def load_fragments():
from residue import Residue
import os
ref = Residue('REF')
ref.append_atom(Atom( 'N', [0.000, 0.300, 0.000]))
ref.append_atom(Atom('CA', [1.181, -0.540, 0.000]))
ref.append_atom(Atom( 'C', [2.440, 0.300, 0.000]))
# load all residues
this_dir, this_filename = os.path.split(__file__)
DATA_PATH = os.path.join(this_dir, "static", "residues.pdb")
residue_container = Molecule.LoadFromFile(DATA_PATH)
for fragment in residue_container.iter_residues():
fit(ref, ('N','CA','C'), fragment, ('N','CA','C'))
FragmentProvider.FRAGMENTS[fragment.name] = fragment
def LoadFromFile(fname):
from residue import Residue
from atom import Atom
def parse_pdb_line(s):
# atname, resname, resid, xyz
return s[12:16].strip(), \
s[17:21].strip(), \
int(s[22:26]), \
np.array([s[i:i+8] for i in (30,38,46)], dtype=float)
rindex = 0
pivot = None
atoms = [None]
is_head = True
molecule = Molecule('mol')
with open(fname, 'r') as fin:
for line in fin:
if line.startswith('TITLE'):
molecule.name = line[5:].strip()
elif line.startswith('ATOM'):
atname,resname,resid,xyz = parse_pdb_line(line)
if is_head or (resid != rindex):
residue = Residue(resname)
molecule.append_residue(residue, is_head)
is_head = False
rindex = resid
atom = Atom(atname, xyz)
atoms.append(atom)
residue.append_atom(atom)
elif line.startswith('TER'):
is_head = True
elif line.startswith('CONECT'):
idxs = map(int, line[6:].split())
pivot = atoms[idxs[0]]
for i in idxs[1:]:
pivot.connect_to(atoms[i])
auto_setup = pivot is None
molecule.compile(auto_setup=auto_setup)
return molecule
