def test_SystemPDB(self):
pdb = T.testRoot('pep', 'pep.pdb')
self.f_out = T.tempDir() + os.sep + 'SystemPDB'
if not os.path.exists(self.f_out): os.mkdir(self.f_out)
T.BROWSER.chdir(self.f_out)
self.r1 = System(amberPDB=pdb)
solvatedsys = self.r1.solvate('WAT', tmp=self.f_out)
def test_OpenMMWriter(self):
"""Create new replica and write MDinput"""
from MDSettings import MDSettings
from Systems import SolvatedSystem
top = osp.join(T.testRoot('pep', 'pep.prmtop'))
crd = osp.join(T.testRoot('pep', 'pep.prmcrd'))
sys = SolvatedSystem(name='pep', top=top, crd=crd)
settings = MDSettings(solvent='WAT',
mdProgram='OpenMM',
restrMode='HA',
restrForce=0.1)
self.testdir = T.tempDir()
self.r1 = sys + settings
self.r1.setName('testOpenMM')
T.BROWSER.chdir(self.testdir)
# write replica folder and check methods of OpenMMWriter
self.r1.createFolder()
self.r1.createMDInput()
writer = OpenMMWriter(self.r1)
self.testdir += os.sep + 'testOpenMM'
def test_NAMDWriter(self):
"""Create new replica and write MDinput"""
from MDSettings import MDSettings
from Systems import SolvatedSystem
top = osp.join(T.testRoot('pep', 'pep.prmtop'))
crd = osp.join(T.testRoot('pep', 'pep.prmcrd'))
sys = SolvatedSystem(name='pep', top=top, crd=crd)
settings = MDSettings(solvent='WAT',
mdProgram='NAMD',
restrMode='HA',
restrForce=0.1)
self.testdir = T.tempDir()
self.r1 = sys + settings
self.r1.setName('testNAMD')
T.BROWSER.chdir(self.testdir)
# write replica folder and check methods of AmberWriter
self.r1.createFolder()
self.r1.createMDInput()
writer = NAMDWriter(self.r1)
# self.assertEqual(writer.getAmberRestrMask(), ':1-8 & !@H=')
# self.assertTrue(writer.writeCommands())
# self.assertTrue(writer.writeReplicaInput())
# self.assertEqual(writer.getReplicaCommands(), checkCommands)
self.testdir += os.sep + 'testNAMD'
def test_SystemOFF(self):
"""Create System from OFF"""
off = T.testRoot('pep', 'pep.off')
self.f_out = T.tempDir() + os.sep + 'SystemOFF'
if not os.path.exists(self.f_out): os.mkdir(self.f_out)
T.BROWSER.chdir(self.f_out)
self.r1 = System(amberOFF=off)
solvatedsys = self.r1.solvate('WAT', tmp=self.f_out)
def test_SolvatedSystem(self):
top = T.testRoot('pep', 'pep.prmtop')
crd = T.testRoot('pep', 'pep.prmcrd')
self.f_out = T.tempDir() + os.sep + 'SolvatedSystem'
if not os.path.exists(self.f_out): os.mkdir(self.f_out)
T.BROWSER.chdir(self.f_out)
solvatedsys = SolvatedSystem(name='pep', top=top, crd=crd)
solvatedsys.setPDBfromTOPCRD()
pdb = solvatedsys.getSolvatedPDB()
def test_CREATEpepProject(self):
"""Create complete test project"""
import shutil
print T.testRoot()
cfg = T.testRoot('pep', 'pep_amber_mdmix.cfg')
off = T.testRoot('pep', 'pep.off')
self.f_out = T.tempDir()
T.BROWSER.chdir(self.f_out)
shutil.copy(cfg, 'pep_amber_mdmix.cfg')
shutil.copy(off, 'pep.off')
proj = createProject('pep_amber_mdmix.cfg', 'pep_test_project')
self.f_out += 'pep_test_project'
def test_SolventCreation(self):
"""SolventManager Solvent creation test"""
f_in = osp.join(T.testRoot(), 'solvents', 'solvent_template.cfg')
self.f_out = osp.join(T.tempDir(), 'solvent.db')
self.m = SolventManager()
solv = self.m.createSolvent(f_in)
# print solv.getProbeByName('CT').mask
self.m.saveSolvent(solv, db=self.f_out)
self.assertEqual(str(solv), str(self.m.getSolvent('ETA', self.f_out)))
def solvate(self, solvent, suffix=None, tmp=True):
"""
Solvate system in OFF using solvent *solvent*. A PRMTOP and PRMCRD files will be saved and paths stored to :attr:`top` and :attr:`crd`.
:arg solvent: Solvent Instance or Name to fetch the Solvent Instance in the database.
:type: str or :class:`~Solvents.Solvent`
:arg str suffix: Suffix for output files. Prefix will be the system name. E.g.: ``systemname_suffix.prmtop`` and ``systemname_suffix.prmcrd``.
:arg bool tmp: Work in temporary folder.
"""
if not self.amberOFF:
raise SystemError, "Can not solvate if no Amber Object File is assigned."
if isinstance(solvent, str): solvent = Solvents.getSolvent(solvent)
if not solvent:
raise SystemError, 'Invalid solvent instance or name.'
# Build a loger just for this method
log = logging.getLogger("SystemLogger")
log.info("Solvating %s with solvent mixture %s"%(self.name, solvent.name))
suffix = suffix or solvent.name
name = '{0}_{1}'.format(self.name, suffix)
prmtop = name+'.prmtop'
prmcrd = name+'.prmcrd'
if tmp:
if isinstance(tmp, str): path = tmp
else: path = T.tempDir()
prmtop = osp.join(path, prmtop)
prmcrd = osp.join(path, prmcrd)
# Initiate AmberCreateSystem with loaded AmberOFF
# Solvate, neutralize
self.__initCreate()
self.create.solvateOrganic(self.unitName, solvent=solvent) # It will work even if its water
self.create.saveAmberParm(self.unitName, prmtop, prmcrd)
# Added by Xiaofeng 01/12/2016
parm = AmberParm(prmtop)
action = HMassRepartition(parm)
action.execute()
log.info(str(action))
parm.write_parm(prmtop)
#
self.__cleanCreate()
s = SolvatedSystem(name, prmtop, prmcrd, solvent=solvent.name, ref=self.ref)
return s
def test_SettingsManager(self):
"""SettingsManager test"""
f_in = osp.join(T.dataRoot(), 'defaults', 'settings.cfg')
self.f_out = osp.join(T.tempDir(), 'settings.cfg')
self.m = SettingsManager(f_in,
self.f_out,
createmissing=True,
verbose=self.local)
ns = locals() ## fetch local namespace
self.m.updateNamespace(ns) ## parse and insert options into namespace
if self.local:
globals().update(locals()) ## publish namespace for debugging
r = self.m.settings2dict()['testparam']
self.assertEqual(r, 42) ## from 'int-testparam = 42' in settings.cfg
def prepare(self):
self.fname = T.testRoot() + '/rec/1A2P_rec_original.pdb'
self.outPath = T.tempDir()
def prepare(self):
self.fname = T.testRoot() + '/rec/1A2P_rec_original.pdb'
self.outPath = T.tempDir()
