def to_task(self):
logger.info1('Creating task for', self.digest)
pxul.os.ensure_dir(self.outputdir)
logger.debug('Ensured', self.outputdir, 'exists')
cmd = 'bash %(script)s > %(log)s' % dict(script = SCRIPT_NAME, log = LOGFILE)
task = wq.Task(cmd)
# input files
task.specify_buffer(SCRIPT_CONTENTS, SCRIPT_NAME , cache=True)
task.specify_buffer(str(self._cpus), SCRIPT_INPUT_NAMES['cpus'],cache=True)
task.specify_input_file(self._x , SCRIPT_INPUT_NAMES['x'] , cache=False, name='x_i')
task.specify_input_file(self._v , SCRIPT_INPUT_NAMES['v'] , cache=False, name='v_i')
task.specify_input_file(self._t , SCRIPT_INPUT_NAMES['t'] , cache=False, name='t_i')
task.specify_input_file(self._tpr , SCRIPT_INPUT_NAMES['tpr'], cache=True , name='tpr')
# output files
task.specify_output_file(self.output_files['log'], LOGFILE , cache=False, name='log')
task.specify_output_file(self.output_files['x'], SCRIPT_OUTPUT_NAMES['x'] , cache=False, name='x_o')
task.specify_output_file(self.output_files['v'], SCRIPT_OUTPUT_NAMES['v'] , cache=False, name='v_o')
task.specify_output_file(self.output_files['t'], SCRIPT_OUTPUT_NAMES['t'] , cache=False, name='t_o')
self.check_binaries()
for path in self._binaries:
task.specify_input_file(path, cache=True)
for name in self._trajfiles:
task.specify_output_file(self.output_path(name), name, cache=False)
logger.debug('Created task:\n', str(task))
return task
def to_task(self):
logger.info1('Creating task for', self.digest)
pxul.os.ensure_dir(self.outputdir)
logger.debug('Ensured', self.outputdir, 'exists')
cmd = 'bash %(script)s > %(log)s' % dict(script=SCRIPT_NAME,
log=LOGFILE)
task = wq.Task(cmd)
# input files
task.specify_buffer(SCRIPT_CONTENTS, SCRIPT_NAME, cache=True)
task.specify_buffer(str(self._cpus),
SCRIPT_INPUT_NAMES['cpus'],
cache=True)
task.specify_input_file(self._x,
SCRIPT_INPUT_NAMES['x'],
cache=False,
name='x_i')
task.specify_input_file(self._v,
SCRIPT_INPUT_NAMES['v'],
cache=False,
name='v_i')
task.specify_input_file(self._t,
SCRIPT_INPUT_NAMES['t'],
cache=False,
name='t_i')
task.specify_input_file(self._tpr,
SCRIPT_INPUT_NAMES['tpr'],
cache=True,
name='tpr')
# output files
task.specify_output_file(self.output_files['log'],
LOGFILE,
cache=False,
name='log')
task.specify_output_file(self.output_files['x'],
SCRIPT_OUTPUT_NAMES['x'],
cache=False,
name='x_o')
task.specify_output_file(self.output_files['v'],
SCRIPT_OUTPUT_NAMES['v'],
cache=False,
name='v_o')
task.specify_output_file(self.output_files['t'],
SCRIPT_OUTPUT_NAMES['t'],
cache=False,
name='t_o')
self.check_binaries()
for path in self._binaries:
task.specify_input_file(path, cache=True)
for name in self._trajfiles:
task.specify_output_file(self.output_path(name), name, cache=False)
logger.debug('Created task:\n', str(task))
return task
def relax(self, mdp, gammas=None, steps=None):
logger.info1('Iterative equilibration')
gammas = [1000, 100, 10, 1] if gammas is None else gammas
name = self.name + '_itr_posres_eq'
mdp_itr = suffix.mdp(name)
mdp.SETUP.define = '-DPOSRES'
if steps is not None:
mdp.nsteps = steps
mdp.set_velocity_generation()
for g in gammas:
mdp.dt = 0.001
mdp.set_gamma(g)
logger.debug('using gamma =', g)
logger.debug('using dt =', mdp.dt)
mdp.save(mdp_itr)
self._cn = name + '_gamma-%d' % g
gmx.grompp(
f = mdp_itr,
c = suffix.gro(self.pn),
t = suffix.trr(self.pn),
p = self.top,
o = suffix.tpr(self.cn)
)
gmx.mdrun(
s = suffix.tpr(self.cn),
deffnm = self.cn,
v = True
)
self._pn = self.cn
mdp.unset_velocity_generation()
def relax(self, mdp, gammas=None, steps=None):
logger.info1('Iterative equilibration')
gammas = [1000, 100, 10, 1] if gammas is None else gammas
name = self.name + '_itr_posres_eq'
mdp_itr = suffix.mdp(name)
mdp.SETUP.define = '-DPOSRES'
if steps is not None:
mdp.nsteps = steps
mdp.set_velocity_generation()
for g in gammas:
mdp.dt = 0.001
mdp.set_gamma(g)
logger.debug('using gamma =', g)
logger.debug('using dt =', mdp.dt)
mdp.save(mdp_itr)
self._cn = name + '_gamma-%d' % g
gmx.grompp(f=mdp_itr,
c=suffix.gro(self.pn),
t=suffix.trr(self.pn),
p=self.top,
o=suffix.tpr(self.cn))
gmx.mdrun(s=suffix.tpr(self.cn), deffnm=self.cn, v=True)
self._pn = self.cn
mdp.unset_velocity_generation()
def tpr_set_scalar(tpr, name, value):
logger.info1('Setting', name, '=', value, 'in', tpr)
tmpfile = os.path.join(os.path.dirname(tpr), name + '.gps')
with open(tmpfile, 'w') as fd:
fd.write('%s\n' % value)
guamps_set(f=tpr, s=name, i=tmpfile, O=True)
os.unlink(tmpfile)
def save(self, path, overwrite=True):
if os.path.exists(path) and not overwrite:
raise ValueError, 'Path exists: %s' % path
with open(path, 'w') as fd:
fd.write(self.format())
logger.info1('Saved file %s' % os.path.abspath(path))
def save(self, path, overwrite=True):
if os.path.exists(path) and not overwrite:
raise ValueError, 'Path exists: %s' % path
with open(path, 'w') as fd:
fd.write(self.format())
logger.info1('Saved file %s' % os.path.abspath(path))
def tpr_get_scalar(tpr, name, mktype):
logger.info1('Getting', name, 'from', tpr)
tmpfile = os.path.join(os.path.dirname(tpr), name+'.gps')
guamps_get(f=tpr, s=name, o=tmpfile)
with open(tmpfile) as fd:
value = fd.readline()
value = mktype(value)
os.unlink(tmpfile)
return value
def wait(self):
result = self.wq.wait(self._timeout)
if result:
logger.info1('%-15s' % 'Received', result.uuid)
taskable = self._table[result.uuid]
taskable.update_task(result)
del self._table[result.uuid]
self._persist(taskable)
return taskable
def tpr_get_scalar(tpr, name, mktype):
logger.info1('Getting', name, 'from', tpr)
tmpfile = os.path.join(os.path.dirname(tpr), name + '.gps')
guamps_get(f=tpr, s=name, o=tmpfile)
with open(tmpfile) as fd:
value = fd.readline()
value = mktype(value)
os.unlink(tmpfile)
return value
def save(self, prefix=None, name='experiment.yaml'):
prefix = self.name if prefix is None else prefix
pxul.os.ensure_dir(prefix)
ypath = os.path.join(prefix, name)
with open(ypath, 'w') as fd:
logger.info('Saving experiments:', fd.name)
yaml.dump(self, fd, default_flow_style=False)
logger.info1('Writing children')
for k, r in self.runs.iteritems():
r.save(prefix=os.path.join(self.name, str(k)))
def save(self, prefix=None, name='experiment.yaml'):
prefix = self.name if prefix is None else prefix
pxul.os.ensure_dir(prefix)
ypath = os.path.join(prefix, name)
with open(ypath, 'w') as fd:
logger.info('Saving experiments:', fd.name)
yaml.dump(self, fd, default_flow_style=False)
logger.info1('Writing children')
for k, r in self.runs.iteritems():
r.save(prefix=os.path.join(self.name, str(k)))
def initialize(self, pdb, ff='amber03', water='tip3p', ignh=True):
logger.info1('Importing to GMX format')
top = suffix.top(self.cn)
gmx.pdb2gmx(f=pdb,
o=suffix.gro(self.cn),
p=top,
ff=ff,
water=water,
ignh=ignh)
self._top = top
self._pn = self.cn
def initialize(self, pdb, ff='amber03', water='tip3p', ignh=True):
logger.info1('Importing to GMX format')
top = suffix.top(self.cn)
gmx.pdb2gmx(
f = pdb,
o = suffix.gro(self.cn),
p = top,
ff = ff,
water = water,
ignh = ignh)
self._top = top
self._pn = self.cn
def minimize_vacuum(self, mdp):
logger.info1('Minimization in vacuum')
self._cn = self.name + '_EMV'
cn, pn = self.cn, self.pn
mdp_path = suffix.mdp(self.cn)
mdp.save(mdp_path)
tpr = suffix.tpr(cn)
gmx.grompp(f=mdp_path, c=suffix.gro(pn), p=suffix.top(pn), o=tpr)
gmx.mdrun(
s=tpr,
deffnm=cn,
c=suffix.pdb(cn),
nt=1,
)
self._pn = self._cn
def equilibrate(self, mdp, steps=None):
logger.info1('Equilibrating')
self._cn = self.name + '_eq'
if steps is not None:
mdp.nsteps = steps
mdp_path = suffix.mdp(self.cn)
mdp.unset_velocity_generation()
mdp.save(mdp_path)
gmx.grompp(f=mdp_path,
c=suffix.gro(self.pn),
t=suffix.trr(self.pn),
p=self.top,
o=suffix.tpr(self.cn))
gmx.mdrun(s=suffix.tpr(self.cn), deffnm=self.cn, v=True)
def main(opts):
if os.path.exists(state.CONFIG):
logger.info1('Loading previous state from', state.CONFIG)
cfg = state.Config.load(path=state.CONFIG)
else:
cfg = state.Config()
cfg.update(
backend = opts.backend,
generations = opts.generations,
time = opts.time,
outputfreq = opts.outputfreq,
cpus = opts.cpus,
binaries = opts.binaries,
seed = opts.seed
)
cfg.write()
logger.info('Configured:\n', str(cfg))
def minimize_vacuum(self, mdp):
logger.info1('Minimization in vacuum')
self._cn = self.name + '_EMV'
cn, pn = self.cn, self.pn
mdp_path = suffix.mdp(self.cn)
mdp.save(mdp_path)
tpr = suffix.tpr(cn)
gmx.grompp(
f = mdp_path,
c = suffix.gro(pn),
p = suffix.top(pn),
o = tpr
)
gmx.mdrun(
s = tpr,
deffnm = cn,
c = suffix.pdb(cn),
nt = 1,
)
self._pn = self._cn
def equilibrate(self, mdp, steps=None):
logger.info1('Equilibrating')
self._cn = self.name + '_eq'
if steps is not None:
mdp.nsteps = steps
mdp_path = suffix.mdp(self.cn)
mdp.unset_velocity_generation()
mdp.save(mdp_path)
gmx.grompp(
f = mdp_path,
c = suffix.gro(self.pn),
t = suffix.trr(self.pn),
p = self.top,
o = suffix.tpr(self.cn)
)
gmx.mdrun(
s = suffix.tpr(self.cn),
deffnm = self.cn,
v = True
)
def prepare(self,
pdb,
ff = 'amber03',
water = 'tip3p',
ignh = True,
mdp_min_vac = None,
mdp_min_sol = None,
mdp_run = None,
iter_gammas = None,
iter_steps = 500,
eq_steps = 500,
seed = None):
cwd = os.getcwd()
logger.info('Preparing %s with %s in %s' % (os.path.relpath(pdb, cwd), ff, cwd))
pdb = os.path.abspath(pdb)
wa = os.path.join(self.workarea)
name = os.path.splitext(os.path.basename(pdb))[0]
mdp_min_vac = mdp_defaults.minimize_vacuum() if mdp_min_vac is None else mdp_min_vac.copy()
mdp_min_sol = mdp_defaults.minimize_solvated() if mdp_min_sol is None else mdp_min_sol.copy()
mdp_run = mdp_defaults.explicit_solvent() if mdp_run is None else mdp_run.copy()
if seed is not None:
mdp_run.seed(seed)
self.name = name
self._cn = name
with pxul.os.StackDir(wa):
self.initialize(pdb, ff=ff, water=water, ignh=ignh)
self.minimize_vacuum(mdp_min_vac)
self.solvate(mdp_min_sol)
self.relax(copy.deepcopy(mdp_run), gammas=iter_gammas, steps=iter_steps)
self.equilibrate(copy.deepcopy(mdp_run), steps=eq_steps)
if not name:
name = self.name
conf = suffix.gro(name), suffix.gro(self.pn)
top = suffix.top(name), self.top
itp = suffix.itp(name), 'posre.itp'
mdp = suffix.mdp(name)
for new, old in [conf, top, itp]:
shutil.copy(os.path.join(self.workarea, old), new)
logger.info1('Saved file %s' % os.path.abspath(new))
with open(mdp, 'w') as fd:
fd.write(str(mdp_run))
logger.info1('Saved file', os.path.abspath(fd.name))
# create tpr with velocities
logger.info1('Creating run tpr')
conf = conf[0]
top = top[0]
mdout = suffix.mdp('{}_mdout'.format(name))
tpr = suffix.tpr(name)
gmx.grompp(f=mdp, c=conf, po=mdout, p=top, o=tpr, t=suffix.trr(os.path.join(self.workarea, self.pn)))
return dict(conf=conf,top=top,mdout=mdout,tpr=tpr)
def task(self,
tpr,
x=None,
v=None,
t=None,
outputdir=None,
seed=None,
digest=None):
outdir = outputdir or tpr + '.mdq'
pxul.os.ensure_dir(outdir)
logger.debug('Ensured', outdir, 'exists')
tpr2 = os.path.join(outdir, 'topol.tpr')
shutil.copy(tpr, tpr2)
logger.debug(tpr, '->', tpr2)
gendir = os.path.join(outdir, '0')
pxul.os.ensure_dir(gendir)
logger.debug('Ensured', gendir, 'exists')
gps = dict(x=os.path.join(gendir, SCRIPT_INPUT_NAMES['x']),
v=os.path.join(gendir, SCRIPT_INPUT_NAMES['v']),
t=os.path.join(gendir, SCRIPT_INPUT_NAMES['t']))
if x is not None:
shutil.copy(x, gps['x'])
logger.debug(x, '->', gps['x'])
if v is not None:
shutil.copy(v, gps['v'])
logger.debug(v, '->', gps['v'])
if t is not None:
if type(t) is float:
with open(gps['t'], 'w') as fd:
fd.write(str(t))
logger.debug('Wrote', t, 'to', gps['t'])
elif type(t) is str:
shutil.copy(t, gps['t'])
logger.debug(t, '->', gps['t'])
else:
raise ValueError, 'Illegal state: invalid time spec %s' % t
for sel, key in SELECTIONS.iteritems():
logger.info1('Getting', sel, 'from', tpr2)
guamps_get(f=tpr2, s=sel, o=gps[key])
if seed:
logger.info1('Setting seed', seed)
tpr_set_scalar(tpr2, 'ld_seed', seed)
dt = tpr_get_scalar(tpr2, 'deltat', float)
if self._picoseconds:
nsteps = int(self._picoseconds / dt)
logger.info1('Running for', self._picoseconds, 'ps as', nsteps,
'nsteps')
tpr_set_scalar(tpr2, 'nsteps', nsteps)
if self._outputfreq:
freq = int(self._outputfreq / dt)
# FIXME nstenergy, see badi/guamps#27
for attr in 'nstxout nstxtcout nstfout nstvout nstlog'.split():
logger.info1('Setting output frequency', self._outputfreq,
'for', attr, 'as', freq, 'steps', 'in', tpr2)
tpr_set_scalar(tpr2, attr, freq)
if not digest:
logger.info1('Computing digest for', tpr2)
sha256 = hashlib.sha256()
sha256.update(open(tpr2, 'rb').read())
digest = sha256.hexdigest()
task = Task(x=gps['x'],
v=gps['v'],
t=gps['t'],
tpr=tpr2,
outputdir=outdir,
cpus=self._cpus,
digest=digest)
task.add_binary(self._mdrun)
task.add_binary(self._guamps_get)
task.add_binary(self._guamps_set)
if self._keep_trajfiles:
task.keep_trajfiles()
logger.info('Prepared', digest, 'from', tpr)
for k in self.__dict__:
logger.info(10 * ' ', k.lstrip('_'), '=', getattr(self, k))
return task
def solvate(self,
mdp, boxtype='triclinic', boxdist=1.0, solv='spc216.gro',
concentration=0.15, neutral=True, pname='NA', nname='CL'):
nbox = self.name + '_box'
nwat = self.name + '_wat'
nsolv = self.name + '_sol'
logger.info1('Solvating')
self._cn = nbox
gmx.editconf(
f = suffix.pdb(self.pn),
o = suffix.gro(nbox),
bt = boxtype,
d = boxdist,
)
self._cn = nwat
gmx.genbox(
cp = suffix.gro(nbox),
cs = solv,
p = self.top,
o = suffix.gro(self.cn)
)
gmx.grompp(
f = suffix.mdp(self.pn),
c = suffix.gro(self.cn),
p = self.top,
o = suffix.tpr(self.cn)
)
# create atom indices for water
pdb = suffix.pdb(self.cn)
gmx.editconf(
f = suffix.tpr(self.cn),
o = pdb
)
top = prody.parsePDB(pdb)
sel = top.select('resname is SOL')
idx = sel.getIndices()
idx += 1 # GMX starts with 1, prody with 0
ndx = suffix.ndx(nwat)
with open(ndx, 'w') as fd:
fd.write('[ SOL ] \n')
# GMX has a limited buffer for read ndx files
idx = map(str, idx)
idx = ' '.join(idx)
idx = textwrap.wrap(idx)
idx = '\n'.join(idx)
fd.write(idx + '\n')
gmx.genion(
n = ndx,
s = suffix.tpr(nwat),
o = suffix.gro(nsolv),
conc = concentration,
neutral = neutral,
pname = pname,
nname = nname
)
# figure out the number of solvent, cation, and anion molecules
logger.info1('Calculating number of solvent, cation, and anion molecules')
conf = open(suffix.gro(nsolv)).readlines()
nsol = count_occurences('SOL', conf) / 3
ncat = count_occurences(pname, conf)
nani = count_occurences(nname, conf)
del conf
# write a new topology file with the updated counts
logger.info1('Generating new topology file')
top = open(self.top).readlines()
top = top[:-1] # the last line containts the number of solvent molecules, which is outdated
top.append('SOL %s\n' % nsol)
top.append('%s %s\n' % (pname, ncat))
top.append('%s %s\n' % (nname, nani))
top = ''.join(top)
self._top = suffix.top(nsolv)
open(self.top, 'w').write(top)
self._pn = nsolv
self._cn = nsolv
# minimize the solvated system
logger.info1('Minimizaing solvated system')
mdp_path = suffix.mdp(self.cn)
mdp.save(mdp_path)
tpr = suffix.tpr(self.cn)
gmx.grompp(
f = mdp_path,
c = suffix.gro(self.cn),
p = self.top,
o = tpr
)
gmx.mdrun(
s = tpr,
deffnm = self.cn,
)
self._pv = self.cn
def save(self, prefix='.', name='run.yaml'):
pxul.os.ensure_dir(prefix)
ypath = os.path.join(prefix, name)
with open(ypath, 'w') as fd:
logger.info1('Saving', fd.name)
yaml.dump(self, fd)
def prepare(self,
pdb,
ff='amber03',
water='tip3p',
ignh=True,
mdp_min_vac=None,
mdp_min_sol=None,
mdp_run=None,
iter_gammas=None,
iter_steps=500,
eq_steps=500,
seed=None):
cwd = os.getcwd()
logger.info('Preparing %s with %s in %s' %
(os.path.relpath(pdb, cwd), ff, cwd))
pdb = os.path.abspath(pdb)
wa = os.path.join(self.workarea)
name = os.path.splitext(os.path.basename(pdb))[0]
mdp_min_vac = mdp_defaults.minimize_vacuum(
) if mdp_min_vac is None else mdp_min_vac.copy()
mdp_min_sol = mdp_defaults.minimize_solvated(
) if mdp_min_sol is None else mdp_min_sol.copy()
mdp_run = mdp_defaults.explicit_solvent(
) if mdp_run is None else mdp_run.copy()
if seed is not None:
mdp_run.seed(seed)
self.name = name
self._cn = name
with pxul.os.StackDir(wa):
self.initialize(pdb, ff=ff, water=water, ignh=ignh)
self.minimize_vacuum(mdp_min_vac)
self.solvate(mdp_min_sol)
self.relax(copy.deepcopy(mdp_run),
gammas=iter_gammas,
steps=iter_steps)
self.equilibrate(copy.deepcopy(mdp_run), steps=eq_steps)
if not name:
name = self.name
conf = suffix.gro(name), suffix.gro(self.pn)
top = suffix.top(name), self.top
itp = suffix.itp(name), 'posre.itp'
mdp = suffix.mdp(name)
for new, old in [conf, top, itp]:
shutil.copy(os.path.join(self.workarea, old), new)
logger.info1('Saved file %s' % os.path.abspath(new))
with open(mdp, 'w') as fd:
fd.write(str(mdp_run))
logger.info1('Saved file', os.path.abspath(fd.name))
# create tpr with velocities
logger.info1('Creating run tpr')
conf = conf[0]
top = top[0]
mdout = suffix.mdp('{}_mdout'.format(name))
tpr = suffix.tpr(name)
gmx.grompp(f=mdp,
c=conf,
po=mdout,
p=top,
o=tpr,
t=suffix.trr(os.path.join(self.workarea, self.pn)))
return dict(conf=conf, top=top, mdout=mdout, tpr=tpr)
def task(self, tpr, x=None, v=None, t=None, outputdir=None, seed=None, digest=None):
outdir = outputdir or tpr + '.mdq'
pxul.os.ensure_dir(outdir)
logger.debug('Ensured', outdir, 'exists')
tpr2 = os.path.join(outdir, 'topol.tpr')
shutil.copy(tpr, tpr2)
logger.debug(tpr, '->', tpr2)
gendir = os.path.join(outdir, '0')
pxul.os.ensure_dir(gendir)
logger.debug('Ensured', gendir, 'exists')
gps = dict(x = os.path.join(gendir, SCRIPT_INPUT_NAMES['x']),
v = os.path.join(gendir, SCRIPT_INPUT_NAMES['v']),
t = os.path.join(gendir, SCRIPT_INPUT_NAMES['t']))
if x is not None:
shutil.copy(x, gps['x'])
logger.debug(x, '->', gps['x'])
if v is not None:
shutil.copy(v, gps['v'])
logger.debug(v, '->', gps['v'])
if t is not None:
if type(t) is float:
with open(gps['t'], 'w') as fd: fd.write(str(t))
logger.debug('Wrote', t, 'to', gps['t'])
elif type(t) is str:
shutil.copy(t, gps['t'])
logger.debug(t, '->', gps['t'])
else: raise ValueError, 'Illegal state: invalid time spec %s' % t
for sel, key in SELECTIONS.iteritems():
logger.info1('Getting', sel, 'from', tpr2)
guamps_get(f=tpr2, s=sel, o=gps[key])
if seed:
logger.info1('Setting seed', seed)
tpr_set_scalar(tpr2, 'ld_seed', seed)
dt = tpr_get_scalar(tpr2, 'deltat', float)
if self._picoseconds:
nsteps = int(self._picoseconds / dt)
logger.info1('Running for', self._picoseconds, 'ps as', nsteps, 'nsteps')
tpr_set_scalar(tpr2, 'nsteps', nsteps)
if self._outputfreq:
freq = int(self._outputfreq / dt)
# FIXME nstenergy, see badi/guamps#27
for attr in 'nstxout nstxtcout nstfout nstvout nstlog'.split():
logger.info1('Setting output frequency', self._outputfreq,
'for', attr, 'as', freq, 'steps', 'in', tpr2)
tpr_set_scalar(tpr2, attr, freq)
if not digest:
logger.info1('Computing digest for', tpr2)
sha256 = hashlib.sha256()
sha256.update(open(tpr2, 'rb').read())
digest = sha256.hexdigest()
task = Task(x=gps['x'], v=gps['v'], t=gps['t'], tpr=tpr2,
outputdir=outdir, cpus=self._cpus, digest=digest)
task.add_binary(self._mdrun)
task.add_binary(self._guamps_get)
task.add_binary(self._guamps_set)
if self._keep_trajfiles:
task.keep_trajfiles()
logger.info('Prepared', digest, 'from', tpr)
for k in self.__dict__:
logger.info(10*' ', k.lstrip('_'), '=', getattr(self, k))
return task
def tpr_set_scalar(tpr, name, value):
logger.info1('Setting', name, '=', value, 'in', tpr)
tmpfile = os.path.join(os.path.dirname(tpr), name +'.gps')
with open(tmpfile, 'w') as fd: fd.write('%s\n' % value)
guamps_set(f=tpr, s=name, i=tmpfile, O=True)
os.unlink(tmpfile)
def save(self, prefix='.', name='run.yaml'):
pxul.os.ensure_dir(prefix)
ypath = os.path.join(prefix, name)
with open(ypath, 'w') as fd:
logger.info1('Saving', fd.name)
yaml.dump(self, fd)
def solvate(self,
mdp,
boxtype='triclinic',
boxdist=1.0,
solv='spc216.gro',
concentration=0.15,
neutral=True,
pname='NA',
nname='CL'):
nbox = self.name + '_box'
nwat = self.name + '_wat'
nsolv = self.name + '_sol'
logger.info1('Solvating')
self._cn = nbox
gmx.editconf(
f=suffix.pdb(self.pn),
o=suffix.gro(nbox),
bt=boxtype,
d=boxdist,
)
self._cn = nwat
gmx.genbox(cp=suffix.gro(nbox),
cs=solv,
p=self.top,
o=suffix.gro(self.cn))
gmx.grompp(f=suffix.mdp(self.pn),
c=suffix.gro(self.cn),
p=self.top,
o=suffix.tpr(self.cn))
# create atom indices for water
pdb = suffix.pdb(self.cn)
gmx.editconf(f=suffix.tpr(self.cn), o=pdb)
top = prody.parsePDB(pdb)
sel = top.select('resname is SOL')
idx = sel.getIndices()
idx += 1 # GMX starts with 1, prody with 0
ndx = suffix.ndx(nwat)
with open(ndx, 'w') as fd:
fd.write('[ SOL ] \n')
# GMX has a limited buffer for read ndx files
idx = map(str, idx)
idx = ' '.join(idx)
idx = textwrap.wrap(idx)
idx = '\n'.join(idx)
fd.write(idx + '\n')
gmx.genion(n=ndx,
s=suffix.tpr(nwat),
o=suffix.gro(nsolv),
conc=concentration,
neutral=neutral,
pname=pname,
nname=nname)
# figure out the number of solvent, cation, and anion molecules
logger.info1(
'Calculating number of solvent, cation, and anion molecules')
conf = open(suffix.gro(nsolv)).readlines()
nsol = count_occurences('SOL', conf) / 3
ncat = count_occurences(pname, conf)
nani = count_occurences(nname, conf)
del conf
# write a new topology file with the updated counts
logger.info1('Generating new topology file')
top = open(self.top).readlines()
top = top[:
-1] # the last line containts the number of solvent molecules, which is outdated
top.append('SOL %s\n' % nsol)
top.append('%s %s\n' % (pname, ncat))
top.append('%s %s\n' % (nname, nani))
top = ''.join(top)
self._top = suffix.top(nsolv)
open(self.top, 'w').write(top)
self._pn = nsolv
self._cn = nsolv
# minimize the solvated system
logger.info1('Minimizaing solvated system')
mdp_path = suffix.mdp(self.cn)
mdp.save(mdp_path)
tpr = suffix.tpr(self.cn)
gmx.grompp(f=mdp_path, c=suffix.gro(self.cn), p=self.top, o=tpr)
gmx.mdrun(
s=tpr,
deffnm=self.cn,
)
self._pv = self.cn