From 9dadfdb3332b073aaff508d126e90200ad09868d Mon Sep 17 00:00:00 2001
From: Navan Chauhan <navanchauhan@gmail.com>
Date: Fri, 11 Sep 2020 16:18:38 +0530
Subject: removed downloaded plip
---
plip/visualization/__init__.py | 0
plip/visualization/chimera.py | 221 --------------------
plip/visualization/pymol.py | 450 ----------------------------------------
plip/visualization/visualize.py | 111 ----------
4 files changed, 782 deletions(-)
delete mode 100644 plip/visualization/__init__.py
delete mode 100644 plip/visualization/chimera.py
delete mode 100644 plip/visualization/pymol.py
delete mode 100644 plip/visualization/visualize.py
(limited to 'plip/visualization')
diff --git a/plip/visualization/__init__.py b/plip/visualization/__init__.py
deleted file mode 100644
index e69de29..0000000
diff --git a/plip/visualization/chimera.py b/plip/visualization/chimera.py
deleted file mode 100644
index a37fffb..0000000
--- a/plip/visualization/chimera.py
+++ /dev/null
@@ -1,221 +0,0 @@
-class ChimeraVisualizer:
- """Provides visualization for Chimera."""
-
- def __init__(self, plcomplex, chimera_module, tid):
- self.chimera = chimera_module
- self.tid = tid
- self.uid = plcomplex.uid
- self.plipname = 'PLIP-%i' % self.tid
- self.hetid, self.chain, self.pos = self.uid.split(':')
- self.pos = int(self.pos)
- self.colorbyname = self.chimera.colorTable.getColorByName
- self.rc = self.chimera.runCommand
- self.getPseudoBondGroup = self.chimera.misc.getPseudoBondGroup
-
- if plcomplex is not None:
- self.plcomplex = plcomplex
- self.protname = plcomplex.pdbid # Name of protein with binding site
- self.ligname = plcomplex.hetid # Name of ligand
- self.metal_ids = plcomplex.metal_ids
- self.water_ids = []
- self.bs_res_ids = []
- self.models = self.chimera.openModels
-
- for md in self.models.list():
- if md.name == self.plipname:
- self.model = md
-
- self.atoms = self.atom_by_serialnumber()
-
- def set_initial_representations(self):
- """Set the initial representations"""
- self.update_model_dict()
- self.rc("background solid white")
- self.rc("setattr g display 0") # Hide all pseudobonds
- self.rc("~display #%i & :/isHet & ~:%s" % (self.model_dict[self.plipname], self.hetid))
-
- def update_model_dict(self):
- """Updates the model dictionary"""
- dct = {}
- models = self.chimera.openModels
- for md in models.list():
- dct[md.name] = md.id
- self.model_dict = dct
-
- def atom_by_serialnumber(self):
- """Provides a dictionary mapping serial numbers to their atom objects."""
- atm_by_snum = {}
- for atom in self.model.atoms:
- atm_by_snum[atom.serialNumber] = atom
- return atm_by_snum
-
- def show_hydrophobic(self):
- """Visualizes hydrophobic contacts."""
- grp = self.getPseudoBondGroup("Hydrophobic Interactions-%i" % self.tid, associateWith=[self.model])
- grp.lineType = self.chimera.Dash
- grp.lineWidth = 3
- grp.color = self.colorbyname('gray')
- for i in self.plcomplex.hydrophobic_contacts.pairs_ids:
- self.bs_res_ids.append(i[0])
-
- def show_hbonds(self):
- """Visualizes hydrogen bonds."""
- grp = self.getPseudoBondGroup("Hydrogen Bonds-%i" % self.tid, associateWith=[self.model])
- grp.lineWidth = 3
- for i in self.plcomplex.hbonds.ldon_id:
- b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
- b.color = self.colorbyname('blue')
- self.bs_res_ids.append(i[0])
- for i in self.plcomplex.hbonds.pdon_id:
- b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
- b.color = self.colorbyname('blue')
- self.bs_res_ids.append(i[1])
-
- def show_halogen(self):
- """Visualizes halogen bonds."""
- grp = self.getPseudoBondGroup("HalogenBonds-%i" % self.tid, associateWith=[self.model])
- grp.lineWidth = 3
- for i in self.plcomplex.halogen_bonds:
- b = grp.newPseudoBond(self.atoms[i[0]], self.atoms[i[1]])
- b.color = self.colorbyname('turquoise')
-
- self.bs_res_ids.append(i.acc_id)
-
- def show_stacking(self):
- """Visualizes pi-stacking interactions."""
- grp = self.getPseudoBondGroup("pi-Stacking-%i" % self.tid, associateWith=[self.model])
- grp.lineWidth = 3
- grp.lineType = self.chimera.Dash
- for i, stack in enumerate(self.plcomplex.pistacking):
-
- m = self.model
- r = m.newResidue("pseudoatoms", " ", 1, " ")
- centroid_prot = m.newAtom("CENTROID", self.chimera.Element("CENTROID"))
- x, y, z = stack.proteinring_center
- centroid_prot.setCoord(self.chimera.Coord(x, y, z))
- r.addAtom(centroid_prot)
-
- centroid_lig = m.newAtom("CENTROID", self.chimera.Element("CENTROID"))
- x, y, z = stack.ligandring_center
- centroid_lig.setCoord(self.chimera.Coord(x, y, z))
- r.addAtom(centroid_lig)
-
- b = grp.newPseudoBond(centroid_lig, centroid_prot)
- b.color = self.colorbyname('forest green')
-
- self.bs_res_ids += stack.proteinring_atoms
-
- def show_cationpi(self):
- """Visualizes cation-pi interactions"""
- grp = self.getPseudoBondGroup("Cation-Pi-%i" % self.tid, associateWith=[self.model])
- grp.lineWidth = 3
- grp.lineType = self.chimera.Dash
- for i, cat in enumerate(self.plcomplex.pication):
-
- m = self.model
- r = m.newResidue("pseudoatoms", " ", 1, " ")
- chargecenter = m.newAtom("CHARGE", self.chimera.Element("CHARGE"))
- x, y, z = cat.charge_center
- chargecenter.setCoord(self.chimera.Coord(x, y, z))
- r.addAtom(chargecenter)
-
- centroid = m.newAtom("CENTROID", self.chimera.Element("CENTROID"))
- x, y, z = cat.ring_center
- centroid.setCoord(self.chimera.Coord(x, y, z))
- r.addAtom(centroid)
-
- b = grp.newPseudoBond(centroid, chargecenter)
- b.color = self.colorbyname('orange')
-
- if cat.protcharged:
- self.bs_res_ids += cat.charge_atoms
- else:
- self.bs_res_ids += cat.ring_atoms
-
- def show_sbridges(self):
- """Visualizes salt bridges."""
- # Salt Bridges
- grp = self.getPseudoBondGroup("Salt Bridges-%i" % self.tid, associateWith=[self.model])
- grp.lineWidth = 3
- grp.lineType = self.chimera.Dash
- for i, sbridge in enumerate(self.plcomplex.saltbridges):
-
- m = self.model
- r = m.newResidue("pseudoatoms", " ", 1, " ")
- chargecenter1 = m.newAtom("CHARGE", self.chimera.Element("CHARGE"))
- x, y, z = sbridge.positive_center
- chargecenter1.setCoord(self.chimera.Coord(x, y, z))
- r.addAtom(chargecenter1)
-
- chargecenter2 = m.newAtom("CHARGE", self.chimera.Element("CHARGE"))
- x, y, z = sbridge.negative_center
- chargecenter2.setCoord(self.chimera.Coord(x, y, z))
- r.addAtom(chargecenter2)
-
- b = grp.newPseudoBond(chargecenter1, chargecenter2)
- b.color = self.colorbyname('yellow')
-
- if sbridge.protispos:
- self.bs_res_ids += sbridge.positive_atoms
- else:
- self.bs_res_ids += sbridge.negative_atoms
-
- def show_wbridges(self):
- """Visualizes water bridges"""
- grp = self.getPseudoBondGroup("Water Bridges-%i" % self.tid, associateWith=[self.model])
- grp.lineWidth = 3
- for i, wbridge in enumerate(self.plcomplex.waterbridges):
- c = grp.newPseudoBond(self.atoms[wbridge.water_id], self.atoms[wbridge.acc_id])
- c.color = self.colorbyname('cornflower blue')
- self.water_ids.append(wbridge.water_id)
- b = grp.newPseudoBond(self.atoms[wbridge.don_id], self.atoms[wbridge.water_id])
- b.color = self.colorbyname('cornflower blue')
- self.water_ids.append(wbridge.water_id)
- if wbridge.protisdon:
- self.bs_res_ids.append(wbridge.don_id)
- else:
- self.bs_res_ids.append(wbridge.acc_id)
-
- def show_metal(self):
- """Visualizes metal coordination."""
- grp = self.getPseudoBondGroup("Metal Coordination-%i" % self.tid, associateWith=[self.model])
- grp.lineWidth = 3
- for i, metal in enumerate(self.plcomplex.metal_complexes):
- c = grp.newPseudoBond(self.atoms[metal.metal_id], self.atoms[metal.target_id])
- c.color = self.colorbyname('magenta')
-
- if metal.location == 'water':
- self.water_ids.append(metal.target_id)
-
- if metal.location.startswith('protein'):
- self.bs_res_ids.append(metal.target_id)
-
- def cleanup(self):
- """Clean up the visualization."""
-
- if not len(self.water_ids) == 0:
- # Hide all non-interacting water molecules
- water_selection = []
- for wid in self.water_ids:
- water_selection.append('serialNumber=%i' % wid)
- self.rc("~display :HOH")
- self.rc("display :@/%s" % " or ".join(water_selection))
-
- # Show all interacting binding site residues
- self.rc("~display #%i & ~:/isHet" % self.model_dict[self.plipname])
- self.rc("display :%s" % ",".join([str(self.atoms[bsid].residue.id) for bsid in self.bs_res_ids]))
- self.rc("color lightblue :HOH")
-
- def zoom_to_ligand(self):
- """Centers the view on the ligand and its binding site residues."""
- self.rc("center #%i & :%s" % (self.model_dict[self.plipname], self.hetid))
-
- def refinements(self):
- """Details for the visualization."""
- self.rc("setattr a color gray @CENTROID")
- self.rc("setattr a radius 0.3 @CENTROID")
- self.rc("represent sphere @CENTROID")
- self.rc("setattr a color orange @CHARGE")
- self.rc("setattr a radius 0.4 @CHARGE")
- self.rc("represent sphere @CHARGE")
- self.rc("display :pseudoatoms")
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()
diff --git a/plip/visualization/visualize.py b/plip/visualization/visualize.py
deleted file mode 100644
index 4cd7a14..0000000
--- a/plip/visualization/visualize.py
+++ /dev/null
@@ -1,111 +0,0 @@
-from pymol import cmd
-
-from plip.basic import config, logger
-from plip.basic.supplemental import start_pymol
-from plip.visualization.pymol import PyMOLVisualizer
-
-logger = logger.get_logger()
-
-
-def visualize_in_pymol(plcomplex):
- """Visualizes the protein-ligand pliprofiler at one site in PyMOL."""
-
- vis = PyMOLVisualizer(plcomplex)
-
- #####################
- # Set everything up #
- #####################
-
- pdbid = plcomplex.pdbid
- lig_members = plcomplex.lig_members
- chain = plcomplex.chain
- if config.PEPTIDES:
- vis.ligname = 'PeptideChain%s' % plcomplex.chain
- if config.INTRA is not None:
- vis.ligname = 'Intra%s' % plcomplex.chain
-
- ligname = vis.ligname
- hetid = plcomplex.hetid
-
- metal_ids = plcomplex.metal_ids
- metal_ids_str = '+'.join([str(i) for i in metal_ids])
-
- ########################
- # Basic visualizations #
- ########################
-
- start_pymol(run=True, options='-pcq', quiet=not config.VERBOSE and not config.SILENT)
- vis.set_initial_representations()
-
- cmd.load(plcomplex.sourcefile)
- current_name = cmd.get_object_list(selection='(all)')[0]
- logger.debug(f'setting current_name to {current_name} and pdbid to {pdbid}')
- cmd.set_name(current_name, pdbid)
- cmd.hide('everything', 'all')
- if config.PEPTIDES:
- cmd.select(ligname, 'chain %s and not resn HOH' % plcomplex.chain)
- else:
- cmd.select(ligname, 'resn %s and chain %s and resi %s*' % (hetid, chain, plcomplex.position))
- logger.debug(f'selecting ligand for PDBID {pdbid} and ligand name {ligname}')
- logger.debug(f'resn {hetid} and chain {chain} and resi {plcomplex.position}')
-
- # Visualize and color metal ions if there are any
- if not len(metal_ids) == 0:
- vis.select_by_ids(ligname, metal_ids, selection_exists=True)
- cmd.show('spheres', 'id %s and %s' % (metal_ids_str, pdbid))
-
- # Additionally, select all members of composite ligands
- if len(lig_members) > 1:
- for member in lig_members:
- resid, chain, resnr = member[0], member[1], str(member[2])
- cmd.select(ligname, '%s or (resn %s and chain %s and resi %s)' % (ligname, resid, chain, resnr))
-
- cmd.show('sticks', ligname)
- cmd.color('myblue')
- cmd.color('myorange', ligname)
- cmd.util.cnc('all')
- if not len(metal_ids) == 0:
- cmd.color('hotpink', 'id %s' % metal_ids_str)
- cmd.hide('sticks', 'id %s' % metal_ids_str)
- cmd.set('sphere_scale', 0.3, ligname)
- cmd.deselect()
-
- vis.make_initial_selections()
-
- vis.show_hydrophobic() # Hydrophobic Contacts
- vis.show_hbonds() # Hydrogen Bonds
- vis.show_halogen() # Halogen Bonds
- vis.show_stacking() # pi-Stacking Interactions
- vis.show_cationpi() # pi-Cation Interactions
- vis.show_sbridges() # Salt Bridges
- vis.show_wbridges() # Water Bridges
- vis.show_metal() # Metal Coordination
-
- vis.refinements()
-
- vis.zoom_to_ligand()
-
- vis.selections_cleanup()
-
- vis.selections_group()
- vis.additional_cleanup()
- if config.DNARECEPTOR:
- # Rename Cartoon selection to Line selection and change repr.
- cmd.set_name('%sCartoon' % plcomplex.pdbid, '%sLines' % plcomplex.pdbid)
- cmd.hide('cartoon', '%sLines' % plcomplex.pdbid)
- cmd.show('lines', '%sLines' % plcomplex.pdbid)
-
- if config.PEPTIDES:
- filename = "%s_PeptideChain%s" % (pdbid.upper(), plcomplex.chain)
- if config.PYMOL:
- vis.save_session(config.OUTPATH, override=filename)
- elif config.INTRA is not None:
- filename = "%s_IntraChain%s" % (pdbid.upper(), plcomplex.chain)
- if config.PYMOL:
- vis.save_session(config.OUTPATH, override=filename)
- else:
- filename = '%s_%s' % (pdbid.upper(), "_".join([hetid, plcomplex.chain, plcomplex.position]))
- if config.PYMOL:
- vis.save_session(config.OUTPATH)
- if config.PICS:
- vis.save_picture(config.OUTPATH, filename)
--
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