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Diffstat (limited to 'plip/visualization/chimera.py')
| -rw-r--r-- | plip/visualization/chimera.py | 221 |
1 files changed, 0 insertions, 221 deletions
diff --git a/plip/visualization/chimera.py b/plip/visualization/chimera.py deleted file mode 100644 index a37fffb..0000000 --- a/plip/visualization/chimera.py +++ /dev/null @@ -1,221 +0,0 @@ -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") |