print("\nFEWPOINTS")
idcons.useFewPointsAlgorithm()
mols = idcons.update(system)
print(mols)
printMolecules(mols)
print("\nMANYPOINTS")
idcons.useManyPointsAlgorithm()
mols = idcons.update(system)
print(mols)
printMolecules(mols)
print("\nAPPLICATION TEST")
idcons = IdentityConstraint( [centers[99], centers[100], centers[101], centers[102]], system[MGIdx(0)] )
mols = idcons.update(system)
print("\nDEFAULT")
print(mols)
printMolecules(mols)
print("\nUPDATING SYSTEM")
print(system.version())
system.update(mols)
print(system.version())
mols = idcons.update(system)
print("\nPOST-UPDATE")
print(mols)
printMolecules(mols)
sampler = PrefSampler(mol0, cljff[MGIdx(0)], 200*angstrom2) sampler.updateFrom(system) mol0 = PartialMolecule(mol0) mol1 = PartialMolecule(mol1) mol2 = PartialMolecule(mol2) p0 = sampler.probabilityOf(mol0) p1 = sampler.probabilityOf(mol1) p2 = sampler.probabilityOf(mol2) print(p0, p1, p2, p0+p1+p2) mol1 = mol1.move().translate( Vector(1,0,0) ).commit() system.update(mol1) sampler.updateFrom(system) p0 = sampler.probabilityOf(mol0) p1 = sampler.probabilityOf(mol1) p2 = sampler.probabilityOf(mol2) print(p0, p1, p2, p0+p1+p2) mol0 = mol0.move().translate( Vector(1,0,0) ).commit() system.update(mol0) sampler.updateFrom(system) p0 = sampler.probabilityOf(mol0) p1 = sampler.probabilityOf(mol1)
def readXmlParameters(pdbfile, xmlfile):
# 1) Read a pdb file describing the system to simulate
p = PDB2(pdbfile)
s = p.toSystem()
molecules = s.molecules()
#print (molecules)
with open(pdbfile, "r") as f:
for line in f:
if line.split()[0] == "CRYST1":
print(line)
pbc_x = float(line.split()[1])
pbc_y = float(line.split()[2])
pbc_z = float(line.split()[3])
space = PeriodicBox(Vector(pbc_x, pbc_y, pbc_z))
break
else:
space = Cartesian()
#print("space:", space)
system = System()
# 2) Now we read the xml file, and store parameters for each molecule
import xml.dom.minidom as minidom
xmldoc = minidom.parse(xmlfile)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~ TAG NAME: TYPE ~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
itemlist_type = xmldoc.getElementsByTagName('Type')
dicts_type = []
for items in itemlist_type:
d = {}
for a in items.attributes.values():
d[a.name] = a.value
dicts_type.append(d)
dicts_tp = str(dicts_type).split()
#print (dicts_tp)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~ TAG NAME: ATOM ~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
itemlist_atom = xmldoc.getElementsByTagName('Atom')
dicts_atom = []
for items in itemlist_atom:
d = {}
for a in items.attributes.values():
d[a.name] = a.value
dicts_atom.append(d)
dicts_at = str(dicts_atom).split()
#print (dicts_at)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~ TAG NAME: BOND ~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
itemlist_bond = xmldoc.getElementsByTagName('Bond')
dicts_bond = []
for items in itemlist_bond:
d = {}
for a in items.attributes.values():
d[a.name] = a.value
dicts_bond.append(d)
dicts_b = str(dicts_bond).split()
#print (dicts_b)
nbond = itemlist_bond.length
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~ TAG NAME: ANGLE ~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
itemlist_angle = xmldoc.getElementsByTagName('Angle')
dicts_angle = []
for items in itemlist_angle:
d = {}
for a in items.attributes.values():
d[a.name] = a.value
dicts_angle.append(d)
dicts_ang = str(dicts_angle).split()
#print (dicts_angle)
nAngles = itemlist_angle.length
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~ TAG NAME: PROPER ~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
itemlist_proper = xmldoc.getElementsByTagName('Proper')
dicts_proper = []
for items in itemlist_proper:
d = {}
for a in items.attributes.values():
d[a.name] = a.value
dicts_proper.append(d)
dicts_pr = str(dicts_proper).split()
#print (dicts_pr)
nProper = itemlist_proper.length
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~ TAG NAME: IMPROPER ~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
itemlist_improper = xmldoc.getElementsByTagName('Improper')
dicts_improper = []
for items in itemlist_improper:
d = {}
for a in items.attributes.values():
d[a.name] = a.value
dicts_improper.append(d)
dicts_impr = str(dicts_improper).split()
#print (dicts_impr)
nImproper = itemlist_improper.length
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~ TAG NAME: VIRTUAL SITES ~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
itemlist_VirtualSite = xmldoc.getElementsByTagName('VirtualSite')
dicts_virtualsite = []
for items in itemlist_VirtualSite:
d = {}
for a in items.attributes.values():
d[a.name] = a.value
dicts_virtualsite.append(d)
#dicts_vs = str(dicts_virtualsite).split()
#print (dicts_vs)
nVirtualSites = itemlist_VirtualSite.length
v_site_CLJ = []
for i in range(0, int(len(dicts_atom))):
if dicts_atom[i]['type'][0] == 'v':
v_site_CLJ = dicts_atom[i]
dicts_virtualsite.append(v_site_CLJ)
for i in range(0, len(itemlist_VirtualSite)):
dicts_virtualsite[i].update(
dicts_virtualsite[i + len(itemlist_VirtualSite)])
dicts_virtualsite[i].update(
dicts_virtualsite[i + 2 * len(itemlist_VirtualSite)])
dict_vs = []
for i in range(0, len(itemlist_VirtualSite)):
dicts_virtualsite[i]
dict_vs.append(dicts_virtualsite[i])
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~ TAG NAME: RESIDUE ~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
itemlist_residue = xmldoc.getElementsByTagName('Residue')
dicts_residue = []
for items in itemlist_residue:
d = {}
for a in items.attributes.values():
d[a.name] = a.value
dicts_residue.append(d)
dicts_res = str(dicts_residue).split()
#print (dicts_res)
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~ TAG NAME: NON BONDED FORCE ~~~~~~~~~~~~~~~~
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
itemlist_nonbond = xmldoc.getElementsByTagName('NonbondedForce')
dicts_nonb = []
for items in itemlist_nonbond:
d = {}
for a in items.attributes.values():
d[a.name] = a.value
dicts_nonb.append(d)
dicts_nb = str(dicts_nonb).split()
#print (dicts_nb)
nNonBonded = itemlist_nonbond.length
# 3) Now we create an Amberparameters object for each molecule
molnums = molecules.molNums()
newmolecules = Molecules()
for molnum in molnums:
mol = molecules.at(molnum)
#print (mol)
# Add potential virtual site parameters
if len(dicts_virtualsite) > 0:
mol = mol.edit().setProperty(
"virtual-sites", vsiteListToProperty(dict_vs)).commit()
# We populate the Amberparameters object with a list of bond, angle, dihedrals
# We look up parameters from the contents of the xml file
# We also have to set the atomic parameters (q, sigma, epsilon)
editmol = mol.edit()
mol_params = AmberParameters(editmol) #SireMol::AmberParameters()
atoms = editmol.atoms()
# We update atom parameters see setAtomParameters in SireIO/amber.cpp l2122
natoms = editmol.nAtoms()
#print("number of atoms is %s" %natoms)
#natoms don't include the virtual sites!
# Loop over each molecule in the molecules object
opls = []
for i in range(0, int(len(dicts_atom) / 2)):
opl = {}
opl = dicts_atom[i]['type']
opls.append(opl)
name = []
for i in range(0, int(len(dicts_atom) / 2)):
nm = {}
nm = dicts_atom[i]['name']
name.append(nm)
two = []
#print(len(name))
for i in range(0, len(name)):
t = (opls[i], name[i])
two.append(t)
import numpy as np
atom_sorted = []
for j in range(0, len(two)):
for i in range(int(len(dicts_atom) / 2), len(dicts_atom)):
if dicts_atom[i]['type'] == two[j][0]:
dic_a = {}
dic_a = dicts_atom[i]
atom_sorted.append(dic_a)
type_sorted = []
for j in range(0, len(two)):
for i in range(0, int(len(dicts_type))):
if dicts_type[i]['name'] == two[j][0]:
dic_t = {}
dic_t = dicts_type[i]
type_sorted.append(dic_t)
print(" ")
print("There are ", natoms, " atoms in this molecule. ")
print("*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*")
for atom in atoms:
editatom = editmol.atom(atom.index())
i = int(str(atom.number()).split('(')[1].replace(")", " "))
editatom.setProperty(
"charge",
float(atom_sorted[i - 1]['charge']) * mod_electron)
editatom.setProperty("mass",
float(type_sorted[i - 1]['mass']) * g_per_mol)
editatom.setProperty(
"LJ",
LJParameter(
float(atom_sorted[i - 1]['sigma']) * 10 * angstrom,
float(atom_sorted[i - 1]['epsilon']) / 4.184 *
kcal_per_mol))
editatom.setProperty("ambertype", dicts_atom[i - 1]['type'])
editmol = editatom.molecule()
# Now we create a connectivity see setConnectivity in SireIO/amber.cpp l2144
# XML data tells us how atoms are bonded in the molecule (Bond 'from' and 'to')
if natoms > 1:
print("Set up connectivity")
con = []
for i in range(0, int(nbond / 2)):
if natoms > 1:
connect_prop = {}
connect_prop = dicts_bond[i]['from'], dicts_bond[i]['to']
con.append(connect_prop)
conn = Connectivity(editmol.info()).edit()
for j in range(0, len(con)):
conn.connect(atoms[int(con[j][0])].index(),
atoms[int(con[j][1])].index())
editmol.setProperty("connectivity", conn.commit()).commit()
mol = editmol.setProperty("connectivity", conn.commit()).commit()
system.update(mol)
# Now we add bond parameters to the Sire molecule. We also update amberparameters see SireIO/amber.cpp l2154
internalff = InternalFF()
bondfuncs = TwoAtomFunctions(mol)
r = internalff.symbols().bond().r()
for j in range(0, len(con)):
bondfuncs.set(
atoms[int(con[j][0])].index(),
atoms[int(con[j][1])].index(),
float(dicts_bond[j + len(con)]['k']) / (2 * 100 * 4.184) *
(float(dicts_bond[j + len(con)]['length']) * 10 - r)**2)
bond_id = BondID(atoms[int(con[j][0])].index(),
atoms[int(con[j][1])].index())
mol_params.add(
bond_id,
float(dicts_bond[j + len(con)]['k']) / (2 * 100 * 4.184),
float(dicts_bond[j + len(con)]['length']) * 10)
editmol.setProperty("bonds", bondfuncs).commit()
molecule = editmol.commit()
mol_params.getAllBonds()
editmol.setProperty(
"amberparameters",
mol_params).commit() # Weird, should work - investigate ?
molecule = editmol.commit()
# Now we add angle parameters to the Sire molecule. We also update amberparameters see SireIO/amber.cpp L2172
if natoms > 2:
print("Set up angles")
anglefuncs = ThreeAtomFunctions(mol)
at1 = []
for i in range(0, nAngles):
a1 = {}
to_str1 = str(re.findall(r"\d+",
str(dicts_angle[i]['class1'])))
if dicts_atom[i]['type'][0] == 'o': #if opls_
a1 = int(
to_str1.replace("[", "").replace("]", "").replace(
"'", "")) - 800
else: #if QUBE_
a1 = int(
to_str1.replace("[", "").replace("]",
"").replace("'", ""))
at1.append(a1)
at2 = []
for i in range(0, nAngles):
a2 = {}
to_str2 = str(re.findall(r"\d+",
str(dicts_angle[i]['class2'])))
if dicts_atom[i]['type'][0] == 'o': #if opls_
a2 = int(
to_str2.replace("[", "").replace("]", "").replace(
"'", "")) - 800
else: #if QUBE_
a2 = int(
to_str2.replace("[", "").replace("]",
"").replace("'", ""))
at2.append(a2)
at3 = []
for i in range(0, nAngles):
a3 = {}
to_str3 = str(re.findall(r"\d+",
str(dicts_angle[i]['class3'])))
if dicts_atom[i]['type'][0] == 'o': #if opls_
a3 = int(
to_str3.replace("[", "").replace("]", "").replace(
"'", "")) - 800
else: #if QUBE_
a3 = int(
to_str3.replace("[", "").replace("]",
"").replace("'", ""))
at3.append(a3)
theta = internalff.symbols().angle().theta()
for j in range(0, nAngles):
anglefuncs.set(
atoms[at1[j]].index(), atoms[at2[j]].index(),
atoms[at3[j]].index(),
float(dicts_angle[j]['k']) / (2 * 4.184) *
((float(dicts_angle[j]['angle']) - theta)**2))
angle_id = AngleID(atoms[int(at1[j])].index(),
atoms[int(at2[j])].index(),
atoms[int(at3[j])].index())
mol_params.add(angle_id,
float(dicts_angle[j]['k']) / (2 * 4.184),
float(dicts_angle[j]['angle']))
# Now we add dihedral parameters to the Sire molecule. We also update amberparameters see SireIO/amber.cpp L2190
if natoms > 3:
print("Set up dihedrals")
di1 = []
for i in range(0, nProper):
d1 = {}
to_str1 = str(
re.findall(r"\d+", str(dicts_proper[i]['class1'])))
if dicts_atom[0]['type'][0] == 'o': #if opls_
d1 = int(
to_str1.replace("[", "").replace("]", "").replace(
"'", "")) - 800
else: #if QUBE_
d1 = int(
to_str1.replace("[", "").replace("]",
"").replace("'", ""))
di1.append(d1)
di2 = []
for i in range(0, nProper):
d2 = {}
to_str2 = str(
re.findall(r"\d+", str(dicts_proper[i]['class2'])))
if dicts_atom[0]['type'][0] == 'o': #if opls_
d2 = int(
to_str2.replace("[", "").replace("]", "").replace(
"'", "")) - 800
else: #if QUBE_
d2 = int(
to_str2.replace("[", "").replace("]",
"").replace("'", ""))
di2.append(d2)
di3 = []
for i in range(0, nProper):
d3 = {}
to_str3 = str(
re.findall(r"\d+", str(dicts_proper[i]['class3'])))
if dicts_atom[0]['type'][0] == 'o': #if opls_
d3 = int(
to_str3.replace("[", "").replace("]", "").replace(
"'", "")) - 800
else: #if QUBE_
d3 = int(
to_str3.replace("[", "").replace("]",
"").replace("'", ""))
di3.append(d3)
di4 = []
for i in range(0, nProper):
d4 = {}
to_str4 = str(
re.findall(r"\d+", str(dicts_proper[i]['class4'])))
if dicts_atom[0]['type'][0] == 'o': #if opls_
d4 = int(
to_str4.replace("[", "").replace("]", "").replace(
"'", "")) - 800
else: #if QUBE_
d4 = int(
to_str4.replace("[", "").replace("]",
"").replace("'", ""))
di4.append(d4)
dihedralfuncs = FourAtomFunctions(mol)
phi = internalff.symbols().dihedral().phi()
for i in range(0, nProper):
if atoms[int(di1[i])].index() != atoms[int(di4[i])].index():
dihedral_id = DihedralID(atoms[int(di1[i])].index(),
atoms[int(di2[i])].index(),
atoms[int(di3[i])].index(),
atoms[int(di4[i])].index())
dih1 = float(dicts_proper[i]['k1']) / 4.184 * (1 + Cos(
int(dicts_proper[i]['periodicity1']) * phi -
float(dicts_proper[i]['phase1'])))
dih2 = float(dicts_proper[i]['k2']) / 4.184 * (1 + Cos(
int(dicts_proper[i]['periodicity2']) * phi -
float(dicts_proper[i]['phase2'])))
dih3 = float(dicts_proper[i]['k3']) / 4.184 * (1 + Cos(
int(dicts_proper[i]['periodicity3']) * phi -
float(dicts_proper[i]['phase3'])))
dih4 = float(dicts_proper[i]['k4']) / 4.184 * (1 + Cos(
int(dicts_proper[i]['periodicity4']) * phi -
float(dicts_proper[i]['phase4'])))
dih_fun = dih1 + dih2 + dih3 + dih4
dihedralfuncs.set(dihedral_id, dih_fun)
for t in range(1, 5):
mol_params.add(
dihedral_id,
float(dicts_proper[i]['k%s' % t]) / 4.184,
int(dicts_proper[i]['periodicity%s' % t]),
float(dicts_proper[i]['phase%s' % t]))
print("Set up impropers")
di_im1 = []
for i in range(0, nImproper):
d1 = {}
to_str1 = str(
re.findall(r"\d+", str(dicts_improper[i]['class1'])))
if dicts_atom[0]['type'][0] == 'o': #if opls_
d1 = int(
to_str1.replace("[", "").replace("]", "").replace(
"'", "")) - 800
else:
d1 = int(
to_str1.replace("[", "").replace("]",
"").replace("'", ""))
di_im1.append(d1)
di_im2 = []
for i in range(0, nImproper):
d2 = {}
to_str2 = str(
re.findall(r"\d+", str(dicts_improper[i]['class2'])))
if dicts_atom[0]['type'][0] == 'o': #if opls_
d2 = int(
to_str2.replace("[", "").replace("]", "").replace(
"'", "")) - 800
else:
d2 = int(
to_str2.replace("[", "").replace("]",
"").replace("'", ""))
di_im2.append(d2)
di_im3 = []
for i in range(0, nImproper):
d3 = {}
to_str3 = str(
re.findall(r"\d+", str(dicts_improper[i]['class3'])))
if dicts_atom[0]['type'][0] == 'o': #if opls_
d3 = int(
to_str3.replace("[", "").replace("]", "").replace(
"'", "")) - 800
else:
d3 = int(
to_str3.replace("[", "").replace("]",
"").replace("'", ""))
di_im3.append(d3)
di_im4 = []
for i in range(0, nImproper):
d4 = {}
to_str4 = str(
re.findall(r"\d+", str(dicts_improper[i]['class4'])))
if dicts_atom[0]['type'][0] == 'o': #if opls_
d4 = int(
to_str4.replace("[", "").replace("]", "").replace(
"'", "")) - 800
else:
d4 = int(
to_str4.replace("[", "").replace("]",
"").replace("'", ""))
di_im4.append(d4)
improperfuncs = FourAtomFunctions(mol)
phi_im = internalff.symbols().improper().phi()
for i in range(0, nImproper):
improper_id = ImproperID(atoms[int(di_im2[i])].index(),
atoms[int(di_im3[i])].index(),
atoms[int(di_im1[i])].index(),
atoms[int(di_im4[i])].index())
imp1 = float(dicts_improper[i]['k1']) * (1 / 4.184) * (1 + Cos(
int(dicts_improper[i]['periodicity1']) * phi_im -
float(dicts_improper[i]['phase1'])))
imp2 = float(dicts_improper[i]['k2']) * (1 / 4.184) * (1 + Cos(
int(dicts_improper[i]['periodicity2']) * phi_im -
float(dicts_improper[i]['phase2'])))
imp3 = float(dicts_improper[i]['k3']) * (1 / 4.184) * (1 + Cos(
int(dicts_improper[i]['periodicity3']) * phi_im -
float(dicts_improper[i]['phase3'])))
imp4 = float(dicts_improper[i]['k4']) * (1 / 4.184) * (1 + Cos(
int(dicts_improper[i]['periodicity4']) * phi_im -
float(dicts_improper[i]['phase4'])))
imp_fun = imp1 + imp2 + imp3 + imp4
improperfuncs.set(improper_id, imp_fun)
#print(improperfuncs.potentials())
for t in range(1, 5):
mol_params.add(
improper_id,
float(dicts_improper[i]['k%s' % t]) * (1 / 4.184),
int(dicts_improper[i]['periodicity%s' % t]),
float(dicts_improper[i]['phase%s' % t]))
mol = editmol.setProperty("bond", bondfuncs).commit()
mol = editmol.setProperty("angle", anglefuncs).commit()
mol = editmol.setProperty("dihedral", dihedralfuncs).commit()
mol = editmol.setProperty("improper", improperfuncs).commit()
system.update(mol)
# Now we work out non bonded pairs see SireIO/amber.cpp L2213
print("Set up nbpairs")
print("*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*")
## Define the bonded pairs in a list that is called are12
#print("Now calculating 1-2 intercactions")
are12 = []
for i in range(0, natoms):
for j in range(0, natoms):
if conn.areBonded(atoms[i].index(),
atoms[j].index()) == True:
#ij = {}
ij = (i, j)
are12.append(ij)
are12_bckup = are12[:]
#print("Now calculating 1-3 intercactions")
are13 = []
for i in range(0, natoms):
for j in range(0, natoms):
if conn.areAngled(atoms[i].index(),
atoms[j].index()) == True:
ij = {}
ij = (i, j)
are13.append(ij)
are13_bckup = are13[:]
# print("Now calculating 1-4 intercactions")
are14 = []
for i in range(0, natoms):
for j in range(0, natoms):
if conn.areDihedraled(
atoms[i].index(),
atoms[j].index()) == True and conn.areAngled(
atoms[i].index(), atoms[j].index()) == False:
ij = {}
ij = (i, j)
are14.append(ij)
are14_bckup = are14[:]
# print("Now calculating the non-bonded intercactions")
bonded_pairs_list = are12_bckup + are13_bckup + are14_bckup
nb_pair_list = []
for i in range(0, natoms):
#print("i=",i)
for j in range(0, natoms):
if i != j and (i, j) not in bonded_pairs_list:
nb_pair_list.append((i, j))
are_nb_bckup = nb_pair_list[:]
nbpairs = CLJNBPairs(editmol.info(), CLJScaleFactor(0, 0))
#print("Now setting 1-2 intercactions")
for i in range(0, len(are12)):
scale_factor1 = 0
scale_factor2 = 0
nbpairs.set(atoms.index(int(are12[i][0])),
atoms.index(int(are12[i][1])),
CLJScaleFactor(scale_factor1, scale_factor2))
#print("Now setting 1-3 intercactions")
for i in range(0, len(are13)):
scale_factor1 = 0
scale_factor2 = 0
nbpairs.set(atoms.index(int(are13[i][0])),
atoms.index(int(are13[i][1])),
CLJScaleFactor(scale_factor1, scale_factor2))
# print("Now setting 1-4 intercactions")
for i in range(0, len(are14)):
scale_factor1 = 1 / 2
scale_factor2 = 1 / 2
nbpairs.set(atoms.index(int(are14[i][0])),
atoms.index(int(are14[i][1])),
CLJScaleFactor(scale_factor1, scale_factor2))
mol_params.add14Pair(
BondID(atoms.index(int(are14[i][0])),
atoms.index(int(are14[i][1]))), scale_factor1,
scale_factor2)
# print("Now setting non-bonded intercactions")
#print("*~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~*")
for i in range(0, len(nb_pair_list)):
scale_factor1 = 1
scale_factor2 = 1
nbpairs.set(atoms.index(int(nb_pair_list[i][0])),
atoms.index(int(nb_pair_list[i][1])),
CLJScaleFactor(scale_factor1, scale_factor2))
# print("~~~~~~~~~~~~~~~~~~`")
mol = editmol.setProperty("intrascale", nbpairs).commit()
system.update(mol)
#print("Setup name of qube FF")
mol = mol.edit().setProperty("forcefield",
ffToProperty("qube")).commit()
system.update(mol)
molecule = editmol.commit()
newmolecules.add(molecule)
return (newmolecules, space)
sampler = PrefSampler(mol0, cljff[MGIdx(0)], 200 * angstrom2) sampler.updateFrom(system) mol0 = PartialMolecule(mol0) mol1 = PartialMolecule(mol1) mol2 = PartialMolecule(mol2) p0 = sampler.probabilityOf(mol0) p1 = sampler.probabilityOf(mol1) p2 = sampler.probabilityOf(mol2) print(p0, p1, p2, p0 + p1 + p2) mol1 = mol1.move().translate(Vector(1, 0, 0)).commit() system.update(mol1) sampler.updateFrom(system) p0 = sampler.probabilityOf(mol0) p1 = sampler.probabilityOf(mol1) p2 = sampler.probabilityOf(mol2) print(p0, p1, p2, p0 + p1 + p2) mol0 = mol0.move().translate(Vector(1, 0, 0)).commit() system.update(mol0) sampler.updateFrom(system) p0 = sampler.probabilityOf(mol0) p1 = sampler.probabilityOf(mol1)
rbmc.setReflectionSphere(center_point, 7.5*angstrom)
moves = SameMoves(rbmc)
PDB().write(grid_system.molecules(), "test0000.pdb")
t = QTime()
for i in range(1,11):
print("Moving the system...")
t.start()
grid_system = moves.move(grid_system, 1000, False)
ms = t.elapsed()
print(("Moves complete! Took %d ms" % ms))
print(("GRID: ",grid_system.energies()))
exp_system.update( grid_system.molecules() )
print(("EXPT: ",exp_system.energies()))
print(("\nGrid energy equals: %s. Explicit energy equals: %s." % \
(grid_system.energy(), exp_system.energy())))
diff = grid_system.energy() - exp_system.energy()
print(("The difference is %s\n" % diff))
PDB().write(grid_system.molecules(), "test%0004d.pdb" % i)
# Save and restore the two systems from binary
import Sire.Stream
print("Saving the grid system...")
Sire.Stream.save( (grid_system, exp_system), "test/SireMM/testgrid.s3" )
print("Reloading the grid system...")
rbmc.setReflectionSphere(center_point, 7.5*angstrom)
moves = SameMoves(rbmc)
PDB().write(grid_system2.molecules(), "test0000.pdb")
t = QTime()
for i in range(1,11):
print("Moving the system...")
t.start()
grid_system2 = moves.move(grid_system2, 1000, False)
ms = t.elapsed()
print("Moves complete! Took %d ms" % ms)
print("NEW GRIDFF: ",grid_system2.energies())
grid_system.update( grid_system2.molecules() )
print("OLD GRIDFF: ",grid_system.energies())
print("\nOld GridFF energy equals: %s. New GridFF energy equals: %s." % \
(grid_system.energy(), grid_system2.energy()))
diff = grid_system.energy() - grid_system2.energy()
print("The difference is %s\n" % diff)
PDB().write(grid_system2.molecules(), "test%0004d.pdb" % i)
# Save and restore the two systems from binary
import Sire.Stream
print("Saving the systems...")
Sire.Stream.save( (grid_system, grid_system2), "test/SireMM/testgrid.s3" )
print("Reloading the grid system...")