def exercise_hybrid_36():
hybrid_36.exercise(hy36enc=pdb.hy36encode, hy36dec=pdb.hy36decode)
for width, s in [(3, "AAA"), (6, "zzzzzz")]:
try:
pdb.hy36encode(width=width, value=0)
except RuntimeError as e:
assert str(e) == "unsupported width."
else:
raise Exception_expected
try:
pdb.hy36decode(width=width, s=s)
except RuntimeError as e:
assert str(e) == "unsupported width."
else:
raise Exception_expected
ups = user_plus_sys_time()
n_ok = pdb.hy36recode_width_4_all()
ups = ups.elapsed()
print("time hy36recode_width_4_all: %.2f s" \
" (%.3f micro s per encode-decode cycle)" % (ups, 1.e6*ups/max(1,n_ok)))
assert n_ok == 999 + 10000 + 2 * 26 * 36**3
#
assert pdb.resseq_decode(s=1234) == 1234
assert pdb.resseq_decode(s="A123") == 11371
assert pdb.resseq_decode(s="1") == 1
pdb.resseq_encode(value=1) == " 1"
pdb.resseq_encode(value=11371) == "A123"
pdb.resseq_encode(value=1234) == "1234"
#
try:
pdb.resseq_decode(s="18A")
except ValueError as e:
assert str(e) == 'invalid residue sequence number: " 18A"'
else:
raise Exception_expected
def exercise_hybrid_36():
hybrid_36.exercise(hy36enc=pdb.hy36encode, hy36dec=pdb.hy36decode)
for width,s in [(3,"AAA"), (6,"zzzzzz")]:
try: pdb.hy36encode(width=width, value=0)
except RuntimeError, e:
assert str(e) == "unsupported width."
else: raise Exception_expected
try: pdb.hy36decode(width=width, s=s)
except RuntimeError, e:
assert str(e) == "unsupported width."
def exercise_hybrid_36():
hybrid_36.exercise(hy36enc=pdb.hy36encode, hy36dec=pdb.hy36decode)
for width, s in [(3, "AAA"), (6, "zzzzzz")]:
try:
pdb.hy36encode(width=width, value=0)
except RuntimeError, e:
assert str(e) == "unsupported width."
else:
raise Exception_expected
try:
pdb.hy36decode(width=width, s=s)
except RuntimeError, e:
assert str(e) == "unsupported width."
def exercise_base_256_ordinal():
o = pdb.utils_base_256_ordinal
assert o(None) == 48
assert o("") == 48
assert o("0") == 48
assert o(" 0") == 48
assert o(" 0") == 48
assert o("1") == 49
assert o("-1") == -49
assert o("123") == (49 * 256 + 50) * 256 + 51
assert o("-123") == -o("123")
#
def po(s):
result = 0
s = s.lstrip()
neg = False
if (len(s) == 0):
s = "0"
elif (s[0] == "-"):
neg = True
s = s[1:]
for c in s:
result *= 256
result += ord(c)
if (neg):
result *= -1
return result
for s in ["780 ", "999 ", "1223 ", "zzzzz"]:
assert o(s) == po(s)
assert o("-" + s) == -o(s)
#
from past.builtins import cmp
from functools import cmp_to_key
def o_cmp(a, b):
return cmp(o(a), o(b))
char4s = ["%4s" % i for i in range(-999, 9999 + 1)]
assert sorted(char4s, key=cmp_to_key(o_cmp)) == char4s
m = pdb.hy36decode(width=4, s="zzzz")
e = pdb.hy36encode
char4s = [e(width=4, value=i) for i in range(-999, m + 1, 51)]
assert sorted(char4s, key=cmp_to_key(o_cmp)) == char4s
def exercise_base_256_ordinal():
o = pdb.utils_base_256_ordinal
assert o(None) == 48
assert o("") == 48
assert o("0") == 48
assert o(" 0") == 48
assert o(" 0") == 48
assert o("1") == 49
assert o("-1") == -49
assert o("123") == (49*256+50)*256+51
assert o("-123") == -o("123")
#
def po(s):
result = 0
s = s.lstrip()
neg = False
if (len(s) == 0):
s = "0"
elif (s[0] == "-"):
neg = True
s = s[1:]
for c in s:
result *= 256
result += ord(c)
if (neg):
result *= -1
return result
for s in ["780 ", "999 ", "1223 ", "zzzzz"]:
assert o(s) == po(s)
assert o("-"+s) == -o(s)
#
def o_cmp(a, b): return cmp(o(a), o(b))
char4s = ["%4s" % i for i in xrange(-999,9999+1)]
assert sorted(char4s, o_cmp) == char4s
m = pdb.hy36decode(width=4, s="zzzz")
e = pdb.hy36encode
char4s = [e(width=4, value=i) for i in xrange(-999,m+1,51)]
assert sorted(char4s, o_cmp) == char4s
def __init__(self, pdb_hierarchy, crystal_symmetry=None,
coordinate_precision=5,
occupancy_precision=3,
b_iso_precision=5,
u_aniso_precision=5):
if crystal_symmetry is None:
crystal_symmetry = crystal.symmetry()
iotbx.cif.crystal_symmetry_as_cif_block.__init__(
self, crystal_symmetry, format="mmcif")
coord_fmt_str = "%%.%if" %coordinate_precision
occ_fmt_str = "%%.%if" %occupancy_precision
b_iso_fmt_str = "%%.%if" %b_iso_precision
u_aniso_fmt_str = "%%.%if" %u_aniso_precision
atom_site_loop = iotbx.cif.model.loop(header=(
'_atom_site.group_PDB',
'_atom_site.id',
'_atom_site.label_atom_id',
'_atom_site.label_alt_id',
'_atom_site.label_comp_id',
'_atom_site.auth_asym_id',
'_atom_site.auth_seq_id',
'_atom_site.pdbx_PDB_ins_code',
'_atom_site.Cartn_x',
'_atom_site.Cartn_y',
'_atom_site.Cartn_z',
'_atom_site.occupancy',
'_atom_site.B_iso_or_equiv',
'_atom_site.type_symbol',
'_atom_site.pdbx_formal_charge',
'_atom_site.phenix_scat_dispersion_real',
'_atom_site.phenix_scat_dispersion_imag',
'_atom_site.label_asym_id',
'_atom_site.label_entity_id',
'_atom_site.label_seq_id',
#'_atom_site.auth_comp_id',
#'_atom_site.auth_atom_id',
'_atom_site.pdbx_PDB_model_num',
))
aniso_loop = iotbx.cif.model.loop(header=(
'_atom_site_anisotrop.id',
'_atom_site_anisotrop.pdbx_auth_atom_id',
'_atom_site_anisotrop.pdbx_label_alt_id',
'_atom_site_anisotrop.pdbx_auth_comp_id',
'_atom_site_anisotrop.pdbx_auth_asym_id',
'_atom_site_anisotrop.pdbx_auth_seq_id',
'_atom_site_anisotrop.pdbx_PDB_ins_code',
'_atom_site_anisotrop.U[1][1]',
'_atom_site_anisotrop.U[2][2]',
'_atom_site_anisotrop.U[3][3]',
'_atom_site_anisotrop.U[1][2]',
'_atom_site_anisotrop.U[1][3]',
'_atom_site_anisotrop.U[2][3]'
))
# cache dictionary lookups to save time in inner loop
atom_site_group_PDB = atom_site_loop['_atom_site.group_PDB']
atom_site_id = atom_site_loop['_atom_site.id']
atom_site_label_atom_id = atom_site_loop['_atom_site.label_atom_id']
atom_site_label_alt_id = atom_site_loop['_atom_site.label_alt_id']
atom_site_label_comp_id = atom_site_loop['_atom_site.label_comp_id']
atom_site_auth_asym_id = atom_site_loop['_atom_site.auth_asym_id']
atom_site_auth_seq_id = atom_site_loop['_atom_site.auth_seq_id']
atom_site_pdbx_PDB_ins_code = atom_site_loop['_atom_site.pdbx_PDB_ins_code']
atom_site_Cartn_x = atom_site_loop['_atom_site.Cartn_x']
atom_site_Cartn_y = atom_site_loop['_atom_site.Cartn_y']
atom_site_Cartn_z = atom_site_loop['_atom_site.Cartn_z']
atom_site_occupancy = atom_site_loop['_atom_site.occupancy']
atom_site_B_iso_or_equiv = atom_site_loop['_atom_site.B_iso_or_equiv']
atom_site_type_symbol = atom_site_loop['_atom_site.type_symbol']
atom_site_pdbx_formal_charge = atom_site_loop['_atom_site.pdbx_formal_charge']
atom_site_phenix_scat_dispersion_real = \
atom_site_loop['_atom_site.phenix_scat_dispersion_real']
atom_site_phenix_scat_dispersion_imag = \
atom_site_loop['_atom_site.phenix_scat_dispersion_imag']
atom_site_label_asym_id = atom_site_loop['_atom_site.label_asym_id']
atom_site_label_entity_id = atom_site_loop['_atom_site.label_entity_id']
atom_site_label_seq_id = atom_site_loop['_atom_site.label_seq_id']
#atom_site_loop['_atom_site.auth_comp_id'].append(comp_id)
#atom_site_loop['_atom_site.auth_atom_id'].append(atom.name.strip())
atom_site_pdbx_PDB_model_num = atom_site_loop['_atom_site.pdbx_PDB_model_num']
atom_site_anisotrop_id = aniso_loop['_atom_site_anisotrop.id']
atom_site_anisotrop_pdbx_auth_atom_id = \
aniso_loop['_atom_site_anisotrop.pdbx_auth_atom_id']
atom_site_anisotrop_pdbx_label_alt_id = \
aniso_loop['_atom_site_anisotrop.pdbx_label_alt_id']
atom_site_anisotrop_pdbx_auth_comp_id = \
aniso_loop['_atom_site_anisotrop.pdbx_auth_comp_id']
atom_site_anisotrop_pdbx_auth_asym_id = \
aniso_loop['_atom_site_anisotrop.pdbx_auth_asym_id']
atom_site_anisotrop_pdbx_auth_seq_id = \
aniso_loop['_atom_site_anisotrop.pdbx_auth_seq_id']
atom_site_anisotrop_pdbx_PDB_ins_code = \
aniso_loop['_atom_site_anisotrop.pdbx_PDB_ins_code']
atom_site_anisotrop_U11 = aniso_loop['_atom_site_anisotrop.U[1][1]']
atom_site_anisotrop_U22 = aniso_loop['_atom_site_anisotrop.U[2][2]']
atom_site_anisotrop_U33 = aniso_loop['_atom_site_anisotrop.U[3][3]']
atom_site_anisotrop_U12 = aniso_loop['_atom_site_anisotrop.U[1][2]']
atom_site_anisotrop_U13 = aniso_loop['_atom_site_anisotrop.U[1][3]']
atom_site_anisotrop_U23 = aniso_loop['_atom_site_anisotrop.U[2][3]']
model_ids = flex.std_string()
unique_chain_ids = set()
auth_asym_ids = flex.std_string()
label_asym_ids = flex.std_string()
label_seq_id = 0
label_asym_id = ""
for model in pdb_hierarchy.models():
model_id = model.id
if model_id == '': model_id = '1'
for chain in model.chains():
auth_asym_id = chain.id
if auth_asym_id.strip() == '': auth_asym_id = '.'
label_asym_id = increment_label_asym_id(label_asym_id)
for residue_group in chain.residue_groups():
seq_id = residue_group.resseq.strip()
label_seq_id += 1
icode = residue_group.icode
if icode == ' ': icode = '?'
for atom_group in residue_group.atom_groups():
alt_id = atom_group.altloc
if alt_id == '': alt_id = '.'
comp_id = atom_group.resname.strip()
entity_id = '?' # XXX how do we determine this?
for atom in atom_group.atoms():
group_pdb = "ATOM"
if atom.hetero: group_pdb = "HETATM"
x, y, z = [coord_fmt_str %i for i in atom.xyz]
atom_charge = atom.charge_tidy()
if atom_charge is None:
atom_charge = "?"
else:
atom_charge = atom_charge.strip()
if atom_charge == "": atom_charge = "?"
fp, fdp = atom.fp, atom.fdp
if fp == 0 and fdp == 0:
fp = '.'
fdp = '.'
else:
fp = "%.4f" %fp
fdp = "%.4f" %fdp
atom_site_group_PDB.append(group_pdb)
atom_site_id.append(str(hy36decode(width=5, s=atom.serial)))
atom_site_label_atom_id.append(atom.name.strip())
atom_site_label_alt_id.append(alt_id)
atom_site_label_comp_id.append(comp_id)
atom_site_auth_asym_id.append(auth_asym_id)
atom_site_auth_seq_id.append(seq_id)
atom_site_pdbx_PDB_ins_code.append(icode)
atom_site_Cartn_x.append(x)
atom_site_Cartn_y.append(y)
atom_site_Cartn_z.append(z)
atom_site_occupancy.append(occ_fmt_str % atom.occ)
atom_site_B_iso_or_equiv.append(b_iso_fmt_str % atom.b)
atom_site_type_symbol.append(atom.element.strip())
atom_site_pdbx_formal_charge.append(atom_charge)
atom_site_phenix_scat_dispersion_real.append(fp)
atom_site_phenix_scat_dispersion_imag.append(fdp)
atom_site_label_asym_id.append(label_asym_id)
atom_site_label_entity_id.append(entity_id)
atom_site_label_seq_id.append(str(label_seq_id))
#atom_site_loop['_atom_site.auth_comp_id'].append(comp_id)
#atom_site_loop['_atom_site.auth_atom_id'].append(atom.name.strip())
atom_site_pdbx_PDB_model_num.append(model_id.strip())
if atom.uij_is_defined():
u11, u22, u33, u12, u13, u23 = [
u_aniso_fmt_str %i for i in atom.uij]
atom_site_anisotrop_id.append(
str(hy36decode(width=5, s=atom.serial)))
atom_site_anisotrop_pdbx_auth_atom_id.append(atom.name.strip())
atom_site_anisotrop_pdbx_label_alt_id.append(alt_id)
atom_site_anisotrop_pdbx_auth_comp_id.append(comp_id)
atom_site_anisotrop_pdbx_auth_asym_id.append(auth_asym_id)
atom_site_anisotrop_pdbx_auth_seq_id.append(seq_id)
atom_site_anisotrop_pdbx_PDB_ins_code.append(icode)
atom_site_anisotrop_U11.append(u11)
atom_site_anisotrop_U22.append(u22)
atom_site_anisotrop_U33.append(u33)
atom_site_anisotrop_U12.append(u12)
atom_site_anisotrop_U13.append(u13)
atom_site_anisotrop_U23.append(u23)
for key in ('_atom_site.phenix_scat_dispersion_real',
'_atom_site.phenix_scat_dispersion_imag'):
if atom_site_loop[key].all_eq('.'):
del atom_site_loop[key]
self.cif_block.add_loop(atom_site_loop)
if aniso_loop.size() > 0:
self.cif_block.add_loop(aniso_loop)
