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from collections import namedtuple
hbonds_info = namedtuple('hbonds_info', 'ldon_id lig_don_id prot_acc_id pdon_id prot_don_id lig_acc_id')
hydrophobic_info = namedtuple('hydrophobic_info', 'bs_ids lig_ids pairs_ids')
halogen_info = namedtuple('halogen_info', 'don_id acc_id')
pistack_info = namedtuple('pistack_info', 'proteinring_atoms, proteinring_center ligandring_atoms '
'ligandring_center type')
pication_info = namedtuple('pication_info', 'ring_center charge_center ring_atoms charge_atoms, protcharged')
sbridge_info = namedtuple('sbridge_info', 'positive_atoms negative_atoms positive_center negative_center protispos')
wbridge_info = namedtuple('wbridge_info', 'don_id acc_id water_id protisdon')
metal_info = namedtuple('metal_info', 'metal_id, target_id location')
class VisualizerData:
"""Contains all information on a complex relevant for visualization. Can be pickled"""
def __init__(self, mol, site):
pcomp = mol
pli = mol.interaction_sets[site]
ligand = pli.ligand
# General Information
self.lig_members = sorted(pli.ligand.members)
self.sourcefile = pcomp.sourcefiles['pdbcomplex']
self.corrected_pdb = pcomp.corrected_pdb
self.pdbid = mol.pymol_name
self.hetid = ligand.hetid
self.ligandtype = ligand.type
self.chain = ligand.chain if not ligand.chain == "0" else "" # #@todo Fix this
self.position = str(ligand.position)
self.uid = ":".join([self.hetid, self.chain, self.position])
self.outpath = mol.output_path
self.metal_ids = [x.m_orig_idx for x in pli.ligand.metals]
self.unpaired_hba_idx = pli.unpaired_hba_orig_idx
self.unpaired_hbd_idx = pli.unpaired_hbd_orig_idx
self.unpaired_hal_idx = pli.unpaired_hal_orig_idx
# Information on Interactions
# Hydrophobic Contacts
# Contains IDs of contributing binding site, ligand atoms and the pairings
hydroph_pairs_id = [(h.bsatom_orig_idx, h.ligatom_orig_idx) for h in pli.hydrophobic_contacts]
self.hydrophobic_contacts = hydrophobic_info(bs_ids=[hp[0] for hp in hydroph_pairs_id],
lig_ids=[hp[1] for hp in hydroph_pairs_id],
pairs_ids=hydroph_pairs_id)
# Hydrogen Bonds
# #@todo Don't use indices, simplify this code here
hbonds_ldon, hbonds_pdon = pli.hbonds_ldon, pli.hbonds_pdon
hbonds_ldon_id = [(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_ldon]
hbonds_pdon_id = [(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_pdon]
self.hbonds = hbonds_info(ldon_id=[(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_ldon],
lig_don_id=[hb[1] for hb in hbonds_ldon_id],
prot_acc_id=[hb[0] for hb in hbonds_ldon_id],
pdon_id=[(hb.a_orig_idx, hb.d_orig_idx) for hb in hbonds_pdon],
prot_don_id=[hb[1] for hb in hbonds_pdon_id],
lig_acc_id=[hb[0] for hb in hbonds_pdon_id])
# Halogen Bonds
self.halogen_bonds = [halogen_info(don_id=h.don_orig_idx, acc_id=h.acc_orig_idx)
for h in pli.halogen_bonds]
# Pistacking
self.pistacking = [pistack_info(proteinring_atoms=pistack.proteinring.atoms_orig_idx,
proteinring_center=pistack.proteinring.center,
ligandring_atoms=pistack.ligandring.atoms_orig_idx,
ligandring_center=pistack.ligandring.center,
type=pistack.type) for pistack in pli.pistacking]
# Pi-cation interactions
self.pication = [pication_info(ring_center=picat.ring.center,
charge_center=picat.charge.center,
ring_atoms=picat.ring.atoms_orig_idx,
charge_atoms=picat.charge.atoms_orig_idx,
protcharged=picat.protcharged)
for picat in pli.pication_paro + pli.pication_laro]
# Salt Bridges
self.saltbridges = [sbridge_info(positive_atoms=sbridge.positive.atoms_orig_idx,
negative_atoms=sbridge.negative.atoms_orig_idx,
positive_center=sbridge.positive.center,
negative_center=sbridge.negative.center,
protispos=sbridge.protispos)
for sbridge in pli.saltbridge_lneg + pli.saltbridge_pneg]
# Water Bridgese('wbridge_info', 'don_id acc_id water_id protisdon')
self.waterbridges = [wbridge_info(don_id=wbridge.d_orig_idx,
acc_id=wbridge.a_orig_idx,
water_id=wbridge.water_orig_idx,
protisdon=wbridge.protisdon) for wbridge in pli.water_bridges]
# Metal Complexes
self.metal_complexes = [metal_info(metal_id=metalc.metal_orig_idx,
target_id=metalc.target_orig_idx,
location=metalc.location) for metalc in pli.metal_complexes]
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