def compute_salt_bridges(self):
salts = []
[
self.reps.remove(index)
for index, rep in reversed(list(enumerate(self.reps.replist)))
]
metr = MetricDistance('sidechain and acidic and element O',
'sidechain and basic and element N',
metric="contacts",
threshold=3.2,
pbc=False)
try:
data = metr.project(self)
mapping = metr.getMapping(self)
if len(np.shape(data)) > 1:
data = data[0].copy() # handling NMR structures
self.reps.add(sel='protein', style='NewCartoon', color=8)
if mapping[data].atomIndexes.values.any():
for salt in mapping[data].atomIndexes.values:
resid1 = self.get(
"resid", sel=f"same residue as index {salt[0]}")[0]
chain1 = self.get(
"chain", sel=f"same residue as index {salt[0]}")[0]
resid2 = self.get(
"resid", sel=f"same residue as index {salt[1]}")[0]
chain2 = self.get(
"chain", sel=f"same residue as index {salt[1]}")[0]
if [resid1, resid2] not in salts:
salts.append({
"residues": [int(resid1), int(resid2)],
"chain": [chain1, chain2]
})
self.reps.add(f"protein and resid {resid1}",
style="Licorice",
color="1")
self.reps.add(f"protein and resid {resid2}",
style="Licorice",
color="0")
except:
logger.error("Molecule has no basic or acidic residues")
raise
graph = make_graph_salts(salts)
comp, _ = label_components(graph)
if comp.a.size != 0:
salts = add_networks_salts(graph, comp)
else:
logger.warning('No salt bridges present in the structure')
return salts
def main(argv):
inputfile = ''
outputfile = ''
try:
opts, args = getopt.getopt(argv, "hi:o:", ["ifile=", "ofile="])
except getopt.GetoptError("usage:"):
print('salt_bridges.py -i <inputfile> -o <outputfile>')
sys.exit(2)
for opt, arg in opts:
if opt == '-h':
print('salt_bridges.py -i <inputfile> -o <outputfile>')
sys.exit()
elif opt in ("-i", "--ifile"):
inputfile = arg
elif opt in ("-o", "--ofile"):
outputfile = arg
#1. Load molecule
logger.info("Filtering and writing PDB")
mol = filter_mol(inputfile)
#2. Compute distances
logger.info("Computing distances among all polar residues")
metr = MetricDistance('chain A and sidechain and acidic and element O',
'chain A and sidechain and basic and element N',
metric="contacts",
threshold=3.2,
pbc=False)
try:
data = metr.project(mol)
except:
logger.error("Molecule has no basic or acidic residues")
raise
if len(np.shape(data)) > 1:
data = data[0].copy() # handling NMR structures
mapping = metr.getMapping(mol)
#3. Write txt and vmd session out
write_salt_bridges(data, mapping, mol, outputfile)
inputfile_processed = f"{inputfile[:-4]}-chainA.pdb"
postprocess_session(inputfile_processed, outputfile)
logger.info("Saving VMD session")
def compute_salt_bridges(self):
salts = []
[
self.reps.remove(index)
for index, rep in reversed(list(enumerate(self.reps.replist)))
]
metr = MetricDistance('sidechain and acidic and element O',
'sidechain and basic and element N',
metric="contacts",
threshold=3.2,
pbc=False)
try:
data = metr.project(self)
except:
logger.error("Molecule has no basic or acidic residues")
raise
if len(np.shape(data)) > 1:
data = data[0].copy() # handling NMR structures
mapping = metr.getMapping(self)
self.reps.add(sel='protein', style='NewCartoon', color=8)
if mapping[data].atomIndexes.values.any():
for bond in mapping[data].atomIndexes.values:
resid1 = self.get("resid",
sel=f"same residue as index {bond[0]}")[0]
resid2 = self.get("resid",
sel=f"same residue as index {bond[1]}")[0]
if [resid1, resid2] not in salts:
salts.append([resid1, resid2])
self.reps.add(f"protein and resid {resid1}",
style="Licorice",
color="1")
self.reps.add(f"protein and resid {resid2}",
style="Licorice",
color="0")
else:
logger.warning("No salt bridges found in this protein")
return salts
class MetricShell(Projection):
""" Calculates the density of atoms around other atoms.
The MetricShell class calculates the density of a set of
interchangeable atoms in concentric spherical shells around some
other atoms. Thus it can treat identical molecules (like water or
ions) and calculate summary values like the changes in water density
around atoms. It produces a n-by-s dimensional vector where n the
number of atoms in the first selection and s the number of shells
around each of the n atoms.
Parameters
----------
sel1 : str
Atom selection string for the first set of atoms around which the shells will be calculated.
See more `here <http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node89.html>`__
sel2 : str
Atom selection string for the second set of atoms whose density will be calculated in shells around `sel1`.
See more `here <http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node89.html>`__
numshells : int, optional
Number of shells to use around atoms of `sel1`
shellwidth : int, optional
The width of each concentric shell in Angstroms
pbc : bool, optional
Set to false to disable distance calculations using periodic distances
gap : int, optional
Not functional yet
truncate : float, optional
Set all distances larger than `truncate` to `truncate`
"""
def __init__(self,
sel1,
sel2,
numshells=4,
shellwidth=3,
pbc=True,
gap=None,
truncate=None):
super().__init__()
from moleculekit.projections.metricdistance import MetricDistance
self.metricdistance = MetricDistance(sel1=sel1,
sel2=sel2,
groupsel1=None,
groupsel2=None,
metric='distances',
threshold=8,
pbc=pbc,
truncate=truncate)
self.numshells = numshells
self.shellwidth = shellwidth
self.description = None
self.shellcenters = None
def _calculateMolProp(self, mol, props='all'):
props = ('shellcenters', 'map') if props == 'all' else props
res = {}
mapping = np.vstack(self.metricdistance.getMapping(mol).atomIndexes)
if 'map' in props:
res['map'] = mapping
if 'shellcenters' in props:
res['shellcenters'] = np.unique(mapping[:, 0])
return res
def project(self, mol):
""" Project molecule.
Parameters
----------
mol : :class:`Molecule <moleculekit.molecule.Molecule>`
A :class:`Molecule <moleculekit.molecule.Molecule>` object to project.
kwargs :
Do not use this argument. Only used for backward compatibility. Will be removed in later versions.
Returns
-------
data : np.ndarray
An array containing the projected data.
"""
molprops = self._getMolProp(mol, 'all')
distances = self.metricdistance.project(mol)
if distances.ndim == 1:
distances = distances[np.newaxis, :]
return _shells(distances, molprops['map'][:,
0], molprops['shellcenters'],
self.numshells, self.shellwidth)
def getMapping(self, mol):
""" Returns the description of each projected dimension.
Parameters
----------
mol : :class:`Molecule <moleculekit.molecule.Molecule>` object
A Molecule object which will be used to calculate the descriptions of the projected dimensions.
Returns
-------
map : :class:`DataFrame <pandas.core.frame.DataFrame>` object
A DataFrame containing the descriptions of each dimension
"""
shellcenters = self.metricdistance._getMolProp(mol, 'sel1')
from pandas import DataFrame
types = []
indexes = []
description = []
for i in np.where(shellcenters)[0]:
for n in range(self.numshells):
types += ['shell']
indexes += [i]
description += [
'Density of sel2 atoms in shell {}-{} A centered on atom {} {} {}'
.format(n * self.shellwidth, (n + 1) * self.shellwidth,
mol.resname[i], mol.resid[i], mol.name[i])
]
return DataFrame({
'type': types,
'atomIndexes': indexes,
'description': description
})
class MetricShell(Projection):
"""Calculates the density of atoms around other atoms.
The MetricShell class calculates the density of a set of
interchangeable atoms in concentric spherical shells around some
other atoms. Thus it can treat identical molecules (like water or
ions) and calculate summary values like the changes in water density
around atoms. It produces a n-by-s dimensional vector where n the
number of atoms in the first selection and s the number of shells
around each of the n atoms.
Parameters
----------
sel1 : str
Atom selection string for the first set of atoms around which the shells will be calculated.
See more `here <http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node89.html>`__
sel2 : str
Atom selection string for the second set of atoms whose density will be calculated in shells around `sel1`.
See more `here <http://www.ks.uiuc.edu/Research/vmd/vmd-1.9.2/ug/node89.html>`__
periodic : str
See the documentation of MetricDistance class for options.
numshells : int, optional
Number of shells to use around atoms of `sel1`
shellwidth : int, optional
The width of each concentric shell in Angstroms
gap : int, optional
Not functional yet
truncate : float, optional
Set all distances larger than `truncate` to `truncate`
"""
def __init__(
self,
sel1,
sel2,
periodic,
numshells=4,
shellwidth=3,
pbc=None,
gap=None,
truncate=None,
):
super().__init__()
if pbc is not None:
raise DeprecationWarning(
"The `pbc` option is deprecated please use the `periodic` option as described in MetricDistance."
)
from moleculekit.projections.metricdistance import MetricDistance
self.symmetrical = sel1 == sel2
self.metricdistance = MetricDistance(
sel1=sel1,
sel2=sel2,
periodic=periodic,
groupsel1=None,
groupsel2=None,
metric="distances",
threshold=8,
truncate=truncate,
)
self.numshells = numshells
self.shellwidth = shellwidth
self.description = None
self.shellcenters = None
def _calculateMolProp(self, mol, props="all"):
props = (
("map", "shellcenters", "shelledges", "shellvol")
if props == "all"
else props
)
res = {}
mapping = np.vstack(self.metricdistance.getMapping(mol).atomIndexes)
if "map" in props:
res["map"] = mapping
if "shellcenters" in props:
res["shellcenters"] = (
np.unique(mapping[:, 0]) if not self.symmetrical else np.unique(mapping)
)
if "shelledges" in props:
res["shelledges"] = np.arange(
self.shellwidth * (self.numshells + 1), step=self.shellwidth
)
if "shellvol" in props:
res["shellvol"] = (
4
/ 3
* np.pi
* (res["shelledges"][1:] ** 3 - res["shelledges"][:-1] ** 3)
)
return res
def project(self, mol):
"""Project molecule.
Parameters
----------
mol : :class:`Molecule <moleculekit.molecule.Molecule>`
A :class:`Molecule <moleculekit.molecule.Molecule>` object to project.
kwargs :
Do not use this argument. Only used for backward compatibility. Will be removed in later versions.
Returns
-------
data : np.ndarray
An array containing the projected data.
"""
molprops = self._getMolProp(mol, "all")
distances = self.metricdistance.project(mol)
if distances.ndim == 1:
distances = distances[np.newaxis, :]
return _shells(
distances,
molprops["map"],
molprops["shellcenters"],
self.numshells,
molprops["shelledges"],
molprops["shellvol"],
self.symmetrical,
)
def getMapping(self, mol):
"""Returns the description of each projected dimension.
Parameters
----------
mol : :class:`Molecule <moleculekit.molecule.Molecule>` object
A Molecule object which will be used to calculate the descriptions of the projected dimensions.
Returns
-------
map : :class:`DataFrame <pandas.core.frame.DataFrame>` object
A DataFrame containing the descriptions of each dimension
"""
shellcenters = self._getMolProp(mol, "shellcenters")
from pandas import DataFrame
types = []
indexes = []
description = []
for i in shellcenters:
for n in range(self.numshells):
types += ["shell"]
indexes += [i]
description += [
"Density of sel2 atoms in shell {}-{} A centered on atom {} {} {}".format(
n * self.shellwidth,
(n + 1) * self.shellwidth,
mol.resname[i],
mol.resid[i],
mol.name[i],
)
]
return DataFrame(
{"type": types, "atomIndexes": indexes, "description": description}
)