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Diffstat (limited to 'plip/visualization/pymol.py')
| -rw-r--r-- | plip/visualization/pymol.py | 450 |
1 files changed, 0 insertions, 450 deletions
diff --git a/plip/visualization/pymol.py b/plip/visualization/pymol.py deleted file mode 100644 index b97912a..0000000 --- a/plip/visualization/pymol.py +++ /dev/null @@ -1,450 +0,0 @@ -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() |