diff options
Diffstat (limited to 'plip/visualization/chimera.py')
| -rw-r--r-- | plip/visualization/chimera.py | 84 |
1 files changed, 56 insertions, 28 deletions
diff --git a/plip/visualization/chimera.py b/plip/visualization/chimera.py index a37fffb..436d0e3 100644 --- a/plip/visualization/chimera.py +++ b/plip/visualization/chimera.py @@ -5,8 +5,8 @@ class ChimeraVisualizer: 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.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 @@ -32,7 +32,10 @@ class ChimeraVisualizer: 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)) + self.rc( + "~display #%i & :/isHet & ~:%s" + % (self.model_dict[self.plipname], self.hetid) + ) def update_model_dict(self): """Updates the model dictionary""" @@ -51,39 +54,47 @@ class ChimeraVisualizer: def show_hydrophobic(self): """Visualizes hydrophobic contacts.""" - grp = self.getPseudoBondGroup("Hydrophobic Interactions-%i" % self.tid, associateWith=[self.model]) + grp = self.getPseudoBondGroup( + "Hydrophobic Interactions-%i" % self.tid, associateWith=[self.model] + ) grp.lineType = self.chimera.Dash grp.lineWidth = 3 - grp.color = self.colorbyname('gray') + 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 = 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') + 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') + 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 = 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') + 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 = 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): @@ -101,13 +112,15 @@ class ChimeraVisualizer: r.addAtom(centroid_lig) b = grp.newPseudoBond(centroid_lig, centroid_prot) - b.color = self.colorbyname('forest green') + 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 = 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): @@ -125,7 +138,7 @@ class ChimeraVisualizer: r.addAtom(centroid) b = grp.newPseudoBond(centroid, chargecenter) - b.color = self.colorbyname('orange') + b.color = self.colorbyname("orange") if cat.protcharged: self.bs_res_ids += cat.charge_atoms @@ -135,7 +148,9 @@ class ChimeraVisualizer: def show_sbridges(self): """Visualizes salt bridges.""" # Salt Bridges - grp = self.getPseudoBondGroup("Salt Bridges-%i" % self.tid, associateWith=[self.model]) + 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): @@ -153,7 +168,7 @@ class ChimeraVisualizer: r.addAtom(chargecenter2) b = grp.newPseudoBond(chargecenter1, chargecenter2) - b.color = self.colorbyname('yellow') + b.color = self.colorbyname("yellow") if sbridge.protispos: self.bs_res_ids += sbridge.positive_atoms @@ -162,14 +177,20 @@ class ChimeraVisualizer: def show_wbridges(self): """Visualizes water bridges""" - grp = self.getPseudoBondGroup("Water Bridges-%i" % self.tid, associateWith=[self.model]) + 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') + 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') + 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) @@ -178,16 +199,20 @@ class ChimeraVisualizer: def show_metal(self): """Visualizes metal coordination.""" - grp = self.getPseudoBondGroup("Metal Coordination-%i" % self.tid, associateWith=[self.model]) + 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') + c = grp.newPseudoBond( + self.atoms[metal.metal_id], self.atoms[metal.target_id] + ) + c.color = self.colorbyname("magenta") - if metal.location == 'water': + if metal.location == "water": self.water_ids.append(metal.target_id) - if metal.location.startswith('protein'): + if metal.location.startswith("protein"): self.bs_res_ids.append(metal.target_id) def cleanup(self): @@ -197,13 +222,16 @@ class ChimeraVisualizer: # Hide all non-interacting water molecules water_selection = [] for wid in self.water_ids: - water_selection.append('serialNumber=%i' % wid) + 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( + "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): |