diff --git a/CanonicalNucleotideAtoms.py b/CanonicalNucleotideAtoms.py
index e8403c05c78dcd2523bbee1d90e17d8d3467e47f..e793888d6b0bac26316167aea4de5a53ef39f99d 100644
--- a/CanonicalNucleotideAtoms.py
+++ b/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'