def worker(self, entry, pdbid):
import lemon
smallm = lemon.select_small_molecules(entry, lemon.small_molecule_types, 10)
# Pruning phase
lemon.prune_identical_residues(entry, smallm)
lemon.prune_cofactors(entry, smallm, lemon.common_cofactors)
lemon.prune_cofactors(entry, smallm, lemon.common_fatty_acids)
# Output phase
return pdbid + lemon.count_print_residue_names(entry, smallm)
def worker(self, entry, pdbid):
import lemon
wat_name = set()
wat_name.add(lemon.ResidueName("HOH"))
hemegs = lemon.select_specific_residues(entry, wat_name)
smallm = lemon.select_small_molecules(entry,
lemon.small_molecule_types, 10)
# Pruning phase
smallm = lemon.prune_identical_residues(entry, smallm)
smallm = lemon.prune_cofactors(entry, smallm, lemon.common_cofactors)
smallm = lemon.prune_cofactors(entry, smallm, lemon.common_fatty_acids)
smallm = lemon.keep_interactions(entry, smallm, hemegs, 6.0)
# Output phase
return pdbid + lemon.count_print_residue_names(entry, smallm) + '\n'
def worker(self, entry, pdbid):
import lemon
heme_names = lemon.ResidueNameSet()
heme_names.append(lemon.ResidueName("HEM"))
heme_names.append(lemon.ResidueName("HEA"))
heme_names.append(lemon.ResidueName("HEB"))
heme_names.append(lemon.ResidueName("HEC"))
hemegs = lemon.select_specific_residues(entry, heme_names)
smallm = lemon.select_small_molecules(entry,
lemon.small_molecule_types, 10)
# Pruning phase
lemon.prune_identical_residues(entry, smallm)
lemon.prune_cofactors(entry, smallm, lemon.common_cofactors)
lemon.prune_cofactors(entry, smallm, lemon.common_fatty_acids)
lemon.keep_interactions(entry, smallm, hemegs, 6.0)
# Output phase
return pdbid + lemon.count_print_residue_names(entry, smallm) + '\n'
def worker(self, entry, pdbid):
import lemon
# Selection phase
smallm = lemon.select_small_molecules(entry, lemon.small_molecule_types, 10)
if (len(smallm) == 0):
return ""
# Pruning phase
lemon.prune_identical_residues(entry, smallm)
lemon.prune_cofactors(entry, smallm, lemon.common_cofactors)
lemon.prune_cofactors(entry, smallm, lemon.common_fatty_acids)
# Output phase
prot = lemon.ResidueIDs()
residues = entry.topology().residues()
for resid in range(0, len(residues)):
prot.append(resid)
result = ""
for smallm_id in smallm:
lig_copy = lemon.ResidueIDs()
lig_copy.append(smallm_id)
# Hack to remove self
prot_copy = lemon.ResidueIDs(prot)
lemon.remove_interactions(entry, prot_copy, lig_copy, 0.001)
vscore = lemon.vina_score(entry, smallm_id, prot_copy, 8.0)
result += pdbid + "\t"
result += residues[smallm_id].name() + "\t"
result += str(vscore.g1) + "\t"
result += str(vscore.g2) + "\t"
result += str(vscore.hydrogen) + "\t"
result += str(vscore.hydrophobic) + "\t"
result += str(vscore.rep) + "\n"
return result