diff options
Diffstat (limited to 'plip/visualization/pymol.py')
| -rw-r--r-- | plip/visualization/pymol.py | 618 |
1 files changed, 384 insertions, 234 deletions
diff --git a/plip/visualization/pymol.py b/plip/visualization/pymol.py index b97912a..2e1b0e3 100644 --- a/plip/visualization/pymol.py +++ b/plip/visualization/pymol.py @@ -7,7 +7,6 @@ from pymol import cmd class PyMOLVisualizer: - def __init__(self, plcomplex): if plcomplex is not None: self.plcomplex = plcomplex @@ -20,57 +19,86 @@ class PyMOLVisualizer: def set_initial_representations(self): """General settings for PyMOL""" self.standard_settings() - cmd.set('dash_gap', 0) # Show not dashes, but lines for the pliprofiler - cmd.set('ray_shadow', 0) # Turn on ray shadows for clearer ray-traced images - cmd.set('cartoon_color', 'mylightblue') + cmd.set("dash_gap", 0) # Show not dashes, but lines for the pliprofiler + cmd.set("ray_shadow", 0) # Turn on ray shadows for clearer ray-traced images + cmd.set("cartoon_color", "mylightblue") # Set clipping planes for full view - cmd.clip('far', -1000) - cmd.clip('near', 1000) + cmd.clip("far", -1000) + cmd.clip("near", 1000) def make_initial_selections(self): """Make empty selections for structures and interactions""" - for group in ['Hydrophobic-P', 'Hydrophobic-L', 'HBondDonor-P', - 'HBondDonor-L', 'HBondAccept-P', 'HBondAccept-L', - 'HalogenAccept', 'HalogenDonor', 'Water', 'MetalIons', 'StackRings-P', - 'PosCharge-P', 'PosCharge-L', 'NegCharge-P', 'NegCharge-L', - 'PiCatRing-P', 'StackRings-L', 'PiCatRing-L', 'Metal-M', 'Metal-P', - 'Metal-W', 'Metal-L', 'Unpaired-HBA', 'Unpaired-HBD', 'Unpaired-HAL', - 'Unpaired-RINGS']: - cmd.select(group, 'None') + for group in [ + "Hydrophobic-P", + "Hydrophobic-L", + "HBondDonor-P", + "HBondDonor-L", + "HBondAccept-P", + "HBondAccept-L", + "HalogenAccept", + "HalogenDonor", + "Water", + "MetalIons", + "StackRings-P", + "PosCharge-P", + "PosCharge-L", + "NegCharge-P", + "NegCharge-L", + "PiCatRing-P", + "StackRings-L", + "PiCatRing-L", + "Metal-M", + "Metal-P", + "Metal-W", + "Metal-L", + "Unpaired-HBA", + "Unpaired-HBD", + "Unpaired-HAL", + "Unpaired-RINGS", + ]: + cmd.select(group, "None") def standard_settings(self): """Sets up standard settings for a nice visualization.""" - cmd.set('bg_rgb', [1.0, 1.0, 1.0]) # White background - cmd.set('depth_cue', 0) # Turn off depth cueing (no fog) - cmd.set('cartoon_side_chain_helper', 1) # Improve combined visualization of sticks and cartoon - cmd.set('cartoon_fancy_helices', 1) # Nicer visualization of helices (using tapered ends) - cmd.set('transparency_mode', 1) # Turn on multilayer transparency - cmd.set('dash_radius', 0.05) + cmd.set("bg_rgb", [1.0, 1.0, 1.0]) # White background + cmd.set("depth_cue", 0) # Turn off depth cueing (no fog) + cmd.set( + "cartoon_side_chain_helper", 1 + ) # Improve combined visualization of sticks and cartoon + cmd.set( + "cartoon_fancy_helices", 1 + ) # Nicer visualization of helices (using tapered ends) + cmd.set("transparency_mode", 1) # Turn on multilayer transparency + cmd.set("dash_radius", 0.05) self.set_custom_colorset() def set_custom_colorset(self): """Defines a colorset with matching colors. Provided by Joachim.""" - cmd.set_color('myorange', '[253, 174, 97]') - cmd.set_color('mygreen', '[171, 221, 164]') - cmd.set_color('myred', '[215, 25, 28]') - cmd.set_color('myblue', '[43, 131, 186]') - cmd.set_color('mylightblue', '[158, 202, 225]') - cmd.set_color('mylightgreen', '[229, 245, 224]') - - def select_by_ids(self, selname, idlist, selection_exists=False, chunksize=20, restrict=None): + cmd.set_color("myorange", "[253, 174, 97]") + cmd.set_color("mygreen", "[171, 221, 164]") + cmd.set_color("myred", "[215, 25, 28]") + cmd.set_color("myblue", "[43, 131, 186]") + cmd.set_color("mylightblue", "[158, 202, 225]") + cmd.set_color("mylightgreen", "[229, 245, 224]") + + def select_by_ids( + self, selname, idlist, selection_exists=False, chunksize=20, restrict=None + ): """Selection with a large number of ids concatenated into a selection list can cause buffer overflow in PyMOL. This function takes a selection name and and list of IDs (list of integers) as input and makes a careful step-by-step selection (packages of 20 by default)""" idlist = list(set(idlist)) # Remove duplicates if not selection_exists: - cmd.select(selname, 'None') # Empty selection first - idchunks = [idlist[i:i + chunksize] for i in range(0, len(idlist), chunksize)] + cmd.select(selname, "None") # Empty selection first + idchunks = [idlist[i : i + chunksize] for i in range(0, len(idlist), chunksize)] for idchunk in idchunks: - cmd.select(selname, '%s or (id %s)' % (selname, '+'.join(map(str, idchunk)))) + cmd.select( + selname, "%s or (id %s)" % (selname, "+".join(map(str, idchunk))) + ) if restrict is not None: - cmd.select(selname, '%s and %s' % (selname, restrict)) + cmd.select(selname, "%s and %s" % (selname, restrict)) def object_exists(self, object_name): """Checks if an object exists in the open PyMOL session.""" @@ -80,40 +108,44 @@ class PyMOLVisualizer: """Visualizes hydrophobic contacts.""" hydroph = self.plcomplex.hydrophobic_contacts if not len(hydroph.bs_ids) == 0: - self.select_by_ids('Hydrophobic-P', hydroph.bs_ids, restrict=self.protname) - self.select_by_ids('Hydrophobic-L', hydroph.lig_ids, restrict=self.ligname) + self.select_by_ids("Hydrophobic-P", hydroph.bs_ids, restrict=self.protname) + self.select_by_ids("Hydrophobic-L", hydroph.lig_ids, restrict=self.ligname) for i in hydroph.pairs_ids: - cmd.select('tmp_bs', 'id %i & %s' % (i[0], self.protname)) - cmd.select('tmp_lig', 'id %i & %s' % (i[1], self.ligname)) - cmd.distance('Hydrophobic', 'tmp_bs', 'tmp_lig') - if self.object_exists('Hydrophobic'): - cmd.set('dash_gap', 0.5, 'Hydrophobic') - cmd.set('dash_color', 'grey50', 'Hydrophobic') + cmd.select("tmp_bs", "id %i & %s" % (i[0], self.protname)) + cmd.select("tmp_lig", "id %i & %s" % (i[1], self.ligname)) + cmd.distance("Hydrophobic", "tmp_bs", "tmp_lig") + if self.object_exists("Hydrophobic"): + cmd.set("dash_gap", 0.5, "Hydrophobic") + cmd.set("dash_color", "grey50", "Hydrophobic") else: - cmd.select('Hydrophobic-P', 'None') + cmd.select("Hydrophobic-P", "None") def show_hbonds(self): """Visualizes hydrogen bonds.""" hbonds = self.plcomplex.hbonds - for group in [['HBondDonor-P', hbonds.prot_don_id], - ['HBondAccept-P', hbonds.prot_acc_id]]: + for group in [ + ["HBondDonor-P", hbonds.prot_don_id], + ["HBondAccept-P", hbonds.prot_acc_id], + ]: if not len(group[1]) == 0: self.select_by_ids(group[0], group[1], restrict=self.protname) - for group in [['HBondDonor-L', hbonds.lig_don_id], - ['HBondAccept-L', hbonds.lig_acc_id]]: + for group in [ + ["HBondDonor-L", hbonds.lig_don_id], + ["HBondAccept-L", hbonds.lig_acc_id], + ]: if not len(group[1]) == 0: self.select_by_ids(group[0], group[1], restrict=self.ligname) for i in hbonds.ldon_id: - cmd.select('tmp_bs', 'id %i & %s' % (i[0], self.protname)) - cmd.select('tmp_lig', 'id %i & %s' % (i[1], self.ligname)) - cmd.distance('HBonds', 'tmp_bs', 'tmp_lig') + cmd.select("tmp_bs", "id %i & %s" % (i[0], self.protname)) + cmd.select("tmp_lig", "id %i & %s" % (i[1], self.ligname)) + cmd.distance("HBonds", "tmp_bs", "tmp_lig") for i in hbonds.pdon_id: - cmd.select('tmp_bs', 'id %i & %s' % (i[1], self.protname)) - cmd.select('tmp_lig', 'id %i & %s' % (i[0], self.ligname)) - cmd.distance('HBonds', 'tmp_bs', 'tmp_lig') - if self.object_exists('HBonds'): - cmd.set('dash_color', 'blue', 'HBonds') + cmd.select("tmp_bs", "id %i & %s" % (i[1], self.protname)) + cmd.select("tmp_lig", "id %i & %s" % (i[0], self.ligname)) + cmd.distance("HBonds", "tmp_bs", "tmp_lig") + if self.object_exists("HBonds"): + cmd.set("dash_color", "blue", "HBonds") def show_halogen(self): """Visualize halogen bonds.""" @@ -122,155 +154,218 @@ class PyMOLVisualizer: for h in halogen: all_don_x.append(h.don_id) all_acc_o.append(h.acc_id) - cmd.select('tmp_bs', 'id %i & %s' % (h.acc_id, self.protname)) - cmd.select('tmp_lig', 'id %i & %s' % (h.don_id, self.ligname)) + cmd.select("tmp_bs", "id %i & %s" % (h.acc_id, self.protname)) + cmd.select("tmp_lig", "id %i & %s" % (h.don_id, self.ligname)) - cmd.distance('HalogenBonds', 'tmp_bs', 'tmp_lig') + cmd.distance("HalogenBonds", "tmp_bs", "tmp_lig") if not len(all_acc_o) == 0: - self.select_by_ids('HalogenAccept', all_acc_o, restrict=self.protname) - self.select_by_ids('HalogenDonor', all_don_x, restrict=self.ligname) - if self.object_exists('HalogenBonds'): - cmd.set('dash_color', 'greencyan', 'HalogenBonds') + self.select_by_ids("HalogenAccept", all_acc_o, restrict=self.protname) + self.select_by_ids("HalogenDonor", all_don_x, restrict=self.ligname) + if self.object_exists("HalogenBonds"): + cmd.set("dash_color", "greencyan", "HalogenBonds") def show_stacking(self): """Visualize pi-stacking interactions.""" stacks = self.plcomplex.pistacking for i, stack in enumerate(stacks): - pires_ids = '+'.join(map(str, stack.proteinring_atoms)) - pilig_ids = '+'.join(map(str, stack.ligandring_atoms)) - cmd.select('StackRings-P', 'StackRings-P or (id %s & %s)' % (pires_ids, self.protname)) - cmd.select('StackRings-L', 'StackRings-L or (id %s & %s)' % (pilig_ids, self.ligname)) - cmd.select('StackRings-P', 'byres StackRings-P') - cmd.show('sticks', 'StackRings-P') - - cmd.pseudoatom('ps-pistack-1-%i' % i, pos=stack.proteinring_center) - cmd.pseudoatom('ps-pistack-2-%i' % i, pos=stack.ligandring_center) - cmd.pseudoatom('Centroids-P', pos=stack.proteinring_center) - cmd.pseudoatom('Centroids-L', pos=stack.ligandring_center) - - if stack.type == 'P': - cmd.distance('PiStackingP', 'ps-pistack-1-%i' % i, 'ps-pistack-2-%i' % i) - if stack.type == 'T': - cmd.distance('PiStackingT', 'ps-pistack-1-%i' % i, 'ps-pistack-2-%i' % i) - if self.object_exists('PiStackingP'): - cmd.set('dash_color', 'green', 'PiStackingP') - cmd.set('dash_gap', 0.3, 'PiStackingP') - cmd.set('dash_length', 0.6, 'PiStackingP') - if self.object_exists('PiStackingT'): - cmd.set('dash_color', 'smudge', 'PiStackingT') - cmd.set('dash_gap', 0.3, 'PiStackingT') - cmd.set('dash_length', 0.6, 'PiStackingT') + pires_ids = "+".join(map(str, stack.proteinring_atoms)) + pilig_ids = "+".join(map(str, stack.ligandring_atoms)) + cmd.select( + "StackRings-P", + "StackRings-P or (id %s & %s)" % (pires_ids, self.protname), + ) + cmd.select( + "StackRings-L", + "StackRings-L or (id %s & %s)" % (pilig_ids, self.ligname), + ) + cmd.select("StackRings-P", "byres StackRings-P") + cmd.show("sticks", "StackRings-P") + + cmd.pseudoatom("ps-pistack-1-%i" % i, pos=stack.proteinring_center) + cmd.pseudoatom("ps-pistack-2-%i" % i, pos=stack.ligandring_center) + cmd.pseudoatom("Centroids-P", pos=stack.proteinring_center) + cmd.pseudoatom("Centroids-L", pos=stack.ligandring_center) + + if stack.type == "P": + cmd.distance( + "PiStackingP", "ps-pistack-1-%i" % i, "ps-pistack-2-%i" % i + ) + if stack.type == "T": + cmd.distance( + "PiStackingT", "ps-pistack-1-%i" % i, "ps-pistack-2-%i" % i + ) + if self.object_exists("PiStackingP"): + cmd.set("dash_color", "green", "PiStackingP") + cmd.set("dash_gap", 0.3, "PiStackingP") + cmd.set("dash_length", 0.6, "PiStackingP") + if self.object_exists("PiStackingT"): + cmd.set("dash_color", "smudge", "PiStackingT") + cmd.set("dash_gap", 0.3, "PiStackingT") + cmd.set("dash_length", 0.6, "PiStackingT") def show_cationpi(self): """Visualize cation-pi interactions.""" for i, p in enumerate(self.plcomplex.pication): - cmd.pseudoatom('ps-picat-1-%i' % i, pos=p.ring_center) - cmd.pseudoatom('ps-picat-2-%i' % i, pos=p.charge_center) + cmd.pseudoatom("ps-picat-1-%i" % i, pos=p.ring_center) + cmd.pseudoatom("ps-picat-2-%i" % i, pos=p.charge_center) if p.protcharged: - cmd.pseudoatom('Chargecenter-P', pos=p.charge_center) - cmd.pseudoatom('Centroids-L', pos=p.ring_center) - pilig_ids = '+'.join(map(str, p.ring_atoms)) - cmd.select('PiCatRing-L', 'PiCatRing-L or (id %s & %s)' % (pilig_ids, self.ligname)) + cmd.pseudoatom("Chargecenter-P", pos=p.charge_center) + cmd.pseudoatom("Centroids-L", pos=p.ring_center) + pilig_ids = "+".join(map(str, p.ring_atoms)) + cmd.select( + "PiCatRing-L", + "PiCatRing-L or (id %s & %s)" % (pilig_ids, self.ligname), + ) for a in p.charge_atoms: - cmd.select('PosCharge-P', 'PosCharge-P or (id %i & %s)' % (a, self.protname)) + cmd.select( + "PosCharge-P", + "PosCharge-P or (id %i & %s)" % (a, self.protname), + ) else: - cmd.pseudoatom('Chargecenter-L', pos=p.charge_center) - cmd.pseudoatom('Centroids-P', pos=p.ring_center) - pires_ids = '+'.join(map(str, p.ring_atoms)) - cmd.select('PiCatRing-P', 'PiCatRing-P or (id %s & %s)' % (pires_ids, self.protname)) + cmd.pseudoatom("Chargecenter-L", pos=p.charge_center) + cmd.pseudoatom("Centroids-P", pos=p.ring_center) + pires_ids = "+".join(map(str, p.ring_atoms)) + cmd.select( + "PiCatRing-P", + "PiCatRing-P or (id %s & %s)" % (pires_ids, self.protname), + ) for a in p.charge_atoms: - cmd.select('PosCharge-L', 'PosCharge-L or (id %i & %s)' % (a, self.ligname)) - cmd.distance('PiCation', 'ps-picat-1-%i' % i, 'ps-picat-2-%i' % i) - if self.object_exists('PiCation'): - cmd.set('dash_color', 'orange', 'PiCation') - cmd.set('dash_gap', 0.3, 'PiCation') - cmd.set('dash_length', 0.6, 'PiCation') + cmd.select( + "PosCharge-L", "PosCharge-L or (id %i & %s)" % (a, self.ligname) + ) + cmd.distance("PiCation", "ps-picat-1-%i" % i, "ps-picat-2-%i" % i) + if self.object_exists("PiCation"): + cmd.set("dash_color", "orange", "PiCation") + cmd.set("dash_gap", 0.3, "PiCation") + cmd.set("dash_length", 0.6, "PiCation") def show_sbridges(self): """Visualize salt bridges.""" for i, saltb in enumerate(self.plcomplex.saltbridges): if saltb.protispos: for patom in saltb.positive_atoms: - cmd.select('PosCharge-P', 'PosCharge-P or (id %i & %s)' % (patom, self.protname)) + cmd.select( + "PosCharge-P", + "PosCharge-P or (id %i & %s)" % (patom, self.protname), + ) for latom in saltb.negative_atoms: - cmd.select('NegCharge-L', 'NegCharge-L or (id %i & %s)' % (latom, self.ligname)) - for sbgroup in [['ps-sbl-1-%i' % i, 'Chargecenter-P', saltb.positive_center], - ['ps-sbl-2-%i' % i, 'Chargecenter-L', saltb.negative_center]]: + cmd.select( + "NegCharge-L", + "NegCharge-L or (id %i & %s)" % (latom, self.ligname), + ) + for sbgroup in [ + ["ps-sbl-1-%i" % i, "Chargecenter-P", saltb.positive_center], + ["ps-sbl-2-%i" % i, "Chargecenter-L", saltb.negative_center], + ]: cmd.pseudoatom(sbgroup[0], pos=sbgroup[2]) cmd.pseudoatom(sbgroup[1], pos=sbgroup[2]) - cmd.distance('Saltbridges', 'ps-sbl-1-%i' % i, 'ps-sbl-2-%i' % i) + cmd.distance("Saltbridges", "ps-sbl-1-%i" % i, "ps-sbl-2-%i" % i) else: for patom in saltb.negative_atoms: - cmd.select('NegCharge-P', 'NegCharge-P or (id %i & %s)' % (patom, self.protname)) + cmd.select( + "NegCharge-P", + "NegCharge-P or (id %i & %s)" % (patom, self.protname), + ) for latom in saltb.positive_atoms: - cmd.select('PosCharge-L', 'PosCharge-L or (id %i & %s)' % (latom, self.ligname)) - for sbgroup in [['ps-sbp-1-%i' % i, 'Chargecenter-P', saltb.negative_center], - ['ps-sbp-2-%i' % i, 'Chargecenter-L', saltb.positive_center]]: + cmd.select( + "PosCharge-L", + "PosCharge-L or (id %i & %s)" % (latom, self.ligname), + ) + for sbgroup in [ + ["ps-sbp-1-%i" % i, "Chargecenter-P", saltb.negative_center], + ["ps-sbp-2-%i" % i, "Chargecenter-L", saltb.positive_center], + ]: cmd.pseudoatom(sbgroup[0], pos=sbgroup[2]) cmd.pseudoatom(sbgroup[1], pos=sbgroup[2]) - cmd.distance('Saltbridges', 'ps-sbp-1-%i' % i, 'ps-sbp-2-%i' % i) + cmd.distance("Saltbridges", "ps-sbp-1-%i" % i, "ps-sbp-2-%i" % i) - if self.object_exists('Saltbridges'): - cmd.set('dash_color', 'yellow', 'Saltbridges') - cmd.set('dash_gap', 0.5, 'Saltbridges') + if self.object_exists("Saltbridges"): + cmd.set("dash_color", "yellow", "Saltbridges") + cmd.set("dash_gap", 0.5, "Saltbridges") def show_wbridges(self): """Visualize water bridges.""" for bridge in self.plcomplex.waterbridges: if bridge.protisdon: - cmd.select('HBondDonor-P', 'HBondDonor-P or (id %i & %s)' % (bridge.don_id, self.protname)) - cmd.select('HBondAccept-L', 'HBondAccept-L or (id %i & %s)' % (bridge.acc_id, self.ligname)) - cmd.select('tmp_don', 'id %i & %s' % (bridge.don_id, self.protname)) - cmd.select('tmp_acc', 'id %i & %s' % (bridge.acc_id, self.ligname)) + cmd.select( + "HBondDonor-P", + "HBondDonor-P or (id %i & %s)" % (bridge.don_id, self.protname), + ) + cmd.select( + "HBondAccept-L", + "HBondAccept-L or (id %i & %s)" % (bridge.acc_id, self.ligname), + ) + cmd.select("tmp_don", "id %i & %s" % (bridge.don_id, self.protname)) + cmd.select("tmp_acc", "id %i & %s" % (bridge.acc_id, self.ligname)) else: - cmd.select('HBondDonor-L', 'HBondDonor-L or (id %i & %s)' % (bridge.don_id, self.ligname)) - cmd.select('HBondAccept-P', 'HBondAccept-P or (id %i & %s)' % (bridge.acc_id, self.protname)) - cmd.select('tmp_don', 'id %i & %s' % (bridge.don_id, self.ligname)) - cmd.select('tmp_acc', 'id %i & %s' % (bridge.acc_id, self.protname)) - cmd.select('Water', 'Water or (id %i & resn HOH)' % bridge.water_id) - cmd.select('tmp_water', 'id %i & resn HOH' % bridge.water_id) - cmd.distance('WaterBridges', 'tmp_acc', 'tmp_water') - cmd.distance('WaterBridges', 'tmp_don', 'tmp_water') - if self.object_exists('WaterBridges'): - cmd.set('dash_color', 'lightblue', 'WaterBridges') - cmd.delete('tmp_water or tmp_acc or tmp_don') - cmd.color('lightblue', 'Water') - cmd.show('spheres', 'Water') + cmd.select( + "HBondDonor-L", + "HBondDonor-L or (id %i & %s)" % (bridge.don_id, self.ligname), + ) + cmd.select( + "HBondAccept-P", + "HBondAccept-P or (id %i & %s)" % (bridge.acc_id, self.protname), + ) + cmd.select("tmp_don", "id %i & %s" % (bridge.don_id, self.ligname)) + cmd.select("tmp_acc", "id %i & %s" % (bridge.acc_id, self.protname)) + cmd.select("Water", "Water or (id %i & resn HOH)" % bridge.water_id) + cmd.select("tmp_water", "id %i & resn HOH" % bridge.water_id) + cmd.distance("WaterBridges", "tmp_acc", "tmp_water") + cmd.distance("WaterBridges", "tmp_don", "tmp_water") + if self.object_exists("WaterBridges"): + cmd.set("dash_color", "lightblue", "WaterBridges") + cmd.delete("tmp_water or tmp_acc or tmp_don") + cmd.color("lightblue", "Water") + cmd.show("spheres", "Water") def show_metal(self): """Visualize metal coordination.""" metal_complexes = self.plcomplex.metal_complexes if not len(metal_complexes) == 0: - self.select_by_ids('Metal-M', self.metal_ids) + self.select_by_ids("Metal-M", self.metal_ids) for metal_complex in metal_complexes: - cmd.select('tmp_m', 'id %i' % metal_complex.metal_id) - cmd.select('tmp_t', 'id %i' % metal_complex.target_id) - if metal_complex.location == 'water': - cmd.select('Metal-W', 'Metal-W or id %s' % metal_complex.target_id) - if metal_complex.location.startswith('protein'): - cmd.select('tmp_t', 'tmp_t & %s' % self.protname) - cmd.select('Metal-P', 'Metal-P or (id %s & %s)' % (metal_complex.target_id, self.protname)) - if metal_complex.location == 'ligand': - cmd.select('tmp_t', 'tmp_t & %s' % self.ligname) - cmd.select('Metal-L', 'Metal-L or (id %s & %s)' % (metal_complex.target_id, self.ligname)) - cmd.distance('MetalComplexes', 'tmp_m', 'tmp_t') - cmd.delete('tmp_m or tmp_t') - if self.object_exists('MetalComplexes'): - cmd.set('dash_color', 'violetpurple', 'MetalComplexes') - cmd.set('dash_gap', 0.5, 'MetalComplexes') + cmd.select("tmp_m", "id %i" % metal_complex.metal_id) + cmd.select("tmp_t", "id %i" % metal_complex.target_id) + if metal_complex.location == "water": + cmd.select("Metal-W", "Metal-W or id %s" % metal_complex.target_id) + if metal_complex.location.startswith("protein"): + cmd.select("tmp_t", "tmp_t & %s" % self.protname) + cmd.select( + "Metal-P", + "Metal-P or (id %s & %s)" + % (metal_complex.target_id, self.protname), + ) + if metal_complex.location == "ligand": + cmd.select("tmp_t", "tmp_t & %s" % self.ligname) + cmd.select( + "Metal-L", + "Metal-L or (id %s & %s)" + % (metal_complex.target_id, self.ligname), + ) + cmd.distance("MetalComplexes", "tmp_m", "tmp_t") + cmd.delete("tmp_m or tmp_t") + if self.object_exists("MetalComplexes"): + cmd.set("dash_color", "violetpurple", "MetalComplexes") + cmd.set("dash_gap", 0.5, "MetalComplexes") # Show water molecules for metal complexes - cmd.show('spheres', 'Metal-W') - cmd.color('lightblue', 'Metal-W') + cmd.show("spheres", "Metal-W") + cmd.color("lightblue", "Metal-W") def selections_cleanup(self): """Cleans up non-used selections""" if not len(self.plcomplex.unpaired_hba_idx) == 0: - self.select_by_ids('Unpaired-HBA', self.plcomplex.unpaired_hba_idx, selection_exists=True) + self.select_by_ids( + "Unpaired-HBA", self.plcomplex.unpaired_hba_idx, selection_exists=True + ) if not len(self.plcomplex.unpaired_hbd_idx) == 0: - self.select_by_ids('Unpaired-HBD', self.plcomplex.unpaired_hbd_idx, selection_exists=True) + self.select_by_ids( + "Unpaired-HBD", self.plcomplex.unpaired_hbd_idx, selection_exists=True + ) if not len(self.plcomplex.unpaired_hal_idx) == 0: - self.select_by_ids('Unpaired-HAL', self.plcomplex.unpaired_hal_idx, selection_exists=True) + self.select_by_ids( + "Unpaired-HAL", self.plcomplex.unpaired_hal_idx, selection_exists=True + ) selections = cmd.get_names("selections") for selection in selections: @@ -281,38 +376,52 @@ class PyMOLVisualizer: if empty: cmd.delete(selection) cmd.deselect() - cmd.delete('tmp*') - cmd.delete('ps-*') + cmd.delete("tmp*") + cmd.delete("ps-*") def selections_group(self): """Group all selections""" - cmd.group('Structures', '%s %s %sCartoon' % (self.protname, self.ligname, self.protname)) - cmd.group('Interactions', 'Hydrophobic HBonds HalogenBonds WaterBridges PiCation PiStackingP PiStackingT ' - 'Saltbridges MetalComplexes') - cmd.group('Atoms', '') - cmd.group('Atoms.Protein', 'Hydrophobic-P HBondAccept-P HBondDonor-P HalogenAccept Centroids-P PiCatRing-P ' - 'StackRings-P PosCharge-P NegCharge-P AllBSRes Chargecenter-P Metal-P') - cmd.group('Atoms.Ligand', 'Hydrophobic-L HBondAccept-L HBondDonor-L HalogenDonor Centroids-L NegCharge-L ' - 'PosCharge-L NegCharge-L ChargeCenter-L StackRings-L PiCatRing-L Metal-L Metal-M ' - 'Unpaired-HBA Unpaired-HBD Unpaired-HAL Unpaired-RINGS') - cmd.group('Atoms.Other', 'Water Metal-W') - cmd.order('*', 'y') + cmd.group( + "Structures", + "%s %s %sCartoon" % (self.protname, self.ligname, self.protname), + ) + cmd.group( + "Interactions", + "Hydrophobic HBonds HalogenBonds WaterBridges PiCation PiStackingP PiStackingT " + "Saltbridges MetalComplexes", + ) + cmd.group("Atoms", "") + cmd.group( + "Atoms.Protein", + "Hydrophobic-P HBondAccept-P HBondDonor-P HalogenAccept Centroids-P PiCatRing-P " + "StackRings-P PosCharge-P NegCharge-P AllBSRes Chargecenter-P Metal-P", + ) + cmd.group( + "Atoms.Ligand", + "Hydrophobic-L HBondAccept-L HBondDonor-L HalogenDonor Centroids-L NegCharge-L " + "PosCharge-L NegCharge-L ChargeCenter-L StackRings-L PiCatRing-L Metal-L Metal-M " + "Unpaired-HBA Unpaired-HBD Unpaired-HAL Unpaired-RINGS", + ) + cmd.group("Atoms.Other", "Water Metal-W") + cmd.order("*", "y") def additional_cleanup(self): """Cleanup of various representations""" cmd.remove('not alt ""+A') # Remove alternate conformations - cmd.hide('labels', 'Interactions') # Hide labels of lines - cmd.disable('%sCartoon' % self.protname) - cmd.hide('everything', 'hydrogens') + cmd.hide("labels", "Interactions") # Hide labels of lines + cmd.disable("%sCartoon" % self.protname) + cmd.hide("everything", "hydrogens") def zoom_to_ligand(self): """Zoom in too ligand and its interactions.""" cmd.center(self.ligname) cmd.orient(self.ligname) - cmd.turn('x', 110) # If the ligand is aligned with the longest axis, aromatic rings are hidden - if 'AllBSRes' in cmd.get_names("selections"): - cmd.zoom('%s or AllBSRes' % self.ligname, 3) + cmd.turn( + "x", 110 + ) # If the ligand is aligned with the longest axis, aromatic rings are hidden + if "AllBSRes" in cmd.get_names("selections"): + cmd.zoom("%s or AllBSRes" % self.ligname, 3) else: if self.object_exists(self.ligname): cmd.zoom(self.ligname, 3) @@ -320,8 +429,10 @@ class PyMOLVisualizer: def save_session(self, outfolder, override=None): """Saves a PyMOL session file.""" - filename = '%s_%s' % (self.protname.upper(), "_".join( - [self.hetid, self.plcomplex.chain, self.plcomplex.position])) + filename = "%s_%s" % ( + self.protname.upper(), + "_".join([self.hetid, self.plcomplex.chain, self.plcomplex.position]), + ) if override is not None: filename = override cmd.save("/".join([outfolder, "%s.pse" % filename])) @@ -331,15 +442,15 @@ class PyMOLVisualizer: Use this function in case neither cmd.ray() or cmd.png() work. """ sys.stdout = sys.__stdout__ - cmd.feedback('disable', 'movie', 'everything') + cmd.feedback("disable", "movie", "everything") cmd.viewport(width, height) - cmd.zoom('visible', 1.5) # Adapt the zoom to the viewport - cmd.set('ray_trace_frames', 1) # Frames are raytraced before saving an image. + cmd.zoom("visible", 1.5) # Adapt the zoom to the viewport + cmd.set("ray_trace_frames", 1) # Frames are raytraced before saving an image. cmd.mpng(filepath, 1, 1) # Use batch png mode with 1 frame only cmd.mplay() # cmd.mpng needs the animation to 'run' cmd.refresh() - originalfile = "".join([filepath, '0001.png']) - newfile = "".join([filepath, '.png']) + originalfile = "".join([filepath, "0001.png"]) + newfile = "".join([filepath, ".png"]) ################################################# # Wait for file for max. 1 second and rename it # @@ -349,29 +460,56 @@ class PyMOLVisualizer: while not os.path.isfile(originalfile) and attempts <= 10: sleep(0.1) attempts += 1 - if os.name == 'nt': # In Windows, make sure there is no file of the same name, cannot be overwritten as in Unix + if ( + os.name == "nt" + ): # In Windows, make sure there is no file of the same name, cannot be overwritten as in Unix if os.path.isfile(newfile): os.remove(newfile) os.rename(originalfile, newfile) # Remove frame number in filename # Check if imagemagick is available and crop + resize the images - if subprocess.call("type convert", shell=True, stdout=subprocess.PIPE, stderr=subprocess.PIPE) == 0: + if ( + subprocess.call( + "type convert", + shell=True, + stdout=subprocess.PIPE, + stderr=subprocess.PIPE, + ) + == 0 + ): attempts, ecode = 0, 1 # Check if file is truncated and wait if that's the case while ecode != 0 and attempts <= 10: - ecode = subprocess.call(['convert', newfile, '/dev/null'], stdout=open('/dev/null', 'w'), - stderr=subprocess.STDOUT) + ecode = subprocess.call( + ["convert", newfile, "/dev/null"], + stdout=open("/dev/null", "w"), + stderr=subprocess.STDOUT, + ) sleep(0.1) attempts += 1 - trim = 'convert -trim ' + newfile + ' -bordercolor White -border 20x20 ' + newfile + ';' # Trim the image + trim = ( + "convert -trim " + + newfile + + " -bordercolor White -border 20x20 " + + newfile + + ";" + ) # Trim the image os.system(trim) - getwidth = 'w=`convert ' + newfile + ' -ping -format "%w" info:`;' # Get the width of the new image - getheight = 'h=`convert ' + newfile + ' -ping -format "%h" info:`;' # Get the hight of the new image + getwidth = ( + "w=`convert " + newfile + ' -ping -format "%w" info:`;' + ) # Get the width of the new image + getheight = ( + "h=`convert " + newfile + ' -ping -format "%h" info:`;' + ) # Get the hight of the new image newres = 'if [ "$w" -gt "$h" ]; then newr="${w%.*}x$w"; else newr="${h%.*}x$h"; fi;' # Set quadratic ratio - quadratic = 'convert ' + newfile + ' -gravity center -extent "$newr" ' + newfile # Fill with whitespace + quadratic = ( + "convert " + newfile + ' -gravity center -extent "$newr" ' + newfile + ) # Fill with whitespace os.system(getwidth + getheight + newres + quadratic) else: - sys.stderr.write('Imagemagick not available. Images will not be resized or cropped.') + sys.stderr.write( + "Imagemagick not available. Images will not be resized or cropped." + ) def save_picture(self, outfolder, filename): """Saves a picture""" @@ -380,26 +518,26 @@ class PyMOLVisualizer: def set_fancy_ray(self): """Give the molecule a flat, modern look.""" - cmd.set('light_count', 6) - cmd.set('spec_count', 1.5) - cmd.set('shininess', 4) - cmd.set('specular', 0.3) - cmd.set('reflect', 1.6) - cmd.set('ambient', 0) - cmd.set('direct', 0) - cmd.set('ray_shadow', 0) # Gives the molecules a flat, modern look - cmd.set('ambient_occlusion_mode', 1) - cmd.set('ray_opaque_background', 0) # Transparent background + cmd.set("light_count", 6) + cmd.set("spec_count", 1.5) + cmd.set("shininess", 4) + cmd.set("specular", 0.3) + cmd.set("reflect", 1.6) + cmd.set("ambient", 0) + cmd.set("direct", 0) + cmd.set("ray_shadow", 0) # Gives the molecules a flat, modern look + cmd.set("ambient_occlusion_mode", 1) + cmd.set("ray_opaque_background", 0) # Transparent background def adapt_for_peptides(self): """Adapt visualization for peptide ligands and interchain contacts""" - cmd.hide('sticks', self.ligname) - cmd.set('cartoon_color', 'lightorange', self.ligname) - cmd.show('cartoon', self.ligname) - cmd.show('sticks', "byres *-L") + cmd.hide("sticks", self.ligname) + cmd.set("cartoon_color", "lightorange", self.ligname) + cmd.show("cartoon", self.ligname) + cmd.show("sticks", "byres *-L") cmd.util.cnc(self.ligname) - cmd.remove('%sCartoon and chain %s' % (self.protname, self.plcomplex.chain)) - cmd.set('cartoon_side_chain_helper', 0) + cmd.remove("%sCartoon and chain %s" % (self.protname, self.plcomplex.chain)) + cmd.set("cartoon_side_chain_helper", 0) def adapt_for_intra(self): """Adapt visualization for intra-protein interactions""" @@ -408,43 +546,55 @@ class PyMOLVisualizer: """Refinements for the visualization""" # Show sticks for all residues interacing with the ligand - cmd.select('AllBSRes', 'byres (Hydrophobic-P or HBondDonor-P or HBondAccept-P or PosCharge-P or NegCharge-P or ' - 'StackRings-P or PiCatRing-P or HalogenAcc or Metal-P)') - cmd.show('sticks', 'AllBSRes') + cmd.select( + "AllBSRes", + "byres (Hydrophobic-P or HBondDonor-P or HBondAccept-P or PosCharge-P or NegCharge-P or " + "StackRings-P or PiCatRing-P or HalogenAcc or Metal-P)", + ) + cmd.show("sticks", "AllBSRes") # Show spheres for the ring centroids - cmd.hide('everything', 'centroids*') - cmd.show('nb_spheres', 'centroids*') + cmd.hide("everything", "centroids*") + cmd.show("nb_spheres", "centroids*") # Show spheres for centers of charge - if self.object_exists('Chargecenter-P') or self.object_exists('Chargecenter-L'): - cmd.hide('nonbonded', 'chargecenter*') - cmd.show('spheres', 'chargecenter*') - cmd.set('sphere_scale', 0.4, 'chargecenter*') - cmd.color('yellow', 'chargecenter*') + if self.object_exists("Chargecenter-P") or self.object_exists("Chargecenter-L"): + cmd.hide("nonbonded", "chargecenter*") + cmd.show("spheres", "chargecenter*") + cmd.set("sphere_scale", 0.4, "chargecenter*") + cmd.color("yellow", "chargecenter*") - cmd.set('valence', 1) # Show bond valency (e.g. double bonds) + cmd.set("valence", 1) # Show bond valency (e.g. double bonds) # Optional cartoon representation of the protein - cmd.copy('%sCartoon' % self.protname, self.protname) - cmd.show('cartoon', '%sCartoon' % self.protname) - cmd.show('sticks', '%sCartoon' % self.protname) - cmd.set('stick_transparency', 1, '%sCartoon' % self.protname) + cmd.copy("%sCartoon" % self.protname, self.protname) + cmd.show("cartoon", "%sCartoon" % self.protname) + cmd.show("sticks", "%sCartoon" % self.protname) + cmd.set("stick_transparency", 1, "%sCartoon" % self.protname) # Resize water molecules. Sometimes they are not heteroatoms HOH, but part of the protein - cmd.set('sphere_scale', 0.2, 'resn HOH or Water') # Needs to be done here because of the copy made - cmd.set('sphere_transparency', 0.4, '!(resn HOH or Water)') - - if 'Centroids*' in cmd.get_names("selections"): - cmd.color('grey80', 'Centroids*') - cmd.hide('spheres', '%sCartoon' % self.protname) - cmd.hide('cartoon', '%sCartoon and resn DA+DG+DC+DU+DT+A+G+C+U+T' % self.protname) # Hide DNA/RNA Cartoon - if self.ligname == 'SF4': # Special case for iron-sulfur clusters, can't be visualized with sticks - cmd.show('spheres', '%s' % self.ligname) - - cmd.hide('everything', 'resn HOH &!Water') # Hide all non-interacting water molecules - cmd.hide('sticks', '%s and !%s and !AllBSRes' % - (self.protname, self.ligname)) # Hide all non-interacting residues - - if self.ligandtype in ['PEPTIDE', 'INTRA']: + cmd.set( + "sphere_scale", 0.2, "resn HOH or Water" + ) # Needs to be done here because of the copy made + cmd.set("sphere_transparency", 0.4, "!(resn HOH or Water)") + + if "Centroids*" in cmd.get_names("selections"): + cmd.color("grey80", "Centroids*") + cmd.hide("spheres", "%sCartoon" % self.protname) + cmd.hide( + "cartoon", "%sCartoon and resn DA+DG+DC+DU+DT+A+G+C+U+T" % self.protname + ) # Hide DNA/RNA Cartoon + if ( + self.ligname == "SF4" + ): # Special case for iron-sulfur clusters, can't be visualized with sticks + cmd.show("spheres", "%s" % self.ligname) + + cmd.hide( + "everything", "resn HOH &!Water" + ) # Hide all non-interacting water molecules + cmd.hide( + "sticks", "%s and !%s and !AllBSRes" % (self.protname, self.ligname) + ) # Hide all non-interacting residues + + if self.ligandtype in ["PEPTIDE", "INTRA"]: self.adapt_for_peptides() - if self.ligandtype == 'INTRA': + if self.ligandtype == "INTRA": self.adapt_for_intra() |