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authordeepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>2020-07-07 14:55:17 +0000
committerGitHub <noreply@github.com>2020-07-07 14:55:17 +0000
commit0d135d611506e81d322596c7827b08bbfd3b7c08 (patch)
treea281b8e1f140ad3de77d818747fce03bcfa5b77b /plip/visualization/pymol.py
parent7059ee2a4ced23e467741cc846eb185886ffca38 (diff)
Format code with Blackdeepsource-transform-b65b5545
Diffstat (limited to 'plip/visualization/pymol.py')
-rw-r--r--plip/visualization/pymol.py618
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()