def worker(self, entry, pdbid):
import lemon
# Selection phase
metals = lemon.select_metal_ions(entry)
# Output phase
return pdbid + lemon.count_print_residue_names(entry, metals) + '\n'
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'