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Diffstat (limited to 'plip/visualization/pymol.py')
| -rw-r--r-- | plip/visualization/pymol.py | 450 |
1 files changed, 450 insertions, 0 deletions
diff --git a/plip/visualization/pymol.py b/plip/visualization/pymol.py new file mode 100644 index 0000000..b97912a --- /dev/null +++ b/plip/visualization/pymol.py @@ -0,0 +1,450 @@ +import os +import subprocess +import sys +from time import sleep + +from pymol import cmd + + +class PyMOLVisualizer: + + def __init__(self, plcomplex): + if plcomplex is not None: + self.plcomplex = plcomplex + self.protname = plcomplex.pdbid # Name of protein with binding site + self.hetid = plcomplex.hetid + self.ligandtype = plcomplex.ligandtype + self.ligname = "Ligand_" + self.hetid # Name of ligand + self.metal_ids = plcomplex.metal_ids + + 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') + + # Set clipping planes for full view + 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') + + 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) + 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): + """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)] + for idchunk in idchunks: + 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)) + + def object_exists(self, object_name): + """Checks if an object exists in the open PyMOL session.""" + return object_name in cmd.get_names("objects") + + def show_hydrophobic(self): + """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) + + 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') + else: + 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]]: + 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]]: + 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') + 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') + + def show_halogen(self): + """Visualize halogen bonds.""" + halogen = self.plcomplex.halogen_bonds + all_don_x, all_acc_o = [], [] + 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.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') + + 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') + + 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) + 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)) + for a in p.charge_atoms: + 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)) + 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') + + 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)) + 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.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) + else: + for patom in saltb.negative_atoms: + 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.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) + + 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)) + 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') + + 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) + 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') + # Show water molecules for metal complexes + 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) + if not len(self.plcomplex.unpaired_hbd_idx) == 0: + 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) + + selections = cmd.get_names("selections") + for selection in selections: + try: + empty = len(cmd.get_model(selection).atom) == 0 + except: + empty = True + if empty: + cmd.delete(selection) + cmd.deselect() + 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') + + 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') + + 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) + else: + if self.object_exists(self.ligname): + cmd.zoom(self.ligname, 3) + cmd.origin(self.ligname) + + 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])) + if override is not None: + filename = override + cmd.save("/".join([outfolder, "%s.pse" % filename])) + + def png_workaround(self, filepath, width=1200, height=800): + """Workaround for (a) severe bug(s) in PyMOL preventing ray-traced images to be produced in command-line mode. + Use this function in case neither cmd.ray() or cmd.png() work. + """ + sys.stdout = sys.__stdout__ + 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.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']) + + ################################################# + # Wait for file for max. 1 second and rename it # + ################################################# + + attempts = 0 + 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.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: + 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) + sleep(0.1) + attempts += 1 + 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 + 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 + os.system(getwidth + getheight + newres + quadratic) + else: + sys.stderr.write('Imagemagick not available. Images will not be resized or cropped.') + + def save_picture(self, outfolder, filename): + """Saves a picture""" + self.set_fancy_ray() + self.png_workaround("/".join([outfolder, filename])) + + 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 + + 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.util.cnc(self.ligname) + 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""" + + def refinements(self): + """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') + # Show spheres for the ring 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*') + + 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) + + # 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']: + self.adapt_for_peptides() + + if self.ligandtype == 'INTRA': + self.adapt_for_intra() |