import numpy as np import sqlite3 eps = 1E-5 class DMS_Data(): def __init__(self,filename): self.conn = sqlite3.connect(filename) self.c = self.conn.cursor() self.get_nonbonded() self.get_bonds() self.get_angles() self.get_dihedral_trigs() self.get_improper_harms() self.get_exceptions() self.get_cmap() def get_exceptions(self): self.c.execute("SELECT * FROM pair_12_6_es_param") ans = self.c.fetchall() self.exception_types = {} for row in ans: aij,bij,qij,fid,typekey,comment,ff = row self.exception_types[fid] = (aij,bij,qij) self.c.execute("SELECT * FROM pair_12_6_es_term") ans = self.c.fetchall() self.exceptions = {} for row in ans: p0,p1,fid,moiety = row a,b,q = self.exception_types[fid] sigma = (a/b)**(1.0/6.0) epsilon = b*b / (4.0*a) self.exceptions[p0,p1] = (sigma,epsilon,q) self.exceptions[p1,p0] = (sigma,epsilon,q) def get_nonbonded(self): self.c.execute("SELECT * FROM nonbonded_param") ans = self.c.fetchall() self.nonbonded_types = {} for row in ans: sigma,epsilon,fid,typekey,comment,ff = row self.nonbonded_types[fid] = (sigma,epsilon) self.c.execute("SELECT * FROM particle") ans = self.c.fetchall() self.resnames = {} self.names = {} self.charges = {} self.resids = {} self.sigmas = {} self.epsilons = {} for row in ans: key, anum, chain, resname, resid, name, x,y,z,vx,vy,vz,mass,charge,nbtype,grp_temperature,grp_energy,grp_ligand,grp_bias,grp_frozen,occupancy,bfactor,formal_charge = row self.resnames[key] = resname self.resids[key] = resid self.charges[key] = charge self.names[key] = name sigma,epsilon = self.nonbonded_types[nbtype] self.sigmas[key] = sigma self.epsilons[key] = epsilon def get_bonds(self): self.c.execute("SELECT * FROM stretch_harm_term") ans = self.c.fetchall() self.bond_param_ids = {} for row in ans: p0,p1,param,constrained,moiety = row self.bond_param_ids[(p0,p1)] = param self.c.execute("SELECT * FROM stretch_harm_param") ans = self.c.fetchall() self.bond_params = {} for row in ans: r0,fc,fid,typekey,comment,ff = row fc = fc * 2.0 self.bond_params[fid] = (r0,fc) self.bonds = {} for key in self.bond_param_ids.keys(): self.bonds[key] = self.bond_params[self.bond_param_ids[key]] p0,p1 = key key1 = (p1,p0) self.bonds[key1] = self.bond_params[self.bond_param_ids[key]] def get_angles(self): self.c.execute("SELECT * FROM angle_harm_term") ans = self.c.fetchall() self.angle_param_ids = {} for row in ans: p0,p1,p2,param,constrained,moiety = row self.angle_param_ids[(p0,p1,p2)] = param self.c.execute("SELECT * FROM angle_harm_param") ans = self.c.fetchall() self.angle_params = {} for row in ans: r0,fc,fid,typekey,comment,ff = row fc = fc * 2.0 self.angle_params[fid] = (r0,fc) self.angles = {} for key in self.angle_param_ids.keys(): self.angles[key] = self.angle_params[self.angle_param_ids[key]] p0,p1,p2 = key key1 = (p2,p1,p0) self.angles[key1] = self.angle_params[self.angle_param_ids[key]] def get_dihedral_trigs(self): self.c.execute("SELECT * FROM dihedral_trig_term") ans = self.c.fetchall() self.dihedral_trig_param_ids = {} for row in ans: p0,p1,p2,p3,param,moiety = row key = (p0,p1,p2,p3) if self.dihedral_trig_param_ids.has_key(key): self.dihedral_trig_param_ids[key].append(param) else: self.dihedral_trig_param_ids[key] = [param] self.c.execute("SELECT * FROM dihedral_trig_param") ans = self.c.fetchall() self.dihedral_trig_params = {} for row in ans: phi0,fc0,fc1,fc2,fc3,fc4,fc5,fc6,fid,typekey,comment,ff = row self.dihedral_trig_params[fid] = (phi0,fc0,fc1,fc2,fc3,fc4,fc5,fc6) self.dihedral_trigs = {} for key in self.dihedral_trig_param_ids.keys(): p0,p1,p2,p3 = key key2 = p3,p2,p1,p0 for term in self.dihedral_trig_param_ids[key]: (phi0,fc0,fc1,fc2,fc3,fc4,fc5,fc6) = self.dihedral_trig_params[term] parms = np.array([fc0,fc1,fc2,fc3,fc4,fc5,fc6]) if np.linalg.norm(parms) > eps: if not self.dihedral_trigs.has_key(key): self.dihedral_trigs[key] = {} self.dihedral_trigs[key2] = {} self.dihedral_trigs[key][phi0] = parms self.dihedral_trigs[key2][phi0] = parms def get_improper_harms(self): self.c.execute("SELECT * FROM improper_harm_term") ans = self.c.fetchall() self.improper_harm_param_ids = {} for row in ans: p0,p1,p2,p3,param,moiety = row key = np.unique([p0,p1,p2,p3]) key = tuple(key) if not self.improper_harm_param_ids.has_key(key): self.improper_harm_param_ids[key] = [] self.improper_harm_param_ids[key].append(param) self.c.execute("SELECT * FROM improper_harm_param") ans = self.c.fetchall() self.improper_harm_params = {} for row in ans: phi0,fc,fid,typekey,comment,ff = row self.improper_harm_params[fid] = (phi0,fc) self.improper_harms = {} for key,fidlist in self.improper_harm_param_ids.iteritems(): philist = [] for fid in fidlist: phi0,fc = self.improper_harm_params[fid] if fc > 0.: if not self.improper_harms.has_key(key): self.improper_harms[key] = (phi0,0.0) oldfc = self.improper_harms[key][1] self.improper_harms[key] = (phi0,fc + oldfc) philist.append(phi0) if np.std(philist) > eps: raise(Exception("Putting multiple improper harmonics on single atom set")) def get_cmap(self): self.c.execute("SELECT * FROM torsiontorsion_cmap_term") ans = self.c.fetchall() self.cmap_param_ids = {} for row in ans: p0,p1,p2,p3,p4,p5,p6,p7,param,moiety = row key = p0,p1,p2,p3,p4,p5,p6,p7 if not self.cmap_param_ids.has_key(key): self.cmap_param_ids[key] = [] self.cmap_param_ids[key].append(param) self.c.execute("SELECT * FROM torsiontorsion_cmap_param") ans = self.c.fetchall() self.cmap_param_string = {} for row in ans: cmapid,fid,typekey,comment,ff = row self.cmap_param_string[fid] = (cmapid) self.cmap_grids = {} for key,cmapstring in self.cmap_param_string.iteritems(): self.c.execute("SELECT * FROM %s"%cmapstring) ans = self.c.fetchall() philist = [] psilist = [] enlist = [] for row in ans: phi,psi,energy = row philist.append(phi) psilist.append(psi) enlist.append(energy) self.cmap_grids[key] = (np.array(philist),np.array(psilist),np.array(enlist))