def get_isomorphisms(reference, lig):
"""Get all isomorphisms of the ligand."""
query = pybel.ob.CompileMoleculeQuery(reference.OBMol)
mappr = pybel.ob.OBIsomorphismMapper.GetInstance(query)
if all:
isomorphs = pybel.ob.vvpairUIntUInt()
mappr.MapAll(lig.OBMol, isomorphs)
else:
isomorphs = pybel.ob.vpairUIntUInt()
mappr.MapFirst(lig.OBMol, isomorphs)
isomorphs = [isomorphs]
logger.debug(f'number of isomorphisms: {len(isomorphs)}')
# @todo Check which isomorphism to take
return isomorphs
def readmol(path, as_string=False):
"""Reads the given molecule file and returns the corresponding Pybel molecule as well as the input file type.
In contrast to the standard Pybel implementation, the file is closed properly."""
supported_formats = ['pdb']
# Fix for Windows-generated files: Remove carriage return characters
if "\r" in path and as_string:
path = path.replace('\r', '')
for sformat in supported_formats:
obc = pybel.ob.OBConversion()
obc.SetInFormat(sformat)
logger.debug(
f'detected {sformat} as format, trying to read file with OpenBabel'
)
# Read molecules with single bond information
if as_string:
try:
mymol = pybel.readstring(sformat, path)
except IOError:
logger.error('no valid file format provided')
sys.exit(1)
else:
read_file = pybel.readfile(format=sformat,
filename=path,
opt={"s": None})
try:
mymol = next(read_file)
except StopIteration:
logger.error('file contains no valid molecules')
sys.exit(1)
logger.debug('molecule successfully read')
# Assign multiple bonds
mymol.OBMol.PerceiveBondOrders()
return mymol, sformat
logger.error('no valid file format provided')
sys.exit(1)
def visualize_in_pymol(plcomplex):
"""Visualizes the given Protein-Ligand complex 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 PDB-ID 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)