def createSimulationInput(jobnames, colvars, psffile, pdbfile):
for jobname in jobnames:
print jobname
jobtype, jobname = jobname.split('/')
if not conf['simulations'].has_key(jobtype) or \
not conf['simulations'][jobtype].has_key(jobname):
continue
basedir = os.path.join(conf['spec']['workdir'], jobtype)
jobdir = os.path.join(basedir, jobname)
inputdir = os.path.join(jobdir, 'input')
outputdir = os.path.join(jobdir, 'output')
colvarfile = os.path.join(inputdir, 'colvars.conf')
if not os.path.exists(jobdir): os.makedirs(jobdir)
if not os.path.exists(inputdir): os.makedirs(inputdir)
if not os.path.exists(outputdir): os.makedirs(outputdir)
spec = conf['simulations'][jobtype][jobname]
spec['inputdir'] = inputdir
spec['outputdir'] = outputdir
spec['colvarfile'] = colvarfile
spec['jobtype'] = jobtype
spec['jobname'] = jobname
spec['psffile'] = psffile
spec['pdbfile'] = pdbfile
for k in conf['spec'].keys():
spec[k] = conf['spec'][k]
for k in conf['simulations'][jobtype]['default'].keys():
if not spec.has_key(k):
spec[k] = conf['simulations'][jobtype]['default'][k]
if spec.has_key('windows'):
for rid in spec['windows'].keys():
if spec['windows'][rid].has_key(k): continue
spec['windows'][rid][k] = conf['simulations'][jobtype]['default'][k]
for k in conf['namd'].keys():
spec[k] = conf['namd'][k]
if conf['receptor'].has_key('selection'):
for k in ('selection', 'rest_selection'):
if not spec.has_key(k): continue
spec[k] = spec[k].replace('receptor', conf['receptor']['selection'])
if conf['ligand'].has_key('selection'):
for k in ('selection', 'rest_selection'):
if not spec.has_key(k): continue
spec[k] = spec[k].replace('ligand', conf['ligand']['selection'])
if jobtype == 'Angles':
angles = {'alpha': ['p1', 'l1', 'l2'],
'beta': ['p1', 'l1', 'l2', 'l3'],
'gamma': ['p2', 'p1', 'l1', 'l2'],
'theta': ['p2', 'p1', 'l1'],
'phi': ['p3', 'p2', 'p1', 'l1']}
spec['angle'] = angles[jobname]
if jobtype == 'Distance':
spec['distance'] = ['p1', 'l1']
#method = getattr('create%s' % jobtype)
method = globals()['create%s' % jobtype]
method(jobname, jobdir, spec, colvars)
colvars.write(colvarfile, inputdir=inputdir)
for cv in colvars:
if cv.spec.has_key('refpdb') and cv.spec.has_key('selected_atoms'):
refpdb = os.path.join(inputdir, os.path.basename(cv.spec['refpdb']))
writer = get_writer_for(format='PDB', multiframe=False)
writer(refpdb).write(cv.spec['selected_atoms'])
def createJobDirs(jobdir, jobname, colvars, colvar_type, spec):
inputdir = spec['inputdir']
outputdir = spec['outputdir']
colvarfile = spec['colvarfile']
spec['receptor'] = conf['receptor']['selection']
spec['ligand'] = conf['ligand']['selection']
spec['jobname'] = jobname
colvar = colvars.append(colvar_type, jobname, **spec)
psffile = os.path.basename(spec['psffile'])
pdbfile = os.path.basename(spec['pdbfile'])
shutil.copyfile(spec['psffile'], os.path.join(inputdir, psffile))
shutil.copyfile(spec['pdbfile'], os.path.join(inputdir, pdbfile))
for prm in spec['parameters']:
prmfile = os.path.basename(prm)
shutil.copyfile(prm, os.path.join(inputdir, prmfile))
spec['pbs'] = conf['pbs']
# PME size
universe = mda.Universe(spec['psffile'], spec['pdbfile'])
bbox = universe.atoms.bbox()
spec['A'], spec['B'], spec['C'] = bbox[1,:] - bbox[0,:]
spec['xcen'], spec['ycen'], spec['zcen'] = np.average(bbox, axis=0)
if spec.has_key('rest_selection'):
sptpdb = os.path.join(inputdir, os.path.basename('spt.pdb'))
writer = get_writer_for(format='PDB', multiframe=False)
selected_atoms = universe.select_atoms(spec['rest_selection'])
selected_atoms.set_bfactors(1)
writer(sptpdb, bonds=False).write(universe.atoms)
# initial structure preparation
use_rest = spec['use_rest']
spec['use_rest'] = True
for fname in ('input/namd.conf', 'input/run.pbs', 'input/prepare.py'):
realname = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'templates', fname)
filename = os.path.join(os.path.join(inputdir, os.path.basename(realname)))
if fname == 'input/run.pbs' and spec['jobtype'] == 'Angles':
# angular restraints has minimum at the middle of the arranged windows
realname = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'templates', 'input/run-Angles.pbs')
template = Template(open(realname).read())
open(filename, 'w').write(template.render(spec, psffile=psffile, pdbfile=pdbfile))
# path optimization input
if spec['jobtype'] == 'Distance':
for fname in ('pathopt/pathopt-run.pbs', 'pathopt/pathopt-base.conf', 'pathopt/pathopt-remd.conf', 'pathopt/pathopt-prepare.py'):
realname = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'templates', fname)
filename = os.path.join(os.path.join(jobdir, os.path.basename(realname)))
template = Template(open(realname).read())
open(filename, 'w').write(template.render(spec, psffile=psffile, pdbfile=pdbfile))
# input files preparation
spec['use_rest'] = use_rest
for i in range(spec['num_windows'] * spec['num_temperature']):
windir = os.path.join(outputdir, str(i))
if not os.path.exists(windir): os.mkdir(windir)
for filename in ('umbrella.namd', 'umbrella_rest.namd'):
if filename == 'umbrella.namd' and spec['use_rest']: continue
if filename == 'umbrella_rest.namd' and not spec['use_rest']: continue
realname = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'static', filename)
shutil.copyfile(realname, os.path.join(jobdir, os.path.basename(realname)))
for filename in ('remd.conf', 'base.conf', 'namd.conf', 'run.pbs'):
realname = os.path.join(os.path.dirname(os.path.realpath(__file__)), 'templates', filename)
filename = os.path.join(os.path.join(jobdir, os.path.basename(realname)))
template = Template(open(realname).read())
open(filename, 'w').write(template.render(spec, psffile=psffile, pdbfile=pdbfile))
return jobdir, inputdir, outputdir, colvars
