def findHbonds(self, angleCutoff=30.0, distanceCutoff=3.4):
"""Return a list of H bonds determined by pdb2pqr.
Lifted from the "hbond.py" extension of pdb2pqr.
Residue information of the donor and acceptor atoms returned are of type pdb2pqr.src.structures.Atom
and their information can be accessed e.g. as follows:
atom.name
atom.serial
atom.residue.__str__()
atom.residue.name
...
Parameters
----------
angleCutoff: float
H-bond angle cut-off (in degrees)
distanceCutoff: float
donor to acceptor distance cut-off (in Å)
Returns
-------
A list of dicts containing donor (Atom), acceptor (Atom), hydrogen (Atom), distance (float), angle (float)
for each hydrogen bond found by pdb2pqr.
Example
-------
>>> m=Molecule("3ptb")
>>> mp, md = proteinPrepare(m, returnDetails=True)
>>> hlist=md.findHbonds()
>>> hlist[0]['donor'].name
'N'
>>> hlist[0]['donor'].residue.__str__()
'VAL A 17'
>>> hlist[0]['acceptor'].name
'O'
>>> hlist[0]['acceptor'].residue.__str__()
'ASP A 189'
"""
from pdb2pqr.src.routines import Cells
from pdb2pqr.src.utilities import distance, getAngle
routines = self.pdb2pqr_routines
cellsize = int(distanceCutoff + 1.0 + 1.0)
# protein = routines.protein
protein = self.pdb2pqr_protein
routines.setDonorsAndAcceptors()
routines.cells = Cells(cellsize)
routines.cells.assignCells(protein)
ret = []
for donor in protein.getAtoms():
# Grab the list of donors
if not donor.hdonor:
continue
donorhs = []
for bond in donor.bonds:
if bond.isHydrogen():
donorhs.append(bond)
if donorhs == []:
continue
# For each donor, grab all acceptors
closeatoms = routines.cells.getNearCells(donor)
for acc in closeatoms:
if not acc.hacceptor:
continue
if donor.residue == acc.residue:
continue
dist = distance(donor.getCoords(), acc.getCoords())
if dist > distanceCutoff:
continue
for donorh in donorhs:
# Do angle check
angle = getAngle(acc.getCoords(), donor.getCoords(), donorh.getCoords())
if angle > angleCutoff:
continue
ret.append({"donor": donor, "acceptor": acc, "hydrogen": donorh,
"distance": dist, "angle": angle})
s = "Donor: %s %s\tAcceptor: %s %s\tdist: %.2f\tAngle: %.2f" % \
(donor.residue, donor.name, acc.residue, acc.name, dist, angle)
logger.debug(s)
return ret
def findHbonds(self, angleCutoff=30.0, distanceCutoff=3.4):
"""Return a list of H bonds determined by pdb2pqr.
Lifted from the "hbond.py" extension of pdb2pqr.
Residue information of the donor and acceptor atoms returned are of type pdb2pqr.src.structures.Atom
and their information can be accessed e.g. as follows:
atom.name
atom.serial
atom.residue.__str__()
atom.residue.name
...
Parameters
----------
angleCutoff: float
H-bond angle cut-off (in degrees)
distanceCutoff: float
donor to acceptor distance cut-off (in Å)
Returns
-------
A list of dicts containing donor (Atom), acceptor (Atom), hydrogen (Atom), distance (float), angle (float)
for each hydrogen bond found by pdb2pqr.
Example
-------
>>> m=Molecule("3ptb")
>>> mp, md = proteinPrepare(m, returnDetails=True)
>>> hlist=md.findHbonds()
>>> hlist[0]['donor'].name
'N'
>>> hlist[0]['donor'].residue.__str__()
'VAL A 17'
>>> hlist[0]['acceptor'].name
'O'
>>> hlist[0]['acceptor'].residue.__str__()
'ASP A 189'
"""
from pdb2pqr.src.routines import Cells
from pdb2pqr.src.utilities import distance, getAngle
routines = self.pdb2pqr_routines
cellsize = int(distanceCutoff + 1.0 + 1.0)
# protein = routines.protein
protein = self.pdb2pqr_protein
routines.setDonorsAndAcceptors()
routines.cells = Cells(cellsize)
routines.cells.assignCells(protein)
ret = []
for donor in protein.getAtoms():
# Grab the list of donors
if not donor.hdonor:
continue
donorhs = []
for bond in donor.bonds:
if bond.isHydrogen():
donorhs.append(bond)
if donorhs == []:
continue
# For each donor, grab all acceptors
closeatoms = routines.cells.getNearCells(donor)
for acc in closeatoms:
if not acc.hacceptor:
continue
if donor.residue == acc.residue:
continue
dist = distance(donor.getCoords(), acc.getCoords())
if dist > distanceCutoff:
continue
for donorh in donorhs:
# Do angle check
angle = getAngle(acc.getCoords(), donor.getCoords(), donorh.getCoords())
if angle > angleCutoff:
continue
ret.append({"donor": donor, "acceptor": acc, "hydrogen": donorh,
"distance": dist, "angle": angle})
s = "Donor: %s %s\tAcceptor: %s %s\tdist: %.2f\tAngle: %.2f" % \
(donor.residue, donor.name, acc.residue, acc.name, dist, angle)
logger.debug(s)
return ret