def SoupFromNamdPsf(psf, in_coor_pdb, in_vel_pdb):
soup = Soup(in_coor_pdb)
load_masses_to_soup(psf, soup)
vel_soup = Soup(in_vel_pdb)
for atom, vel_atom in zip(soup.atoms(), vel_soup.atoms()):
v = vel_atom.pos
atom.vel.set(v.x, v.y, v.z)
return soup
def SoupFromPsf(psf):
"read a psf and parse into protein chains."
f = open(psf, "r")
line = f.readline()
while 'NATOM' not in line:
line = f.readline()
n_atom = int(line[0:8])
lines = [f.readline() for i in range(0, n_atom)]
f.close
# work out the chains in the psf file
chain_info_list = []
chain_char = ""
res_num = -1
chain_type = ""
for i, line in enumerate(lines):
word_list = line.split()
new_chain_type = word_list[1]
new_res_num = int(word_list[2])
if chain_type == "":
chain_type = new_chain_type
res_num = new_res_num
chain_info_list.append([chain_type, i, i+1])
elif chain_type is "WATERS" and new_chain_type is "WATERS" and \
res_num <> new_res_num:
res_num = new_res_num
chain_info_list.append([chain_type, i, i+1])
elif chain_type <> new_chain_type:
chain_type = new_chain_type
chain_info_list.append([chain_type, i, i+1])
else:
chain_info_list[-1][2] = i+1
# make a list of chains using the objects in protein
chains = []
for name, first, last in chain_info_list:
if "WATERS" in name:
chain = polymer.Polymer()
else:
chain = protein.Protein()
curr_res_num = -1
for i, line in enumerate(lines[first:last]):
word_list = line.split()
atom = molecule.Atom()
atom.res_num = int(word_list[2])
atom.res_type = word_list[3][0:3]
atom.type = word_list[4]
atom.element = atom.type[0]
atom.type = atom.type.strip(" ")
atom.num = i + first
try:
atom.mass = float(word_list[7])
except:
atom.mass = 0.0
if curr_res_num != atom.res_num:
res = polymer.Residue(atom.res_type, atom.chain_id, atom.res_num, '')
chain.append_residue_no_renum(res)
curr_res_num = atom.res_num
chain.insert_atom(chain.n_residue()-1, atom)
chains.append(chain)
soup = Soup()
for chain in chains:
soup.append_chain(chain)
# load masses in [a.m.u.]
masses = [float(line[47:60]) for line in open(psf, "r") if "CHAIN" in line]
for a, m in zip(soup.atoms(), masses):
a.mass = m
return soup
