def get_SCOP_domain(domain):
"""
:param domain: str. The SCOPe domain to download as pdb
:return:
"""
logger.info(f'Attempting to download domain {domain} from the SCOP server')
url = f'https://scop.berkeley.edu/astral/pdbstyle/ver=2.07&id={domain}&output=text'
connected = False
while not connected:
try:
response = urllib.request.urlopen(url)
text = response.read()
except Exception as e:
import time
logger.warning(
f'Failed to connect to SCOP with error {e}. Sleeping 5s and retrying.'
)
time.sleep(5)
continue
connected = True
filepath = string_to_tempfile(text.decode('ascii'), 'pdb')
logger.info(f"File downloaded as {filepath}")
return filepath
def get_FUZZLE_hhs(domain):
"""
:param domain: str. The domain to download from Fuzzle as hhs
:return: filepath: path where the file is located.
"""
logger.info(
f'Attempting to download hhs file for {domain} from the FUZZLE server')
url = f'https://fuzzle.uni-bayreuth.de/hhs/scop95_2.07.psi.hhs/{domain}.hhs'
connected = False
while not connected:
try:
response = urllib.request.urlopen(url)
text = response.read()
except Exception as e:
import time
logger.warning(
f'Failed to connect to FUZZLE with error {e}. Sleeping 5s and retrying.'
)
time.sleep(5)
continue
connected = True
filepath = string_to_tempfile(text.decode('ascii'), 'hhs')
logger.info(f"File downloaded as {filepath}")
return filepath
def opm(pdb, keep=False, keepaltloc="A"):
"""Download a molecule from the OPM.
Parameters
----------
pdb: str
The 4-letter PDB code
keep: bool
If False, removes the DUM atoms. If True, it keeps them.
Returns
-------
mol: Molecule
The oriented molecule
thickness: float or None
The bilayer thickness (both layers)
Examples
--------
>>> mol, thickness = opm("1z98")
>>> mol.numAtoms
7902
>>> thickness
28.2
>>> _, thickness = opm('4u15')
>>> thickness is None
True
"""
import urllib.request
import re
from moleculekit.support import string_to_tempfile
from moleculekit.molecule import Molecule
response = urllib.request.urlopen(
f"https://storage.googleapis.com/opm-assets/pdb/{pdb.lower()}.pdb"
)
text = response.read()
tempfile = string_to_tempfile(text.decode("ascii"), "pdb")
mol = Molecule(tempfile, keepaltloc=keepaltloc)
if not keep:
mol.filter("not resname DUM")
# Assuming the half-thickness is the last word in the matched line
# REMARK 1/2 of bilayer thickness: 14.1
tmp = open(tempfile)
pattern = re.compile("^REMARK.+thickness")
thickness = None
for line in tmp:
if re.match(pattern, line):
thickness = 2.0 * float(line.split()[-1])
break
tmp.close()
os.unlink(tempfile)
return mol, thickness
def getRCSBLigandByLigname(ligname, returnMol2=False):
"""
Returns a SmallMol object of a ligand by its three letter lignane. This molecule is retrieve from RCSB and a mol2
written. It is possible to return also the mol2 filename.
Parameters
----------
ligname: str
The three letter ligand name
returnMol2: bool
If True, the mol2 filename is returned
Returns
-------
sm: moleculekit.smallmol.smallmol.SmallMol
The SmallMol object
mol2filename: str
The mol2 filename
Example
-------
>>> from moleculekit.molecule import Molecule
>>> mol = Molecule('4eiy')
>>> np.unique(mol.get('resname', 'not protein and not water'))
array(['CLR', 'NA', 'OLA', 'OLB', 'OLC', 'PEG', 'ZMA'], dtype=object)
>>> sm = getRCSBLigandByLigname('ZMA') # doctest: +ELLIPSIS
SmallMol module...
>>> sm.numAtoms
40
>>> sm, mol2filename = getRCSBLigandByLigname('ZMA', returnMol2=True)
>>> mol2filename # doctest: +ELLIPSIS
'/tmp/tmp....mol2'
"""
from moleculekit.support import string_to_tempfile
from moleculekit.smallmol.smallmol import SmallMol
from moleculekit.rcsb import _getRCSBtext
from moleculekit.tools.obabel_tools import openbabelConvert
url = f"https://files.rcsb.org/ligands/view/{ligname}_ideal.sdf"
sdf_text = _getRCSBtext(url).decode("ascii")
tempfile = string_to_tempfile(sdf_text, "sdf")
mol2 = openbabelConvert(tempfile, "sdf", "mol2")
sm = SmallMol(mol2)
if returnMol2:
return sm, mol2
return sm
def send(self, command):
"""Send a tcl command to VMD
Parameters
----------
command : str
The tcl command which to send
"""
if self.done:
return
# print( command )
fn = string_to_tempfile(command, "tcl")
# print(fn)
cc = f"if {{ [ catch {{ source {fn}}} ] }} {{ unlink {fn} }} else {{ unlink {fn} }}\n"
self.vmd.stdin.write(cc.encode("ascii"))
self.vmd.stdin.flush()
while os.path.isfile(fn) and not self.done:
time.sleep(0.01)