initial commit

4 files changed, 782 insertions, 0 deletions

diff --git a/plip/visualization/__init__.py b/plip/visualization/__init__.py
new file mode 100644
index 0000000..e69de29
--- /dev/null
+++ b/plip/visualization/__init__.py
diff --git a/plip/visualization/chimera.py b/plip/visualization/chimera.py
new file mode 100644
index 0000000..a37fffb
--- /dev/null
+++ b/plip/visualization/chimera.py
@@ -0,0 +1,221 @@
+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
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()
diff --git a/plip/visualization/visualize.py b/plip/visualization/visualize.py
new file mode 100644
index 0000000..4cd7a14
--- /dev/null
+++ b/plip/visualization/visualize.py
@@ -0,0 +1,111 @@
+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)