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qube_to_prmRst.py
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qube_to_prmRst.py
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import os
import re
import sys
import argparse
from Sire.Base import *
from datetime import datetime
# Make sure that the OPENMM_PLUGIN_DIR enviroment variable is set correctly.
os.environ["OPENMM_PLUGIN_DIR"] = getLibDir() + "/plugins"
from Sire.IO import *
from Sire.Mol import *
from Sire.CAS import *
from Sire.System import *
from Sire.Move import *
from Sire.MM import *
from Sire.FF import *
from Sire.Units import *
from Sire.Vol import *
from Sire.Maths import *
from Sire.Qt import *
from Sire.ID import *
from Sire.Config import *
from Sire.Analysis import *
from Sire.Tools.DCDFile import *
from Sire.Tools import Parameter, resolveParameters
import Sire.Stream
import time
import numpy as np
#########################################
# Config file parameters #
#########################################
combining_rules = Parameter("combining rules", "geometric",
"""Combining rules to use for the non-bonded interactions.""")
cutoff_type = Parameter("cutoff type", "nocutoff", """The cutoff method to use during the simulation.""")
cutoff_dist = Parameter("cutoff distance", 500 * angstrom,
"""The cutoff distance to use for the non-bonded interactions.""")
use_restraints = Parameter("use restraints", False, """Whether or not to use harmonic restaints on the solute atoms.""")
def createSystem(molecules):
#print("Applying flexibility and zmatrix templates...")
print("Creating the system...")
moleculeNumbers = molecules.molNums()
moleculeList = []
for moleculeNumber in moleculeNumbers:
molecule = molecules.molecule(moleculeNumber)[0].molecule()
moleculeList.append(molecule)
molecules = MoleculeGroup("molecules")
ions = MoleculeGroup("ions")
for molecule in moleculeList:
natoms = molecule.nAtoms()
if natoms == 1:
ions.add(molecule)
else:
molecules.add(molecule)
all = MoleculeGroup("all")
all.add(molecules)
all.add(ions)
# Add these groups to the System
system = System()
system.add(all)
system.add(molecules)
system.add(ions)
return system
def setupForcefields(system, space):
print("Creating force fields... ")
all = system[MGName("all")]
molecules = system[MGName("molecules")]
ions = system[MGName("ions")]
# - first solvent-solvent coulomb/LJ (CLJ) energy
internonbondedff = InterCLJFF("molecules:molecules")
if (cutoff_type.val != "nocutoff"):
internonbondedff.setUseReactionField(True)
internonbondedff.setReactionFieldDielectric(rf_dielectric.val)
internonbondedff.add(molecules)
inter_ions_nonbondedff = InterCLJFF("ions:ions")
if (cutoff_type.val != "nocutoff"):
inter_ions_nonbondedff.setUseReactionField(True)
inter_ions_nonbondedff.setReactionFieldDielectric(rf_dielectric.val)
inter_ions_nonbondedff.add(ions)
inter_ions_molecules_nonbondedff = InterGroupCLJFF("ions:molecules")
if (cutoff_type.val != "nocutoff"):
inter_ions_molecules_nonbondedff.setUseReactionField(True)
inter_ions_molecules_nonbondedff.setReactionFieldDielectric(rf_dielectric.val)
inter_ions_molecules_nonbondedff.add(ions, MGIdx(0))
inter_ions_molecules_nonbondedff.add(molecules, MGIdx(1))
# Now solute bond, angle, dihedral energy
intrabondedff = InternalFF("molecules-intrabonded")
intrabondedff.add(molecules)
# Now solute intramolecular CLJ energy
intranonbondedff = IntraCLJFF("molecules-intranonbonded")
if (cutoff_type.val != "nocutoff"):
intranonbondedff.setUseReactionField(True)
intranonbondedff.setReactionFieldDielectric(rf_dielectric.val)
intranonbondedff.add(molecules)
# solute restraint energy
#
# We restrain atoms based ont he contents of the property "restrainedatoms"
#
restraintff = RestraintFF("restraint")
if use_restraints.val:
molnums = molecules.molecules().molNums()
for molnum in molnums:
mol = molecules.molecule(molnum)[0].molecule()
try:
mol_restrained_atoms = propertyToAtomNumVectorList(mol.property("restrainedatoms"))
except UserWarning as error:
error_type = re.search(r"(Sire\w*::\w*)", str(error)).group(0)
if error_type == "SireBase::missing_property":
continue
else:
raise error
for restrained_line in mol_restrained_atoms:
atnum = restrained_line[0]
restraint_atom = mol.select(atnum)
restraint_coords = restrained_line[1]
restraint_k = restrained_line[2] * kcal_per_mol / (angstrom * angstrom)
restraint = DistanceRestraint.harmonic(restraint_atom, restraint_coords, restraint_k)
restraintff.add(restraint)
# Here is the list of all forcefields
forcefields = [internonbondedff, intrabondedff, intranonbondedff, inter_ions_nonbondedff,
inter_ions_molecules_nonbondedff, restraintff]
for forcefield in forcefields:
system.add(forcefield)
system.setProperty("space", space)
system.setProperty("switchingFunction", CHARMMSwitchingFunction(cutoff_dist.val))
system.setProperty("combiningRules", VariantProperty(combining_rules.val))
total_nrg = internonbondedff.components().total() + \
intranonbondedff.components().total() + intrabondedff.components().total() + \
inter_ions_nonbondedff.components().total() + inter_ions_molecules_nonbondedff.components().total() + \
restraintff.components().total()
e_total = system.totalComponent()
system.setComponent(e_total, total_nrg)
# Add a monitor that calculates the average total energy and average energy
# deltas - we will collect both a mean average and an zwanzig average
system.add("total_energy", MonitorComponent(e_total, Average()))
return system
def vsiteListToProperty(list):
prop = Properties()
i = 0
for entry in list:
for key, value in entry.items():
prop.setProperty("%s(%d)" % (key,i), VariantProperty(value))
i += 1
prop.setProperty("nvirtualsites",VariantProperty(i))
return prop
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)
def ffToProperty(string):
prop = Properties()
prop.setProperty("forcefield",VariantProperty("qube"))
return prop
if __name__ == '__main__':
parser = argparse.ArgumentParser(description="Read parameters and coordinates from xml and pdb files ",
epilog=" ",
prog="readXmlParameters")
parser.add_argument('-p', '--pdbfile', nargs="?", help="The pdb file with the coordinates of the molecule.")
parser.add_argument('-x', '--xmlfile', nargs="?", help="The xml file with the parameters of the molecule.")
args = parser.parse_args()
(lig1, space) = readXmlParameters(args.pdbfile, args.xmlfile)
system = createSystem(lig1) # Sire.System._System.System
system = setupForcefields(system, space)
rst = Sire.IO.AmberRst7(system)
prm = AmberPrm(system)
print("Writing the prm7 and rst7 files")
pdb_name = str(args.pdbfile).split('.')[0]
prm.writeToFile("%s.prm7"%pdb_name)
rst.writeToFile("%s.rst7"%pdb_name)
print("Process completed!")
print(" You can now continue your simulations with the files %s.prm7 and %s.rst7!"%(pdb_name, pdb_name))
print("Energy computed with the ",combining_rules.val, "combining rules is: ", system.energy())
print("_________________________________________________________________________________________")