def __str__(self):
data = ''
for chain in self.__iter__():
for rnum, residue in enumerate(chain):
for offset, atom in enumerate(residue):
data += PDB_util.Atom2pdb(atom)
ter = atom
ter.set_param('atm_type', 'TER')
ter.set_param('atm_name', ' ')
data += PDB_util.Atom2pdb(atom)[0:26] + '\n'
data += 'END'
return data
def read_pdb(self):
model = 1
self.__models[ model ] = Pose.Pose( model )
for line in open( self.__inputFile, 'r'):
if "MODEL" == line[0:5]:
model = int(string.split(line)[1])
self.__models[ model ] = Pose.Pose( model )
elif ( ("ATOM" == line[0:4]) or ( "HETATM" ==line[0:6]) ):
self.__models[ model ].add_atom( PDB_util.pdb2Atom(line) )
elif ( ("TER" == line[0:3] ) or ( "ENDMDL" == line[0:6] ) or ("END" == line[0:3] ) ):
continue
else: self.__header += line
def read_pdb(self):
model = 1
self.__models[model] = Pose.Pose(model)
for line in open(self.__inputFile, 'r'):
if "MODEL" == line[0:5]:
model = int(string.split(line)[1])
self.__models[model] = Pose.Pose(model)
elif (("ATOM" == line[0:4]) or ("HETATM" == line[0:6])):
self.__models[model].add_atom(PDB_util.pdb2Atom(line))
elif (("TER" == line[0:3]) or ("ENDMDL" == line[0:6])
or ("END" == line[0:3])):
continue
else:
self.__header += line
def __str__(self):
data = ''
for atom in self.__iter__():
data += PDB_util.Atom2pdb(atom)
return data
from numpy import array def apply_rotation( self, RotMatrix, c0 = array( [0, 0, 0] ) ): for chain in self.__iter__(): for resi in chain: for atm in chain: print RotMatrix * (atm.pos - c0) def build_pose( atom_objs ): pose = Pose() for atm in atom_objs: pose.add_atom( atm ) return pose if __name__ == '__main__': data=[] path1='/Users/Josh/Documents/pdb/1FOS_cln.pdb' path2='/Users/Josh/Downloads/1HGD.pdb' for line in open(path2,'r'): if line[0:4] != 'ATOM': continue data.append( PDB_util.pdb2Atom(line) ) pose = build_pose( data ) pose.renumber() #`for r in pose['A'][8:40]: # print r['N'] print pose.seq()
from numpy import array
def apply_rotation(self, RotMatrix, c0=array([0, 0, 0])):
for chain in self.__iter__():
for resi in chain:
for atm in chain:
print RotMatrix * (atm.pos - c0)
def build_pose(atom_objs):
pose = Pose()
for atm in atom_objs:
pose.add_atom(atm)
return pose
if __name__ == '__main__':
data = []
path1 = '/Users/Josh/Documents/pdb/1FOS_cln.pdb'
path2 = '/Users/Josh/Downloads/1HGD.pdb'
for line in open(path2, 'r'):
if line[0:4] != 'ATOM': continue
data.append(PDB_util.pdb2Atom(line))
pose = build_pose(data)
pose.renumber()
#`for r in pose['A'][8:40]:
# print r['N']
print pose.seq()
def __str__(self):
return PDB_util.Atom2pdb(self)
