valid : True if all the atoms are within the valid indices
"""
for atom_index in atoms:
if atom_index not in valid_indices:
return False
return True
#valid_indices = np.concatenate((np.arange(1,48), np.arange(88,91)))
valid_indices = np.arange(1, 42)
valid_indices = ['{}'.format(val) for val in valid_indices]
#renumber_indices = {"88": "48", "89":"49", "90":"50"}
original_itp = open('dppc.itp', 'r').readlines()
itplines = itp_utils.remove_comments(original_itp)
newitp = []
newitp.append('; Made by alex on {}\n'.format(datetime.datetime.now()))
newitp.append('[ moleculetype ]\n')
newitp.append(' ; name nrexcl\n')
newitp.append('pchd 3\n')
atoms_section = itp_utils.read_section('atoms', itplines)
newitp.append('[ atoms ]\n')
newitp.append('; nr type resnr residu atom cgnr charge mass\n')
for line in atoms_section:
first = line.split()[0]
if _is_valid([first], valid_indices):
newline = line.split()
## Pull the atomtypes from the itp files
## Print out the atomtypes that aren't yet included in types.txt
## This is useful for expanding our lammps charmm36 forcefield with
## Atomtypes from new gromacs itp files
####################
atomtype_dict = xml_utils.parse_type_dict(xml_utils.ATOMTYPES_FILE())
curr_dir = os.getcwd()
atomtypes = []
# Iterate through all prottype folders, picking out the atomtypes from the itp file
all_folders = [thing for thing in os.listdir() if os.path.isdir(thing)]
for folder in all_folders:
os.chdir(os.path.join(curr_dir, folder))
itpfile = [thing for thing in os.listdir() if os.path.isfile(thing) \
and 'itp' in thing[-4:]]
if itpfile:
itpfile = glob.glob('*.itp')[0]
itplines = open(itpfile, 'r').readlines()
itplines = itp_utils.remove_comments(itplines)
atomtype_lines = itp_utils.read_section('atoms', itplines)
for line in atomtype_lines:
atomtypes.append(line.split()[1])
# Look for all the new and unique atomtypes
atomtypes = set(atomtypes)
atomtype_dict = set(atomtype_dict)
uniques = atomtypes - atomtype_dict
for i in sorted(list(uniques)):
print(i)
import networkx as nx
import pdb
import scripts.itp_utils as itp_utils
itpfile = open('ecer3.itp','r').readlines()
itpfile = itp_utils.remove_comments(itpfile)
bonds = itp_utils.read_section('bonds', itpfile)
pairs = itp_utils.read_section('pairs', itpfile) # For verification
# Make a Network X graph by adding edges for each bond
bondgraph = nx.Graph()
for line in bonds:
first = line.split()[0]
second = line.split()[1]
bondgraph.add_edge(first,second)
# Cool, we are definitely getting all the bonds here
count =0
# all pairs is actually a set of quadruples corresponding to the atoms (and
# the ones in between) that make the pair
all_quadruples = set()
all_pairs = set()
for n1 in bondgraph.nodes_iter():
for n2 in bondgraph.nodes_iter():
path = nx.shortest_path(bondgraph, n1,n2)
if len(path) == 4:
pair = (sorted((n1,n2))[0], sorted((n1,n2))[1])
if pair not in all_pairs: