def cartoonize(color, rep):
"""draw a cartoon representation of glycans"""
stored.ResiduesNumber = []
cmd.iterate('name c1', 'stored.ResiduesNumber.append((resi))')
resn_list = [int(i) for i in stored.ResiduesNumber]
bonds = get_glyco_bonds(resn_list[0], resn_list[-1]+1)
con_matrix = writer(bonds)
#con_matrix = writer2(bonds)
rings = find_rings(resn_list)
rings_coords = get_ring_coords(resn_list, rings)
bonds_coords = get_bonds_coords(resn_list, con_matrix)
colors = get_colors_c1(resn_list, color)
bonds_colors = get_bonds_colors(resn_list, con_matrix, color)
cmd.set('suspend_updates', 'on')
for state, coords in enumerate(rings_coords):
obj = []
if rep == 'beads':
radius_s = 1.8
radius_b = 0.18
obj = beads(obj, coords, colors[state], radius_s)
obj = cylinder(obj, bonds_coords[state], bonds_colors[state], radius_b)
else:
if rep == 'cartoon':
radius = 0.075
else:
radius = 0.035
obj = hexagon(obj, coords, colors[state], rep, radius)
obj = cylinder(obj, bonds_coords[state], bonds_colors[state], radius)
cmd.load_cgo(obj,'cgo01', state+1)
cmd.select('glycan', 'byres name C1')
cmd.delete('glycan')
cmd.delete('tmp')
cmd.set('two_sided_lighting', 1)
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)