def Get_atom_list(filename,crd_file=""):
'''
Read in a structure file like pdb,gro. return a Simple_atom class dict.
rewrite from Get_Simple_atom_list, use dict but not list. for the bug
which may happen when the atom serial in pdb file not start from 1.
'''
atom_list=list()
if filename.endswith(".pdb"):
atom_list=PDB.Get_Atom_list(filename)
elif filename.endswith(".gro"):
atom_list=GRO.Get_Atom_list(filename)
elif filename.endswith(".top"):
if crd_file == "":
atom_list=amber_top.Read_top(filename)
else:
atom_list=amber_top.Read_crd(filename,crd_file)
else:
print "file name %s in invalid." %filename
return []
simple_list=dict()
for atom in atom_list:
simple=unit_atom.unit_atom(atom_name=atom.atom_name,\
atom_serial=atom.atom_serial,\
residue_name=atom.residue_name,\
residue_serial=atom.residue_serial,\
atom_coor_x=atom.atom_coor_x,\
atom_coor_y=atom.atom_coor_y,\
atom_coor_z=atom.atom_coor_z)
simple_list[simple.atom_serial]=simple
return simple_list
def Get_atom_list(filename, crd_file=""):
'''
Read in a structure file like pdb,gro. return a Simple_atom class dict.
rewrite from Get_Simple_atom_list, use dict but not list. for the bug
which may happen when the atom serial in pdb file not start from 1.
'''
atom_list = list()
if filename.endswith(".pdb"):
atom_list = PDB.Get_Atom_list(filename)
elif filename.endswith(".gro"):
atom_list = GRO.Get_Atom_list(filename)
elif filename.endswith(".top"):
if crd_file == "":
atom_list = amber_top.Read_top(filename)
else:
atom_list = amber_top.Read_crd(filename, crd_file)
else:
print "file name %s in invalid." % filename
return []
simple_list = dict()
for atom in atom_list:
simple=unit_atom.unit_atom(atom_name=atom.atom_name,\
atom_serial=atom.atom_serial,\
residue_name=atom.residue_name,\
residue_serial=atom.residue_serial,\
atom_coor_x=atom.atom_coor_x,\
atom_coor_y=atom.atom_coor_y,\
atom_coor_z=atom.atom_coor_z)
simple_list[simple.atom_serial] = simple
return simple_list
def Get_Simple_atom_list(filename,crd_file=""):
'''
Read in a structure file like pdb,gro. return a Simple_atom class list.
'''
atom_list=[]
if filename.endswith(".pdb"):
atom_list=PDB.Get_Atom_list(filename)
elif filename.endswith(".gro"):
atom_list=GRO.Get_Atom_list(filename)
elif filename.endswith(".top"):
if crd_file == "":
atom_list=amber_top.Read_top(filename)
else:
atom_list=amber_top.Read_crd(filename,crd_file)
else:
print "file name %s in invalid." %filename
return []
simple_list=[]
for atom in atom_list:
simple=unit_atom.unit_atom(atom_name=atom.atom_name,\
atom_serial=atom.atom_serial,\
residue_name=atom.residue_name,\
residue_serial=atom.residue_serial,\
atom_coor_x=atom.atom_coor_x,\
atom_coor_y=atom.atom_coor_y,\
atom_coor_z=atom.atom_coor_z)
simple_list.append(simple)
return simple_list
def Get_Simple_atom_list(filename, crd_file=""):
'''
Read in a structure file like pdb,gro. return a Simple_atom class list.
'''
atom_list = []
if filename.endswith(".pdb"):
atom_list = PDB.Get_Atom_list(filename)
elif filename.endswith(".gro"):
atom_list = GRO.Get_Atom_list(filename)
elif filename.endswith(".top"):
if crd_file == "":
atom_list = amber_top.Read_top(filename)
else:
atom_list = amber_top.Read_crd(filename, crd_file)
else:
print "file name %s in invalid." % filename
return []
simple_list = []
for atom in atom_list:
simple=unit_atom.unit_atom(atom_name=atom.atom_name,\
atom_serial=atom.atom_serial,\
residue_name=atom.residue_name,\
residue_serial=atom.residue_serial,\
atom_coor_x=atom.atom_coor_x,\
atom_coor_y=atom.atom_coor_y,\
atom_coor_z=atom.atom_coor_z)
simple_list.append(simple)
return simple_list