From 4be08f7bdd77991e9e453c1cda863c3f20c338d5 Mon Sep 17 00:00:00 2001
From: Navan Chauhan <navanchauhan@gmail.com>
Date: Thu, 2 Jul 2020 20:48:33 +0530
Subject: initial commit

---
 plip/visualization/visualize.py | 111 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 111 insertions(+)
 create mode 100644 plip/visualization/visualize.py

(limited to 'plip/visualization/visualize.py')

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)
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