def calculate_single(pdb_id, cid, seq_marker):
seq_marker = int(seq_marker)
pdb_data = pdb_interface.get_info_for(pdb_id)
if pdb_data is None:
raise Exception(f"PDB file download fail for {pdb_id}.")
ATOM, HETATM, hb = pdb_data
try:
dsr_snos = _get_sno_range(ATOM, cid, seq_marker)
if dsr_snos is None or len(dsr_snos) != 30 or dsr_snos[0] != seq_marker:
msg = f"ATOM lines not found in range({seq_marker}, "
f"{seq_marker + 30}) for {pdb_id}:{cid}.<br>"
raise Exception(msg)
res, C, CA, N = _from_considered_elements_single(ATOM, dsr_snos, cid)
pept_bonds = _get_pept_bonds(CA, dsr_snos)
# For filling descr df
res_CA = _get_res_CA(res, CA, dsr_snos)
angles, CA = dihedrals.get_descr_dihedrals(C, CA, N, dsr_snos)
hbond_descr = hbonds.get_descr_hb(hb, ATOM, HETATM, dsr_snos)
heavy_atom_contacts, hetatom_contacts, hetatom_covalent = \
contacts.get_contacts(ATOM, HETATM, cid, dsr_snos)
descr = _assemble_descr(hetatom_contacts, hetatom_covalent,
heavy_atom_contacts, angles, hbond_descr,
res_CA, pept_bonds)
full_descr = _add_columns(descr, pdb_id, seq_marker, cid)
except Exception as e:
msg = f"Exception caught in descriptor calculation. Traceback: " \
f"<{traceback.format_exc()}>. Error: <{e}>"
raise Exception(msg)
return full_descr
def calculate(motif_pos_map):
descrs = pd.DataFrame()
print(f"Total length: {len(motif_pos_map)}.")
print(len(motif_pos_map))
for i, (pdb_id, motif_cid_map) in enumerate(motif_pos_map.items()):
if not (i % 10):
print(i)
print(f"{len(motif_pos_map) - i}: {pdb_id}")
motif_pos_s = motif_cid_map['sno_markers']
cids = motif_cid_map['cid']
pdb_data = pdb_interface.get_info_for(pdb_id)
if pdb_data is None:
continue
ATOM, HETATM, hb = pdb_data
if not isinstance(motif_pos_s, list):
motif_pos_s = [motif_pos_s]
cids = [cids]
for motif_pos, cid in zip(motif_pos_s, cids):
try:
dsr_snos = _get_sno_range(ATOM, cid, motif_pos)
if dsr_snos is None:
continue
res, C, CA, N = _from_considered_elements(ATOM, dsr_snos, cid)
pept_bonds = _get_pept_bonds(CA, dsr_snos)
# For filling descr df
res_CA = _get_res_CA(res, CA, dsr_snos)
angles, CA = dihedrals.get_descr_dihedrals(C, CA, N, dsr_snos)
hbond_descr = hbonds.get_descr_hb(hb, ATOM, HETATM, dsr_snos)
heavy_atom_contacts, hetatom_contacts, hetatom_covalent = \
contacts.get_contacts(ATOM, HETATM, cid, dsr_snos)
descr = _assemble_descr(hetatom_contacts, hetatom_covalent,
heavy_atom_contacts, angles, hbond_descr,
res_CA, pept_bonds)
full_descr = _add_columns(descr, pdb_id, motif_pos, cid)
descrs = descrs.append(full_descr, ignore_index=True)
except Exception as e:
print(e)
print(f"Calc_descr failed for {pdb_id}:{cid}")
pdb_suffix = pdb_id.lower().strip()
if pdb_suffix+".pkl" in paths.PDB_PARSED_SET:
os.remove(os.path.join(paths.PDB_PARSED,
pdb_suffix + ".pkl"))
# raise
continue
return descrs
def calculate(motif_pos_map):
descrs = pd.DataFrame()
i = 0
for pdb_id, motif_cid_map in motif_pos_map.items():
i += 1
# if pdb_id != "2xsx":
# continue
motif_pos = motif_cid_map['sno_markers']
cid = motif_cid_map['cid']
pdb_data = pdb_interface.get_info_for(pdb_id)
if pdb_data is None:
continue
ATOM, HETATM, hb = pdb_data
try:
motif_pos = motif_pos[0]
dsr_snos = _get_sno_range(ATOM, cid, motif_pos)
if dsr_snos is None:
continue
res, C, CA, N = _from_considered_elements(ATOM, dsr_snos, cid)
pept_bonds = _get_pept_bonds(CA, dsr_snos)
# For filling descr df
res_CA = _get_res_CA(res, CA, dsr_snos)
angles, CA = dihedrals.get_descr_dihedrals(C, CA, N, dsr_snos)
hbond_descr = hbonds.get_descr_hb(hb, ATOM, HETATM, dsr_snos)
heavy_atom_contacts, hetatom_contacts, hetatom_covalent = \
contacts.get_contacts(ATOM, HETATM, cid, dsr_snos)
descr = _assemble_descr(hetatom_contacts, hetatom_covalent,
heavy_atom_contacts, angles, hbond_descr,
res_CA, pept_bonds)
full_descr = _add_columns(descr, pdb_id, motif_pos, cid)
descrs = descrs.append(full_descr, ignore_index=True)
except:
print(f"Calc_descr failed for {pdb_id}:{cid}")
raise
continue
return descrs