def get_topologies(toplist):
topfiles = [
currdir + "/oplsx-top.json",
currdir + "/dna-rna-top.json",
]
for f in toplist:
print(f, file=sys.stderr)
assert os.path.exists(f), f
topfiles.append(f)
topologies = []
for f in topfiles:
try:
topologies.append(topology.load(json.load(open(f))))
except:
print(f, file=sys.stderr)
raise
top_residues, top_patches = topology.merge(topologies)
return top_residues, top_patches
raise ValueError("--readpatch and explicit patch specification via --patch are mutually incompatible")
for f in args.topfile:
assert os.path.exists(f), f
topfiles.append(f)
for f in args.transfile:
transfiles.append(f)
topologies = []
for f in topfiles:
try:
topologies.append(topology.load(json.load(open(f))))
except:
print(f, file=sys.stderr)
raise
top_residues, top_patches = topology.merge(topologies)
for f in transfiles:
name = os.path.splitext(os.path.split(f)[1])[0]
parse_transfile(f, name)
mutations={}
for f in args.mutatefiles:
assert os.path.exists(f), f
for l in open(f):
h = l.find("#")
if h != -1: l = l[:h]
ll = l.split()
if len(ll) == 0: continue
assert len(ll) == 2, l
mutations[ll[0]] = ll[1]
currdir = os.path.abspath(os.path.split(__file__)[0])
allatomdir = currdir + "/../allatom"
sys.path.append(allatomdir)
import topology as topology_lib
topfiles = [
allatomdir + "/oplsx-top.json",
allatomdir + "/dna-rna-top.json",
]
topologies = []
for f in topfiles:
try:
topologies.append(topology_lib.load(json.load(open(f))))
except:
print >> sys.stderr, f
raise
topology = topology_lib.merge(topologies)
def make_interfacelist(ilist, pdb):
# Read interface residues from files
data = open(ilist).readlines()
data = [l for l in data if not l[0] == '#']
if len(data) == 0:
return [], []
rlist = np.loadtxt(ilist, dtype=int)
# Make list of corresponding atoms
ratoms = []
receptorid = []
data = open(pdb).readlines()
data = [x for x in data if 'ATOM' in x]