
cmd.bond("/1-tess/lig/0/0/C1", "/1-tess/lig/0/0/C5")
cmd.bond("/1-tess/lig/0/0/C1", "/1-tess/lig/0/0/O1")
cmd.bond("/1-tess/lig/0/0/C1", "/1-tess/lig/0/0/O2")
cmd.bond("/1-tess/lig/0/0/C1", "/1-tess/lig/0/0/O5")
cmd.bond("/1-tess/lig/0/0/C1", "/1-tess/lig/0/0/O11")
cmd.bond("/1-tess/lig/0/0/C2", "/1-tess/lig/0/0/O1")
cmd.bond("/1-tess/lig/0/0/C2", "/1-tess/lig/0/0/O2")
cmd.bond("/1-tess/lig/0/0/C2", "/1-tess/lig/0/0/O3")
cmd.bond("/1-tess/lig/0/0/C2", "/1-tess/lig/0/0/O4")
cmd.bond("/1-tess/lig/0/0/C2", "/1-tess/lig/0/0/O5")
cmd.bond("/1-tess/pro/A/29/OG", "/1-tess/lig/0/0/O3")
cmd.bond("/1-tess/lig/0/0/C3", "/1-tess/lig/0/0/C4")
cmd.bond("/1-tess/lig/0/0/C3", "/1-tess/lig/0/0/C5")
cmd.bond("/1-tess/lig/0/0/C3", "/1-tess/lig/0/0/O2")
def create_object_with_flipkin_coords(mpobj, which_flips='NQ'):
'''Duplicate the mpobj molecule and apply the flipNQ/H group coordinates.
PARAMETERS
mpobj An MPObject instance
which_flips Either 'NQ' or 'H' to specify which flipkin to use
'''
flipkin_name = 'flipkin{}'.format(which_flips)
flipkin = mpobj.kin[flipkin_name]
flip_group = 'flip{}'.format(which_flips)
reduced_obj = mpobj.pdb['reduce']
flipped_obj = mpobj.pdb[flipkin_name]
cmd.create(flipped_obj, reduced_obj)
for vl in flipkin.vectorlists():
# Skip if not coordinates
if vl[0].vectorlist_name == 'x':
msg = 'skipping non-coords vectorlist {}'
logger.debug(msg.format(vl[0].vectorlist_name))
continue
# Skip everything except the'flipNQ' (or 'flipH') group
if vl[0].group[0] != flip_group:
msg = 'skipping non-{} vectorlist'.format(flip_group)
logger.debug(msg)
continue
logger.debug('begin flipping vectorlist')
for v in vl:
if not (v.atom[0] and v.atom[1]):
msg = 'vector {} was missing atoms: {}'.format(v, v.atom)
logger.warning(msg)
continue
macro = v.macro(1)
sel = v.sel(1)
logger.debug('atom to be flipped: {}\n sel: {}'.format(
macro, sel))
source_coords = v.coords[1]
target_sel = '{} and {}'.format(flipped_obj, sel)
msg = 'flipping atom {} to {}'.format(target_sel, source_coords)
logger.debug(msg)
ret = cmd.load_coords([source_coords], target_sel)
if ret == -1:
success = 0
a = v.atom[1]
if a['resn'] == 'HIS':
his_h = {
'HD1': {
'old_h': 'HE2',
'old_n': 'NE2',
'new_h': 'HD1',
'new_n': 'ND1',
},
'HE2': {
'old_h': 'HD1',
'old_n': 'ND1',
'new_h': 'HE2',
'new_n': 'NE2',
}
}
if a['name'] in his_h.keys():
# Reduce has switched which N is protonated. Let's move
# the old H atom and rename it.
resi_sel = '{} and chain {} and resi {}'.format(
flipped_obj, a['chain'], a['resi'])
h = his_h[a['name']]
old_h = '{} and name {}'.format(resi_sel, h['old_h'])
old_n = '{} and name {}'.format(resi_sel, h['old_n'])
new_h = '{} and name {}'.format(resi_sel, h['new_h'])
new_n = '{} and name {}'.format(resi_sel, h['new_n'])
# Break the old bond
cmd.unbond(old_h, old_n)
# Rename the atom
cmd.alter(old_h, 'name="{}"'.format(a['name']))
# Make the new bond
cmd.bond(new_h, new_n)
# Retry loading coordinates
ret = cmd.load_coords([source_coords], target_sel)
if not ret == -1:
success = 1
if not success:
msg = 'failed to load coords for {}!'.format(macro)
logger.warning(msg)
logger.debug('end flipping vectorlist')
CTERM_tuple: [CTERM_bonds_all, CTERM_bonds_double],
ARG_tuple: [ARG_bonds_all, ARG_bonds_double]
}
if bonds != 2:
lines = 4
print "Formating as delocalized bonds"
else:
lines = 1
print "Formating as double bonds"
# for all tuples (i.e format_dict.keys())
for p in format_dict.keys():
# go through list except ID at pos 1
for q in p[1:]:
# format bonds
for r in format_dict[p][0]:
cmd.unbond('%s and name %s' % (q, r[0]), '%s and name %s' % (q, r[1]))
cmd.bond('%s and name %s' % (q, r[0]), '%s and name %s' % (q, r[1]), lines)
if lines == 1:
# add double bonds
for r in format_dict[p][1]:
cmd.unbond('%s and name %s' % (q, r[0]), '%s and name %s' % (q, r[1]))
cmd.bond('%s and name %s' % (q, r[0]), '%s and name %s' % (q, r[1]), 2)
return bonds
cmd.extend("format_bonds", format_bonds)
cmd.auto_arg[0]['format_bonds'] = [lambda: cmd.Shortcut(['all', 'resn PHE+TYR+PTR+NIY+PNIY+TRP+NIW+HIS', 'resn GLU+ASP', 'resn ARG', 'last all']), 'selection=', ', ']
cmd.auto_arg[1]['format_bonds'] = [lambda: cmd.Shortcut(['4', '2', '1']), 'bonds=', '']
################################################################################
def format_bonds(
selection='all',
bonds=4,
):
'''
DESCRIPTION
Formats bonds in aromatic or charged residues
EXAMPLE
frag PHE
format_bonds
USAGE
format_bonds [ selection [, bonds ]]
ARGUMENTS
selection: <str> input selection {default: 'all'}
bonds: <int> toogles format of bonds
1: single bonds (deactivates valence display)
2: regular double bonds (activates valence display)
>=3: delocalized (activates valence display)
'''
# Selection
try:
# group selection with bracketing and select complete residues
selection = '(byres (' + str(selection) + '))'
# checks functional selection
cmd.count_atoms(selection)
except:
print("invalid selection")
return False
# PARAMETERS
try:
bonds = int(bonds)
except:
pass
if (not (bonds in [1, 2])):
bonds = 4
if bonds == 1:
cmd.set('valence', 0)
print("Valence display disabled!")
return bonds
else:
cmd.set('valence', 1)
print("Valence display enabled!")
# proceed
##### SELECTION BY OBJECT AND CHAIN #####
# variable for the selections
# get the names of the proteins in the selection
objects = cmd.get_object_list(selection)
# include chains
# subselect chains
names = []
for p in objects:
for chain in cmd.get_chains('model ' + p) or ['']:
names.append("(model %s and chain '%s')" % (p, chain))
##### SELECTION LISTS #####
# get TRP
stored.temp = []
for p in names:
cmd.iterate(('(%s) and (resn TRP+NIW) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p)
# the integer is to ensure unique keys
TRP_tuple = (1, ) + tuple(stored.temp)
# get PHETYR
stored.temp = []
for p in names:
cmd.iterate(('(%s) and (resn PHE+TYR+PTR+NIY+PNIY) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p)
PHETYR_tuple = (2, ) + tuple(stored.temp)
# get HIS
stored.temp = []
for p in names:
cmd.iterate(('(%s) and (resn HIS) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p)
HIS_tuple = (3, ) + tuple(stored.temp)
# get NITRO
stored.temp = []
for p in names:
cmd.iterate(('(%s) and (resn NIY+PNIY+NIW) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p)
NITRO_tuple = (4, ) + tuple(stored.temp)
# get GLU
stored.temp = []
for p in names:
cmd.iterate(('(%s) and (resn GLU) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p)
GLU_tuple = (5, ) + tuple(stored.temp)
# get ASP
stored.temp = []
for p in names:
cmd.iterate(('(%s) and (resn ASP) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p)
ASP_tuple = (6, ) + tuple(stored.temp)
# get CTERM
stored.temp = []
for p in names:
cmd.iterate(
'(byres (last %s)) and (not (hetatm)) '
'and (name OXT)' % (p),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p)
CTERM_tuple = (7, ) + tuple(stored.temp)
# get ARG
stored.temp = []
for p in names:
cmd.iterate(('(%s) and (resn ARG) '
'and (name CA)' % (p)),
'stored.temp.append("(%s and resi "+str(resi)+")")' % p)
ARG_tuple = (8, ) + tuple(stored.temp)
##### SELECTION TUPLES DONE #####
##### ATOM LISTS #####
TRP_bonds_all = [['CG', 'CD1'], ['CD1', 'NE1'], ['NE1', 'CE2'],
['CE2', 'CD2'], ['CD2', 'CG'], ['CD2', 'CE3'],
['CE3', 'CZ3'], ['CZ3', 'CH2'], ['CH2', 'CZ2'],
['CZ2', 'CE2']]
TRP_bonds_double = [['CG', 'CD1'], ['CE2', 'CD2'], ['CE3', 'CZ3'],
['CH2', 'CZ2']]
PHETYR_bonds_all = [['CG', 'CD1'], ['CD1', 'CE1'], ['CE1', 'CZ'],
['CZ', 'CE2'], ['CE2', 'CD2'], ['CD2', 'CG']]
PHETYR_bonds_double = [['CG', 'CD1'], ['CE1', 'CZ'], ['CE2', 'CD2']]
HIS_bonds_all = [
['CG', 'CD2'],
['CD2', 'NE2'],
['NE2', 'CE1'],
['CE1', 'ND1'],
['ND1', 'CG'],
]
HIS_bonds_double = [['CG', 'CD2'], ['CE1', 'ND1']]
NITRO_bonds_all = [['NN', 'O1'], ['NN', 'O2']]
NITRO_bonds_double = [['NN', 'O1']]
GLU_bonds_all = [['CD', 'OE1'], ['CD', 'OE2']]
GLU_bonds_double = [['CD', 'OE1']]
ASP_bonds_all = [['CG', 'OD1'], ['CG', 'OD2']]
ASP_bonds_double = [['CG', 'OD1']]
CTERM_bonds_all = [['C', 'O'], ['C', 'OXT']]
CTERM_bonds_double = [['C', 'O']]
ARG_bonds_all = [['CZ', 'NH1'], ['CZ', 'NH2']]
ARG_bonds_double = [['CZ', 'NH1']]
##### FORMATING #####
# dictionary: entries:atoms
format_dict = {
TRP_tuple: [TRP_bonds_all, TRP_bonds_double],
PHETYR_tuple: [PHETYR_bonds_all, PHETYR_bonds_double],
HIS_tuple: [HIS_bonds_all, HIS_bonds_double],
NITRO_tuple: [NITRO_bonds_all, NITRO_bonds_double],
GLU_tuple: [GLU_bonds_all, GLU_bonds_double],
ASP_tuple: [ASP_bonds_all, ASP_bonds_double],
CTERM_tuple: [CTERM_bonds_all, CTERM_bonds_double],
ARG_tuple: [ARG_bonds_all, ARG_bonds_double]
}
if bonds != 2:
lines = 4
print("Formating as delocalized bonds")
else:
lines = 1
print("Formating as double bonds")
# for all tuples (i.e format_dict.keys())
for p in list(format_dict.keys()):
# go through list except ID at pos 1
for q in p[1:]:
# format bonds
for r in format_dict[p][0]:
cmd.unbond('%s and name %s' % (q, r[0]),
'%s and name %s' % (q, r[1]))
cmd.bond('%s and name %s' % (q, r[0]),
'%s and name %s' % (q, r[1]), lines)
if lines == 1:
# add double bonds
for r in format_dict[p][1]:
cmd.unbond('%s and name %s' % (q, r[0]),
'%s and name %s' % (q, r[1]))
cmd.bond('%s and name %s' % (q, r[0]),
'%s and name %s' % (q, r[1]), 2)
return bonds
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 add_missing_atoms(selection='all', cycles=200, quiet=1):
'''
DESCRIPTION
Mutate those residues to themselves which have missing atoms
SEE ALSO
stub2ala
'''
from collections import defaultdict
from chempy import fragments
cycles, quiet = int(cycles), int(quiet)
reference = {
'ALA': set(['CB']),
'ARG': set(['CB', 'CG', 'NE', 'CZ', 'NH1', 'NH2', 'CD']),
'ASN': set(['CB', 'CG', 'OD1', 'ND2']),
'ASP': set(['CB', 'CG', 'OD1', 'OD2']),
'CYS': set(['CB', 'SG']),
'GLN': set(['CB', 'CG', 'CD', 'NE2', 'OE1']),
'GLU': set(['CB', 'CG', 'OE2', 'CD', 'OE1']),
'GLY': set([]),
'HIS': set(['CE1', 'CB', 'CG', 'CD2', 'ND1', 'NE2']),
'ILE': set(['CB', 'CD1', 'CG1', 'CG2']),
'LEU': set(['CB', 'CG', 'CD1', 'CD2']),
'LYS': set(['CB', 'CG', 'NZ', 'CE', 'CD']),
'MET': set(['CB', 'CG', 'CE', 'SD']),
'PHE': set(['CE1', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
'PRO': set(['CB', 'CG', 'CD']),
'SER': set(['OG', 'CB']),
'THR': set(['CB', 'OG1', 'CG2']),
'TRP': set(['CZ2', 'CB', 'CG', 'CH2', 'CE3', 'CD1', 'CD2', 'CZ3', 'NE1', 'CE2']),
'TYR': set(['CE1', 'OH', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
'VAL': set(['CB', 'CG1', 'CG2']),
}
namedsele = cmd.get_unused_name('_')
cmd.select(namedsele, selection, 0)
namelists = defaultdict(list)
cmd.iterate('(%s) and polymer' % namedsele,
'namelists[model,segi,chain,resn,resi,resv].append(name)',
space=locals())
sele_dict = defaultdict(list)
tmp_name = cmd.get_unused_name('_')
for key, namelist in namelists.items():
resn = key[3]
if resn not in reference:
if not quiet:
print(' Unknown residue:', resn)
continue
if not reference[resn].issubset(namelist):
try:
frag = fragments.get(resn.lower())
for a in frag.atom:
a.segi = key[1]
a.chain = key[2]
a.resi = key[4]
a.resi_number = key[5]
cmd.load_model(frag, tmp_name, 1, zoom=0)
skey = '/%s/%s/%s/%s`%s' % key[:5]
cmd.remove(skey + ' and not name N+C+O+OXT+CA')
cmd.align(tmp_name, skey + ' and name N+C+CA', cycles=0)
cmd.remove(tmp_name + ' and (name N+C+O+CA or hydro)')
cmd.fuse('name CB and ' + tmp_name, 'name CA and ' + skey, move=0)
if resn == 'PRO':
cmd.bond(skey + '/N', skey + '/CD')
cmd.unpick()
cmd.delete(tmp_name)
sele_dict[key[0]].append(skey)
if not quiet:
print(' Mutated ', skey)
except:
print(' Mutating', skey, 'failed')
for model in sele_dict:
cmd.sort(model)
sculpt_relax(' '.join(sele_dict[model]), 0, 0, model, cycles)
cmd.delete(namedsele)
def load_ff(filename):
"""
Load a fDynamo force field file (.ff)
Re-bond ligands accordingly
Alter properties of all atoms:
- 'text_type' : atomtypes
- 'partial_charges' : charges
Parameters
----------
filename : str
file path
"""
print(f" pyDYNAMON: reading \"{filename}\"")
# residue names excluded from re-bonding
rebond_excluded = []
rebond_excluded.extend(aa_dict.keys())
rebond_excluded.extend(["SOL", "NA", "CL"])
# read file as list of strings
with open(filename, "rt") as f:
ff_file = f.readlines()
# remove comment lines and blank lines
ff_file = [
line.strip() for line in ff_file
if line.strip() and not line.startswith("!")
]
# read residue atoms and bonds
topology = dict()
current_sect = None
for line in ff_file:
line = line.split("!")
keyword = line[0].split()[0].lower()
content = line[0].split()
if keyword == 'end':
current_sect = None
elif keyword == 'residues':
current_sect = keyword
elif current_sect == 'residues' or keyword == 'residue':
if keyword == 'residue': # new residue
current_sect = 'residues'
resname = content[1]
topology[resname] = dict()
continue
top = topology[resname]
if not topology[resname]: # first line (numbers)
top['natoms'] = int(content[0])
top['nbonds'] = int(content[1])
top['nimpropers'] = int(content[2])
top['atoms'] = dict()
top['bonds'] = []
top['impropers'] = []
elif len(top['atoms']) < top['natoms']:
param = {
'atomtype': str(content[1]).upper(),
'charge': float(content[2])
}
top['atoms'][str(content[0]).upper()] = param
elif len(top['bonds']) < top['nbonds']:
bonds = [(b.split()[0].upper(), b.split()[1].upper())
for b in " ".join(content).split(";") if b.strip()]
top['bonds'].extend(bonds)
elif len(top['impropers']) < top['nimpropers']:
impropers = [(i.split()[0].upper(), i.split()[1].upper(),
i.split()[2].upper(), i.split()[3].upper())
for i in " ".join(content).split(";")
if i.strip()]
top['impropers'].extend(impropers)
for resname, top in topology.items():
# atomtypes and partial charges
for name, param in top['atoms'].items():
cmd.alter(f"resn {resname} & name {name}",
f"partial_charge={param['charge']}")
cmd.alter(f"resn {resname} & name {name}",
f"text_type=\'{param['atomtype']}\'")
# unbond all and re-bond
if resname in rebond_excluded: continue
cmd.unbond(f"resn {resname}", f"resn {resname}")
for bond in top['bonds']:
cmd.bond(f"resn {resname} & name {bond[0]}",
f"resn {resname} & name {bond[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 do_library(self):
cmd=self.cmd
pymol=cmd._pymol
if not ((cmd.count_atoms("(%s) and name N"%src_sele)==1) and
(cmd.count_atoms("(%s) and name C"%src_sele)==1) and
(cmd.count_atoms("(%s) and name O"%src_sele)==1)):
self.clear()
return 1
cmd.feedback("push")
cmd.feedback("disable","selector","everythin")
cmd.feedback("disable","editor","actions")
self.prompt = [ 'Loading rotamers...']
self.bump_scores = []
state_best = 0
pymol.stored.name = 'residue'
cmd.iterate("first (%s)"%src_sele,'stored.name=model+"/"+segi+"/"+chain+"/"+resn+"`"+resi')
self.res_text = pymol.stored.name
cmd.select("_seeker_hilight",src_sele)
auto_zoom = cmd.get_setting_text('auto_zoom')
cmd.set('auto_zoom',"0",quiet=1)
cmd.frame(0)
cmd.delete(frag_name)
if self.auto_center:
cmd.center(src_sele,animate=-1)
self.lib_mode = self.mode
if self.lib_mode=="current":
pymol.stored.resn=""
cmd.iterate("(%s & name CA)"%src_sele,"stored.resn=resn")
rot_type = _rot_type_xref.get(pymol.stored.resn,pymol.stored.resn)
if (self.c_cap!='none') or (self.n_cap!='none') or (self.hyd != 'auto'):
self.lib_mode = rot_type # force fragment-based load
else:
cmd.create(frag_name,src_sele,1,1)
if self.c_cap=='open':
cmd.remove("%s and name OXT"%frag_name)
if self.lib_mode!='current':
rot_type = self.lib_mode
frag_type = self.lib_mode
if (self.n_cap == 'posi') and (frag_type[0:3]!='NT_'):
if not ( cmd.count_atoms(
"elem C & !(%s) & (bto. (name N & (%s))) &! resn ACE"%
(src_sele,src_sele))):
# use N-terminal fragment
frag_type ="NT_"+frag_type
if (self.c_cap == 'nega') and (frag_type[0:3]!='CT_'):
if not ( cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele))):
# use C-terminal fragment
frag_type ="CT_"+frag_type
if rot_type[0:3] in [ 'NT_', 'CT_' ]:
rot_type = rot_type[3:]
rot_type = _rot_type_xref.get(rot_type, rot_type)
cmd.fragment(frag_type.lower(), frag_name, origin=0)
# trim off hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# copy identifying information
cmd.alter("?%s & name CA" % src_sele, "stored.identifiers = (segi, chain, resi, ss, color)", space=self.space)
cmd.alter("?%s" % frag_name, "(segi, chain, resi, ss) = stored.identifiers[:4]", space=self.space)
# move the fragment
if ((cmd.count_atoms("(%s & name CB)"%frag_name)==1) and
(cmd.count_atoms("(%s & name CB)"%src_sele)==1)):
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name CB)"%frag_name,
"(%s & name CB)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
else:
cmd.pair_fit("(%s & name CA)"%frag_name,
"(%s & name CA)"%src_sele,
"(%s & name C)"%frag_name,
"(%s & name C)"%src_sele,
"(%s & name N)"%frag_name,
"(%s & name N)"%src_sele)
# fix the carbonyl position...
cmd.iterate_state(1,"(%s & name O)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name O)"%frag_name,"(x,y,z)=stored.list")
if cmd.count_atoms("(%s & name OXT)"%src_sele):
cmd.iterate_state(1,"(%s & name OXT)"%src_sele,"stored.list=[x,y,z]")
cmd.alter_state(1,"(%s & name OXT)"%frag_name,"(x,y,z)=stored.list")
elif cmd.count_atoms("(%s & name OXT)"%frag_name): # place OXT if no template exists
angle = cmd.get_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name O)"%frag_name)
cmd.protect("(%s & name O)"%frag_name)
cmd.set_dihedral("(%s & name N)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name C)"%frag_name,
"(%s & name OXT)"%frag_name,180.0+angle)
cmd.deprotect(frag_name)
# fix the hydrogen position (if any)
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%frag_name)==1:
if cmd.count_atoms("(hydro and bound_to (name N & (%s)))"%src_sele)==1:
cmd.iterate_state(1,"(hydro and bound_to (name N & (%s)))"%src_sele,
"stored.list=[x,y,z]")
cmd.alter_state(1,"(hydro and bound_to (name N & (%s)))"%frag_name,
"(x,y,z)=stored.list")
elif cmd.select(tmp_sele1,"(name C & bound_to (%s and elem N))"%src_sele)==1:
# position hydro based on location of the carbonyl
angle = cmd.get_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
tmp_sele1)
cmd.set_dihedral("(%s & name C)"%frag_name,
"(%s & name CA)"%frag_name,
"(%s & name N)"%frag_name,
"(%s & name H)"%frag_name,180.0+angle)
cmd.delete(tmp_sele1)
# add c-cap (if appropriate)
if self.c_cap in [ 'amin', 'nmet' ]:
if not cmd.count_atoms("elem N & !(%s) & (bto. (name C & (%s))) & !resn NME+NHH"%
(src_sele,src_sele)):
if cmd.count_atoms("name C & (%s)"%(frag_name))==1:
if self.c_cap == 'amin':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nhh')
elif self.c_cap == 'nmet':
editor.attach_amino_acid("name C & (%s)"%(frag_name), 'nme')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & bound_to (name C & (%s))"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
# add n-cap (if appropriate)
if self.n_cap in [ 'acet' ]:
if not cmd.count_atoms("elem C & !(%s) & (bto. (name N & (%s))) & !resn ACE "%
(src_sele,src_sele)):
if cmd.count_atoms("name N & (%s)"%(frag_name))==1:
if self.n_cap == 'acet':
editor.attach_amino_acid("name N & (%s)"%(frag_name), 'ace')
if cmd.count_atoms("hydro & bound_to (name N & bound_to (name C & (%s)))"%frag_name):
cmd.h_fix("name N & (%s)"%frag_name)
# trim hydrogens
if (self.hyd == 'none'):
cmd.remove("("+frag_name+" and hydro)")
elif (self.hyd == 'auto'):
if cmd.count_atoms("("+src_sele+") and hydro")==0:
cmd.remove("("+frag_name+" and hydro)")
cartoon = (cmd.count_atoms("(%s & name CA & rep cartoon)"%src_sele)>0)
sticks = (cmd.count_atoms("(%s & name CA & rep sticks)"%src_sele)>0)
cmd.delete(obj_name)
key = rot_type
lib = None
if self.dep == 'dep':
try:
result = cmd.phi_psi("%s"%src_sele)
if len(result)==1:
(phi,psi) = list(result.values())[0]
(phi,psi) = (int(10*round(phi/10)),int(10*(round(psi/10))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(20*round(phi/20)),int(20*(round(psi/20))))
key = (rot_type,phi,psi)
if key not in self.dep_library:
(phi,psi) = (int(60*round(phi/60)),int(60*(round(psi/60))))
key = (rot_type,phi,psi)
lib = self.dep_library.get(key,None)
except:
pass
if lib == None:
key = rot_type
lib = self.ind_library.get(key,None)
if (lib!= None) and self.dep == 'dep':
print(' Mutagenesis: no phi/psi, using backbone-independent rotamers.')
if lib != None:
state = 1
for a in lib:
cmd.create(obj_name,frag_name,1,state)
if state == 1:
cmd.select(mut_sele,"(byres (%s like %s))"%(obj_name,src_sele))
if rot_type=='PRO':
cmd.unbond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
for b in a.keys():
if b!='FREQ':
cmd.set_dihedral("(%s & n;%s)"%(mut_sele,b[0]),
"(%s & n;%s)"%(mut_sele,b[1]),
"(%s & n;%s)"%(mut_sele,b[2]),
"(%s & n;%s)"%(mut_sele,b[3]),
a[b],state=state)
else:
cmd.set_title(obj_name,state,"%1.1f%%"%(a[b]*100))
if rot_type=='PRO':
cmd.bond("(%s & name N)"%mut_sele,"(%s & name CD)"%mut_sele)
state = state + 1
cmd.delete(frag_name)
print(" Mutagenesis: %d rotamers loaded."%len(lib))
if self.bump_check:
cmd.delete(bump_name)
cmd.create(bump_name,
"(((byobj %s) within 6 of (%s and not name N+C+CA+O+H+HA)) and (not (%s)))|(%s)"%
(src_sele,mut_sele,src_sele,mut_sele),singletons=1)
cmd.color("gray50",bump_name+" and elem C")
cmd.set("seq_view",0,bump_name,quiet=1)
cmd.hide("everything",bump_name)
if ((cmd.select(tmp_sele1, "(name N & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2, "(name C & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
if ((cmd.select(tmp_sele1,"(name C & (%s in (neighbor %s)))"%
(bump_name,src_sele)) == 1) and
(cmd.select(tmp_sele2,"(name N & (%s in %s))"%
(bump_name,mut_sele)) == 1)):
cmd.bond(tmp_sele1,tmp_sele2)
cmd.delete(tmp_sele1)
cmd.delete(tmp_sele2)
cmd.protect("%s and not (%s in (%s and not name N+C+CA+O+H+HA))"%
(bump_name,bump_name,mut_sele))
cmd.sculpt_activate(bump_name)
cmd.show("cgo",bump_name)
# draw the bumps
cmd.set("sculpt_vdw_vis_mode",1,bump_name)
state = 1
score_best = 1e6
for a in lib:
score = cmd.sculpt_iterate(bump_name, state, 1)
self.bump_scores.append(score)
if score < score_best:
state_best = state
score_best = score
state = state + 1
cmd.delete(mut_sele)
else:
cmd.create(obj_name,frag_name,1,1)
print(" Mutagenesis: no rotamers found in library.")
cmd.set("seq_view",0,obj_name,quiet=1)
pymol.util.cbaw(obj_name)
cmd.hide("("+obj_name+")")
cmd.show(self.rep,obj_name)
cmd.show('lines',obj_name) #neighbor always show lines
if cartoon:
cmd.show("cartoon",obj_name)
if sticks:
cmd.show("sticks",obj_name)
cmd.set('auto_zoom',auto_zoom,quiet=1)
cmd.delete(frag_name)
cmd.frame(state_best)
cmd.unpick()
cmd.feedback("pop")
def 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 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 visualize_path((path, freq, pdb, outfile)):
nodes = path.split('=>')
save_pse = True
#print outfile
#print freq
#sys.exit()
#print nodes
node_color = sns.color_palette("Reds", n_colors=len(nodes))
node_color.reverse()
#print node_color
cmd.reinitialize()
cmd.load(pdb)
cmd.hide("everything")
# cmd.show("ribbon")
cmd.show("cartoon")
#resa = re.sub(r':\w', ':', nodes[0])
(chain, resnum) = re.split(':\w', nodes[0])
a = "chain {} and resi {} and name CA".format(chain, resnum)
cmd.show("spheres", a)
colorname = "color" + str(0)
cmd.set_color(colorname, node_color[0])
cmd.color(colorname, a)
cmd.label(a, '" %s:%s" % (resi, resn)')
cmd.set("label_color", "red", a)
#cmd.label(a, '"%s" % (resi)')
for i in range(1, len(nodes)):
#resb = re.sub(r':\w', ':', nodes[i])
(chain, resnum) = re.split(':\w', nodes[i])
b = "chain {} and resi {} and name CA".format(chain, resnum)
#print a,b
cmd.bond(a, b)
cmd.set_bond("line_width", 5, a, b)
cmd.set_bond("line_color", "red", a, b)
cmd.show("lines", a)
cmd.show("spheres", a)
cmd.show("lines", b)
cmd.show("spheres", b)
colorname = "color" + str(i)
cmd.set_color(colorname, node_color[i])
cmd.color(colorname, b)
#cmd.label(b,'" %s:%s" % (resi, resn)')
cmd.label(b, '" %s%s" % (one_letter[resn],resi)')
#cmd.label(b, '"%s" % (resi)')
a = b
#cmd.color(node_color[len)],b)
#cmd.space("cmyk")
cmd.set("ray_shadow", "off")
#cmd.bg_color("white")
#cmd.label_position([3,2,1])
cmd.set("label_position", (2, 2, 2))
sele = "chain A and resi 131 and not name H*"
cmd.show("sticks", sele)
norm_factor = freq[nodes[0]]
node_freqs = {k: freq[k] for k in nodes}
#print node_freqs
#print freq[nodes]
#print sorted(node_freqs.values())
node_freq_min = min(node_freqs.values())
#print node_freq_min
#sys.exit()
scale_cutoff = min(0.25, min(node_freqs.values()) / norm_factor)
#print nodes
#print node_freqs
#print freq
#sys.exit()
for res in freq.keys():
scale = freq[res] / norm_factor
#print res,freq[res],scale,scale_cutoff
if scale > scale_cutoff:
(chain, resnum) = re.split(':\w', res)
sele = "chain {} and resi {} and name CA".format(chain, resnum)
cmd.show("spheres", sele)
cmd.set("sphere_scale", scale, selection=sele)
if not res in nodes: #give residue not on highest freq path a different color
last_color = len(nodes) - 1
#colorname="color"+str(last_color)
colorname = "grey60" #color" + str(last_color)
cmd.color(colorname, sele)
cmd.label(sele, '" %s%s" % (one_letter[resn],resi)')
cmd.util.cnc(sele)
#cmd.center("chain A")
cmd.deselect()
### cut below here and paste into script ###
cmd.set_view([\
0.354133159, -0.915425777, 0.191264138,\
-0.626513124, -0.384070098, -0.678214610,\
0.694314659, 0.120348796, -0.709537089,\
-0.000188543, -0.000061929, -119.472831726,\
33.501632690, 81.432159424, 143.041992188,\
87.118530273, 151.834289551, -20.000000000\
])
### cut above here and paste into script ###
#outfile="{}cluster{}-{}.png".format(outfolder,cut,freq)
# if ray:
# cmd.ray()
# cmd.sync(10)
cmd.save(outfile)
cmd.sync(10)
if save_pse:
outfile_pse = re.sub('.png', '.pse', outfile)
cmd.save(outfile_pse)
cmd.sync(10)
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
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 add_missing_atoms(selection='all', cycles=200, quiet=1):
'''
DESCRIPTION
Mutate those residues to themselves which have missing atoms
SEE ALSO
stub2ala
'''
from collections import defaultdict
from chempy import fragments
cycles, quiet = int(cycles), int(quiet)
reference = {
'ALA': set(['CB']),
'ARG': set(['CB', 'CG', 'NE', 'CZ', 'NH1', 'NH2', 'CD']),
'ASN': set(['CB', 'CG', 'OD1', 'ND2']),
'ASP': set(['CB', 'CG', 'OD1', 'OD2']),
'CYS': set(['CB', 'SG']),
'GLN': set(['CB', 'CG', 'CD', 'NE2', 'OE1']),
'GLU': set(['CB', 'CG', 'OE2', 'CD', 'OE1']),
'GLY': set([]),
'HIS': set(['CE1', 'CB', 'CG', 'CD2', 'ND1', 'NE2']),
'ILE': set(['CB', 'CD1', 'CG1', 'CG2']),
'LEU': set(['CB', 'CG', 'CD1', 'CD2']),
'LYS': set(['CB', 'CG', 'NZ', 'CE', 'CD']),
'MET': set(['CB', 'CG', 'CE', 'SD']),
'PHE': set(['CE1', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
'PRO': set(['CB', 'CG', 'CD']),
'SER': set(['OG', 'CB']),
'THR': set(['CB', 'OG1', 'CG2']),
'TRP': set(['CZ2', 'CB', 'CG', 'CH2', 'CE3', 'CD1', 'CD2', 'CZ3', 'NE1', 'CE2']),
'TYR': set(['CE1', 'OH', 'CB', 'CG', 'CZ', 'CD1', 'CD2', 'CE2']),
'VAL': set(['CB', 'CG1', 'CG2']),
}
namedsele = cmd.get_unused_name('_')
cmd.select(namedsele, selection, 0)
namelists = defaultdict(list)
cmd.iterate('(%s) and polymer' % namedsele,
'namelists[model,segi,chain,resn,resi,resv].append(name)',
space=locals())
sele_dict = defaultdict(list)
tmp_name = cmd.get_unused_name('_')
for key, namelist in namelists.items():
resn = key[3]
if resn not in reference:
if not quiet:
print(' Unknown residue: + ' + resn)
continue
if not reference[resn].issubset(namelist):
try:
frag = fragments.get(resn.lower())
for a in frag.atom:
a.segi = key[1]
a.chain = key[2]
a.resi = key[4]
a.resi_number = key[5]
cmd.load_model(frag, tmp_name, 1, zoom=0)
skey = '/%s/%s/%s/%s`%s' % key[:5]
cmd.remove(skey + ' and not name N+C+O+OXT+CA')
cmd.align(tmp_name, skey + ' and name N+C+CA', cycles=0)
cmd.remove(tmp_name + ' and (name N+C+O+CA or hydro)')
cmd.fuse('name CB and ' + tmp_name, 'name CA and ' + skey, move=0)
if resn == 'PRO':
cmd.bond(skey + '/N', skey + '/CD')
cmd.unpick()
cmd.delete(tmp_name)
sele_dict[key[0]].append(skey)
if not quiet:
print(' Mutated ' + skey)
except:
print(' Mutating ' + skey + ' failed')
for model in sele_dict:
cmd.sort(model)
sculpt_relax(' '.join(sele_dict[model]), 0, 0, model, cycles)
cmd.delete(namedsele)
def garnish(file="topol.top", selection='all', gmx=None, fix_elastics=1, guess_prot=1, show=1):
"""
DESCRIPTION
Allow a coarse grained structure to be visualized in pymol like an atomistic structure
by drawing bonds and elastic network.
Without a top/tpr file, this function only adds bonds between the backbone beads
so they can be nicely visualized using line or stick representation.
Adding a top/tpr file provides topology information that can be used
to draw side chain and elastic bonds.
USAGE
garnish [file [, selection [, gmx]]]
ARGUMENTS
file = a tpr or topology file to extract bond information from (default: None)
selection = any selection to act upon (default: all)
gmx = gmx executable path (default: inferred by `which gmx`)
fix_elastics = fix elastic bonds based on atom id. Disable if your beads are
numbered non-sequentially (default: 1)
guess_prot = if file is not present, simply draw bonds between backbone atoms of a protein (default: 1)
show = adjust representation after drawing bonds (default: 1)
"""
fix_elastics = bool(int(fix_elastics))
guess_prot = bool(int(guess_prot))
show = bool(int(show))
# Retain order so pymol does not sort the atoms, giving a different result when saving the file
cmd.set("retain_order", 1)
if file:
# parse the file
sys_dict = parse(file, gmx)
# create System object and draw all the bonds
system = System(sys_dict, fix_elastics=fix_elastics)
system.draw_bonds(selection)
system.transfer_attributes(selection)
elif guess_prot:
bb_beads = get_chain_bb(selection)
# For each object and chain, draw bonds between BB beads
for obj, chains in bb_beads.items():
for _, bbs in chains.items():
# create bond tuples for "adjacent" backbone beads
bonds = [(bbs[i], bbs[i+1]) for i in range(len(bbs) - 1)]
for a, b in bonds:
try:
cmd.add_bond(obj, a, b)
except AttributeError:
cmd.bond(f"{obj} and ID {a}", f"{obj} and ID {b}")
else:
# show as spheres if no info on bonds is present
if show:
cmd.show_as('spheres', selection)
return
if show:
cmd.hide("everything", selection)
cmd.show_as("sticks", selection)
# Fix the view for elastics
cmd.color('orange', '*_elastics')
cmd.show_as("lines", '*_elastics')
# We could use this for debugging
return system
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')