aboutsummaryrefslogtreecommitdiff
path: root/plip/visualization/chimera.py
diff options
context:
space:
mode:
authorNavan Chauhan <navanchauhan@gmail.com>2020-07-02 20:48:33 +0530
committerNavan Chauhan <navanchauhan@gmail.com>2020-07-02 20:48:33 +0530
commit4be08f7bdd77991e9e453c1cda863c3f20c338d5 (patch)
tree083e8e91622221185a28fd50754abc2f86b1df43 /plip/visualization/chimera.py
initial commit
Diffstat (limited to 'plip/visualization/chimera.py')
-rw-r--r--plip/visualization/chimera.py221
1 files changed, 221 insertions, 0 deletions
diff --git a/plip/visualization/chimera.py b/plip/visualization/chimera.py
new file mode 100644
index 0000000..a37fffb
--- /dev/null
+++ b/plip/visualization/chimera.py
@@ -0,0 +1,221 @@
+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")