1 files changed, 0 insertions, 111 deletions
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)