def makeForceField(self, phys, *args):
"""
Create a new MDL force field.
@type phys: Physical
@param phys: The physical system.
@type args: tuple
@param args: Python tuple, may have no values or a string \"charmm\"
@rtype: ForceField
@return: Newly instantiated MDL force field.
"""
ff = ForceField()
ff.charmm = 0
ff.forceFactory = ForceFactory()
if (args.__len__() > 0):
ff.charmm = 1
ff.theforces = self
self.phys = ff.phys = phys
ff.bc = phys.bc
ff.setDefaults()
self.energies.initialize(phys)
ff.thisown = 0
#self.myForceFields.append(ff)
return ff
def makeForceField(self, phys, *args):
"""
Create a new MDL force field.
@type phys: Physical
@param phys: The physical system.
@type args: tuple
@param args: Python tuple, may have no values or a string \"charmm\"
@rtype: ForceField
@return: Newly instantiated MDL force field.
"""
ff = ForceField()
ff.charmm = 0
ff.forceFactory = ForceFactory()
if (args.__len__() > 0):
ff.charmm = 1
ff.theforces = self
self.phys = ff.phys = phys
ff.bc = phys.bc
ff.setDefaults()
self.energies.initialize(phys)
ff.thisown = 0
#self.myForceFields.append(ff)
return ff
def run(infile):
if os.path.isfile(infile) != 1:
print("ERROR: setup file not found!")
sys.exit(1)
#parse input file
params = Parser()
params.set_default_values()
params.parse(infile) #parse input file
params.check_variables() #check consistency of defined variables
#folder name equal path + system name
folder = "%s/%s" % (params.output_folder, params.output)
#if output folder does not exist, create it
if os.path.isdir(folder) != 1:
try:
os.makedirs(folder)
except:
print("\n> could not create output folder %s!" % folder)
return
else:
print(
"\n> WARNING: found folder %s. Existing files will be overwritten..."
% folder)
#prepare logger
logname = '%s/%s.log' % (folder, params.output)
if os.path.isfile(logname):
os.remove(logname)
#@todo kill all previous handles and close logfiles before proceeding (in case an unexpected crash happened before)
logger = logging.getLogger('assemble')
logger.setLevel(logging.INFO)
fh = logging.FileHandler(logname)
ch = logging.StreamHandler()
logger.addHandler(fh)
logger.addHandler(ch)
logger.info("> Assemble v1.0 <")
logger.info("> (c) 2014, Matteo Degiacomi and Valentina Erastova <")
if params.mode == "gromacs":
ff = ForceField()
ff.load(params.ff)
ff.default_bond = params.default_bond
ff.default_angle = params.default_angle
ff.default_dihedral = params.default_dihedral
else:
ff = ""
#load molecules objects into hash table from database list
db = Database()
if params.db != "":
try:
db.load(params.db, params.mode)
except Exception as e:
logger.exception(e)
fh.close()
logger.removeHandler(fh)
logger.removeHandler(ch)
sys.exit(1)
if len(params.residue.keys()) > 0:
logger.info("\n> adding residues in database...")
for r in params.residue.keys():
try:
if params.mode == "pdb":
db.add(r, params.residue[r])
if params.mode == "gromacs":
db.add(r, params.residue[r][0], params.residue[r][1])
except:
logger.exception(e)
fh.close()
logger.removeHandler(fh)
logger.removeHandler(ch)
#create random chains for all the molecules not having a chain explicitly defined
for m in params.molecule:
if m not in params.chain:
logger.info("\n> randomizing polymer chain for molecule %s..." % m)
params.chain[m] = make_chain(params.length[m],
params.percentage[m])
polymers = []
for m in params.molecule:
try:
#generate polymer
poly = Polymer(db, ff, m, params.mode, params.gromacs_nrxl)
poly.clash_thresh = params.clash_thresh
poly.make(params.chain[m])
if params.mode == "pdb":
poly.write_polymer(typef="pdb", mypath=folder)
elif params.mode == "gromacs":
poly.write_polymer(typef="gromacs", mypath=folder)
poly.write_gromacs(mypath=folder)
polymers.append(poly)
except Exception as e:
logger.exception(e)
fh.close()
logger.removeHandler(fh)
logger.removeHandler(ch)
if np.any(params.box_grid_shape == 0):
logger.warning(
"\n> no box size information provided, skipping system generation..."
)
fh.close()
logger.removeHandler(fh)
logger.removeHandler(ch)
return
if params.mode == "gromacs":
logger.info("\n> generating system...\n")
system = System(polymers, ff, params)
system.create_system(mypath=folder)
logger.info("\n> All done! Thank you for using Assemble! <")
fh.close()
logger.removeHandler(fh)
logger.removeHandler(ch)
def setUpMM3(input, mol, types):
masses = mol.get_masses() * amu
nAtoms = len(masses)
topology = app.topology.Topology()
f = ff.MM3(mol,types)
chain = topology.addChain('Main')
res = topology.addResidue('mm3', chain)
atoms = []
for a,t in zip(masses, f.types):
elem = app.element.Element.getByMass(a)
atoms.append(topology.addAtom(str('mm3_')+str(t),elem,res))
# Create a system and add particles to it
system = openmm.System()
for index in range(nAtoms):
# Particles are added one at a time
# Their indices in the System will correspond with their indices in the Force objects we will add later
system.addParticle(masses[index])
# Add Lennard-Jones interactions using a NonbondedForce. Only required so that openMM can set up exclusions.
force = openmm.NonbondedForce()
force.setUseDispersionCorrection(False) # use long-range isotropic dispersion correction
force.addParticle(0.5,1,4.184)
# Add custom bond term
bondForce = openmm.CustomBondForce("k*0.5*(r-r_eq)*(r-r_eq)*(1.0+cs*(r-r_eq) + (7.0/12.0)*cs*cs*(r-r_eq)*(r-r_eq))")
bondForce.addPerBondParameter("k")#Force constant
bondForce.addPerBondParameter("r_eq")#Equilibrium distance
#cs converted from 1/A to 1/nm
bondForce.addGlobalParameter("cs",-2.55 *10.0)
# Add custom force to system
system.addForce(bondForce)
# Iterate through bond list
bondPairs = []
for bond in f.bondList:
#Add bond term to forces. Fields 1 and 2 are the atom indicies and fields 3 and 4 are parameters k and r_eq
bondForce.addBond(bond[0],bond[1], [bond[2]*602.3*AngstromsPerNm*AngstromsPerNm, bond[3]*NmPerAngstrom])
bondPairs.append((bond[0],bond[1]))
id1,id2 = bond[0],bond[1]
topology.addBond(atoms[id1],atoms[id2])
# Custom angle term
angleForce = openmm.CustomAngleForce("k *0.5 *dtheta*dtheta*expansion;""expansion= 1.0 -0.014*dtor*dtheta+ 5.6e-5*dtor^2*dtheta^2-1.0e-6*dtor^3*dtheta^3+2.2e-8*dtor^4*dtheta^4;""dtor=57.295779;""dtheta = theta- theta_eq")
angleForce.addPerAngleParameter("k")
angleForce.addPerAngleParameter("theta_eq")
system.addForce(angleForce)
for angle in f.angleList:
#Add bond term to forces. Fields 1, 2 and 3 are the atom indicies and fields 4 and 5 are parameters k and r_eq
angleForce.addAngle(angle[0],angle[1],angle[2], [angle[3]*602.3,angle[4]*RadiansPerDegree])
# Custom angle term
# dihedralForce = openmm.CustomTorsionForce("0.5*V1*(1-cos(theta)) + 0.5*V2*(1-cos(2* (theta-3.141592)))+0.5*V3*(1-cos(3*theta))")
# dihedralForce.addPerTorsionParameter("V1")
# dihedralForce.addPerTorsionParameter("V2")
# dihedralForce.addPerTorsionParameter("V3")
# system.addForce(dihedralForce)
# for dihedral in f.dihedralList:
# #Add bond term to forces. Fields 1, 2 and 3 are the atom indicies and fields 4 and 5 are parameters k and r_eq
# dihedralForce.addTorsion(dihedral[0],dihedral[1],dihedral[2],dihedral[3], [dihedral[4]*4.184,dihedral[5]*4.184,dihedral[6]*4.184])
LJforce = openmm.CustomNonbondedForce("4.0*epsilon*(sigma^12/r^12 - sigma^6/r^6);"
"sigma=((sig1+sig2)/2.0);"
"epsilon=sqrt(eps1*eps2)")
#Add any required parameters
LJforce.addPerParticleParameter("sig")
LJforce.addPerParticleParameter("eps")
#Pass each particle params
for LJ in f.LJList:
LJforce.addParticle([LJ[0]*NmPerAngstrom,LJ[1]*4.184])
#After we've defined the LJ, we need to tell OpenMM to skip calculation where a bond or angle exists between to the two particles
num_exceptions = force.getNumExceptions()
LJforce.setNonbondedMethod(openmm.CustomNonbondedForce.CutoffNonPeriodic)
#Set cutoff distance in nm
LJforce.setCutoffDistance(3.0*NmPerAngstrom)
#Create exceptions for non-bonded interactions
for b in bondPairs:
force.addException(b[0], b[1], 1, 1.0/1.2, 1.0/2.0)
LJforce.addExclusion(b[0],b[1])
system.addForce(LJforce)
#dihedralForce = openmm.CustomTorsionForce()
#for index in range(nAtoms): # all particles must have parameters assigned for the NonbondedForce
# Particles are assigned properties in the same order as they appear in the System object
# force4.addParticle(charge, sigma, epsilon)
#force_index4 = system.addForce(force4)
return system,topology
def run(infile):
if os.path.isfile(infile)!=1 :
print "ERROR: setup file not found!"
sys.exit(1)
#parse input file
params=Parser()
params.set_default_values()
params.parse(infile) #parse input file
params.check_variables() #check consistency of defined variables
#folder name equal path + system name
folder="%s/%s"%(params.output_folder,params.output)
#if output folder does not exist, create it
if os.path.isdir(folder)!=1 :
try:
os.makedirs(folder)
except:
print "\n> could not create output folder %s!"%folder
return
else:
print "\n> WARNING: found folder %s. Existing files will be overwritten..."%folder
#prepare logger
logname='%s/%s.log'%(folder,params.output)
if os.path.isfile(logname):
os.remove(logname)
#@todo kill all previous handles and close logfiles before proceeding (in case an unexpected crash happened before)
logger = logging.getLogger('assemble')
logger.setLevel(logging.INFO)
fh = logging.FileHandler(logname)
ch = logging.StreamHandler()
logger.addHandler(fh)
logger.addHandler(ch)
logger.info("> Assemble v1.0 <")
logger.info("> (c) 2014, Matteo Degiacomi and Valentina Erastova <")
if params.mode=="gromacs":
ff=ForceField()
ff.load(params.ff)
ff.default_bond=params.default_bond
ff.default_angle=params.default_angle
ff.default_dihedral=params.default_dihedral
else:
ff=""
#load molecules objects into hash table from database list
db=Database()
if params.db!="":
try:
db.load(params.db,params.mode)
except Exception, e:
logger.exception(e)
fh.close()
logger.removeHandler(fh)
logger.removeHandler(ch)
sys.exit(1)
def run(infile):
if os.path.isfile(infile) != 1:
print "ERROR: setup file not found!"
sys.exit(1)
#parse input file
params = Parser()
params.set_default_values()
params.parse(infile) #parse input file
params.check_variables() #check consistency of defined variables
#folder name equal path + system name
folder = "%s/%s" % (params.output_folder, params.output)
#if output folder does not exist, create it
if os.path.isdir(folder) != 1:
try:
os.makedirs(folder)
except:
print "\n> could not create output folder %s!" % folder
return
else:
print "\n> WARNING: found folder %s. Existing files will be overwritten..." % folder
#prepare logger
logname = '%s/%s.log' % (folder, params.output)
if os.path.isfile(logname):
os.remove(logname)
#@todo kill all previous handles and close logfiles before proceeding (in case an unexpected crash happened before)
logger = logging.getLogger('assemble')
logger.setLevel(logging.INFO)
fh = logging.FileHandler(logname)
ch = logging.StreamHandler()
logger.addHandler(fh)
logger.addHandler(ch)
logger.info("> Assemble v1.0 <")
logger.info("> (c) 2014, Matteo Degiacomi and Valentina Erastova <")
if params.mode == "gromacs":
ff = ForceField()
ff.load(params.ff)
ff.default_bond = params.default_bond
ff.default_angle = params.default_angle
ff.default_dihedral = params.default_dihedral
else:
ff = ""
#load molecules objects into hash table from database list
db = Database()
if params.db != "":
try:
db.load(params.db, params.mode)
except Exception, e:
logger.exception(e)
fh.close()
logger.removeHandler(fh)
logger.removeHandler(ch)
sys.exit(1)