Fixed bug in atomic structure builder

CanonicalNucleotideAtoms.py

@@ -8,9 +8,6 @@ seqComplement = dict(A='T',G='C')
 resnames = dict(A="ADE", G="GUA", C="CYY", T="THY")
 for x,y in list(seqComplement.items()): seqComplement[y] = x
 
-
-atomic_types = dict()
-
 def stringToIntTuples(string, tupleLen, offset):
     l = string.split()
     # for i in range(0,len(l),tupleLen):
@@ -43,10 +40,10 @@ class CanonicalNucleotideFactory(Group):
         for i in range(len(tns)):
             tn = tns[i]
             if tn not in atomic_types:
-                atomic_types[tn] = ParticleType(tn.decode('UTF-8'),
-                                                charge = d['f3'][i],
-                                                mass   = d['f4'][i])
-            p = PointParticle( type_ = atomic_types[tn],
+                type_ = ParticleType(tn.decode('UTF-8'),
+                                     charge = d['f3'][i],
+                                     mass   = d['f4'][i])
+            p = PointParticle( type_ = type_,
                                position = [xs[i],ys[i],zs[i]],
                                name = names[i].decode('UTF-8'),
                                beta = 1)
@@ -83,107 +80,6 @@ class CanonicalNucleotideFactory(Group):
             nt.add_improper( atoms[i], atoms[j], atoms[k], atoms[l], None )
         return nt
 
-class CanonicalNucleotide(Group):
-    DefaultOrientation = rotationAboutAxis([0,0,1], 80)
-    def __init__(self, prefix, seq):
-        self.sequence = seq     # TODO: used?
-        self.resname = resnames[seq]
-        Group.__init__(self, orientation = CanonicalNucleotide.DefaultOrientation)
-                
-        ## idx, type,   
-        d = np.loadtxt("%s.dat" % prefix, dtype='i4,S4,S4,f4,f4,f4,f4,f4')
-
-        ids = d['f0']
-        assert( np.all(ids == sorted(ids)) )
-
-        names = d['f1']
-        tns = d['f2']
-        xs = d['f5']
-        ys = d['f6']
-        zs = d['f7']
-
-        type_list = []
-        for i in range(len(tns)):
-            tn = tns[i]
-            if tn not in atomic_types:
-                atomic_types[tn] = ParticleType(tn.decode('UTF-8'),
-                                                charge = d['f3'][i],
-                                                mass   = d['f4'][i])
-            p = PointParticle( type_ = atomic_types[tn],
-                               position = [xs[i],ys[i],zs[i]],
-                               name = names[i].decode('UTF-8') )
-            self.add( p )
-
-        
-        atoms = self.children
-        self.atoms_by_name = {a.name:a for a in atoms}
-        
-
-        # minIdx = np.min(self.indices) - 1
-        b = np.loadtxt("%s.bonds.txt" % prefix, dtype='i4') # - minIdx
-        for i,j in zip(b[::2],b[1::2]):
-            self.add_bond( atoms[i], atoms[j], None )
-
-        a = np.loadtxt("%s.angles.txt" % prefix, dtype='i4') # - minIdx
-        for i,j,k in zip(a[::3],a[1::3],a[2::3]):
-            self.add_angle( atoms[i], atoms[j], atoms[k], None )
-
-        d = np.loadtxt("%s.dihedrals.txt" % prefix, dtype='i4')# - minIdx
-        for i,j,k,l in zip(d[::4],d[1::4],d[2::4],d[3::4]):
-            self.add_dihedral( atoms[i], atoms[j], atoms[k], atoms[l], None )
-
-        i = np.loadtxt("%s.impropers.txt" % prefix, dtype='i4')# - minIdx
-        for i,j,k,l in zip(d[::4],d[1::4],d[2::4],d[3::4]):
-            self.add_improper( atoms[i], atoms[j], atoms[k], atoms[l], None )
-    
-    ## TODO: remove this!
-    def transformed(self, orientation, translation, scale=0.5, singleStranded=False):
-        # rotationAboutZ -= 68
-        c = copy.copy(self)
-        c.props = copy.deepcopy(self.props)
-
-        ## Find transformation
-        R = CanonicalNucleotide.DefaultOrientation.dot( orientation )
-        
-        ## Find offset of nt (shift for ssDNA)
-        center = np.array((0,0,0))
-        if singleStranded:
-            i0 = self.index("C3'")-1
-            center = np.array([c.props[k][i0] for k in ('x','y','z')])
-
-
-        ## Apply transformation
-        for i in range(len(c)):
-            rvec = np.array([c.props[k][i] for k in ('x','y','z')]) - center
-            rvec = rvec.dot( R )
-            for k,r,o in zip(('x','y','z'), rvec, translation):
-                c.props[k][i] = r + o
-
-        if scale != 1:
-            if singleStranded:
-                i0 = self.index("C3'")-1
-                r0 = np.array([c.props[k][i0] for k in ('x','y','z')])
-                for i in range(len(c)):
-                    rvec = np.array([c.props[k][i] for k in ('x','y','z')])
-                    rvec = scale*(rvec-r0) + r0
-                    for k,r in zip(('x','y','z'), rvec):
-                        c.props[k][i] = r
-                    c.props["beta"][i] = 0
-            else:
-                if self.sequence in ("A","G"):
-                    i0 = self.index("N9")-1
-                else:
-                    i0 = self.index("N1")-1
-                r0 = np.array([c.props[k][i0] for k in ('x','y','z')])
-                for i in range(len(c)):
-                    if c.props['name'][i][-1] in ("'","P","T"):
-                        rvec = np.array([c.props[k][i] for k in ('x','y','z')])
-                        rvec = scale*(rvec-r0) + r0
-                        for k,r in zip(('x','y','z'), rvec):
-                            c.props[k][i] = r
-                        c.props["beta"][i] = 0
-        
-        return c
     
 canonicalNtFwd = dict()
 direction = 'fwd'