def _pre_exec(self):
if self.occupancy_one:
occ_file = "occupancy_one.pdb"
npdb = NumPdb(self.pdb_input)
npdb['occupancy'] = 1.0
npdb.write(occ_file)
self.pdb_input = self.outpath(occ_file)
def _post_exec(self):
print('TEST 1')
print(self.relpath(self.dowser_file))
if '++' in self.relpath(self.dowser_file):
print('TEST !!!')
print('Dowser++ not looked at!')
return None
self._make_provi_file(input_file=self.relpath(self.input_file),
wat_file=self.relpath(self.wat_file),
watall_file=self.relpath(self.watall_file),
intsurf_file=self.relpath(self.intsurf_file))
# make sure all file exist
for f in [self.wat_file, self.watall_file, self.intsurf_file]:
with open(f, "a"):
pass
# write a pdb with all dowser waters but no others
with open(self.dowser_file, "w") as fp:
with open(self.pdb_file, "r") as fp_pdb:
for line in fp_pdb:
if (line[0:6] in ["ATOM ", "HETATM"]
and line[17:20] != "HOH"):
fp.write(line)
with open(self.wat_file, "r") as fp_wat:
for line in fp_wat:
if line[0:6] in ["HETATM"]:
fp.write(line)
# rename HOH.OW atoms to HOH.O and
# repair atom index
npdb = NumPdb(self.dowser_file)
for i, a in enumerate(npdb._atoms, start=1):
if a["atomname"] == " OW " and a["resname"] == "HOH":
a["atomname"] = " O "
a["atomno"] = i
npdb.write(self.dowser_file)
def _crop_pdb( self ):
npdb = NumPdb( self.pdb_file )
npdb.write(
self.cropped_pdb,
chain=self.res1["chain"],
resno=[ self.res1["resno"] + 1, self.res2["resno"] - 1 ],
invert=True
)