def get_dihedral_subset_mask(self, flexible_residues, mtype):
'''
This method creates an array of ones and/or zeros
of the length of the number of atoms in "self". It
uses the user-supplied flexible_residue array to
determine which atoms to include in the mask.
This version is hard-wired for proteins or rna to choose
the C(n-1), N(n), CA(n), C(n), and N(n+1) atoms
or the O3'(n-1), P(n), O5'(n), C5'(n), C4'(n),
C3'(n), O3'(n) and P(n+1) atoms that form the basis set
for the rotation phi & psi or alpha, beta, delta, epsilon, and eta
angles respectively. This method calles a c-method called
mask to speed up the calculation (24.5 X faster).
'''
natoms = self.natoms()
name = self.name()
resid = self.resid().astype(numpy.long)
nflexible = len(flexible_residues)
nresidues = int(self.resid()[-1] - self.resid()[0] + 1)
farray = numpy.zeros((nflexible, natoms), numpy.long)
mask.get_mask_array(farray, name, resid, flexible_residues, nresidues,
mtype)
return farray
def cee_way():
m1 = sasmol.SasMol(0)
m1.read_pdb("min3.pdb")
natoms = m1.natoms()
resid = m1.resid()
name = m1.name()
nresidues = m1.resid()[-1] - m1.resid()[0] + 1
flexible_residues = numpy.arange(2, 8).tolist()
# print 'getting rotation indices for molecule'
residue_rotation_indices = {}
residue_rotation_mask = {}
# print 'number of flexible residues = ',len(flexible_residues)
nflexible = len(flexible_residues)
atomlist = numpy.arange(0, natoms).tolist()
# import cee_mask
import mask
farray = numpy.zeros((nflexible, natoms), numpy.int32)
nresidues = int(nresidues)
mask.get_mask_array(farray, name, resid, flexible_residues, nresidues)
for i in xrange(nflexible):
for j in xrange(natoms):
if farray[i][j] != 0:
print farray[i][j],
def get_dihedral_subset_mask(self,flexible_residues,mtype): ''' This method creates an array of ones and/or zeros of the length of the number of atoms in "self". It uses the user-supplied flexible_residue array to determine which atoms to include in the mask. This version is hard-wired for proteins or rna to choose the C(n-1), N(n), CA(n), C(n), and N(n+1) atoms or the O3'(n-1), P(n), O5'(n), C5'(n), C4'(n), C3'(n), O3'(n) and P(n+1) atoms that form the basis set for the rotation phi & psi or alpha, beta, delta, epsilon, and eta angles respectively. This method calles a c-method called mask to speed up the calculation (24.5 X faster). ''' natoms=self.natoms() name=self.name() resid=self.resid().astype(numpy.long) nflexible=len(flexible_residues) nresidues=int(self.resid()[-1] - self.resid()[0]+1) farray=numpy.zeros((nflexible,natoms),numpy.long) mask.get_mask_array(farray,name,resid,flexible_residues,nresidues,mtype) return farray
def cee_way():
m1 = sasmol.SasMol(0)
m1.read_pdb('min3.pdb')
natoms = m1.natoms()
resid = m1.resid()
name = m1.name()
nresidues = m1.resid()[-1] - m1.resid()[0] + 1
flexible_residues = numpy.arange(2, 8).tolist()
# print 'getting rotation indices for molecule'
residue_rotation_indices = {}
residue_rotation_mask = {}
# print 'number of flexible residues = ',len(flexible_residues)
nflexible = len(flexible_residues)
atomlist = numpy.arange(0, natoms).tolist()
#import cee_mask
import mask
farray = numpy.zeros((nflexible, natoms), numpy.int32)
nresidues = int(nresidues)
mask.get_mask_array(farray, name, resid, flexible_residues, nresidues)
for i in xrange(nflexible):
for j in xrange(natoms):
if (farray[i][j] != 0):
print farray[i][j],
