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
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()