diff options
Diffstat (limited to 'plip/visualization/chimera.py')
| -rw-r--r-- | plip/visualization/chimera.py | 221 |
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") |