def get_pdbs_with_ftp(*pdbs):
"""
Fetches PDB files using FTP from a list of pdb-codes/text-files.
"""
pdbs = expand_pdbs(*pdbs)
entries = ['pdb%s.ent.gz' % pdb for pdb in pdbs]
mget_scripts = ["get %s" % entry for entry in entries]
substitutions = {
'host': 'ftp.wwpdb.org',
'mget_str': '\n'.join(mget_scripts),
}
ftp_script = template % substitutions
open('ftp.sh', 'w').write(ftp_script)
util.run_with_output('chmod +x ftp.sh')
util.run_with_output('./ftp.sh')
for pdb, entry in zip(pdbs, entries):
fname = pdb + '.pdb'
if os.path.isfile(entry):
out_f = open(fname, 'w')
for line in gzip.open(entry):
out_f.write(line)
util.clean_fname(entry)
print fname
else:
print "Failed: %s" % fname
util.clean_fname('ftp.sh')
def calculate_energy(top, crd):
"""
Returns potential energy of top and crd by running sander
and parsing the sander output.
"""
top = os.path.abspath(top)
crd = os.path.abspath(crd)
util.goto_dir('energy-temp')
parms = minimization_parms.copy()
parms.extend({
'topology': top,
'input_crds': crd,
'output_basename': 'energy',
'n_step_minimization': 0,
'n_step_steepest_descent': 0})
run(parms)
blocks = read_minimization_sander_out('energy.sander.out')
util.goto_dir('..')
util.clean_fname('energy-temp')
return blocks[0]['ENERGY']
def soup_to_bfactor_png(
soup, png, bfactors, lower_bfactor=None, upper_bfactor=None,
highlight_res=None, is_putty=False):
temp_pdb = util.temp_fname('.pdb')
soup.load_residue_bfactors(bfactors)
max_bfactor = rescale_positive_bfactors_pdb(soup, temp_pdb,
lower_bfactor, upper_bfactor)
temp2_pdb = strip_solvent_pdb(temp_pdb)
script = bgcolor_script('white')
script += bfactor_script(
temp2_pdb, lower_bfactor, upper_bfactor, max_bfactor, is_putty)
if highlight_res is not None:
script += highlight_res_script(highlight_res)
script += hide_backbone_sticks_script()
if 'frame_pymol_script' in soup.__dict__:
script += soup.frame_pymol_script
script += "clip far, -20\n"
script += "save %s\n" % png
script += "quit"
width, height = 480, 480
if 'width' in soup.__dict__:
width = soup.width
if 'height' in soup.__dict__:
height = soup.height
run_pymol_script(script, width, height)
util.clean_fname(temp_pdb, temp2_pdb)
def calculate_energy(top, crd):
"""
Returns potential energy of top and crd by running sander
and parsing the sander output.
"""
top = os.path.abspath(top)
crd = os.path.abspath(crd)
util.goto_dir('energy-temp')
parms = minimization_parms.copy()
parms.extend({
'topology': top,
'input_crds': crd,
'output_basename': 'energy',
'n_step_minimization': 0,
'n_step_steepest_descent': 0
})
run(parms)
blocks = read_minimization_sander_out('energy.sander.out')
util.goto_dir('..')
util.clean_fname('energy-temp')
return blocks[0]['ENERGY']
def get_pdbs_with_ftp(*pdbs):
"""
Fetches PDB files using FTP from a list of pdb-codes/text-files.
"""
pdbs = expand_pdbs(*pdbs)
entries = ['pdb%s.ent.gz' % pdb for pdb in pdbs]
mget_scripts = ["get %s" % entry for entry in entries]
substitutions = {
'host': 'ftp.wwpdb.org',
'mget_str': '\n'.join(mget_scripts),
}
ftp_script = template % substitutions
open('ftp.sh', 'w').write(ftp_script)
util.run_with_output('chmod +x ftp.sh')
util.run_with_output('./ftp.sh')
for pdb, entry in zip(pdbs, entries):
fname = pdb + '.pdb'
if os.path.isfile(entry):
out_f = open(fname, 'w')
for line in gzip.open(entry):
out_f.write(line)
util.clean_fname(entry)
print fname
else:
print "Failed: %s" % fname
util.clean_fname('ftp.sh')
def make_pdbs_png(png,
pdbs,
bgcolor="white",
center_res=None,
top_res=None,
highlight_res=None,
is_sticks=True,
is_putty=False,
width=480,
height=480):
if 'transparent' in bgcolor:
script = 'set opaque_background, off\n'
else:
script = make_bgcolor_script(bgcolor)
temp_fnames = []
if center_res and top_res:
transform = get_pdb_transform(pdbs[0], center_res, top_res)
for i in range(len(pdbs)):
soup = pdbatoms.Soup(pdbs[i])
soup.transform(transform)
new_pdb = util.fname_variant(pdbs[i])
soup.write_pdb(new_pdb)
temp_fnames.append(new_pdb)
pdbs[i] = new_pdb
del soup
script += make_load_pdbs_script(pdbs)
script += make_separate_chain_colors_script(pdbs)
if is_putty:
script += make_putty_script(get_scale_max(max_bfactor, upper_bfactor))
else:
script += cartoon_script
if not is_sticks:
script += "hide stick\n"
else:
script += "show stick\n"
script += make_ligands_as_sticks_script(pdbs)
if highlight_res:
script += make_highlight_res_script(highlight_res)
script += hide_backbone_sticks_script
# script += "clip far, 5\n"
script += "save %s\n" % png
script += "quit"
pml = util.fname_variant('temp.pml')
open(pml, 'w').write(script)
run_pymol_script(pml, width, height)
temp_fnames.append(pml)
util.clean_fname(*temp_fnames)
def make_pdbs_png(
png, pdbs, bgcolor="white", center_res=None, top_res=None,
highlight_res=None, is_sticks=True, is_putty=False,
width=480, height=480):
if 'transparent' in bgcolor:
script = 'set opaque_background, off\n'
else:
script = make_bgcolor_script(bgcolor)
temp_fnames = []
if center_res and top_res:
transform = get_pdb_transform(pdbs[0], center_res, top_res)
for i in range(len(pdbs)):
soup = pdbatoms.Soup(pdbs[i])
soup.transform(transform)
new_pdb = util.fname_variant(pdbs[i])
soup.write_pdb(new_pdb)
temp_fnames.append(new_pdb)
pdbs[i] = new_pdb
del soup
script += make_load_pdbs_script(pdbs)
script += make_separate_chain_colors_script(pdbs)
if is_putty:
script += make_putty_script(get_scale_max(
max_bfactor, upper_bfactor))
else:
script += cartoon_script
if not is_sticks:
script += "hide stick\n"
else:
script += "show stick\n"
script += make_ligands_as_sticks_script(pdbs)
if highlight_res:
script += make_highlight_res_script(highlight_res)
script += hide_backbone_sticks_script
# script += "clip far, 5\n"
script += "save %s\n" % png
script += "quit"
pml = util.fname_variant('temp.pml')
open(pml, 'w').write(script)
run_pymol_script(pml, width, height)
temp_fnames.append(pml)
util.clean_fname(*temp_fnames)
def pdb_to_bfactor_png(bfactor_pdb,
png,
lower_bfactor=None,
upper_bfactor=None,
highlight_res=None,
is_putty=False,
is_sticks=True,
center_res=None,
top_res=None,
height=480,
width=480):
"""
Generates a bfactor-colored .png using the standard white-to-red
color scheme with a useful set of options. highlight_res,
center_res & top_res follow the 'A:10' style of residue naming.
"""
pdb, max_bfactor = rescale_positive_bfactors_pdb(bfactor_pdb,
lower_bfactor,
upper_bfactor)
temp_fnames = [pdb]
if center_res or top_res:
pdb = get_pdb_transform(pdb, center_res, top_res)
temp_fnames.append(pdb)
script = ""
script += bfactor_script(pdb, lower_bfactor, upper_bfactor, max_bfactor,
is_putty)
if highlight_res is not None:
pymol_res_id = get_pymol_id_from_res_tag(highlight_res)
script += make_highlight_res_script(pymol_res_id)
script += hide_backbone_sticks_script
script += "clip far, -20\n"
script += "save %s\n" % png
script += "quit"
pml = util.fname_variant('temp.pml')
open(pml, 'w').write(script)
run_pymol_script(pml, width, height)
temp_fnames.append(pml)
util.clean_fname(*temp_fnames)
def soup_to_bfactor_png(
soup, png, bfactors, lower_bfactor=None, upper_bfactor=None,
highlight_res=None, is_putty=False, is_sticks=True,
center_res=None, top_res=None, height=480, width=480):
"""
Wrapper around pdb_to_bfactor that loads in external values
for the residue bfactors with a reusable soup object.
"""
pdb = util.temp_fname('.pdb')
temp_fnames = [pdb]
soup.load_residue_bfactors(bfactors)
soup.write_pdb(pdb)
pdb_to_bfactor_png(
pdb, png, lower_bfactor, upper_bfactor,
highlight_res, is_putty, is_sticks,
center_res, top_res, height, width)
util.clean_fname(*temp_fnames)
def pdb_to_bfactor_png(
bfactor_pdb, png, lower_bfactor=None, upper_bfactor=None,
highlight_res=None, is_putty=False, is_sticks=True,
center_res=None, top_res=None, height=480, width=480):
"""
Generates a bfactor-colored .png using the standard white-to-red
color scheme with a useful set of options. highlight_res,
center_res & top_res follow the 'A:10' style of residue naming.
"""
pdb, max_bfactor = rescale_positive_bfactors_pdb(
bfactor_pdb, lower_bfactor, upper_bfactor)
temp_fnames = [pdb]
if center_res or top_res:
pdb = get_pdb_transform(pdb, center_res, top_res)
temp_fnames.append(pdb)
script = ""
script += bfactor_script(
pdb, lower_bfactor, upper_bfactor,
max_bfactor, is_putty)
if highlight_res is not None:
pymol_res_id = get_pymol_id_from_res_tag(highlight_res)
script += make_highlight_res_script(pymol_res_id)
script += hide_backbone_sticks_script
script += "clip far, -20\n"
script += "save %s\n" % png
script += "quit"
pml = util.fname_variant('temp.pml')
open(pml, 'w').write(script)
run_pymol_script(pml, width, height)
temp_fnames.append(pml)
util.clean_fname(*temp_fnames)
def soup_to_bfactor_png(soup,
png,
bfactors,
lower_bfactor=None,
upper_bfactor=None,
highlight_res=None,
is_putty=False,
is_sticks=True,
center_res=None,
top_res=None,
height=480,
width=480):
"""
Wrapper around pdb_to_bfactor that loads in external values
for the residue bfactors with a reusable soup object.
"""
pdb = util.temp_fname('.pdb')
temp_fnames = [pdb]
soup.load_residue_bfactors(bfactors)
soup.write_pdb(pdb)
pdb_to_bfactor_png(pdb, png, lower_bfactor, upper_bfactor, highlight_res,
is_putty, is_sticks, center_res, top_res, height, width)
util.clean_fname(*temp_fnames)
def pulse(
force_field, in_basename, basename, n_step, pulse_fn,
n_step_per_pulse=100, restraint_pdb="", restraint_force=None):
"""
Runs a pulse simulation that uses the restart-file modification
strategy to manage a steered-molecular dynamics simulation.
The pulsed approacha pplies external forces in pulses, which is
practically carried out be running short constant-energy
simulations and directly modifying the restart velocities
between each simulation.
Pulse simulations has certain advantages: for instance, the
system can respond to the forces between pulses, and the
incredibly flexibility in applying forces. The disadvantage is
the costly setup which is hopefully, mitigated by this library.
Reference: Bosco K. Ho and David A. Agard (2010) "An improved
strategy for generating forces in steered molecular dynamics:
the mechanical unfolding of titin, e2lip3 and ubiquitin" PLoS
ONE 5(9):e13068.
"""
# Grab the simulation prameters for a constant energy
# simulation. Constant energy is preferred as we want to ensure
# energy changes come only from our velocity modification.
top, crds, vels = get_restart_files(in_basename)
# use dummy top and crds, which will be overriden
overall_config_parms = fetch_simulation_parameters(
force_field, top, crds, restraint_pdb,
'constant_energy', basename, restraint_force)
overall_config_parms.update({
'input_md_name': in_basename,
'input_vels': vels,
'n_step_dynamics': n_step,
'n_step_per_snapshot': n_step_per_pulse // 2,
'n_step_per_pulse': n_step_per_pulse
})
# Check if the simulation has already run as the config
# file is not written until the very end
config = basename + ".config"
if util.is_same_dict_in_file(overall_config_parms, config):
print "Skipping: pulsing simulation already run."
return
# The overall_config_parms will be written out at the end.
# We make a copy for internal use
pulse_parms = copy.deepcopy(overall_config_parms)
# Calculate steps for each pulse, esp for last step
n_pulse = pulse_parms['n_step_dynamics'] / n_step_per_pulse
n_step_list = [n_step_per_pulse for i in range(n_pulse)]
n_excess_step = pulse_parms['n_step_dynamics'] % n_step_per_pulse
if n_excess_step > 0:
n_pulse += 1
n_step_list.append(n_excess_step)
# Prepare restart files for first step
pulse_parms['topology'] = os.path.abspath(pulse_parms['topology'])
in_basename = pulse_parms['input_md_name']
pulse_parms['input_md_name'] = os.path.abspath(in_basename)
# Now loop through pulses
timer = util.Timer()
save_dir = os.getcwd()
pulses = ["pulse%d" % i for i in range(n_pulse)]
for pulse, n_step in zip(pulses, n_step_list):
print "Pulse: %s/%d" % (pulse, n_pulse)
os.chdir(save_dir)
util.goto_dir(pulse)
pulse_parms['n_step_dynamics'] = n_step
soup = soup_from_restart_files(pulse_parms['input_md_name'])
# Apply forces by modifying the velocities directly
pulse_fn(soup)
crds, vels = write_soup_to_crds_and_vels(
force_field, soup, basename + '.pulse.in')
pulse_parms['input_crds'] = crds
pulse_parms['input_vels'] = vels
run_simulation_with_parameters(pulse_parms)
# Setup new restart files based on just-finished pulse
pulse_parms['input_md_name'] = os.path.abspath(basename)
os.chdir(save_dir)
merge_simulations(force_field, basename, pulses)
# cleanup pulses after merging
util.clean_fname(*pulses)
# everything worked, no exceptions thrown
open(basename+'.time', 'w').write(timer.str()+'\n')
util.write_dict(config, overall_config_parms)
def delete_backup_files(tag):
util.clean_fname(*util.re_glob('*', '^#' + tag))
def delete_backup_files(tag):
util.clean_fname(*util.re_glob('*', '^#' + tag))
