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class ChimeraVisualizer:
"""Provides visualization for Chimera."""
def __init__(self, plcomplex, chimera_module, tid):
self.chimera = chimera_module
self.tid = tid
self.uid = plcomplex.uid
self.plipname = "PLIP-%i" % self.tid
self.hetid, self.chain, self.pos = self.uid.split(":")
self.pos = int(self.pos)
self.colorbyname = self.chimera.colorTable.getColorByName
self.rc = self.chimera.runCommand
self.getPseudoBondGroup = self.chimera.misc.getPseudoBondGroup
if plcomplex is not None:
self.plcomplex = plcomplex
self.protname = plcomplex.pdbid # Name of protein with binding site
self.ligname = plcomplex.hetid # Name of ligand
self.metal_ids = plcomplex.metal_ids
self.water_ids = []
self.bs_res_ids = []
self.models = self.chimera.openModels
for md in self.models.list():
if md.name == self.plipname:
self.model = md
self.atoms = self.atom_by_serialnumber()
def set_initial_representations(self):
"""Set the initial representations"""
self.update_model_dict()
self.rc("background solid white")
self.rc("setattr g display 0") # Hide all pseudobonds
self.rc(
"~display #%i & :/isHet & ~:%s"
% (self.model_dict[self.plipname], self.hetid)
)
def update_model_dict(self):
"""Updates the model dictionary"""
dct = {}
models = self.chimera.openModels
for md in models.list():
dct[md.name] = md.id
self.model_dict = dct
def atom_by_serialnumber(self):
"""Provides a dictionary mapping serial numbers to their atom objects."""
atm_by_snum = {}
for atom in self.model.atoms:
atm_by_snum[atom.serialNumber] = atom
return atm_by_snum
def show_hydrophobic(self):
"""Visualizes hydrophobic contacts."""
grp = self.getPseudoBondGroup(
"Hydrophobic Interactions-%i" % self.tid, associateWith=[self.model]
)
grp.lineType = self.chimera.Dash
grp.lineWidth = 3
grp.color = self.colorbyname("gray")
for i in self.plcomplex.hydrophobic_contacts.pairs_ids:
self.bs_res_ids.append(i[0])
def show_hbonds(self):
"""Visualizes hydrogen bonds."""
grp = self.getPseudoBondGroup(
"Hydrogen Bonds-%i" % self.tid, associateWith=[self.model]
)
grp.lineWidth = 3
for i in self.plcomplex.hbonds.ldon_id:
b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
b.color = self.colorbyname("blue")
self.bs_res_ids.append(i[0])
for i in self.plcomplex.hbonds.pdon_id:
b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
b.color = self.colorbyname("blue")
self.bs_res_ids.append(i[1])
def show_halogen(self):
"""Visualizes halogen bonds."""
grp = self.getPseudoBondGroup(
"HalogenBonds-%i" % self.tid, associateWith=[self.model]
)
grp.lineWidth = 3
for i in self.plcomplex.halogen_bonds:
b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
b.color = self.colorbyname("turquoise")
self.bs_res_ids.append(i.acc_id)
def show_stacking(self):
"""Visualizes pi-stacking interactions."""
grp = self.getPseudoBondGroup(
"pi-Stacking-%i" % self.tid, associateWith=[self.model]
)
grp.lineWidth = 3
grp.lineType = self.chimera.Dash
for i, stack in enumerate(self.plcomplex.pistacking):
m = self.model
r = m.newResidue("pseudoatoms", " ", 1, " ")
centroid_prot = m.newAtom("CENTROID", self.chimera.Element("CENTROID"))
x, y, z = stack.proteinring_center
centroid_prot.setCoord(self.chimera.Coord(x, y, z))
r.addAtom(centroid_prot)
centroid_lig = m.newAtom("CENTROID", self.chimera.Element("CENTROID"))
x, y, z = stack.ligandring_center
centroid_lig.setCoord(self.chimera.Coord(x, y, z))
r.addAtom(centroid_lig)
b = grp.newPseudoBond(centroid_lig, centroid_prot)
b.color = self.colorbyname("forest green")
self.bs_res_ids += stack.proteinring_atoms
def show_cationpi(self):
"""Visualizes cation-pi interactions"""
grp = self.getPseudoBondGroup(
"Cation-Pi-%i" % self.tid, associateWith=[self.model]
)
grp.lineWidth = 3
grp.lineType = self.chimera.Dash
for i, cat in enumerate(self.plcomplex.pication):
m = self.model
r = m.newResidue("pseudoatoms", " ", 1, " ")
chargecenter = m.newAtom("CHARGE", self.chimera.Element("CHARGE"))
x, y, z = cat.charge_center
chargecenter.setCoord(self.chimera.Coord(x, y, z))
r.addAtom(chargecenter)
centroid = m.newAtom("CENTROID", self.chimera.Element("CENTROID"))
x, y, z = cat.ring_center
centroid.setCoord(self.chimera.Coord(x, y, z))
r.addAtom(centroid)
b = grp.newPseudoBond(centroid, chargecenter)
b.color = self.colorbyname("orange")
if cat.protcharged:
self.bs_res_ids += cat.charge_atoms
else:
self.bs_res_ids += cat.ring_atoms
def show_sbridges(self):
"""Visualizes salt bridges."""
# Salt Bridges
grp = self.getPseudoBondGroup(
"Salt Bridges-%i" % self.tid, associateWith=[self.model]
)
grp.lineWidth = 3
grp.lineType = self.chimera.Dash
for i, sbridge in enumerate(self.plcomplex.saltbridges):
m = self.model
r = m.newResidue("pseudoatoms", " ", 1, " ")
chargecenter1 = m.newAtom("CHARGE", self.chimera.Element("CHARGE"))
x, y, z = sbridge.positive_center
chargecenter1.setCoord(self.chimera.Coord(x, y, z))
r.addAtom(chargecenter1)
chargecenter2 = m.newAtom("CHARGE", self.chimera.Element("CHARGE"))
x, y, z = sbridge.negative_center
chargecenter2.setCoord(self.chimera.Coord(x, y, z))
r.addAtom(chargecenter2)
b = grp.newPseudoBond(chargecenter1, chargecenter2)
b.color = self.colorbyname("yellow")
if sbridge.protispos:
self.bs_res_ids += sbridge.positive_atoms
else:
self.bs_res_ids += sbridge.negative_atoms
def show_wbridges(self):
"""Visualizes water bridges"""
grp = self.getPseudoBondGroup(
"Water Bridges-%i" % self.tid, associateWith=[self.model]
)
grp.lineWidth = 3
for i, wbridge in enumerate(self.plcomplex.waterbridges):
c = grp.newPseudoBond(
self.atoms[wbridge.water_id], self.atoms[wbridge.acc_id]
)
c.color = self.colorbyname("cornflower blue")
self.water_ids.append(wbridge.water_id)
b = grp.newPseudoBond(
self.atoms[wbridge.don_id], self.atoms[wbridge.water_id]
)
b.color = self.colorbyname("cornflower blue")
self.water_ids.append(wbridge.water_id)
if wbridge.protisdon:
self.bs_res_ids.append(wbridge.don_id)
else:
self.bs_res_ids.append(wbridge.acc_id)
def show_metal(self):
"""Visualizes metal coordination."""
grp = self.getPseudoBondGroup(
"Metal Coordination-%i" % self.tid, associateWith=[self.model]
)
grp.lineWidth = 3
for i, metal in enumerate(self.plcomplex.metal_complexes):
c = grp.newPseudoBond(
self.atoms[metal.metal_id], self.atoms[metal.target_id]
)
c.color = self.colorbyname("magenta")
if metal.location == "water":
self.water_ids.append(metal.target_id)
if metal.location.startswith("protein"):
self.bs_res_ids.append(metal.target_id)
def cleanup(self):
"""Clean up the visualization."""
if not len(self.water_ids) == 0:
# Hide all non-interacting water molecules
water_selection = []
for wid in self.water_ids:
water_selection.append("serialNumber=%i" % wid)
self.rc("~display :HOH")
self.rc("display :@/%s" % " or ".join(water_selection))
# Show all interacting binding site residues
self.rc("~display #%i & ~:/isHet" % self.model_dict[self.plipname])
self.rc(
"display :%s"
% ",".join([str(self.atoms[bsid].residue.id) for bsid in self.bs_res_ids])
)
self.rc("color lightblue :HOH")
def zoom_to_ligand(self):
"""Centers the view on the ligand and its binding site residues."""
self.rc("center #%i & :%s" % (self.model_dict[self.plipname], self.hetid))
def refinements(self):
"""Details for the visualization."""
self.rc("setattr a color gray @CENTROID")
self.rc("setattr a radius 0.3 @CENTROID")
self.rc("represent sphere @CENTROID")
self.rc("setattr a color orange @CHARGE")
self.rc("setattr a radius 0.4 @CHARGE")
self.rc("represent sphere @CHARGE")
self.rc("display :pseudoatoms")
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