#filename = "1ivs.cif"
cleaned_filename = filename[:-4] + "_cleaned.cif"
if not os.path.exists(cleaned_filename):
chain_id = sys.argv[2]
if chain_id is None:
raise Exception("Chain ID must be provided!")
clean_pdb(filename, cleaned_filename, chain_id, parameters)
h = float(sys.argv[3])
steps = int(sys.argv[4])
save_step = int(sys.argv[5])
# Load PDB file
print("initializing")
pdb = PDB(cleaned_filename)
N = pdb.positions.shape[0]
def parse_name(name):
if name == "OP1":
name = "O1P"
if name == "OP2":
name = "O2P"
return name
#get neighbours of i and then angles
all_angles = []
for i in range(0, N):
neighbours = []
from mpi4py import MPI
from pdb import PDB
from numpy import array, zeros
comm = MPI.COMM_WORLD
size = comm.Get_size()
rank = comm.Get_rank()
if rank == 0:
pdb = PDB('5ire.pdb')
n = len(pdb)
# how many atoms should each process get?
chunk = 3 * (n / size)
left = 3 * (n % size)
# calculate send counts and offsets
counts = [chunk] * size
counts[-1] += left
counts = tuple(counts)
offsets = [x * chunk for x in range(size)]
offsets = tuple(offsets)
# send chunk size to everyone and prepare a receive array
comm.bcast(counts, root=0)
comm.bcast(offsets, root=0)
my_coords = zeros((counts[rank], 3), float)
# scatter coordinates to all processes
comm.Scatterv([pdb.coordinates, counts, offsets, MPI.DOUBLE], my_coords)
# calculate the sum of coordinates
result = sum(my_coords)
# 2 (e)
# / \
# 3---1
# \ /
# 4
#
# tetrahedral (f)
# 3-2
# |X|
# 4-1
if __name__ == "__main__":
from pdb import PDB
pdb = PDB([("1", 1, 'H3'), ("2", 1, 'H3'), ("3", 1, 'H3'), ("4", 1, 'C3'),
("5", 1, 'H2'), ("6", 1, 'H2'), ("7", 1, 'C2'), ("8", 1, 'H2'),
("9", 1, 'H2'), ("10", 1, 'C2'), ("11", 1, 'H3'),
("12", 1, 'H3'), ("13", 1, 'H3'), ("14", 1, 'C3')], [], [],
edge=[(0, 3), (1, 3), (2, 3), (3, 6), (4, 6), (5, 6), (6, 9),
(7, 9), (8, 9), (9, 13), (10, 13), (11, 13), (12, 13)])
#def f(i,j):
# return i == 4 or j == 4
#sel = Conn(1,2) * Type('C', 'H') | Conn(1,3) * IdFn(f)
#sel = OOP()
#sel = Conn(1,2,3)
#sel = Conn(1,3)
#sel = ( Conn(1,2,3,4) | (Conn(1,3,2,1) & Id(1,None,None,1)) ) \
# & Type(None, 'C', 'C', None)
#sel = Conn(1,2) | Conn(1,3) | Conn(1,4)
#print set(sel.run(pdb))
top = read_terms(pdb, '../share/vanilla.py')
from cg_topol import show_index
show_index(top)