def start():
check_output('%s qdisc add dev %s root handle %i: htb default %i'\
% (TC, args.interface, ROOT_Q_HANDLE, DEFAULT_CLASS))
# make a default class for normal traffic
check_output('%s class replace dev %s parent %i: classid %i:%i htb rate 1000mbit ceil 1000mbit'\
% (TC, args.interface, ROOT_Q_HANDLE, ROOT_Q_HANDLE, DEFAULT_CLASS))
def install_filters(links_file):
with open(links_file, 'r') as linksf:
for line in strip_comments(linksf):
elems = line.split(' ')
check_output('%s update %s %s -c %i'\
% (TC_SETUP, elems[0], elems[2], int(elems[1].split('link')[1])))
linksf.closed
def start_network():
if network_running():
logging.getLogger(__name__).info("Some network components already running...")
stop_network()
logging.getLogger(__name__).info("Starting simulated network...")
# Create fake NICs
logging.getLogger(__name__).info("Creating network interfaces...")
autogen_click_conf(get_topo_file("servers"), get_topo_file("clients"), get_topo_file("dns"))
if os.path.isfile(CLICK):
run_bg("%s %s" % (CLICK, CLICK_CONF))
else:
run_bg("%s %s" % (CLICK_LOCAL, CLICK_CONF))
# Set up traffic shaping
logging.getLogger(__name__).info("Enabling traffic shaping...")
try:
check_output("%s start" % TC_SETUP)
install_filters(get_topo_file("bottlenecks"))
except Exception as e:
logging.getLogger(__name__).error(e)
# Launch apache instances
logging.getLogger(__name__).info("Configuring apache...")
try:
configure_apache(get_server_ip_list())
restart_apache()
except Exception as e:
logging.getLogger(__name__).error(e)
logging.getLogger(__name__).info("Network started.")
def start_network():
if network_running():
logging.getLogger(__name__).info('Some network components already running...')
stop_network()
logging.getLogger(__name__).info('Starting simulated network...')
# Create fake NICs
logging.getLogger(__name__).info('Creating network interfaces...')
autogen_click_conf(get_topo_file('servers'), get_topo_file('clients'), get_topo_file('dns'))
run_bg('%s %s' % (CLICK, CLICK_CONF))
# Set up traffic shaping
logging.getLogger(__name__).info('Enabling traffic shaping...')
try:
check_output('%s start' % TC_SETUP)
install_filters(get_topo_file('bottlenecks'))
except Exception as e:
logging.getLogger(__name__).error(e)
# Launch apache instances
logging.getLogger(__name__).info('Configuring apache...')
try:
configure_apache(get_server_ip_list())
restart_apache()
except Exception as e:
logging.getLogger(__name__).error(e)
logging.getLogger(__name__).info('Network started.')
def stop_network():
logging.getLogger(__name__).info('Stopping simulated network...')
# stop apache instances
logging.getLogger(__name__).info('Stopping apache...')
try:
reset_apache(get_server_ip_list())
restart_apache()
except Exception as e:
logging.getLogger(__name__).error(e)
# Stop traffic shaping
logging.getLogger(__name__).info('Disabling traffic shaping...')
try:
check_output('%s stop' % TC_SETUP)
except Exception as e:
logging.getLogger(__name__).error(e)
# Destroy fake NICs
logging.getLogger(__name__).info('Destroying network interfaces...')
try:
check_both('killall -9 click', shouldPrint=False)
time.sleep(0.1)
except:
pass
logging.getLogger(__name__).info('Network stopped.')
def run_events(self, events_file=None, bg=False):
cmd = '%s %s run' % (NETSIM, self.topo_dir)
if events_file:
cmd += ' -e %s' % events_file
if bg:
run_bg(cmd)
else:
check_output(cmd)
def execute_event(event):
logging.getLogger(__name__).info("Updating link: %s" % " ".join(event))
try:
check_output("%s update -c %i -b %s -l %s" % (TC_SETUP, int(event[1].split("link")[1]), event[2], event[3]))
if args.log:
with open(args.log, "a") as logfile:
logfile.write("%f %s %s %s\n" % (time.time(), event[1], bw_to_kbps(event[2]), lat_to_ms(event[3])))
logfile.closed
except Exception as e:
logging.getLogger(__name__).error(e)
def pdb_to_top_and_crds(force_field, pdb, basename, solvent_buffer=10.0):
"""
Creates CHARMM .coor and .psf file for NAMD simulation.
"""
solv_dir = basename + '.solvate'
save_dir = os.getcwd()
pdb = os.path.abspath(pdb)
util.goto_dir(solv_dir)
# Remove all but protein heavy atoms in a single clean conformation
stripped_pdb = basename + '.clean.pdb'
pdbtext.clean_pdb(pdb, stripped_pdb)
# Make input script for psfgen
psfgen_psf = basename+'.psfgen.psf'
psfgen_pdb = basename+'.psfgen.pdb'
script = module_load_script
script += make_chain_loading_script(stripped_pdb, basename)
script += make_disulfide_script(stripped_pdb)
script += write_script
script = script % {
# load the included CHARMM2 atom topologies
'topology': os.path.join(data.data_dir, 'charmm22.topology'),
'out_pdb': psfgen_pdb,
'out_psf': psfgen_psf
}
psfgen_in = basename+".psfgen.in"
open(psfgen_in, "w").write(script)
data.binary('psfgen', psfgen_in, basename+'.psfgen')
util.check_output(psfgen_psf)
util.check_output(psfgen_pdb)
solvate_psf(psfgen_psf, psfgen_pdb, basename, solvent_buffer)
psf = basename+'.psf'
coor = basename+'.coor'
pdb = basename+'.pdb'
os.rename(pdb, coor)
convert_restart_to_pdb(basename, pdb)
shutil.copy(psf, save_dir)
shutil.copy(coor, save_dir)
shutil.copy(pdb, save_dir)
os.chdir(save_dir)
return psf, coor
def read_top(top):
"""
Returns a list of (mass, charge, chain_id) for the atoms
in the topology file.
"""
util.check_output(top)
lines = open(top).readlines()
atoms = []
is_chain_topologies = False
chain=" "
top_dir = os.path.dirname(top)
for l in lines:
if not is_chain_topologies:
if 'chain topologies' in l:
is_chain_topologies = True
continue
if l.startswith("#include"):
itp = l.split()[1][1:-1]
itp = os.path.join(top_dir, itp)
if os.path.isfile(itp):
full_chain_name = os.path.splitext(itp)[0]
chain = full_chain_name.split('_')[-1]
these_atoms = read_top(itp, chain)
atoms.extend(these_atoms)
if l.startswith(";"):
break
is_atoms = False
qtot = None
for l in lines:
if not is_atoms:
if '[ atoms ]' in l:
is_atoms = True
continue
if l.startswith('['):
break
if l.startswith(";"):
continue
if not l.strip():
continue
words = l.split()
n = int(words[0])
res_num = int(words[2])
res_type = words[3]
q = float(words[6])
mass = float(words[7])
atoms.append((mass, q, chain))
return atoms
def update():
# Figure out which traffic class we're updating
if args.traffic_class:
traffic_class = args.traffic_class
elif args.ip_pair:
traffic_class = class_for_ip_pair(args.ip_pair)
else:
traffic_class = DEFAULT_CLASS
# Update the queues for the traffic class with the new BW/latency
check_output('%s class replace dev %s parent %i: classid %i:%i htb rate %s ceil %s'\
% (TC, args.interface, ROOT_Q_HANDLE, ROOT_Q_HANDLE, traffic_class,\
args.bandwidth, args.bandwidth))
check_output('%s qdisc replace dev %s parent %i:%i handle %i: netem delay %s'\
% (TC, args.interface, ROOT_Q_HANDLE, traffic_class, traffic_class,\
args.latency))
# Update the rules mapping IP address pairs to the traffic class
if args.ip_pair:
U32='%s filter replace dev %s protocol ip parent %i: prio 1 u32'\
% (TC, args.interface, ROOT_Q_HANDLE)
check_output('%s match ip dst %s match ip src %s flowid %i:%i'
% (U32, args.ip_pair[0], args.ip_pair[1], ROOT_Q_HANDLE, traffic_class))
check_output('%s match ip dst %s match ip src %s flowid %i:%i'
% (U32, args.ip_pair[1], args.ip_pair[0], ROOT_Q_HANDLE, traffic_class))
def solvate_psf(in_psf, in_pdb, basename, solvent_buffer=10.0):
"""
Uses VMD to add explicit waters to a .psf topology file
"""
parms = {
'in_psf': in_psf,
'in_pdb': in_pdb,
'name': basename,
'solvent_buffer': solvent_buffer,
}
tcl = basename + '.vmd.tcl'
open(tcl, 'w').write(solvate_vmd_script % parms)
data.binary('vmd', '-dispdev text -eofexit', basename+'.vmd', tcl)
util.check_output(basename+'.vmd.pdb')
util.check_output(basename+'.pdb')
def _regenerate_dependency_cache(self):
"""Regenerate the Maven dependencies for this project.
This normally happens when the cached dependencies are determined to be stale."""
# Bootstrap with our skeleton environment
shutil.copytree(os.path.join(os.path.dirname(__file__), "skeleton"), self.__cached_project_root)
# Use skeleton environment Maven to copy dependencies into output dir
cmd = ". %s; which mvn" % os.path.join(self.__cached_project_root, "environment.source")
logger.info("Detecting environment mvn via `%s`", cmd)
env_mvn = util.check_output(cmd, shell=True, cwd=self.__cached_project_root)
if env_mvn.endswith("\n"):
env_mvn = env_mvn[:-1]
env_mvn = env_mvn + " " + self.__maven_flags
cached_m2_repo = os.path.join(self.__cached_project_root, Packager._MAVEN_REL_ROOT)
settings_xml = os.path.join(self.__cached_project_root, "settings.xml")
# copy-dependencies
copy_deps_flags = ""
if self.__maven_repo is not None:
copy_deps_flags += "-Dmaven.repo.local=%s" % self.__maven_repo
quiet_flag = "-q"
if self.__verbose:
quiet_flag = ""
cmd = """%s --settings %s %s dependency:copy-dependencies -Dmdep.useRepositoryLayout=true -Dmdep.copyPom -DoutputDirectory=%s %s"""
cmd = cmd % (env_mvn, settings_xml, quiet_flag, cached_m2_repo, copy_deps_flags)
Packager.__shell(cmd, self.__project_root)
# mvn test without running tests
cmd = """%s --settings %s %s -Dmaven.repo.local=%s -Dmaven.artifact.threads=100 surefire:test -DskipTests"""
cmd = cmd % (env_mvn, settings_xml, quiet_flag, cached_m2_repo)
Packager.__shell(cmd, self.__project_root)
def run(in_parms):
"""
Runs a NAMD simulation using the PDBREMIX in_parms dictionary.
"""
parms = copy.deepcopy(in_parms)
name = parms['output_basename']
# load the included CHARMM2 energy parameters
parms['parameter'] = os.path.join(data.data_dir, 'charmm22.parameter')
parms['psf_type'] = 'paraTypeCharmm on'
# copy over input xsc and topology files (same basename)
xsc = parms['topology'].replace('.psf', '.xsc')
if os.path.isfile(xsc):
shutil.copy(xsc, name + '.in.xsc')
parms['xsc'] = name + '.in.xsc'
else:
parms['xsc'] = ''
shutil.copy(parms['topology'], name + '.psf')
parms['topology'] = name + '.psf'
# copy over coordinates
shutil.copy(parms['input_crds'], name + '.in.coor')
parms['input_crds'] = name + '.in.coor'
# copy over velocities
if 'input_vels' in parms and parms['input_vels']:
shutil.copy(parms['input_vels'], name + '.in.vel')
parms['input_vels'] = name + '.in.vel'
else:
parms['input_vels'] = ''
# copy over restraint coordinates
if 'restraint_pdb' in parms and parms['restraint_pdb']:
shutil.copy(parms['restraint_pdb'], name + '.restraint.coor')
parms['restraint_pdb'] = name + '.restraint.coor'
else:
parms['restraint_pdb'] = ''
namd_in = name + ".namd2.in"
open(namd_in, "w").write(make_namd_input_file(parms))
data.binary('namd2', namd_in, name + '.namd2')
top, crds, vels = get_restart_files(name)
util.check_output(top)
util.check_output(crds)
def execute(self):
try:
self._output = util.check_output(self._command_line(), shell=True)
self.reset()
except subprocess.CalledProcessError as e:
print e
return False
return True
def soup_from_top_gro(top, gro, skip_solvent=False):
"""
Returns a Soup built from GROMACS restart files.
If skip_solvent=True, will skip all solvent molecules.
"""
util.check_output(top)
util.check_output(gro)
soup = pdbatoms.Soup()
soup.remaining_text = ""
soup.n_remaining_text = 0
atoms = []
# Read from .gro because .top does not contain water
# residue information, which is "inferred"
lines = open(gro, 'r').readlines()
for i_line, line in enumerate(lines[2:-1]):
atom = AtomFromGroLine(line)
if skip_solvent and atom.res_type == "SOL":
soup.remaining_text = "".join(lines[i_line+2:-1])
soup.n_remaining_text = len(lines[i_line+2:-1])
break
atoms.append(atom)
soup.box = [float(w) for w in lines[-1].split()]
for atom, (mass, q, chain_id) in zip(atoms, read_top(top)):
atom.mass = mass
atom.charge = q
curr_res_num = -1
for a in atoms:
if curr_res_num != a.res_num:
res = pdbatoms.Residue(
a.res_type, a.chain_id, a.res_num)
soup.append_residue(res.copy())
curr_res_num = a.res_num
soup.insert_atom(-1, a)
convert_to_pdb_atom_names(soup)
protein.find_chains(soup)
return soup
def link_jars(libs, directory):
makedirs(directory)
cp = check_output(['buck', 'audit', 'classpath'] + libs)
for j in cp.strip().splitlines():
if j not in jars:
jars.add(j)
n = path.basename(j)
if j.startswith('buck-out/gen/gerrit-'):
n = j.split('/')[2] + '-' + n
symlink(path.join(root, j), path.join(directory, n))
def make_restraint_script(pdb, force=100.0):
"""
Generates sander input fragment that specifies the atoms
that will be restrained.
The function reads a PDB file that was generated from the
topology functions above, and uses the B-factor field B>0 to
determine which atom is to be restrained. The atoms will
be restrained by a spring of force in kcal/mol/angs**2
"""
util.check_output(pdb)
script = "Restrained atoms from %s\n" % pdb
script += "%s\n" % force
script += restraint_script
for i, atom in enumerate(pdbatoms.read_pdb(pdb)):
if atom.bfactor > 0.0:
script += "ATOM %d %d\n" % (i+1, i+1)
script += "END\n"
script += "END\n"
return script
def show():
print '=============== Queue Disciplines ==============='
check_output('%s -s qdisc show dev %s' % (TC, args.interface))
print '\n================ Traffic Classes ================'
check_output('%s -s class show dev %s' % (TC, args.interface))
print '\n==================== Filters ===================='
check_output('%s -s filter show dev %s' % (TC, args.interface))
def build_from_project(project_root):
retcode = subprocess.call("git show-ref --quiet", shell=True, cwd=project_root)
if retcode != 0:
raise Exception("Directory %s is not a git repository" % project_root)
grind_git_hash = util.check_output("git show-ref --head -s HEAD", shell=True, cwd=os.path.dirname(__file__))
if grind_git_hash.endswith("\n"):
grind_git_hash = grind_git_hash[:-1]
git_hash = util.check_output("git show-ref --head -s HEAD", shell=True, cwd=project_root)
if git_hash.endswith("\n"):
git_hash = git_hash[:-1]
git_branch = "(no branch)"
try:
git_branch = util.check_output("git symbolic-ref HEAD", shell=True, cwd=project_root)
except:
# Ignore an error here, can happen if we're on a detached HEAD
pass
if git_branch.endswith("\n"):
git_branch = git_branch[:-1]
# Hash the deps file to look for changes
deps_checksum = None
return Manifest(grind_git_hash, os.path.normpath(project_root), git_branch, git_hash, datetime.datetime.now(), deps_checksum)
def disulfide_script_and_rename_cysteines(in_pdb, out_pdb):
"""
Returns the tleap script for disulfide bonds in the in_pdb file.
This function opens in_pdb in a Soup, and searches for
CYS residues where the SG-SG distance < 3 angs. These residues
are then renamed to CYX and written to out_pdb. The disulfide bonds
are then returned in a .tleap script fragment.
"""
soup = pdbatoms.Soup(in_pdb)
script = " # disulfide bonds\n"
n = len(soup.residues())
for i in range(n):
for j in range(i+1, n):
if soup.residue(i).type in 'CYS' and soup.residue(j).type in 'CYS':
p1 = soup.residue(i).atom('SG').pos
p2 = soup.residue(j).atom('SG').pos
if v3.distance(p1, p2) < 3.0:
soup.residue(i).set_type('CYX')
soup.residue(j).set_type('CYX')
script += "bond pdb.%d.SG pdb.%d.SG\n" % (i+1, j+1)
soup.write_pdb(out_pdb)
util.check_output(out_pdb)
return script
def get_rev(repo, rev):
validate_rev(rev)
return check_output(["git", "-C", repo, "rev-parse", rev],
stdin=DEVNULL).decode(PREFERREDENCODING).strip()
cmd = mvn(args.a) + [
'deploy:deploy-file',
'-DrepositoryId=%s' % args.repository,
'-Durl=%s' % args.url,
] + common
else:
print("unknown action -a %s" % args.a, file=stderr)
exit(1)
for spec in args.s:
artifact, packaging_type, src = spec.split(':')
cmds = cmd + [
'-DartifactId=%s' % artifact,
'-Dpackaging=%s' % packaging_type,
'-Dfile=%s' % src,
]
try:
check_output(cmds)
except Exception as e:
cmds_str = ' '.join(pipes.quote(c) for c in cmds)
print("%s command failed: `%s`: %s" % (args.a, cmds_str, e),
file=stderr)
exit(1)
with open(args.o, 'w') as fd:
if args.repository:
print('Repository: %s' % args.repository, file=fd)
if args.url:
print('URL: %s' % args.url, file=fd)
print('Version: %s' % args.v, file=fd)
def install_filters(links_file):
with open(links_file, "r") as linksf:
for line in strip_comments(linksf):
elems = line.split(" ")
check_output("%s update %s %s -c %i" % (TC_SETUP, elems[0], elems[2], int(elems[1].split("link")[1])))
linksf.closed
def restart_apache_script(script):
check_output('%s restart' % script, shouldPrint=False)
def restart_apache_binary(bin):
check_output('%s -k restart' % bin, shouldPrint=True)
jar = ['-Dpackaging=jar']
src = ['-Dpackaging=java-source']
cmd = {
'deploy': ['mvn',
'deploy:deploy-file',
'-DrepositoryId=gerrit-api-repository',
'-Durl=%s' % URL],
'install': ['mvn',
'install:install-file'],
}
try:
check_output(cmd[action] +
plugin +
common +
jar +
['-Dfile=%s' % plugin_jar])
check_output(cmd[action] +
plugin +
common +
src +
['-Dfile=%s' % plugin_src])
check_output(cmd[action] +
extension +
common +
jar +
['-Dfile=%s' % extension_jar])
check_output(cmd[action] +
extension +
common +
def run(in_parms):
"""
Run a GROMACS simulations using the PDBREMIX parms dictionary.
"""
parms = copy.deepcopy(in_parms)
basename = parms['output_basename']
# Copies across topology and related *.itp files, with appropriate
# filename renaming in #includes
top = basename + '.top'
in_top = parms['topology']
shutil.copy(in_top, top)
in_name = os.path.basename(in_top).replace('.top', '')
in_dir = os.path.dirname(in_top)
file_tag = "%s/%s_*itp" % (in_dir, in_name)
new_files = [top]
for f in glob.glob(file_tag):
new_f = os.path.basename(f)
new_f = new_f.replace(in_name, basename)
shutil.copy(f, new_f)
new_files.append(new_f)
for f in new_files:
replace_include_file(f, in_name + "_", basename + "_")
# Copy over input coordinates/velocities
in_gro = basename + '.in.gro'
shutil.copy(parms['input_crds'], in_gro)
# Generates a postiional-restraint topology file
if parms['restraint_pdb']:
# 1kcal*mol*A**-2 = 4.184 kJ*mol*(0.1 nm)**-2
kcalmolang2_to_kJmolnm2 = 400.184
open(basename + '_posre.itp', 'w').write(
make_restraint_itp(
parms['restraint_pdb'],
parms['restraint_force'] * kcalmolang2_to_kJmolnm2))
# Generate .mdp file based on parms
in_mdp = basename + '.grompp.mdp'
open(in_mdp, 'w').write(make_mdp(parms))
# Now run .grompp to generate this .tpr file
tpr = basename + '.tpr'
# .mdp to save complete set of parameters
mdp = basename + '.mdrun.mdp'
data.binary(
'grompp',
'-f %s -po %s -c %s -p %s -o %s' \
% (in_mdp, mdp, in_gro, top, tpr),
basename + '.grompp')
util.check_files(tpr)
# Run simulation with the .tpr file
data.binary(
'mdrun',
'-v -deffnm %s' % (basename),
basename + '.mdrun')
top, crds, vels = get_restart_files(basename)
util.check_output(top)
util.check_output(crds)
# Cleanup
delete_backup_files(basename)
def run(in_parms):
"""
Run a AMBER simulations using the PDBREMIX in_parms dictionary.
"""
parms = copy.deepcopy(in_parms)
basename = parms['output_basename']
# Copies across topology file
input_top = parms['topology']
util.check_files(input_top)
new_top = basename + '.top'
shutil.copy(input_top, new_top)
# Copies over coordinate/velocity files
input_crd = parms['input_crds']
util.check_files(input_crd)
if input_crd.endswith('.crd'):
new_crd = basename + '.in.crd'
else:
new_crd = basename + '.in.rst'
shutil.copy(input_crd, new_crd)
# Decide on type of output coordinate/velocity file
if 'n_step_minimization' in parms:
rst = basename + ".crd"
else:
rst = basename + ".rst"
# Construct the long list of arguments for sander
trj = basename + ".trj"
vel_trj = basename + ".vel.trj"
ene = basename + ".ene"
inf = basename + ".inf"
sander_out = basename + ".sander.out"
sander_in = basename + ".sander.in"
args = "-O -i %s -o %s -p %s -c %s -r %s -x %s -v %s -e %s -inf %s" \
% (sander_in, sander_out, new_top, new_crd, rst, trj, vel_trj, ene, inf)
# Make the input script
script = make_sander_input_file(parms)
# If positional restraints
if parms['restraint_pdb']:
# Generate the AMBER .crd file that stores the constrained coordinates
pdb = parms['restraint_pdb']
soup = pdbatoms.Soup(pdb)
ref_crd = basename + '.restraint.crd'
write_soup_to_rst(soup, ref_crd)
util.check_output(ref_crd)
# Add the restraints .crd to the SANDER arguments
args += " -ref %s" % ref_crd
# Add the restraint forces and atom indices to the SANDER input file
script += make_restraint_script(pdb, parms['restraint_force'])
open(sander_in, "w").write(script)
# Run the simulation
data.binary('sander', args, basename)
# Check if output is okay
util.check_output(sander_out, ['FATAL'])
top, crds, vels = get_restart_files(basename)
util.check_output(top)
util.check_output(crds)
def run_tleap(
force_field, pdb, name, solvent_buffer=0.0, excess_charge=0):
"""
Generates AMBER topology and coordinate files from PDB.
Depending on whether excess_charge is non-zero, will also generate
counterions. If solvent_buffer is non-zero, will generate explicit
waters, otherwise, no waters generated. No waters is used for
implicit solvent simulations.
"""
util.check_output(pdb)
# Remove all but protein heavy atoms in a single clean conformation
tleap_pdb = name + '.clean.pdb'
pdbtext.clean_pdb(pdb, tleap_pdb)
# The restart files to be generated
top = name + '.top'
crd = name + '.crd'
# Dictionary to substitute into tleap scripts
params = {
'top': top,
'crd': crd,
'pdb': tleap_pdb,
'data_dir':data.data_dir,
'solvent_buffer': solvent_buffer,
}
# use best force-field for the 2 versions of AMBER author has tested
if 'AMBER11' in force_field:
params['amber_ff'] = "leaprc.ff99SB"
elif 'AMBER14' in force_field:
params['amber_ff'] = "leaprc.ff14SB"
elif 'AMBER8' in force_field:
params['amber_ff'] = "leaprc.ff96"
else:
raise Exception("Don't know which version of AMBER(8|11|14) to use.")
# make the tleap input script
script = force_field_script
# check for a few non-standard residue that have been included
residues = [r.type for r in pdbatoms.Soup(tleap_pdb).residues()]
if 'PHD' in residues:
leaprc = open("%s/phd.leaprc" % data.data_dir).read()
script += leaprc
if 'ZNB' in residues:
leaprc = open("%s/znb.leaprc" % data.data_dir).read()
script += leaprc
script += "pdb = loadpdb %(pdb)s\n"
script += disulfide_script_and_rename_cysteines(tleap_pdb, tleap_pdb)
if 'GBSA' not in force_field:
# Add explicit waters as not GBSA implicit solvent
if excess_charge != 0:
# Add script to add counterions, must specify + or -
if excess_charge > 0:
script += "addions pdb Cl- 0\n"
else:
script += "addions pdb Na+ 0\n"
solvent_buffer = 10
params['solvent_buffer'] = solvent_buffer
script += explicit_water_box_script
script += save_and_quit_script
script = script % params
# Now write script to input file
tleap_in = name + ".tleap.in"
open(tleap_in, "w").write(script)
# Now run tleap with tleap_in
data.binary('tleap', "-f "+tleap_in, name+'.tleap')
# Check output is okay
if os.path.isfile('leap.log'):
os.rename('leap.log', name + '.tleap.log')
util.check_output(name+'.tleap.log', ['FATAL'])
util.check_output(top)
util.check_output(crd)
return top, crd
def restart_apache_script(script):
check_output('%s restart' % script, shouldPrint=False)
def get_file_contents(repo, rev, path):
validate_rev(rev)
return check_output(["git", "-C", repo, "show", rev + ":" + path],
stdin=DEVNULL)
elif 'deploy' == args.a:
cmd = mvn(args.a) + [
'deploy:deploy-file',
'-DrepositoryId=%s' % args.repository,
'-Durl=%s' % args.url,
] + common
else:
print("unknown action -a %s" % args.a, file=stderr)
exit(1)
for spec in args.s:
artifact, packaging_type, src = spec.split(':')
cmds = cmd + [
'-DartifactId=%s' % artifact,
'-Dpackaging=%s' % packaging_type,
'-Dfile=%s' % src,
]
try:
check_output(cmds)
except Exception as e:
cmds_str = ' '.join(pipes.quote(c) for c in cmds)
print("%s command failed: `%s`: %s" % (args.a, cmds_str, e), file=stderr)
exit(1)
with open(args.o, 'w') as fd:
if args.repository:
print('Repository: %s' % args.repository, file=fd)
if args.url:
print('URL: %s' % args.url, file=fd)
print('Version: %s' % args.v, file=fd)
def restart_apache_binary(bin):
check_output('%s -k restart' % bin, shouldPrint=True)