def predict(self, temp=None, distance_cutoff=5.5, acc_threshold=0.05):
if temp is not None:
self.temp = temp
# Make selection dict from user option or PDB chains
selection_dict = {}
for igroup, group in enumerate(self.selection):
chains = group.split(',')
for chain in chains:
if chain in selection_dict:
errmsg = 'Selections must be disjoint sets: {0} is repeated'.format(chain)
raise ValueError(errmsg)
selection_dict[chain] = igroup
# Contacts
self.ic_network = calculate_ic(self.structure, d_cutoff=distance_cutoff, selection=selection_dict)
self.bins = analyse_contacts(self.ic_network)
# SASA
_, cmplx_sasa = execute_freesasa(self.structure, selection=selection_dict)
self.nis_a, self.nis_c, _ = analyse_nis(cmplx_sasa, acc_threshold=acc_threshold)
# Affinity Calculation
self.ba_val = IC_NIS(self.bins['CC'], self.bins['AC'], self.bins['PP'], self.bins['AP'], self.nis_a, self.nis_c)
self.kd_val = dg_to_kd(self.ba_val, self.temp)
errmsg = 'Selections must be disjoint sets: {0} is repeated'.format(
chain)
raise ValueError(errmsg)
selection_dict[chain] = igroup
else:
selection_dict = dict([(c.id, nc)
for nc, c in enumerate(structure.get_chains())])
# Contacts
ic_network = calculate_ic(structure, selection=selection_dict)
print('[+] No. of intermolecular contacts: {0}'.format(len(ic_network)))
bins = analyse_contacts(ic_network)
# SASA
_, cmplx_sasa = execute_freesasa(structure, selection=selection_dict)
# Print out features
print('[+] No. of charged-charged contacts: {0}'.format(bins['CC']))
print('[+] No. of charged-polar contacts: {0}'.format(bins['CP']))
print('[+] No. of charged-apolar contacts: {0}'.format(bins['AC']))
print('[+] No. of polar-polar contacts: {0}'.format(bins['PP']))
print('[+] No. of apolar-polar contacts: {0}'.format(bins['AP']))
print('[+] No. of apolar-apolar contacts: {0}'.format(bins['AA']))
for aa in [
'ALA', 'CYS', 'GLU', 'ASP', 'GLY', 'PHE', 'ILE', 'HIS', 'LYS',
'MET', 'LEU', 'ASN', 'GLN', 'PRO', 'SER', 'ARG', 'THR', 'TRP',
'VAL', 'TYR'
]:
print('[+] ' + aa + ': ' + str(bins[aa]))
# Make groups from user option or PDB chains
if cmd.selection:
selection_dict = {}
for igroup, group in enumerate(cmd.selection):
chains = group.split(',')
for chain in chains:
if chain in selection_dict:
errmsg = 'Selections must be disjoint sets: {0} is repeated'.format(chain)
raise ValueError(errmsg)
selection_dict[chain] = igroup
else:
selection_dict = dict([(c.id, nc) for nc, c in enumerate(structure.get_chains())])
# Complex SASA
cmplx_asa, cmplx_rsa = execute_freesasa(structure, selection=selection_dict)
_, nis_c, nis_p = analyse_nis(cmplx_rsa, acc_threshold=cmd.acc_threshold, selection=selection_dict)
# Interface atoms
free_asa = {}
for group in selection_dict:
group_asa, _ = execute_freesasa(structure, selection=group)
free_asa.update(group_asa)
interface_atoms = calculate_interface_atoms(cmplx_asa, free_asa)
# Affinity Calculation
ba_val = NIS(nis_c, nis_p, interface_atoms)
print('[+] Percentage of polar NIS residues: {0:3.2f}'.format(nis_p))
print('[+] Percentage of charged NIS residues: {0:3.2f}'.format(nis_c))
print('[+] No. of (buried) interface atoms: {0}'.format(interface_atoms))
for chain in chains:
if chain in selection_dict:
errmsg = 'Selections must be disjoint sets: {0} is repeated'.format(chain)
raise ValueError(errmsg)
selection_dict[chain] = igroup
else:
selection_dict = dict([(c.id, nc) for nc, c in enumerate(structure.get_chains())])
# Contacts
ic_network = calculate_ic(structure, d_cutoff=cmd.distance_cutoff, selection=selection_dict)
print('[+] No. of intermolecular contacts: {0}'.format(len(ic_network)))
bins = analyse_contacts(ic_network)
# SASA
_, cmplx_sasa = execute_freesasa(structure, selection=selection_dict)
nis_a, nis_c, _ = analyse_nis(cmplx_sasa, acc_threshold=cmd.acc_threshold, selection=selection_dict)
# Affinity Calculation
ba_val = IC_NIS(bins['CC'], bins['AC'], bins['PP'], bins['AP'], nis_a, nis_c)
kd_val = dg_to_kd(ba_val, cmd.temperature)
print('[+] No. of charged-charged contacts: {0}'.format(bins['CC']))
print('[+] No. of charged-polar contacts: {0}'.format(bins['CP']))
print('[+] No. of charged-apolar contacts: {0}'.format(bins['AC']))
print('[+] No. of polar-polar contacts: {0}'.format(bins['PP']))
print('[+] No. of apolar-polar contacts: {0}'.format(bins['AP']))
print('[+] No. of apolar-apolar contacts: {0}'.format(bins['AA']))
print('[+] Percentage of apolar NIS residues: {0:3.2f}'.format(nis_a))
print('[+] Percentage of charged NIS residues: {0:3.2f}'.format(nis_c))
print('[++] Predicted binding affinity (kcal.mol-1): {0:8.3f}'.format(ba_val))
print ('[++] Predicted dissociation constant (M): {0:8.3e}'.format(kd_val))
if cmd.selection:
selection_dict = {}
for igroup, group in enumerate(cmd.selection):
chains = group.split(',')
for chain in chains:
if chain in selection_dict:
errmsg = 'Selections must be disjoint sets: {0} is repeated'.format(
chain)
raise ValueError(errmsg)
selection_dict[chain] = igroup
else:
selection_dict = dict([(c.id, nc)
for nc, c in enumerate(structure.get_chains())])
# Complex SASA
cmplx_asa, cmplx_rsa = execute_freesasa(structure,
selection=selection_dict)
_, nis_c, nis_p = analyse_nis(cmplx_rsa,
acc_threshold=cmd.acc_threshold,
selection=selection_dict)
# Interface atoms
free_asa = {}
for group in selection_dict:
group_asa, _ = execute_freesasa(structure, selection=group)
free_asa.update(group_asa)
interface_atoms = calculate_interface_atoms(cmplx_asa, free_asa)
# Affinity Calculation
ba_val = NIS(nis_c, nis_p, interface_atoms)
print('[+] Percentage of polar NIS residues: {0:3.2f}'.format(nis_p))