def opm(pdb):
"""Download a molecule from the OPM.
Removes DUM atoms.
Parameters
----------
pdb: str
The 4-letter PDB code
Returns
-------
mol: Molecule
The oriented molecule
thickness: float
The bilayer thickness (both layers)
Examples
--------
>>> mol, thickness = opm("1z98")
>>> mol.numAtoms
7902
>>> thickness
28.2
"""
from htmd.molecule.support import string_to_tempfile
from htmd.molecule.molecule import Molecule
# http://opm.phar.umich.edu/pdb/1z98.pdb
r = requests.get("http://opm.phar.umich.edu/pdb/{:s}.pdb".format(
pdb.lower()))
if r.status_code != 200:
raise NameError('PDB code not found in the OPM database')
tempfile = string_to_tempfile(r.content.decode('ascii'), "pdb")
mol = Molecule(tempfile)
mol.filter("not resname DUM")
# Assuming the half-thickness is the last word in the first line
# REMARK 1/2 of bilayer thickness: 14.1
f = open(tempfile)
h = f.readline()
f.close()
os.unlink(tempfile)
hs = h.split()
thickness = 2.0 * float(hs[-1])
return mol, thickness
def opm(pdb):
"""Download a molecule from the OPM.
Removes DUM atoms.
Parameters
----------
pdb: str
The 4-letter PDB code
Returns
-------
mol: Molecule
The oriented molecule
thickness: float
The bilayer thickness (both layers)
Examples
--------
>>> mol, thickness = opm("1z98")
>>> mol.numAtoms
7902
>>> thickness
28.2
"""
from htmd.molecule.support import string_to_tempfile
from htmd.molecule.molecule import Molecule
# http://opm.phar.umich.edu/pdb/1z98.pdb
r = requests.get("http://opm.phar.umich.edu/pdb/{:s}.pdb".format(pdb.lower()))
if r.status_code != 200:
raise NameError('PDB code not found in the OPM database')
tempfile = string_to_tempfile(r.content.decode('ascii'), "pdb")
mol = Molecule(tempfile)
mol.filter("not resname DUM")
# Assuming the half-thickness is the last word in the first line
# REMARK 1/2 of bilayer thickness: 14.1
f = open(tempfile)
h = f.readline()
f.close()
os.unlink(tempfile)
hs = h.split()
thickness = 2.0 * float(hs[-1])
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: htmd.smallmol.smallmol.SmallMol
The SmallMol object
mol2filename: str
The mol2 filename
Example
-------
>>> from htmd.molecule.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'
"""
import requests
from htmd.molecule.support import string_to_tempfile
from htmd.smallmol.smallmol import SmallMol
r = requests.get(
"https://files.rcsb.org/ligands/view/{}_ideal.sdf".format(ligname))
sdf_text = r.content.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 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: htmd.smallmol.smallmol.SmallMol
The SmallMol object
mol2filename: str
The mol2 filename
Example
-------
>>> from htmd.molecule.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'
"""
import requests
from htmd.molecule.support import string_to_tempfile
from htmd.smallmol.smallmol import SmallMol
r = requests.get("https://files.rcsb.org/ligands/view/{}_ideal.sdf".format(ligname))
sdf_text = r.content.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 _getPDB(pdbid):
import requests
from htmd.molecule.support import string_to_tempfile
from htmd.home import home
# Try loading it from the pdb data directory
tempfile = False
localpdb = os.path.join(home(dataDir='pdb'), pdbid.lower() + '.pdb')
if os.path.isfile(localpdb):
logger.info('Using local copy for {:s}: {:s}'.format(pdbid, localpdb))
filepath = localpdb
else:
# or the PDB website
logger.info('Attempting PDB query for {:s}'.format(pdbid))
r = requests.get('https://files.rcsb.org/download/{}.pdb'.format(pdbid))
if r.status_code == 200:
filepath = string_to_tempfile(r.content.decode('ascii'), 'pdb')
tempfile = True
else:
raise NameError('Invalid PDB code')
return filepath, tempfile
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 = "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)
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 = "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)
def _getPDB(pdbid):
import requests
from htmd.molecule.support import string_to_tempfile
from htmd.home import home
# Try loading it from the pdb data directory
tempfile = False
localpdb = os.path.join(home(dataDir='pdb'), pdbid.lower() + '.pdb')
if os.path.isfile(localpdb):
logger.info('Using local copy for {:s}: {:s}'.format(pdbid, localpdb))
filepath = localpdb
else:
# or the PDB website
logger.info('Attempting PDB query for {:s}'.format(pdbid))
r = requests.get('https://files.rcsb.org/download/{}.pdb'.format(pdbid))
if r.status_code == 200:
filepath = string_to_tempfile(r.content.decode('ascii'), 'pdb')
tempfile = True
else:
raise NameError('Invalid PDB code')
return filepath, tempfile
def opm(pdb, keep=False, keepaltloc='A'):
"""Download a molecule from the OPM.
Removes DUM atoms.
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
"""
from htmd.molecule.support import string_to_tempfile
from htmd.molecule.molecule import Molecule
# http://opm.phar.umich.edu/pdb/1z98.pdb
r = requests.get("http://opm.phar.umich.edu/pdb/{:s}.pdb".format(pdb.lower()))
if r.status_code != 200:
raise NameError('PDB code not found in the OPM database')
tempfile = string_to_tempfile(r.content.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')
match = None
for line in tmp:
if re.match(pattern, line):
match = line
tmp.close()
os.unlink(tempfile)
if not match:
thickness = None
else:
split_line = match.split()
thickness = 2.0 * float(split_line[-1])
return mol, thickness
def opm(pdb, keep=False, keepaltloc='A'):
"""Download a molecule from the OPM.
Removes DUM atoms.
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
"""
from htmd.molecule.support import string_to_tempfile
from htmd.molecule.molecule import Molecule
# http://opm.phar.umich.edu/pdb/1z98.pdb
r = requests.get("http://opm.phar.umich.edu/pdb/{:s}.pdb".format(
pdb.lower()))
if r.status_code != 200:
raise NameError('PDB code not found in the OPM database')
tempfile = string_to_tempfile(r.content.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')
match = None
for line in tmp:
if re.match(pattern, line):
match = line
tmp.close()
os.unlink(tempfile)
if not match:
thickness = None
else:
split_line = match.split()
thickness = 2.0 * float(split_line[-1])
return mol, thickness