def mutate_peptide(new_seq):
'''
mutate peptide to new_seq starting at second residue in the peptide
'''
cmd.copy(new_seq, "peptide_template")
aa1 = list("ACDEFGHIKLMNPQRSTVWY")
aa3 = "ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR".split(
)
aa123 = dict(zip(aa1, aa3))
for ind, aa in enumerate(new_seq, 2):
cmd.wizard("mutagenesis")
cmd.do("refresh_wizard")
print ind
print aa
# lets mutate residue 104 to GLN
cmd.get_wizard().set_mode(aa123[aa])
cmd.get_wizard().do_select("/{0}//B/{1}".format(new_seq, ind))
# Select the rotamer
#cmd.frame(1)
# Apply the mutation
cmd.get_wizard().apply()
def testSaveRef(self, format):
# for rms_cur (not all formats save all identifiers)
m = -1
cmd.set('retain_order')
cmd.fragment('ala', 'm1')
cmd.copy('m2', 'm1')
cmd.copy('m3', 'm1')
cmd.rotate('y', 90, 'm2')
cmd.align('m3', 'm2')
# with ref=m3
with testing.mktemp('.' + format) as filename:
cmd.save(filename, 'm2', ref='m3')
cmd.load(filename, 'm4')
self.assertAlmostEqual(cmd.rms_cur('m4', 'm1', matchmaker=m), 0.00, delta=1e-2)
self.assertAlmostEqual(cmd.rms_cur('m4', 'm2', matchmaker=m), 1.87, delta=1e-2)
# without ref
with testing.mktemp('.' + format) as filename:
cmd.save(filename, 'm2')
cmd.load(filename, 'm5')
self.assertAlmostEqual(cmd.rms_cur('m5', 'm2', matchmaker=m), 0.00, delta=1e-2)
self.assertAlmostEqual(cmd.rms_cur('m5', 'm1', matchmaker=m), 1.87, delta=1e-2)
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 builderMicelle(detergent, r, numberOfDetergents):
i = 0
numberOfDetergents = (int)(numberOfDetergents)
#FIXME: if number of detergents > 360, molecules may clash in space
if numberOfDetergents > 360:
x1 = range(-180, 180)
x2 = range(0, 360)
theta = ([random.choice(x1) for _ in range(numberOfDetergents)])
phi = ([random.choice(x2) for _ in range(numberOfDetergents)])
else:
theta = random.sample(range(-180, 180), numberOfDetergents)
phi = random.sample(range(0, 360), numberOfDetergents)
for t, p in zip(theta, phi):
i += 1
cmd.copy(f"seg{i}", detergent)
# randomly sample on a sphere
cmd.translate(f"[0,{r},0]", f"seg{i}")
cmd.rotate("x", f"{t}", f"seg{i}")
cmd.rotate("z", f"{p}", f"seg{i}")
s = f"micelle_{detergent}_{(int)(r)}_{(int)(numberOfDetergents)}"
cmd.create(f"{s}", "seg*")
cmd.delete("seg*")
#center(f"{s}")
#cmd.show_as("sticks","org")
# could be streched if necessary
# affineStretch(s, 10)
return s
def prepare(model, resi1, resi2, resi3, segis_for_save, segis_for_del):
resi1,resi2,resi3 = sorted((resi1,resi2,resi3))
cmd.fetch(model, async=0)
cmd.remove('not alt a+""')
# delete additional protein segis
if segis_for_del != '':
cmd.remove('segi {}'.format(segis_for_del.replace(' ', '+')))
# all_segis contains segis which are included to that protein part (symmetric) we need
all_segis = []
for resi in (resi1, resi2, resi3):
all_segis.append([])
cmd.iterate('/{}///{}/CA'.format(model, resi), \
'all_segis[-1].append(segi)', \
space={'all_segis': all_segis})
all_segis = [set(x) for x in all_segis]
all_segis = all_segis[0] | all_segis[1] | all_segis[2]
cmd.remove('not segi {}'.format(str_riffle(list(all_segis), '+')))
if type(segis_for_save) == list:
segis_for_save_fact = set(segis_for_save)
absent_segis_names = sorted(all_segis - segis_for_save_fact)
else:
segis_for_save_fact = absent_segis_names = sorted(all_segis)
model_save = '{}_save'.format(model)
cmd.copy(model_save, model)
cmd.remove('{} and not segi {}'.format(model, str_riffle(list(segis_for_save_fact), '+')))
return sorted(all_segis)
def object_tfm_interpolate(object_properties, number_of_frames, frameno):
tmpnames = []
for objnm, properties in object_properties.items():
[source_tfm, target_tfm, reverse, color,
small_molecule] = properties[:5]
transparency_range = properties[5] if len(properties) > 5 else None
frame = frameno
if reverse: frame = number_of_frames - frame
tfm = intermediate_tfm(source_tfm, target_tfm, number_of_frames, frame)
if objnm == "lipid": lipid_decimate(number_of_frames, frameno)
tmpnm = objnm + str(frameno)
cmd.copy(tmpnm, objnm, zoom=0)
cmd.transform_selection(tmpnm, tfm)
transparency = -1
if transparency_range:
transparency = transparency_range[0] \
+ float(frameno)/number_of_frames*(transparency_range[1]-transparency_range[0])
if small_molecule:
if objnm == "lipid":
style_lipid(tmpnm)
else:
style_substrate(tmpnm, mol_color[objnm], transparency)
else:
clump_representation([tmpnm],
color,
tmpnm,
small_molecule=small_molecule,
transparency=transparency)
tmpnames.append(tmpnm)
return tmpnames
def testSaveRef(self, format):
# for rms_cur (not all formats save all identifiers)
m = -1
cmd.set('retain_order')
cmd.fragment('ala', 'm1')
cmd.copy('m2', 'm1')
cmd.copy('m3', 'm1')
cmd.rotate('y', 90, 'm2')
cmd.align('m3', 'm2')
# with ref=m3
with testing.mktemp('.' + format) as filename:
cmd.save(filename, 'm2', ref='m3')
cmd.load(filename, 'm4')
self.assertAlmostEqual(cmd.rms_cur('m4', 'm1', matchmaker=m), 0.00, delta=1e-2)
self.assertAlmostEqual(cmd.rms_cur('m4', 'm2', matchmaker=m), 1.87, delta=1e-2)
# without ref
with testing.mktemp('.' + format) as filename:
cmd.save(filename, 'm2')
cmd.load(filename, 'm5')
self.assertAlmostEqual(cmd.rms_cur('m5', 'm2', matchmaker=m), 0.00, delta=1e-2)
self.assertAlmostEqual(cmd.rms_cur('m5', 'm1', matchmaker=m), 1.87, delta=1e-2)
def sewalign(first,second):
#hide waters
cmd.hide("(solvent and (all))")
#hide hydrogens
cmd.hide( 'sticks', 'elem H' )
cmd.hide( 'lines', 'elem H' )
#show cartoon
cmd.show("cartoon" ,"all")
#create duplicate of first
first_copy = first + "_copy"
cmd.copy(first_copy, first)
#select first 14 residues
cmd.select('node_9_selection', '(obj *_9_* and resi 1-14)')
cmd.select('node_12_selection', '(obj *_12_* and resi 1-14)')
cmd.select('node_15_selection', '(obj *_15_* and resi 1-14)')
alignment_1 = cmd.align(first, 'node_9_selection')
print alignment_1[0]
alignment_2 = cmd.align(second, 'node_12_selection')
print alignment_2[0]
alignment_3 = cmd.align(first_copy, 'node_15_selection')
print alignment_3[0]
def testIgnoreCase(self):
# check defaults
self.assertEqual(cmd.get_setting_int('ignore_case'), 1)
self.assertEqual(cmd.get_setting_int('ignore_case_chain'), 0)
# data
natoms = 10
cmd.fragment('ala', 'm1')
cmd.copy('m2', 'm1')
cmd.alter('m1', 'chain, segi = "C", "S"')
cmd.alter('m2', 'chain, segi = "c", "s"')
cmd.alter('m2', 'resn, name = resn.lower(), name.lower()')
self.assertEqual(cmd.count_atoms('chain C'), natoms)
self.assertEqual(cmd.count_atoms('segi S'), natoms)
self.assertEqual(cmd.count_atoms('chain c'), natoms)
self.assertEqual(cmd.count_atoms('segi s'), natoms)
self.assertEqual(cmd.count_atoms('resn ALA'), natoms * 2)
self.assertEqual(cmd.count_atoms('resn ala'), natoms * 2)
self.assertEqual(cmd.count_atoms('name CA'), 2)
self.assertEqual(cmd.count_atoms('name ca'), 2)
cmd.set('ignore_case_chain')
self.assertEqual(cmd.count_atoms('chain C'), natoms * 2)
self.assertEqual(cmd.count_atoms('segi S'), natoms * 2)
self.assertEqual(cmd.count_atoms('chain c'), natoms * 2)
self.assertEqual(cmd.count_atoms('segi s'), natoms * 2)
cmd.set('ignore_case', 0)
self.assertEqual(cmd.count_atoms('resn ALA'), natoms)
self.assertEqual(cmd.count_atoms('resn ala'), natoms)
self.assertEqual(cmd.count_atoms('name CA'), 1)
self.assertEqual(cmd.count_atoms('name ca'), 1)
def mutate_peptide( new_seq ):
'''
mutate peptide to new_seq starting at second residue in the peptide
'''
cmd.copy(new_seq, "peptide_template")
aa1 = list("ACDEFGHIKLMNPQRSTVWY")
aa3 = "ALA CYS ASP GLU PHE GLY HIS ILE LYS LEU MET ASN PRO GLN ARG SER THR VAL TRP TYR".split()
aa123 = dict(zip(aa1,aa3))
for ind, aa in enumerate(new_seq,2):
cmd.wizard("mutagenesis")
cmd.do("refresh_wizard")
print ind
print aa
# lets mutate residue 104 to GLN
cmd.get_wizard().set_mode(aa123[aa])
cmd.get_wizard().do_select("/{0}//B/{1}".format(new_seq, ind))
# Select the rotamer
#cmd.frame(1)
# Apply the mutation
cmd.get_wizard().apply()
def testIgnoreCase(self):
# check defaults
self.assertEqual(cmd.get_setting_int('ignore_case'), 1)
self.assertEqual(cmd.get_setting_int('ignore_case_chain'), 0)
# data
natoms = 10
cmd.fragment('ala', 'm1')
cmd.copy('m2', 'm1')
cmd.alter('m1', 'chain, segi = "C", "S"')
cmd.alter('m2', 'chain, segi = "c", "s"')
cmd.alter('m2', 'resn, name = resn.lower(), name.lower()')
self.assertEqual(cmd.count_atoms('chain C'), natoms)
self.assertEqual(cmd.count_atoms('segi S'), natoms)
self.assertEqual(cmd.count_atoms('chain c'), natoms)
self.assertEqual(cmd.count_atoms('segi s'), natoms)
self.assertEqual(cmd.count_atoms('resn ALA'), natoms * 2)
self.assertEqual(cmd.count_atoms('resn ala'), natoms * 2)
self.assertEqual(cmd.count_atoms('name CA'), 2)
self.assertEqual(cmd.count_atoms('name ca'), 2)
cmd.set('ignore_case_chain')
self.assertEqual(cmd.count_atoms('chain C'), natoms * 2)
self.assertEqual(cmd.count_atoms('segi S'), natoms * 2)
self.assertEqual(cmd.count_atoms('chain c'), natoms * 2)
self.assertEqual(cmd.count_atoms('segi s'), natoms * 2)
cmd.set('ignore_case', 0)
self.assertEqual(cmd.count_atoms('resn ALA'), natoms)
self.assertEqual(cmd.count_atoms('resn ala'), natoms)
self.assertEqual(cmd.count_atoms('name CA'), 1)
self.assertEqual(cmd.count_atoms('name ca'), 1)
def apply_symmetry(R, t, inchain, outchain):
cmd.copy('symm', f'inpdb')
coords = cmd.get_coords('symm')
cmd.remove(f'symm and not chain {inchain}')
coords_symm = (R.dot(coords.T)).T + t
cmd.load_coords(coords_symm, 'symm')
myspace = {'outchain': outchain}
cmd.alter('symm', 'chain=f"{outchain}"', space=myspace)
def growShape(self, lastNode, idList, newNode):
rel = self.xDB['pairsData'][lastNode][newNode]
self.transformPymolShape(idList, [0, 0, 0], rel['rot'], rel['tran'])
copyNodeName = newNode + '#' + str(len(idList))
cmd.copy(copyNodeName, newNode)
idList = np.append(idList, copyNodeName)
return idList, rel['rot'], rel['tran'], copyNodeName
def builder(residues, bonds, mol_name):
"""Using the list generated by read_input connects monosacharides in
a single oligosaccharide"""
cmd.set('suspend_updates', 'on')
cmd.feedback('disable', 'executive', 'actions')
every_object = cmd.get_object_list('all')
if mol_name in every_object:
cmd.delete(mol_name)
every_object.remove(mol_name)
if every_object:
sel = 'not (' + ' or '.join(every_object) + ') and'
else:
sel = ''
for i in range(0, len(residues)):
res_name = residues[i]
cmd.load(os.path.join(path, 'db_glycans', '%s.pdb' % res_name))
cmd.set_name(res_name,
i) #rename object (necessary to avoid repeating names)
cmd.alter(i, 'resi = %s' % i) #name residues for further referencing
cmd.sort(i)
for i in range(0, len(bonds)):
resi_i, resi_j, atom_i, atom_j = bonds[i][0], bonds[i][2], bonds[i][
4], bonds[i][5]
if atom_i > atom_j:
cmd.remove('%s (resi %s and name O%s+H%so)' %
(sel, resi_j, atom_j, atom_j))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_i, atom_i))
cmd.fuse('%s (resi %s and name O%s)' % (sel, resi_i, atom_i),
'%s (resi %s and name C%s)' % (sel, resi_j, atom_j),
mode=2)
else:
cmd.remove('%s (resi %s and name O%s+H%so)' %
(sel, resi_i, atom_i, atom_i))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_j, atom_j))
cmd.fuse('%s (resi %s and name C%s)' % (sel, resi_i, atom_i),
'%s (resi %s and name O%s)' % (sel, resi_j, atom_j),
mode=2)
cmd.delete('%s' % i)
cmd.copy(mol_name, '%s' % resi_j)
cmd.delete('%s' % resi_j)
for i in range(0, len(bonds)):
set_phi(mol_name, bonds[i], -60)
set_psi(mol_name, bonds[i], 120)
cmd.delete('pk1')
cmd.delete('pk2')
cmd.delete('pkbond')
cmd.delete('pkmol')
if babel:
fast_min(mol_name, 5000)
minimize(mol_name)
else:
fast_min(mol_name, 5000)
cmd.feedback('enable', 'executive', 'actions')
cmd.set('suspend_updates', 'off')
def refinements(self):
"""Refinements for the visualization"""
# Show sticks for all residues interacing with the ligand
cmd.select(
'AllBSRes',
'byres (Hydrophobic-P or HBondDonor-P or HBondAccept-P or PosCharge-P or NegCharge-P or '
'StackRings-P or PiCatRing-P or HalogenAcc or Metal-P)')
cmd.show('sticks', 'AllBSRes')
# Show spheres for the ring centroids
cmd.hide('everything', 'centroids*')
cmd.show('nb_spheres', 'centroids*')
# Show spheres for centers of charge
if self.object_exists('Chargecenter-P') or self.object_exists(
'Chargecenter-L'):
cmd.hide('nonbonded', 'chargecenter*')
cmd.show('spheres', 'chargecenter*')
cmd.set('sphere_scale', 0.4, 'chargecenter*')
cmd.color('yellow', 'chargecenter*')
cmd.set('valence', 1) # Show bond valency (e.g. double bonds)
# Optional cartoon representation of the protein
cmd.copy('%sCartoon' % self.protname, self.protname)
cmd.show('cartoon', '%sCartoon' % self.protname)
cmd.show('sticks', '%sCartoon' % self.protname)
cmd.set('stick_transparency', 1, '%sCartoon' % self.protname)
# Resize water molecules. Sometimes they are not heteroatoms HOH, but part of the protein
cmd.set('sphere_scale', 0.2, 'resn HOH or Water'
) # Needs to be done here because of the copy made
cmd.set('sphere_transparency', 0.4, '!(resn HOH or Water)')
if 'Centroids*' in cmd.get_names("selections"):
cmd.color('grey80', 'Centroids*')
cmd.hide('spheres', '%sCartoon' % self.protname)
cmd.hide('cartoon', '%sCartoon and resn DA+DG+DC+DU+DT+A+G+C+U+T' %
self.protname) # Hide DNA/RNA Cartoon
if self.ligname == 'SF4': # Special case for iron-sulfur clusters, can't be visualized with sticks
cmd.show('spheres', '%s' % self.ligname)
cmd.hide(
'everything',
'resn HOH &!Water') # Hide all non-interacting water molecules
cmd.hide(
'sticks', '%s and !%s and !AllBSRes' %
(self.protname, self.ligname)) # Hide all non-interacting residues
if self.ligandtype in ['PEPTIDE', 'INTRA']:
self.adapt_for_peptides()
if self.ligandtype == 'INTRA':
self.adapt_for_intra()
def series_resfile(color="orange"):
# Main PDB File Name
object = cmd.get_names()[0]
counter = 0
# Read Rosetta Resfile
for fname in glob.glob('*.resfile'):
counter += 1
if counter == 1:
fname_rem = fname
cmd.copy(fname, object)
for line in open(fname):
# Split Resfile Line by Tab
data = line.split('\t')
# Only Consider Lines that Start with Residue Numbers
if data[0].isdigit():
# Get Revalent Data
pos = data[0]
chain = data[1]
mut = data[3]
# Generate Mutation Label
label = mut
label_list = list(label)
label_list.insert(1, "%s" % (pos))
label = ''.join(label_list)
# PyMOL Color and Label
cmd.color(color,
"resi %s and chain %s and %s" % (pos, chain, fname))
cmd.label(
"resi %s and chain %s and name ca and %s" %
(pos, chain, fname), "\'%s\'" % (label))
# Output Comments to the Console
elif line[:1] == "#":
# Remove newline feeds
line.rstrip("\n")
print "\n%s" % (line)
cmd.disable('all')
cmd.enable(fname_rem)
cmd.orient
cmd.set_key('pgup', move_up)
cmd.set_key('pgdn', move_down)
def sample_uniform(pose, con_matrix, angles_prob):
random_angle = np.random.choice(['phi', 'psi', 'chi'], p=angles_prob)
random_res = np.random.random_integers(0, len(con_matrix) - 1)
bond = con_matrix[random_res]
cmd.copy('tmp', pose)
if random_angle == "phi":
phi = get_phi('tmp', bond)
angle_value = np.random.normal(phi, 30)
set_phi('tmp', bond, angle_value)
elif random_angle == "psi":
psi = get_psi('tmp', bond)
angle_value = np.random.normal(psi, 30)
set_psi('tmp', bond, angle_value)
else:
set_chi('tmp', bond)
set_chi('tmp', bond)
def sample_uniform(pose, con_matrix, angles_prob):
random_angle = np.random.choice(['phi', 'psi', 'chi'], p=angles_prob)
random_res = np.random.random_integers(0, len(con_matrix)-1)
bond = con_matrix[random_res]
cmd.copy('tmp', pose)
if random_angle == "phi":
phi = get_phi('tmp', bond)
angle_value = np.random.normal(phi, 30)
set_phi('tmp', bond, angle_value)
elif random_angle == "psi":
psi = get_psi('tmp', bond)
angle_value = np.random.normal(psi, 30)
set_psi('tmp', bond, angle_value)
else:
set_chi('tmp', bond)
set_chi('tmp', bond)
def _check_optimzer_results_pairwise_5(self, exit_test_mode=False):
'''Creates groups for all pairs which are connected. And show them all in grid mode
:warning: only designed for pairwise restraints
'''
self.check_results_mode = 5
# 1) Check which molecule pairs have connections
pair_exists = {}
for i_m1 in range(len(self.pymol_molecule_objects)):
for i_m2 in range(len(self.pymol_molecule_objects)):
pair_exists.update({str(i_m1 + 1) + str(i_m2 + 1): False})
for r in self.logic_handler.selected_restraints:
pair_exists.update({str(r.atoms[0].resi) + str(r.atoms[1].resi): True})
mol_pairs = [(str(i_m1 + 1), str(i_m2 + 1)) for i_m1 in range(len(self.pymol_molecule_objects) - 1) for i_m2 in
range(i_m1, len(self.pymol_molecule_objects)) if
pair_exists[str(i_m1 + 1) + str(i_m2 + 1)] or pair_exists[str(i_m2 + 1) + str(i_m1 + 1)]]
print(mol_pairs, mv=1)
cmd.disable('all')
for p in mol_pairs:
m1, m2 = p[0], p[1]
m1_name = m1 + '-' + m2 + 'mol_' + m1
m2_name = m1 + '-' + m2 + 'mol_' + m2
cmd.copy(m1 + '-' + m2 + 'mol_' + m1, 'mol_' + m1)
cmd.copy(m1 + '-' + m2 + 'mol_' + m2, 'mol_' + m2)
group_expression = m1_name + ' ' + m2_name
cmd.group('pair_' + m1 + '_' + m2, group_expression)
cmd.enable(group_expression)
cmd.set('grid_mode', 1)
cmd.reset()
if (exit_test_mode):
self.check_results_mode = 0
for p in mol_pairs:
m1_name = m1 + '-' + m2 + 'mol_' + m1
m2_name = m1 + '-' + m2 + 'mol_' + m2
group_expression = m1_name + ' ' + m2_name
cmd.delete(m1_name)
cmd.delete(m2_name)
cmd.ungroup('group_expression')
cmd.set('grid_mode', 0)
cmd.enable('all')
def builderCorona(theta, fi, detergent, r, detR):
# Build symmates with desired rotations
thetaSteps = len(theta)
angleVer = np.linspace(-90, 90, thetaSteps)
i = 0
for t, a in zip(theta, angleVer):
for f in fi:
i += 1
cmd.copy(f"seg{i}", detergent)
# corona
cmd.rotate("x", f"{a}", f"seg{i}")
cmd.translate(f"[0,{r + 0.5*detR*np.cos(np.deg2rad(a))},0]",
f"seg{i}")
cmd.translate(f"[0,0,{(r+detR)*np.sin(np.deg2rad(t))}]", f"seg{i}")
cmd.rotate("z", f"{f}", f"seg{i}")
cmd.create("corona", "seg*")
cmd.delete("seg*")
def builder(residues, bonds, mol_name):
"""Using the list generated by read_input connects monosacharides in
a single oligosaccharide"""
cmd.set('suspend_updates', 'on')
cmd.feedback('disable', 'executive', 'actions')
every_object = cmd.get_object_list('all')
if mol_name in every_object:
cmd.delete(mol_name)
every_object.remove(mol_name)
if every_object:
sel = 'not (' + ' or '.join(every_object) + ') and'
else:
sel = ''
for i in range(0, len(residues)):
res_name = residues[i]
cmd.load(os.path.join(path, 'db_glycans', '%s.pdb' % res_name))
cmd.set_name(res_name, i) #rename object (necessary to avoid repeating names)
cmd.alter(i, 'resi = %s' % i) #name residues for further referencing
cmd.sort(i)
for i in range(0, len(bonds)):
resi_i, resi_j, atom_i, atom_j = bonds[i][0], bonds[i][2], bonds[i][4], bonds[i][5]
if atom_i > atom_j:
cmd.remove('%s (resi %s and name O%s+H%so)' % (sel, resi_j, atom_j, atom_j))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_i, atom_i))
cmd.fuse('%s (resi %s and name O%s)' % (sel, resi_i, atom_i), '%s (resi %s and name C%s)' % (sel, resi_j, atom_j), mode=2)
else:
cmd.remove('%s (resi %s and name O%s+H%so)' % (sel, resi_i, atom_i, atom_i))
cmd.remove('%s (resi %s and name H%so)' % (sel, resi_j, atom_j))
cmd.fuse('%s (resi %s and name C%s)' % (sel, resi_i, atom_i), '%s (resi %s and name O%s)' % (sel, resi_j, atom_j), mode=2)
cmd.delete('%s' % i)
cmd.copy(mol_name, '%s' % resi_j)
cmd.delete('%s' % resi_j)
for i in range(0, len(bonds)):
set_phi(mol_name, bonds[i], -60)
set_psi(mol_name, bonds[i], 120)
cmd.delete('pk1')
cmd.delete('pk2')
cmd.delete('pkbond')
cmd.delete('pkmol')
if babel:
fast_min(mol_name, 5000)
minimize(mol_name)
else:
fast_min(mol_name, 5000)
cmd.feedback('enable', 'executive', 'actions')
cmd.set('suspend_updates', 'off')
def builderMicelle(detergent, r, numberOfDetergents):
refresh()
i = 0
numberOfDetergents = int(numberOfDetergents)
# FIXME: if number of detergents > 360, molecules may clash in space
points = fibonacci_sphere(numberOfDetergents)
print("Rotating detergent molecule for build protocol...")
for x,y,z in points:
i += 1
t = np.degrees(np.arccos(z))
p = np.degrees(np.arctan(y/x))
cmd.copy("seg{}".format(i), detergent)
cmd.alter("seg{}".format(i), "resi={}".format(i)) # assign residue numbers
# put to to knot of fibonacci grid
center("seg{}".format(i))
cmd.translate("[0,{},0]".format(r), "seg{}".format(i))
if x < 0: cmd.rotate("z", 180, "seg{}".format(i))
cmd.rotate("z", str(t), "seg{}".format(i))
cmd.rotate("y", str(p), "seg{}".format(i))
#cmd.translate("[{},{},{}]".format(r * x, r * y, r * z), "seg{}".format(i))
# if numberOfDetergents > 360:
# x1 = range(-180, 180)
# x2 = range(0, 360)
# theta = ([random.choice(x1) for _ in range(numberOfDetergents)])
# phi = ([random.choice(x2) for _ in range(numberOfDetergents)])
# else:
# theta = random.sample(range(-180, 180), numberOfDetergents)
# phi = random.sample(range(0, 360), numberOfDetergents)
# for t, p in zip(theta, phi):
# i += 1
# cmd.copy("seg{}".format(i), detergent)
# cmd.alter("seg{}".format(i), "resi={}".format(i)) # assign residue numbers
# # randomly sample on a sphere
# cmd.translate("[0,{},0]".format(r), "seg{}".format(i))
# cmd.rotate("x", str(t), "seg{}".format(i))
# cmd.rotate("z", str(p), "seg{}".format(i))
s = "micelle_{}_{}_{}".format(detergent, int(r), int(numberOfDetergents))
cmd.create(s, "seg*")
cmd.delete("seg*")
# center(f"{s}")
# cmd.show_as("sticks","org")
# could be streched if necessary
# affineStretch(s, 10)
return s
def show_result(tmpdir, ligname):
n = 10 # number of positions of ligand
ft_file = tmpdir + "/ft.000.0.0"
rm_file = tmpdir + "/rm.000.0.0"
ft_data = np.loadtxt(ft_file)
rm_data = np.loadtxt(rm_file)
for i in range(n):
num_state = i + 1
name_copy = "copy_ligand_" + str(i)
cmd.copy(name_copy, ligname)
tv = ft_data[i, 1:4]
rm = rm_data[i].reshape((3, 3))
en = ft_data[i, 4]
cmd.translate(list(tv), name_copy)
cmd.rotate(list(get_axis(rm)), get_angle(rm), name_copy)
cmd.create("result", name_copy, 0, num_state)
cmd.delete(name_copy)
result = tmpdir + "/result_dock.pdb"
cmd.save(result, "result")
cmd.mplay()
def builderNanodisc(protein, membrane, scaffold, prefixName, runNumber, x=0, y=0, refine=False):
"""
builds a MP-nanodisc systems
scaffold in this case is a double belt of MSP
"""
# Checking time of builder function execution
if protein != None:
print('protein is: ' + protein)
print('scaffold is: ' + scaffold)
print('membrane is: ' + membrane)
empty = False
if protein is None: empty = True
if not empty:
tmp_prot = "tmp_prot" + str(runNumber)
cmd.copy(tmp_prot, protein) # store initial
cmd.translate("[{},{},0]".format(x, y), tmp_prot)
print("State of empty/not-empty: {}".format(empty))
# copies to delete later
tmp_scaffold = "tmp_scaffold" + str(runNumber)
tmp_memb = "tmp_memb" + str(runNumber)
tmp_origin = "origin" + str(runNumber)
cmd.copy(tmp_scaffold, scaffold) # store initial
cmd.copy(tmp_memb, membrane) # store initial
center(tmp_memb)
center(tmp_scaffold)
cmd.pseudoatom(tmp_origin, pos=[0, 0, 0])
cmd.origin(tmp_origin)
#outRadius = findAverDist(tmp_scaffold) #doubles time for each run
outRadius = TMdistCheck(tmp_scaffold, 0.2)
print("Max distance from origin to scaffold in xy plane: {}".format(outRadius))
# remove lipids beyond border encased by MSP
cmd.remove("br. org and {} beyond {} of {}".format(tmp_memb, outRadius, tmp_origin))
# remove lipids clashing with tmp_protein core
if not empty:
avXY = TMdistCheck(tmp_prot, 0.2)
if avXY == -1: return "bad model"
minXY = avXY / 2.0
# remove lipids inside pore
cmd.remove("br. org and {} within {} of {}".format(tmp_memb, minXY, tmp_origin))
print("Mean distance if TM cross-section in xy plane: {}".format(avXY))
if empty:
cmd.remove("br. org and {} within 0.4 of {} and not hydro".format(tmp_memb, tmp_scaffold))
s = "empty_{}_{}".format(membrane, scaffold)
else:
cmd.remove("br. org and {} within 0.3 of pol. and not hydro".format(tmp_memb))
s = "{}_{}_{}".format(protein, membrane, scaffold)
if refine: s += "{}_{}".format(int(x), int(y))
if prefixName:
s = "{}{}".format(prefixName, s)
cmd.create(s, "({},{}, {})".format(protein, tmp_scaffold, tmp_memb))
cmd.save(s + ".pdb", s)
cmd.delete(tmp_memb)
cmd.delete(tmp_scaffold)
cmd.delete(tmp_prot)
cmd.delete(tmp_origin)
return s
def test_update(self):
# 3 states
cmd.fragment('gly', 'm1')
cmd.create('m1', 'm1', 1, 2)
cmd.create('m1', 'm1', 1, 3)
# second object, 90 degree rotates
cmd.copy('m2', 'm1')
cmd.rotate('x', 90, '(m2)', state=0)
# reference coordsets
cs = cmd.get_coordset
cs1 = cs('m1', 1)
cs2 = cs('m2', 1)
# m2/3 will change (pre-check)
self.assertArrayEqual(cs2, cs('m2', 3))
self.assertArrayNotEqual(cs1, cs('m2', 3))
# update explicit state
cmd.update('m2', 'm1', 3, 2)
# m2/3 has changed
self.assertArrayEqual(cs1, cs('m2', 3))
self.assertArrayNotEqual(cs2, cs('m2', 3))
# these haven't changed
self.assertArrayEqual(cs2, cs('m2', 1))
self.assertArrayEqual(cs2, cs('m2', 2))
# reset m2/3
cmd.load_coordset(cs2, 'm2', 3)
self.assertArrayEqual(cs2, cs('m2', 3))
# update all states
cmd.update('m2', 'm1', 0, 0)
self.assertArrayEqual(cs1, cs('m2', 1))
self.assertArrayEqual(cs1, cs('m2', 2))
self.assertArrayEqual(cs1, cs('m2', 3))
def test_update(self):
# 3 states
cmd.fragment('gly', 'm1')
cmd.create('m1', 'm1', 1, 2)
cmd.create('m1', 'm1', 1, 3)
# second object, 90 degree rotates
cmd.copy('m2', 'm1')
cmd.rotate('x', 90, '(m2)', state=0)
# reference coordsets
cs = cmd.get_coordset
cs1 = cs('m1', 1)
cs2 = cs('m2', 1)
# m2/3 will change (pre-check)
self.assertArrayEqual(cs2, cs('m2', 3))
self.assertArrayNotEqual(cs1, cs('m2', 3))
# update explicit state
cmd.update('m2', 'm1', 3, 2)
# m2/3 has changed
self.assertArrayEqual(cs1, cs('m2', 3))
self.assertArrayNotEqual(cs2, cs('m2', 3))
# these haven't changed
self.assertArrayEqual(cs2, cs('m2', 1))
self.assertArrayEqual(cs2, cs('m2', 2))
# reset m2/3
cmd.load_coordset(cs2, 'm2', 3)
self.assertArrayEqual(cs2, cs('m2', 3))
# update all states
cmd.update('m2', 'm1', 0, 0)
self.assertArrayEqual(cs1, cs('m2', 1))
self.assertArrayEqual(cs1, cs('m2', 2))
self.assertArrayEqual(cs1, cs('m2', 3))
def Add_VDW(object, radii=""):
cmd.copy(object + "_vdw", object)
cmd.alter(object + "_vdw and elem H", "vdw=1.09")
radii = radii.lower()
if radii == "cpk" or radii == "bondi":
# retrieve the data (coords and atomtypes)
ATOMTYPES = []
CARTESIANS = []
atomslist = cmd.get_model(object + "_vdw")
for i in range(0, len(atomslist.atom)):
ATOMTYPES.append(atomslist.atom[i].symbol)
CARTESIANS.append(atomslist.atom[i].coord)
for i in range(0, len(ATOMTYPES)):
atomid = i + 1 # careful, pymol numbering starts at 1, but list starts at 0
cmd.alter(
"%s_vdw & id %s" % (object, atomid), "vdw=%.2f" %
atomicModelRadius(ATOMTYPES, CARTESIANS, radii, i))
cmd.rebuild()
cmd.set("sphere_scale", 1, object + "_vdw")
cmd.hide("nonbonded", object + "_vdw")
cmd.hide("lines", object + "_vdw")
cmd.hide("sticks", object + "_vdw")
cmd.set("sphere_transparency", 0.7, object + "_vdw")
def builderMembrane(lipid, runNumber):
"""
build membrane bilayer from single lipid PDB file
"""
refresh()
cmd.load(lipid + ".pdb", "start_lipid")
cmd.alter("start_lipid", "chain = 'X'")
cmd.alter("start_lipid", "segi = 'mema'")
# cmd.rotate('x', 90, "start_lipid")
dmax = findMaxDist("start_lipid")
# create lipid copies and translate them to new position
nlip = 20 # number of lipids forming edge of bilayer
s0 = range(1, nlip, 1)
s1 = range(1, nlip + 1, 1) # excludes first lipid
step_x = 0 # translation in x (TODO: automatic determination of spacing without clashes)
step_y = 7
step_z = 0
step_x2 = 7
step_y2 = 0
step_z2 = 0
for i in s1:
# first column
cmd.copy("lip{}".format(i), "start_lipid") # row of lipids
cmd.alter("lip{}".format(i), "resi={}".format(i)) # change residue numbers
y = i * step_y
cmd.translate("[{},{},{}]".format(step_x, y, step_z), "lip{}".format(i))
# generate remaining rows/columns in same leaflet
for j in s0:
k = int(nlip) * i + j # TODO: general counter to write correct lipid number
cmd.copy("lip{}".format(k), "lip{}".format(i)) # adjacent row of lipids
cmd.alter("lip{}".format(k), "resi={}".format(k)) # change residue numbers
x2 = j * step_x2
cmd.translate("[{},{},{}]".format(x2, step_y2, step_z2), "lip{}".format(k))
cmd.sort() # sort atom order
# create second leaflet
# simple method by creating a single leaflet object:
cmd.create("mema", "(lip*)")
cmd.delete("lip*")
cmd.copy("memb", "mema")
cmd.alter("memb", "segi = 'memb'")
cmd.rotate("x", 180, "memb")
cmd.translate("[0,0,{}]".format((-1.0 * (dmax + 0.5))), "memb")
# cmd.color("yellow", "segi = 'mema'")
# cmd.color("blue", "segi = 'memb'")
cmd.translate("[3.5,3.5,0]", "memb") # optional shift of single leaflet to avoid aliphatic clashes
s = "{}_bilayer".format(lipid)
cmd.create(s, "(mema,memb)")
cmd.delete("mema ,memb, start_lipid")
center(s)
cmd.save(s + ".pdb", s)
cmd.reset()
return s
def extract_state_to_object(morph, state, new_object):
number_of_states = cmd.count_states(morph)
if number_of_states < state:
print("in extract_state_to_object() requested state " +
"{} > number of states ({}) available in {}".format(
state, number_of_states, morph))
exit()
if morph == new_object:
print("in extract_state_to_object() please picked different " +
"name for extraction (currently bouth '{}') ".format(morph))
exit()
# after this I will have each state available as its own object, called "{morphname}_000x" (padded to length of 4)
# x starts with 1 --> not clear - that might depend on the numbering in the input file
cmd.split_states(morph)
state_name = morph + "_" + str(state).zfill(4)
cmd.copy(new_object, state_name)
for statenum in range(1, number_of_states + 1):
state_name = morph + "_" + str(statenum).zfill(4)
cmd.delete(state_name)
cmd.delete(morph)
return
def builderNanodisc(protein,
membrane,
scaffold,
prefixName,
offset=0,
refine=False):
"""
builds a MP-nanodisc systems
scaffold in this case is a double belt of MSP
"""
# Checking time of builder function execution
print(f'protein is: {protein}')
print(f'scaffold is: {scaffold}')
print(f'membrane is: {membrane}')
empty = False
if protein == None: empty = True
# copies to delete later
cmd.copy("tmp_scaffold", scaffold) # store initial
cmd.copy("tmp_memb", membrane) # store initial
cmd.copy("tmp_prot", protein) # store initial
center("tmp_memb")
center("tmp_scaffold")
cmd.pseudoatom("origin0", pos=[0, 0, 0])
cmd.origin("origin0")
outRadius = findAverDist("tmp_scaffold")
cmd.translate(f"[0,0,{offset}]", f"tmp_scaffold")
print(f"Max distance from origin to scaffold in xy plane: {outRadius}")
# remove lipids beyond border encased by MSP
cmd.remove(f"org and tmp_memb beyond {outRadius} of origin0")
print(f"State of empty/not-empty: {empty}")
# remove lipids clashing with tmp_protein core
if not empty:
avXY = TMdistCheck("tmp_prot", 0.2)
minXY = avXY / 2.0
# remove lipids inside pore
cmd.remove(f"org and tmp_memb within {minXY} of origin0")
print(f"Mean distance if TM cross-section in xy plane: {avXY}")
if empty:
cmd.remove("org and tmp_memb within 0.4 of tmp_scaffold and not hydro")
s = f"{prefixName}empty_{membrane}_{scaffold}"
else:
cmd.remove("org and tmp_memb within 0.3 of pol. and not hydro")
s = f"{prefixName}{protein}_{membrane}_{scaffold}"
if refine: s += str(int(offset))
cmd.create(s, f"({protein},tmp_scaffold, tmp_memb)")
cmd.save(s + ".pdb", s)
cmd.delete("tmp_memb")
cmd.delete("tmp_scaffold")
cmd.delete("tmp_prot")
cmd.delete("origin0")
return s
def my_mutate(rec_name, lig_name, dist):
# select residues in rec_name within dist of lig_name
# and show them as lines, the rest as cartoon
rec_pocket = f'byres {rec_name} within {dist} of {lig_name}'
# get the names and indices of the pocket residues
space = dict(residues=set())
cmd.iterate(rec_pocket, 'residues.add((resv, resn))', space=space)
residues = sorted(space['residues'])
res_idxs = [str(i) for i, n in residues]
res_idxs = '(resi ' + '+'.join(res_idxs) + ')'
# create a mapping from charged residues to
# oppositely charged residues of similar size
charge_map = {
'ARG': 'GLU',
'HIS': 'ASP',
'LYS': 'GLU',
'ASP': 'LYS',
'GLU': 'LYS',
}
# mutate each pocket residue individually
for res_idx, res_name in residues:
# make a mutant with the residue as alanine
mut_name = f'{rec_name}_mut_{res_idx}_{res_name}_ALA'
cmd.copy(mut_name, rec_name)
mutate(mut_name, res_idx, 'ALA')
cmd.save(mut_name + '.pdb', mut_name)
if res_name in charge_map:
# make another mutant with the charge flipped
inv_name = charge_map[res_name]
mut_name = f'{rec_name}_mut_{res_idx}_{res_name}_{inv_name}'
cmd.copy(mut_name, rec_name)
mutate(mut_name, res_idx, inv_name)
cmd.save(mut_name + '.pdb', mut_name)
# create one final mutant with ALL charges flipped
mut_name = f'{rec_name}_mut_all_charges'
cmd.copy(mut_name, rec_name)
for res_idx, res_name in residues:
if res_name in charge_map:
inv_name = charge_map[res_name]
mutate(mut_name, res_idx, inv_name)
cmd.save(mut_name + '.pdb', mut_name)
cmd.zoom(rec_pocket)
print(res_idxs)
def testCopy(self):
cmd.fragment('ala', 'm1')
cmd.copy('m2', 'm1')
self.assertEqual(
cmd.count_atoms('m1'),
cmd.count_atoms('m2'))
def phenotype_scene(gnao_cartoon=True): # shared between movie and xlsx
all_structures = ["AC", "RGS", "GPCR", "substrate", "gnao"]
load_structures(structure_home, structure_filename, all_structures)
cmd.bg_color("white")
#style_substrate("substrate", mol_color["substrate"])
if gnao_cartoon:
cmd.copy("gnao-cartoon", "gnao")
cmd.show("cartoon", "gnao-cartoon")
cmd.color("white", "gnao-cartoon")
cmd.set("ray_shadows", "off")
if gnao_cartoon:
cmd.remove("gnao-cartoon and resi 58-170")
cmd.remove("gnao-cartoon and resi 347-350") # see below
cmd.remove("gnao and resi 58-170")
cmd.remove("gnao and resi 347-350"
) # the isosurface at the GPCR interface won't close otherwise
# substrate
interface_clump("substrate",
"gnao",
mol_color["substrate"],
depth=5,
transparency=0.5)
#clump_representation(["substrate"], mol_color["substrate"], "substrate", transparency=0.2)
cmd.set("stick_radius", 0.5, "substrate")
cmd.show_as("sticks", "substrate")
cmd.show_as("spheres", "substrate and name MG")
cmd.color(mol_color["substrate"], "substrate")
cmd.remove("AC and (resi 1-1065 or resi 1175-1500)")
interface_clump("AC", "gnao", mol_color["AC"], depth=5, transparency=0.6)
if gnao_cartoon:
interface_clump("GPCR",
"gnao",
mol_color["GPCR"],
depth=5,
transparency=0.6)
else: # I get a hole in the mesh here
interface_clump("GPCR",
"gnao",
mol_color["GPCR"],
depth=5,
transparency=0.6,
grid_spacing=0.8)
interface_clump("RGS",
"gnao",
mol_color["RGS"],
depth=5,
transparency=0.6,
grid_spacing=0.7)
residue_cluster_clump("gnao",
conserved,
"gnao-conserved",
"aquamarine",
transparency=0.6)
#############################
residue_cluster_clump("gnao",
conserved,
"gnao-conserved",
"aquamarine",
transparency=0.6)
pheno_residues()
return
def testAlignto(self):
cmd.fragment("gly", "m1")
cmd.copy("m2", "m1")
cmd.alignto(method="fit", mobile_state=1, target_state=1)
def make_GDP(in_name, new_name):
cmd.copy(new_name, in_name, zoom=0)
cmd.remove("{} and not resn GDP".format(new_name))
return
def mcm(pose, mc_steps, SASA, randomize):
################################# MCM Parameters ##########################
T = 300. # Temperature
k = 0.0019872041 # Boltzmann constant
kT = k * T
# probability to sample phi, psi or chi
angles_prob = [1 / 3, 1 / 3, 1 / 3]
accepted = 0
##########################################################################
#
first, last = pose_from_pdb(pose)
if first or last:
print('Starting MCM')
from energy import minimize, set_sasa, get_sasa
sus_updates = cmd.get('suspend_updates')
cmd.set('suspend_updates', 'on')
# uncomment for debugging
cmd.feedback('disable', 'executive', 'everything')
pdb_conect = cmd.get('pdb_conect_all')
cmd.set('pdb_conect_all', 1)
glyco_bonds = get_glyco_bonds(first, last)
con_matrix = writer(glyco_bonds)
# Remove previous pdb files
prev_files = glob.glob('mcm_*.pdb')
for prev_file in prev_files:
os.remove(prev_file)
# set all paramenters for sasa-energy computation
if SASA:
params, points, const = set_sasa(n=1000)
# randomize initial conformation
if randomize:
for i in range(len(con_matrix) - 1):
bond = con_matrix[i]
angle_values = np.random.uniform(-180, 180, size=2)
set_psi(pose, bond, angle_values[0])
set_phi(pose, bond, angle_values[1])
for i in range(6):
set_chi(pose, bond)
# minimize energy of starting conformation and save it
NRG_old = minimize(pose, nsteps=5000, rigid_geometry=False)
NRG_min = NRG_old
cmd.save('mcm_%08d.pdb' % accepted)
# start MCM routine
fd = open("mcm_log.txt", "w")
print('# iterations remaining = %s' % (mc_steps))
for i in range(1, mc_steps + 1):
if i % (mc_steps // 10) == 0:
print('#remaining iterations = %s' % (mc_steps - i))
if True:
sample_uniform(pose, con_matrix, angles_prob)
NRG_new = minimize('tmp', nsteps=100, rigid_geometry=False)
if SASA:
solvatation_nrg = get_sasa(params,
points,
const,
selection='all',
probe=0)[0]
NRG_new = NRG_new + solvatation_nrg
if NRG_new < NRG_old:
NRG_old = NRG_new
fd.write('%8d%10.2f\n' % (accepted, NRG_new))
cmd.copy(pose, 'tmp')
cmd.delete('tmp')
cmd.save('mcm_%08d.pdb' % accepted)
accepted += 1
else:
delta = np.exp(-(NRG_new - NRG_old) / (kT))
if delta > np.random.uniform(0, 1):
NRG_old = NRG_new
fd.write('%8d%10.2f\n' % (accepted, NRG_new))
cmd.copy(pose, 'tmp')
cmd.delete('tmp')
cmd.save('mcm_%08d.pdb' % accepted)
accepted += 1
cmd.delete('tmp')
if NRG_new < NRG_min:
NRG_min = NRG_new
cmd.save('mcm_min.pdb')
fd.close()
cmd.delete('all')
print('Savings all accepted conformations on a single file')
de_builds = cmd.get('defer_builds_mode')
cmd.set('defer_builds_mode', 5)
for i in range(0, accepted):
cmd.load('mcm_%08d.pdb' % i, 'mcm_trace')
cmd.save('mcm_trace.pdb', 'all', state=0)
cmd.delete('all')
cmd.load('mcm_trace.pdb')
cmd.intra_fit('mcm_trace')
print('MCM completed')
# restore settings
cmd.set('suspend_updates', sus_updates)
cmd.set('pdb_conect_all', pdb_conect)
cmd.set('defer_builds_mode', de_builds)
def symset(prefix="sym", object=-1, x=0, y=0, z=0, opList=[]):
if object == -1:
object = cmd.get_names()[0]
cell = [float(x), float(y), float(z)]
view = cmd.get_view()
cmd.show("lines", object)
sgInfo = cmd.get_symmetry(object)
raw_ops = []
for s in sgtbx.space_group_info(sgInfo[6]).group():
raw_ops.append(str(s))
if len(opList) == 0:
for i in range(len(raw_ops)):
opList.append(i)
opMatrices = []
vars = ["x", "y", "z"]
#CREATE 4X4 MATRICES FOR SYMMETRY OPERATORS
for i, raw_op in enumerate(raw_ops):
ops = raw_op.split(",")
matrix = [[0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 0], [0, 0, 0, 1]]
for j in range(len(ops)):
for k in range(len(vars)):
index = ops[j].find(vars[k])
if index != -1:
if index == 0:
matrix[k][j] = 1
elif ops[j][index - 1] == "-":
matrix[k][j] = -1
else:
matrix[k][j] = 1
index = ops[j].find("/")
if index != -1:
matrix[3][j] = float(ops[j][index - 1]) / float(
ops[j][index + 1])
opMatrices.append(matrix)
a, b, c, alpha, beta, gamma = sgInfo[0:6]
ca = math.cos(math.radians(alpha))
cb = math.cos(math.radians(beta))
cg = math.cos(math.radians(gamma))
sb = math.sin(math.radians(beta))
sg = math.sin(math.radians(gamma))
fracToOrt = N.array([[a, b * cg, c * cb, 0.0],
[0.0, b * sg, c * (ca - cb * cg) / sg, 0.0],
[
0.0, 0.0,
c * sb * math.sqrt(1.0 - ((cb * cg - ca) /
(sb * sg))**2), 0.0
], [0.0, 0.0, 0.0, 1.0]])
fracToOrt = fracToOrt.transpose()
ortToFrac = inv(fracToOrt)
stored.atoms = []
cmd.iterate_state(1, object, "stored.atoms.append([x,y,z,1])")
stored.atoms = N.array(stored.atoms)
fracCoords = N.dot(stored.atoms, ortToFrac)
for i in opList:
try:
op = opMatrices[i]
except:
print("Bad symmetry partner numbers. Try again.")
quit()
copy = "%s%02d_%d_%d_%d" % (prefix, i, x, y, z)
cmd.copy(copy, object)
newCoordsFrac = N.dot(fracCoords, op)
stored.newCoords = N.dot(newCoordsFrac, fracToOrt)
stored.j = 0
cmd.alter_state(
1, copy,
"x,y,z = stored.newCoords[stored.j][0], stored.newCoords[stored.j][1], stored.newCoords[stored.j][2]; stored.j = stored.j + 1"
)
xSum = ySum = zSum = 0.0
for a, b, c in newCoordsFrac:
xSum += a
ySum += b
zSum += c
center = N.array([xSum, ySum, zSum])
center = center / len(stored.newCoords)
shift = [
cell[0] - math.floor(center[0]), cell[1] - math.floor(center[1]),
cell[2] - math.floor(center[2])
]
cell_shift(copy, shift[0], shift[1], shift[2], 0)
'''
#COPIES COORDINATES OF EACH ATOM TO CORRESPONDING ONE IN GIVEN SYMMETRY PARTNER
#cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)")
#MOVES SYMMETRY PARTNER TO PROPER LATTICE COORDINATES AND CORRECTS FOR NATIVE LATTICE POSITION ERROR
#stored.xSum,stored.ySum,stored.zSum = 0.0,0.0,0.0
#atoms = cmd.count_atoms(copy)
#cmd.iterate_state(1, copy, "stored.xSum = stored.xSum + x; stored.ySum = stored.ySum + y; stored.zSum = stored.zSum + z")
#xMean = stored.xSum / atoms
#yMean = stored.ySum / atoms
#zMean = stored.zSum / atoms
#xError, yError, zError = N.dot(N.array([xMean,yMean,zMean]), stored.ortToFrac)
#dX,dY,dZ = cell[0]-math.floor(xError), cell[1]-math.floor(yError), cell[2]-math.floor(zError)
#cell_shift(copy,dX,dY,dZ, 0)
'''
cmd.hide("everything", object)
cmd.set_view(view)
def testCopyMap(self):
cmd.load(self.datafile('emd_1155.ccp4'), 'map1')
cmd.copy('map2', 'map1')
self.assertEqual(cmd.get_symmetry('map1'), cmd.get_symmetry('map2'))
self.assertArrayEqual(cmd.get_volume_field('map1'), cmd.get_volume_field('map2'))
def mcm(pose, mc_steps, SASA, randomize):
################################# MCM Parameters ##########################
T = 300. # Temperature
k = 0.0019872041 # Boltzmann constant
angles_prob = [1/3, 1/3, 1/3] # probability to sample phi, psi or chi
accepted = 0
############################################################################
#
first, last = pose_from_pdb(pose)
if first or last:
print('Starting MCM')
from energy import minimize, set_sasa, get_sasa
cmd.set('suspend_updates', 'on')
cmd.feedback('disable', 'executive', 'everything') ##uncomment for debugging
cmd.set('pdb_conect_all', 1)
glyco_bonds = get_glyco_bonds(first, last)
con_matrix = writer(glyco_bonds)
# Remove previous pdb files
prev_files = glob.glob('mcm_*.pdb')
for prev_file in prev_files:
os.remove(prev_file)
# set all paramenters for sasa-energy computation
if SASA:
params, points, const = set_sasa(n=1000)
## randomize initial conformation
if randomize:
for i in range(len(con_matrix)-1):
bond = con_matrix[i]
angle_values = np.random.uniform(-180, 180, size=2)
set_psi(pose, bond, angle_values[0])
set_phi(pose, bond, angle_values[1])
for i in range(6):
set_chi(pose, bond)
# minimize energy of starting conformation and save it
NRG_old = minimize(pose, nsteps=5000, rigid_geometry=False)
NRG_min = NRG_old
cmd.save('mcm_%08d.pdb' % accepted)
## start MCM routine
fd = open("mcm_log.txt", "w")
print('# iterations remaining = %s' % (mc_steps))
for i in range(1, mc_steps+1):
if i % (mc_steps//10) == 0:
print('#remaining iterations = %s' % (mc_steps-i))
if True:
sample_uniform(pose, con_matrix, angles_prob)
NRG_new = minimize('tmp', nsteps=100, rigid_geometry=False)
if SASA:
solvatation_nrg = get_sasa(params, points, const, selection='all',
probe=0)[0]
NRG_new = NRG_new + solvatation_nrg
if NRG_new < NRG_old:
NRG_old = NRG_new
fd.write('%8d%10.2f\n' % (accepted, NRG_new))
cmd.copy(pose, 'tmp')
cmd.delete('tmp')
cmd.save('mcm_%08d.pdb' % accepted)
accepted += 1
else:
delta = np.exp(-(NRG_new-NRG_old)/(T*k))
if delta > np.random.uniform(0, 1):
NRG_old = NRG_new
fd.write('%8d%10.2f\n' % (accepted, NRG_new))
cmd.copy(pose, 'tmp')
cmd.delete('tmp')
cmd.save('mcm_%08d.pdb' % accepted)
accepted += 1
cmd.delete('tmp')
if NRG_new < NRG_min:
NRG_min = NRG_new
cmd.save('mcm_min.pdb')
fd.close()
cmd.delete('all')
print('Savings all accepted conformations on a single file')
cmd.set('defer_builds_mode', 5)
for i in range(0, accepted):
cmd.load('mcm_%08d.pdb' % i, 'mcm_trace')
cmd.save('mcm_trace.pdb', 'all', state=0)
cmd.delete('all')
cmd.load('mcm_trace.pdb')
cmd.intra_fit('mcm_trace')
print(' MCM completed')
cmd.set('suspend_updates', 'off')
def symset(prefix = "sym", object = -1, x=0,y=0,z=0, opList = []):
if object == -1:
object = cmd.get_names()[0]
cell = [float(x),float(y),float(z)]
view = cmd.get_view()
cmd.show("lines", object)
sgInfo = cmd.get_symmetry(object)
raw_ops = []
for s in sgtbx.space_group_info(sgInfo[6]).group():
raw_ops.append(str(s))
if (len(opList) == 0):
for i in range(len(raw_ops)):
opList.append(i)
opMatrices = []
vars = ["x","y","z"]
i = 0
j = 0
k = 0
#CREATE 4X4 MATRICES FOR SYMMETRY OPERATORS
for raw_op in raw_ops:
ops = raw_op.split(",")
matrix = [[0,0,0,0],[0,0,0,0],[0,0,0,0],[0,0,0,1]]
for j in range(len(ops)):
for k in range(len(vars)):
index = ops[j].find(vars[k])
if index != -1:
if index == 0:
matrix[k][j] = 1
elif ops[j][index - 1] == "-":
matrix[k][j] = -1
else:
matrix[k][j] = 1
index = ops[j].find("/")
if index != -1:
matrix[3][j] = float(ops[j][index - 1]) / float(ops[j][index + 1])
opMatrices.append(matrix)
i=i+1
a,b,c,alpha,beta,gamma = sgInfo[0:6]
ca = math.cos(math.radians(alpha))
cb = math.cos(math.radians(beta))
cg = math.cos(math.radians(gamma))
sb = math.sin(math.radians(beta))
sg = math.sin(math.radians(gamma))
fracToOrt = N.array([[a, b * cg, c * cb, 0.0],
[0.0, b * sg, c * (ca - cb * cg) / sg, 0.0],
[0.0, 0.0, c * sb * math.sqrt(1.0 - ((cb * cg - ca) / (sb * sg))**2), 0.0],
[0.0,0.0,0.0,1.0]])
fracToOrt = fracToOrt.transpose()
ortToFrac = inv(fracToOrt)
stored.atoms = []
cmd.iterate_state(1,object,"stored.atoms.append([x,y,z,1])")
stored.atoms = N.array(stored.atoms)
fracCoords = N.dot(stored.atoms,ortToFrac)
for i in opList:
try:
op = opMatrices[i]
except:
print "Bad symmetry partner numbers. Try again."
quit()
if i > 9:
copy = prefix + str(i) + "_" + str(x) + "_" + str(y) + "_" + str(z)
else:
copy = prefix + "0" + str(i) + "_" + str(x) + "_" + str(y) + "_" + str(z)
cmd.copy(copy, object)
newCoordsFrac = N.dot(fracCoords, op)
stored.newCoords = N.dot(newCoordsFrac, fracToOrt)
stored.j = 0
cmd.alter_state(1,copy,"x,y,z = stored.newCoords[stored.j][0], stored.newCoords[stored.j][1], stored.newCoords[stored.j][2]; stored.j = stored.j + 1")
xSum=ySum=zSum=0.0
for k in range(len(newCoordsFrac)):
xSum = newCoordsFrac[k][0] + xSum
ySum = newCoordsFrac[k][1] + ySum
zSum = newCoordsFrac[k][2] + zSum
center = N.array([xSum,ySum,zSum])
center = center/len(stored.newCoords)
shift = [-math.floor(center[0]) + cell[0], -math.floor(center[1]) + cell[1], -math.floor(center[2]) + cell[2]]
cell_shift(copy,shift[0],shift[1],shift[2],0)
'''
#COPIES COORDINATES OF EACH ATOM TO CORRESPONDING ONE IN GIVEN SYMMETRY PARTNER
#cmd.alter_state(1, copy, "x,y,z = cmd.sym_partner([x,y,z], stored.tmpOp)")
#MOVES SYMMETRY PARTNER TO PROPER LATTICE COORDINATES AND CORRECTS FOR NATIVE LATTICE POSITION ERROR
#stored.xSum,stored.ySum,stored.zSum = 0.0,0.0,0.0
#atoms = cmd.count_atoms(copy)
#cmd.iterate_state(1, copy, "stored.xSum = stored.xSum + x; stored.ySum = stored.ySum + y; stored.zSum = stored.zSum + z")
#xMean = (stored.xSum / atoms)
#yMean = (stored.ySum / atoms)
#zMean = (stored.zSum / atoms)
#xError, yError, zError = N.dot(N.array([xMean,yMean,zMean]), stored.ortToFrac)
#dX,dY,dZ = -math.floor(xError) + cell[0], -math.floor(yError) + cell[1], -math.floor(zError) + cell[2]
#cell_shift(copy,dX,dY,dZ, 0)
'''
cmd.hide("everything", object)
cmd.set_view(view)