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 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 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 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)
