def run():
from libtbx.utils import format_cpu_times
from mmtbx.rotamer import rotamer_eval
from mmtbx.rotamer import ramachandran_eval
initial_current_working_directory = os.getcwd()
rotamer_data_dir = rotamer_eval.find_rotarama_data_dir(optional=True)
if rotamer_data_dir is None:
print(' Rebuilding rotarama library skipped. Needs rotamer library.')
return
target_db = rotamer_eval.open_rotarama_dlite(
rotarama_data_dir=rotamer_data_dir)
# rebuild_pickle_files(data_dir=rotamer_data_dir,
# file_prefix="rota500-",
# target_db=target_db,
# amino_acids=rotamer_eval.aminoAcids)
rebuild_pickle_files(data_dir=rotamer_data_dir,
file_prefix="rota8000-",
target_db=target_db,
amino_acids=rotamer_eval.aminoAcids)
#
ramachandran_data_dir = rotamer_eval.find_rotarama_data_dir()
target_db = rotamer_eval.open_rotarama_dlite(
rotarama_data_dir=ramachandran_data_dir)
rebuild_pickle_files(data_dir=rotamer_data_dir,
file_prefix="rama8000-",
target_db=target_db,
amino_acids=ramachandran_eval.aminoAcids_8000)
# rebuild_pickle_files(data_dir=rotamer_data_dir,
# file_prefix="rama500-",
# target_db=target_db,
# amino_acids=ramachandran_eval.aminoAcids)
os.chdir(initial_current_working_directory)
print(format_cpu_times())
def run():
initial_current_working_directory = os.getcwd()
rotamer_data_dir = rotamer_eval.find_rotarama_data_dir(optional=True)
if rotamer_data_dir is None:
print ' Rebuilding rotarama library skipped. Needs rotamer library.'
return
target_db = rotamer_eval.open_rotarama_dlite(
rotarama_data_dir=rotamer_data_dir)
# rebuild_pickle_files(data_dir=rotamer_data_dir,
# file_prefix="rota500-",
# target_db=target_db,
# amino_acids=rotamer_eval.aminoAcids)
rebuild_pickle_files(data_dir=rotamer_data_dir,
file_prefix="rota8000-",
target_db=target_db,
amino_acids=rotamer_eval.aminoAcids)
#
ramachandran_data_dir = rotamer_eval.find_rotarama_data_dir()
target_db = rotamer_eval.open_rotarama_dlite(
rotarama_data_dir=ramachandran_data_dir)
rebuild_pickle_files(data_dir=rotamer_data_dir,
file_prefix="rama8000-",
target_db=target_db,
amino_acids=ramachandran_eval.aminoAcids_8000)
# rebuild_pickle_files(data_dir=rotamer_data_dir,
# file_prefix="rama500-",
# target_db=target_db,
# amino_acids=ramachandran_eval.aminoAcids)
os.chdir(initial_current_working_directory)
print format_cpu_times()
def get_rotarama_data(residue_type=None,
pos_type=None,
db="rama",
convert_to_numpy_array=False):
from mmtbx.rotamer import ramachandran_eval
from mmtbx.rotamer.rotamer_eval import find_rotarama_data_dir
# backwards compatibility
if (pos_type == "proline"): pos_type = "trans-proline"
if (pos_type == "prepro"): pos_type = "pre-proline"
assert (pos_type in [
"general", "cis-proline", "trans-proline", "glycine",
"isoleucine or valine", "pre-proline", None
])
assert (db in ["rama", "rota"])
assert (residue_type is not None) or (pos_type is not None)
if pos_type is not None:
residue_type = ramachandran_eval.aminoAcids_8000[pos_type]
if residue_type.lower() in ["phe", "tyr"]:
residue_type = "phetyr"
assert (residue_type is not None)
rama_data_dir = find_rotarama_data_dir()
if (db == "rama"):
pkl_file = "%s8000-%s.pickle" % (db, residue_type)
else:
pkl_file = "%s8000-%s.pickle" % (db, residue_type.lower())
ndt = easy_pickle.load(os.path.join(rama_data_dir, pkl_file))
if convert_to_numpy_array:
if (db == "rama"):
return export_ramachandran_distribution(ndt)
else:
return export_rotamer_distribution(ndt)
else:
return ndt
def __init__(self):
main_aaTables = RamachandranEval.aaTables
self.aaTables = {}
for aa,ndt_weakref in main_aaTables.items():
# convert existing weak references to strong references
self.aaTables[aa] = ndt_weakref()
rama_data_dir = find_rotarama_data_dir()
target_db = open_rotarama_dlite(rotarama_data_dir=rama_data_dir)
no_update = os.path.exists(os.path.join(rama_data_dir, "NO_UPDATE"))
for aa, aafile in aminoAcids_8000.items():
if (self.aaTables.get(aa) is not None): continue
data_file = "rama8000-"+aafile+".data"
pickle_file = "rama8000-"+aafile+".pickle"
pair_info = target_db.pair_info(
source_path=data_file,
target_path=pickle_file,
path_prefix=rama_data_dir)
if (((pair_info.needs_update) and (not no_update)) or not
os.path.exists(os.path.join(rama_data_dir, pickle_file))) :
raise Sorry(
"chem_data/rotarama_data/*.pickle files are missing or out of date.\n"
" Please run\n"
" mmtbx.rebuild_rotarama_cache\n"
" to resolve this problem.\n")
ndt = easy_pickle.load(file_name=os.path.join(
rama_data_dir, pair_info.target.path))
self.aaTables[aa] = ndt
main_aaTables[aa] = weakref.ref(ndt)
def get_rotarama_data (residue_type=None, pos_type=None, db="rama",
convert_to_numpy_array=False) :
from mmtbx.rotamer import ramachandran_eval
from mmtbx.rotamer.rotamer_eval import find_rotarama_data_dir
# backwards compatibility
if (pos_type == "proline") : pos_type = "trans-proline"
if (pos_type == "prepro") : pos_type = "pre-proline"
assert (pos_type in ["general", "cis-proline", "trans-proline", "glycine",
"isoleucine or valine", "pre-proline",None])
assert (db in ["rama", "rota"])
assert (residue_type is not None) or (pos_type is not None)
if pos_type is not None :
residue_type = ramachandran_eval.aminoAcids_8000[pos_type]
if residue_type.lower() in ["phe", "tyr"] :
residue_type = "phetyr"
assert (residue_type is not None)
rama_data_dir = find_rotarama_data_dir()
if (db == "rama") :
pkl_file = "%s8000-%s.pickle" % (db, residue_type)
else :
pkl_file = "%s8000-%s.pickle" % (db, residue_type.lower())
ndt = easy_pickle.load(os.path.join(rama_data_dir, pkl_file))
if convert_to_numpy_array :
if (db == "rama") :
return export_ramachandran_distribution(ndt)
else :
return export_rotamer_distribution(ndt)
else :
return ndt
def __init__(self):
main_aaTables = RamachandranEval.aaTables
self.aaTables = {}
for aa, ndt_weakref in main_aaTables.items():
# convert existing weak references to strong references
self.aaTables[aa] = ndt_weakref()
rama_data_dir = find_rotarama_data_dir()
target_db = open_rotarama_dlite(rotarama_data_dir=rama_data_dir)
no_update = os.path.exists(os.path.join(rama_data_dir, "NO_UPDATE"))
for aa, aafile in aminoAcids_8000.items():
if (self.aaTables.get(aa) is not None): continue
data_file = "rama8000-" + aafile + ".data"
pickle_file = "rama8000-" + aafile + ".pickle"
pair_info = target_db.pair_info(source_path=data_file,
target_path=pickle_file,
path_prefix=rama_data_dir)
if (((pair_info.needs_update) and (not no_update))
or not os.path.exists(
os.path.join(rama_data_dir, pickle_file))):
raise Sorry(
"chem_data/rotarama_data/*.pickle files are missing or out of date.\n"
" Please run\n"
" mmtbx.rebuild_rotarama_cache\n"
" to resolve this problem.\n")
ndt = easy_pickle.load(
file_name=os.path.join(rama_data_dir, pair_info.target.path))
self.aaTables[aa] = ndt
main_aaTables[aa] = weakref.ref(ndt)
def exercise_rotalyze():
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/jcm.pdb", test=os.path.isfile)
if (regression_pdb is None):
print "Skipping exercise_rotalyze(): input pdb (jcm.pdb) not available"
return
if (find_rotarama_data_dir(optional=True) is None):
print "Skipping exercise_rotalyze(): rotarama_data directory not available"
return
pdb_in = file_reader.any_file(file_name=regression_pdb)
hierarchy = pdb_in.file_object.hierarchy
pdb_io = pdb.input(file_name=regression_pdb)
r = rotalyze.rotalyze(pdb_hierarchy=hierarchy, outliers_only=True)
out = StringIO()
r.show_old_output(out=out, verbose=False)
output = out.getvalue()
assert output.count("OUTLIER") == 246, output.count("OUTLIER")
assert output.count(":") == 984, output.count(":")
output_lines = output.splitlines()
assert len(output_lines) == 123
for lines in output_lines:
assert float(lines[12:15]) <= 1.0
r = rotalyze.rotalyze(pdb_hierarchy=hierarchy, outliers_only=False)
for unpickle in [False, True]:
if unpickle:
r = loads(dumps(r))
out = StringIO()
r.show_old_output(out=out, verbose=False)
for outlier in r.results:
assert (len(outlier.xyz) == 3)
output = out.getvalue()
assert output.count("OUTLIER") == 246
assert output.count(":") == 5144, output.count(":")
assert output.count("p") == 120
assert output.count("m") == 324
assert output.count("t") == 486
output_lines = output.splitlines()
#for line in output_lines:
# print line
#STOP()
assert len(output_lines) == 643
line_indices = [0, 1, 2, 42, 43, 168, 169, 450, 587, 394, 641, 642]
# top500 version
line_values = [
" A 14 MET:1.00:3.3:29.2:173.3:287.9::Favored:ptm",
" A 15 SER:1.00:0.1:229.0::::OUTLIER:OUTLIER",
" A 16 SER:1.00:4.2:277.9::::Favored:m",
" A 58 ASN:1.00:2.0:252.4:343.6:::Favored:m-20",
" A 59 ILE:1.00:2.0:84.2:186.7:::Allowed:pt",
" A 202 GLU:1.00:0.4:272.7:65.9:287.8::OUTLIER:OUTLIER",
" A 203 ILE:1.00:5.0:292.9:199.6:::Favored:mt",
" B 154 THR:1.00:0.1:356.0::::OUTLIER:OUTLIER",
" B 316 TYR:1.00:5.4:153.7:68.6:::Favored:t80",
" B 86 ASP:1.00:2.2:321.4:145.1:::Favored:m-20",
" B 377 GLU:1.00:45.3:311.7:166.2:160.1::Favored:mt-10",
" B 378 THR:1.00:23.5:309.4::::Favored:m"
]
# top8000 version
line_values = [
" A 14 MET:1.00:1.3:29.2:173.3:287.9::Allowed:ptm",
" A 15 SER:1.00:0.1:229.0::::OUTLIER:OUTLIER",
" A 16 SER:1.00:3.0:277.9::::Favored:m",
" A 58 ASN:1.00:1.0:252.4:343.6:::Allowed:m-40",
" A 59 ILE:1.00:0.5:84.2:186.7:::Allowed:pt",
" A 202 GLU:1.00:0.0:272.7:65.9:287.8::OUTLIER:OUTLIER",
" A 203 ILE:1.00:1.0:292.9:199.6:::Allowed:mt",
" B 154 THR:1.00:0.0:356.0::::OUTLIER:OUTLIER",
" B 316 TYR:1.00:4.1:153.7:68.6:::Favored:t80",
" B 86 ASP:1.00:0.4:321.4:145.1:::Allowed:m-30",
" B 377 GLU:1.00:15.0:311.7:166.2:160.1::Favored:mt-10",
" B 378 THR:1.00:17.0:309.4::::Favored:m",
]
for idx, val in zip(line_indices, line_values):
assert (output_lines[idx] == val), (idx, output_lines[idx])
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/pdb1jxt.ent", test=os.path.isfile)
if (regression_pdb is None):
print "Skipping exercise_ramalyze(): input pdb (pdb1jxt.ent) not available"
return
pdb_in = file_reader.any_file(file_name=regression_pdb)
hierarchy = pdb_in.file_object.hierarchy
pdb_io = pdb.input(file_name=regression_pdb)
r = rotalyze.rotalyze(pdb_hierarchy=hierarchy, outliers_only=True)
out = StringIO()
r.show_old_output(out=out, verbose=False)
output = out.getvalue().strip()
assert output == ""
r = rotalyze.rotalyze(pdb_hierarchy=hierarchy, outliers_only=False)
for unpickle in [False, True]:
if unpickle:
r = loads(dumps(r))
out = StringIO()
r.show_old_output(out=out, verbose=False)
output = out.getvalue()
assert not show_diff(
output, """\
A 1 THR:1.00:95.4:299.5::::Favored:m
A 2 ATHR:0.67:49.5:56.1::::Favored:p
A 2 BTHR:0.33:90.4:298.1::::Favored:m
A 3 CYS:1.00:12.9:310.5::::Favored:m
A 4 CYS:1.00:91.6:293.1::::Favored:m
A 5 PRO:1.00:78.8:30.2:319.7:33.8::Favored:Cg_endo
A 6 SER:1.00:90.1:68.4::::Favored:p
A 7 AILE:0.45:49.6:290.8:178.2:::Favored:mt
A 7 BILE:0.55:6.5:284.4:298.4:::Favored:mm
A 8 AVAL:0.50:1.1:156.7::::Allowed:t
A 8 BVAL:0.30:5.1:71.3::::Favored:p
A 8 CVAL:0.20:69.8:172.1::::Favored:t
A 10 AARG:0.65:24.7:176.8:66.5:63.9:180.0:Favored:tpp-160
A 10 BARG:0.35:17.5:176.8:72.8:66.4:171.9:Favored:tpp-160
A 11 SER:1.00:51.6:300.9::::Favored:m
A 12 AASN:0.50:93.9:286.1:343.8:::Favored:m-40
A 12 BASN:0.50:98.9:288.4:337.6:::Favored:m-40
A 13 APHE:0.65:45.1:187.2:276.4:::Favored:t80
A 13 BPHE:0.35:86.1:179.6:263.1:::Favored:t80
A 14 ASN:1.00:95.2:289.6:333.0:::Favored:m-40
A 15 VAL:1.00:42.3:168.2::::Favored:t
A 16 CYS:1.00:40.8:176.5::::Favored:t
A 17 ARG:1.00:21.4:289.7:282.8:288.6:158.7:Favored:mmm160
A 18 LEU:1.00:65.0:287.2:173.3:::Favored:mt
A 19 PRO:1.00:43.6:24.4:324.8:31.6::Favored:Cg_endo
A 21 THR:1.00:5.7:314.0::::Favored:m
A 22 APRO:0.55:87.5:333.5:34.0:333.8::Favored:Cg_exo
A 23 AGLU:0.50:86.9:290.9:187.1:341.8::Favored:mt-10
A 23 BGLU:0.50:91.7:292.0:183.8:339.2::Favored:mt-10
A 25 ALEU:0.50:95.7:294.4:173.6:::Favored:mt
A 26 CYS:1.00:83.0:295.0::::Favored:m
A 28 THR:1.00:29.6:52.9::::Favored:p
A 29 ATYR:0.65:18.5:161.8:67.8:::Favored:t80
A 29 BTYR:0.35:0.4:191.3:322.7:::Allowed:t80
A 30 ATHR:0.70:60.8:57.4::::Favored:p
A 30 BTHR:0.30:6.6:78.1::::Favored:p
A 32 CYS:1.00:61.4:301.7::::Favored:m
A 33 ILE:1.00:36.6:66.5:173.4:::Favored:pt
A 34 AILE:0.70:60.9:303.6:167.6:::Favored:mt
A 34 BILE:0.30:31.4:308.5:296.8:::Favored:mm
A 35 ILE:1.00:45.6:62.4:170.0:::Favored:pt
A 36 PRO:1.00:36.2:22.5:330.5:24.8::Favored:Cg_endo
A 39 ATHR:0.70:14.0:311.0::::Favored:m
A 39 BTHR:0.30:13.1:288.8::::Favored:m
A 40 CYS:1.00:81.4:294.4::::Favored:m
A 41 PRO:1.00:35.4:34.4:317.5:33.1::Favored:Cg_endo
A 43 AASP:0.75:24.8:56.5:340.3:::Favored:p0
A 43 BASP:0.25:43.2:59.6:349.3:::Favored:p0
A 44 TYR:1.00:85.3:290.9:85.1:::Favored:m-80
A 46 ASN:1.00:38.7:301.6:117.9:::Favored:m110
""")
def exercise_ramalyze():
from mmtbx.rotamer.rotamer_eval import find_rotarama_data_dir
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/jcm.pdb", test=os.path.isfile)
if (regression_pdb is None):
print "Skipping exercise_ramalyze(): input pdb (jcm.pdb) not available"
return
if (find_rotarama_data_dir(optional=True) is None):
print "Skipping exercise_ramalyze(): rotarama_data directory not available"
return
from iotbx import file_reader
# Exercise 1
pdb_in = file_reader.any_file(file_name=regression_pdb)
hierarchy = pdb_in.file_object.hierarchy
pdb_io = pdb.input(file_name=regression_pdb)
hierarchy.atoms().reset_i_seq()
r = ramalyze.ramalyze(pdb_hierarchy=hierarchy, outliers_only=True)
out = StringIO()
r.show_old_output(out=out)
output = out.getvalue()
assert output.count("OUTLIER") == 100
assert output.count("Favored") == 0
assert output.count("Allowed") == 0
assert output.count("General") == 64
assert output.count("Glycine") == 6
assert output.count("Trans-proline") == 1
assert output.count("Cis-proline") == 0
assert output.count("Pre-proline") == 4
assert output.count("Isoleucine or valine") == 25
assert (len(r.outlier_selection()) == 494)
outlier_ids = set([])
atoms = hierarchy.atoms()
for i_seq in r.outlier_selection():
atom = atoms[i_seq]
atom_group = atoms[i_seq].parent()
outlier_ids.add(atom_group.id_str())
outliers1 = sorted([o.atom_group_id_str() for o in r.results])
outliers2 = sorted(list(outlier_ids))
assert (outliers1 == outliers2)
r = ramalyze.ramalyze(pdb_hierarchy=hierarchy, outliers_only=False)
for unpickle in [False, True]:
if unpickle:
r = loads(dumps(r))
for outlier in r.results:
assert (len(outlier.xyz) == 3)
out = StringIO()
r.show_old_output(out=out, verbose=False)
output = out.getvalue()
assert output.count("OUTLIER") == 100
assert output.count("Favored") == 463
assert output.count("Allowed") == 162
assert output.count("General") == 514
assert output.count("Glycine") == 39
assert output.count("Trans-proline") == 23
assert output.count("Cis-proline") == 0
assert output.count("Pre-proline") == 21
assert output.count("Isoleucine or valine") == 128
numtotal = r.get_phi_psi_residues_count()
assert r.get_outliers_count_and_fraction() == (100, 100. / numtotal)
assert r.get_allowed_count_and_fraction() == (162, 162. / numtotal)
assert r.get_favored_count_and_fraction() == (463, 463. / numtotal)
assert r.get_general_count_and_fraction() == (514, 514. / numtotal)
assert r.get_gly_count_and_fraction() == (39, 39. / numtotal)
assert r.get_trans_pro_count_and_fraction() == (23, 23. / numtotal)
assert r.get_cis_pro_count_and_fraction() == (0, 0. / numtotal)
assert r.get_prepro_count_and_fraction() == (21, 21. / numtotal)
assert r.get_ileval_count_and_fraction() == (128, 128. / numtotal)
#assert numtotal == 75+154+494 #reasons for this math unclear
assert numtotal == 725
output_lines = output.splitlines()
assert len(output_lines) == 725
selected_lines = []
for x in [
0, 1, 168, 169, 715, 716, 717, 718, 719, 720, 721, 722, 723,
724
]:
selected_lines.append(output_lines[x])
assert not show_diff(
"\n".join(selected_lines), """\
A 15 SER:35.07:-83.26:131.88:Favored:General
A 16 SER:0.74:-111.53:71.36:Allowed:General
A 191 ASP:2.66:-42.39:121.87:Favored:Pre-proline
A 192 PRO:0.31:-39.12:-31.84:Allowed:Trans-proline
B 368 LYS:56.44:-62.97:-53.28:Favored:General
B 369 GLU:8.89:-44.36:-45.50:Favored:General
B 370 LYS:40.00:-50.00:-39.06:Favored:General
B 371 VAL:68.24:-60.38:-51.85:Favored:Isoleucine or valine
B 372 LEU:0.02:-61.13:-170.23:OUTLIER:General
B 373 ARG:0.02:60.09:-80.26:OUTLIER:General
B 374 ALA:0.13:-37.21:-36.12:Allowed:General
B 375 LEU:11.84:-89.81:-41.45:Favored:General
B 376 ASN:84.33:-58.30:-41.39:Favored:General
B 377 GLU:30.88:-56.79:-21.74:Favored:General""")
assert (len(r.outlier_selection()) == 494)
# Exercise 2
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/pdb1jxt.ent", test=os.path.isfile)
pdb_in = file_reader.any_file(file_name=regression_pdb)
hierarchy = pdb_in.file_object.hierarchy
hierarchy.atoms().reset_i_seq()
r = ramalyze.ramalyze(pdb_hierarchy=hierarchy, outliers_only=True)
out = StringIO()
r.show_old_output(out=out)
output = out.getvalue()
assert output.count("Favored") == 0
assert output.count("Allowed") == 0
assert output.count("OUTLIER") == 0
r = ramalyze.ramalyze(pdb_hierarchy=hierarchy, outliers_only=False)
for unpickle in [False, True]:
if unpickle:
r = loads(dumps(r))
out = StringIO()
r.show_old_output(out=out, verbose=False)
output = out.getvalue()
assert output.count("Favored") == 50
assert output.count("Allowed") == 1
assert output.count("OUTLIER") == 0
assert output.count("General") == 29
assert output.count("Glycine") == 4
assert output.count("Trans-proline") == 5
assert output.count("Cis-proline") == 0
assert output.count("Pre-proline") == 5
assert output.count("Isoleucine or valine") == 8
numtotal = r.get_phi_psi_residues_count()
assert r.get_outliers_count_and_fraction() == (0, 0. / numtotal)
assert r.get_allowed_count_and_fraction() == (1, 1. / numtotal)
assert r.get_favored_count_and_fraction() == (43, 43. / numtotal)
#print r.get_general_count_and_fraction()
assert r.get_general_count_and_fraction() == (25, 25. / numtotal)
assert r.get_gly_count_and_fraction() == (4, 4. / numtotal)
assert r.get_trans_pro_count_and_fraction() == (5, 5. / numtotal)
assert r.get_cis_pro_count_and_fraction() == (0, 0. / numtotal)
assert r.get_prepro_count_and_fraction() == (5, 5. / numtotal)
assert r.get_ileval_count_and_fraction() == (5, 5. / numtotal)
output_lines = output.splitlines()
assert len(output_lines) == 51
selected_lines = []
for x in [0, 1, 5, 6, 7, 8, 9, 47, 48, 49, 50]:
selected_lines.append(output_lines[x])
assert not show_diff(
"\n".join(selected_lines), """\
A 2 ATHR:33.85:-106.92:144.23:Favored:General
A 3 ACYS:47.07:-132.54:137.26:Favored:General
A 7 AILE:98.76:-61.91:-44.35:Favored:Isoleucine or valine
A 7 BILE:61.50:-56.21:-51.56:Favored:Isoleucine or valine
A 8 AVAL:23.11:-50.35:-49.64:Favored:Isoleucine or valine
A 8 BVAL:12.01:-83.20:-12.14:Favored:Isoleucine or valine
A 8 CVAL:73.11:-61.22:-36.49:Favored:Isoleucine or valine
A 43 AASP:51.81:-94.64:5.45:Favored:General
A 43 BASP:56.98:-88.69:-0.12:Favored:General
A 44 TYR:1.76:-133.10:58.75:Allowed:General
A 45 ALA:57.37:-86.61:-8.57:Favored:General""")
# Exercise 3: 2plx excerpt (unusual icode usage)
import iotbx.pdb.hierarchy
pdb_io = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1468 N GLY A 219 3.721 21.322 10.752 1.00 14.12 N
ATOM 1469 CA GLY A 219 3.586 21.486 12.188 1.00 14.85 C
ATOM 1470 C GLY A 219 4.462 20.538 12.995 1.00 15.63 C
ATOM 1471 O GLY A 219 5.513 20.090 12.512 1.00 14.55 O
ATOM 1472 N CYS A 220 4.036 20.213 14.235 1.00 15.02 N
ATOM 1473 CA CYS A 220 4.776 19.228 15.068 1.00 15.56 C
ATOM 1474 C CYS A 220 3.773 18.322 15.741 1.00 14.69 C
ATOM 1475 O CYS A 220 2.799 18.828 16.338 1.00 15.54 O
ATOM 1476 CB CYS A 220 5.620 19.906 16.174 1.00 15.72 C
ATOM 1477 SG CYS A 220 6.762 21.133 15.448 1.00 15.45 S
ATOM 1478 N ALA A 221A 4.054 17.017 15.707 1.00 14.77 N
ATOM 1479 CA ALA A 221A 3.274 16.015 16.507 1.00 14.01 C
ATOM 1480 C ALA A 221A 1.774 15.992 16.099 1.00 14.50 C
ATOM 1481 O ALA A 221A 0.875 15.575 16.881 1.00 14.46 O
ATOM 1482 CB ALA A 221A 3.440 16.318 17.935 1.00 12.28 C
ATOM 1483 N GLN A 221 1.523 16.390 14.848 1.00 14.52 N
ATOM 1484 CA GLN A 221 0.159 16.391 14.325 1.00 15.19 C
ATOM 1485 C GLN A 221 -0.229 15.044 13.717 1.00 14.43 C
ATOM 1486 O GLN A 221 0.641 14.280 13.307 1.00 16.88 O
ATOM 1487 CB GLN A 221 0.002 17.491 13.272 1.00 16.41 C
ATOM 1488 CG GLN A 221 0.253 18.906 13.805 1.00 16.52 C
ATOM 1489 CD GLN A 221 -0.640 19.181 14.995 1.00 17.87 C
ATOM 1490 OE1 GLN A 221 -1.857 19.399 14.826 1.00 13.54 O
ATOM 1491 NE2 GLN A 221 -0.050 19.149 16.228 1.00 16.18 N
ATOM 1492 N LYS A 222 -1.537 14.773 13.694 1.00 14.34 N
ATOM 1493 CA LYS A 222 -2.053 13.536 13.125 1.00 15.07 C
ATOM 1494 C LYS A 222 -1.679 13.455 11.655 1.00 14.88 C
ATOM 1495 O LYS A 222 -1.856 14.424 10.883 1.00 14.32 O
""")
r = ramalyze.ramalyze(pdb_hierarchy=pdb_io.hierarchy, outliers_only=False)
assert (len(r.results) == 3)
def exercise_ramalyze():
from mmtbx.rotamer.rotamer_eval import find_rotarama_data_dir
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/jcm.pdb",
test=os.path.isfile)
if (regression_pdb is None):
print "Skipping exercise_ramalyze(): input pdb (jcm.pdb) not available"
return
if (find_rotarama_data_dir(optional=True) is None):
print "Skipping exercise_ramalyze(): rotarama_data directory not available"
return
from iotbx import file_reader
# Exercise 1
pdb_in = file_reader.any_file(file_name=regression_pdb)
hierarchy = pdb_in.file_object.hierarchy
pdb_io = pdb.input(file_name=regression_pdb)
hierarchy.atoms().reset_i_seq()
r = ramalyze.ramalyze(
pdb_hierarchy=hierarchy,
outliers_only=True)
out = StringIO()
r.show_old_output(out=out)
output = out.getvalue()
assert output.count("OUTLIER") == 100
assert output.count("Favored") == 0
assert output.count("Allowed") == 0
assert output.count("General") == 64
assert output.count("Glycine") == 6
assert output.count("Trans-proline") == 1
assert output.count("Cis-proline") == 0
assert output.count("Pre-proline") == 4
assert output.count("Isoleucine or valine") == 25
assert (len(r.outlier_selection()) == 788)
outlier_ids = set([])
atoms = hierarchy.atoms()
for i_seq in r.outlier_selection() :
atom = atoms[i_seq]
atom_group = atoms[i_seq].parent()
outlier_ids.add(atom_group.id_str())
outliers1 = sorted([ o.atom_group_id_str() for o in r.results ])
outliers2 = sorted(list(outlier_ids))
assert (outliers1 == outliers2)
r = ramalyze.ramalyze(
pdb_hierarchy=hierarchy,
outliers_only=False)
for unpickle in [False, True] :
if unpickle :
r = loads(dumps(r))
for outlier in r.results :
assert (len(outlier.xyz) == 3)
out = StringIO()
r.show_old_output(out=out, verbose=False)
output = out.getvalue()
assert output.count("OUTLIER") == 100
assert output.count("Favored") == 461
assert output.count("Allowed") == 162
assert output.count("General") == 513
assert output.count("Glycine") == 39
assert output.count("Trans-proline") == 23
assert output.count("Cis-proline") == 0
assert output.count("Pre-proline") == 21
assert output.count("Isoleucine or valine") == 127
numtotal = r.get_phi_psi_residues_count()
assert r.get_outliers_count_and_fraction() == (100, 100./numtotal)
assert r.get_allowed_count_and_fraction() == (162, 162./numtotal)
assert r.get_favored_count_and_fraction() == (461, 461./numtotal)
assert r.get_general_count_and_fraction() == (513, 513./numtotal)
assert r.get_gly_count_and_fraction() == (39, 39./numtotal)
assert r.get_trans_pro_count_and_fraction() == (23, 23./numtotal)
assert r.get_cis_pro_count_and_fraction() == (0, 0./numtotal)
assert r.get_prepro_count_and_fraction() == (21, 21./numtotal)
assert r.get_ileval_count_and_fraction() == (127, 127./numtotal)
assert numtotal == 75+154+494
output_lines = output.splitlines()
assert len(output_lines) == 723
selected_lines = []
for x in [0, 1, 168, 169, 713, 714, 715, 716, 717, 718, 719, 720, 721, 722]:
selected_lines.append(output_lines[x])
assert not show_diff("\n".join(selected_lines), """\
A 15 SER:35.07:-83.26:131.88:Favored:General
A 16 SER:0.74:-111.53:71.36:Allowed:General
A 191 ASP:2.66:-42.39:121.87:Favored:Pre-proline
A 192 PRO:0.31:-39.12:-31.84:Allowed:Trans-proline
B 368 LYS:56.44:-62.97:-53.28:Favored:General
B 369 GLU:8.89:-44.36:-45.50:Favored:General
B 370 LYS:40.00:-50.00:-39.06:Favored:General
B 371 VAL:68.24:-60.38:-51.85:Favored:Isoleucine or valine
B 372 LEU:0.02:-61.13:-170.23:OUTLIER:General
B 373 ARG:0.02:60.09:-80.26:OUTLIER:General
B 374 ALA:0.13:-37.21:-36.12:Allowed:General
B 375 LEU:11.84:-89.81:-41.45:Favored:General
B 376 ASN:84.33:-58.30:-41.39:Favored:General
B 377 GLU:30.88:-56.79:-21.74:Favored:General""")
assert (len(r.outlier_selection()) == 788)
# Exercise 2
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/pdb1jxt.ent",
test=os.path.isfile)
pdb_in = file_reader.any_file(file_name=regression_pdb)
hierarchy = pdb_in.file_object.hierarchy
hierarchy.atoms().reset_i_seq()
r = ramalyze.ramalyze(
pdb_hierarchy=hierarchy,
outliers_only=True)
out = StringIO()
r.show_old_output(out=out)
output = out.getvalue()
assert output.count("Favored") == 0
assert output.count("Allowed") == 0
assert output.count("OUTLIER") == 0
r = ramalyze.ramalyze(
pdb_hierarchy=hierarchy,
outliers_only=False)
for unpickle in [False, True] :
if unpickle :
r = loads(dumps(r))
out = StringIO()
r.show_old_output(out=out, verbose=False)
output = out.getvalue()
assert output.count("Favored") == 47
assert output.count("Allowed") == 1
assert output.count("OUTLIER") == 0
assert output.count("General") == 27
assert output.count("Glycine") == 4
assert output.count("Trans-proline") == 4
assert output.count("Cis-proline") == 0
assert output.count("Pre-proline") == 5
assert output.count("Isoleucine or valine") == 8
numtotal = r.get_phi_psi_residues_count()
assert r.get_outliers_count_and_fraction() == (0, 0./numtotal)
assert r.get_allowed_count_and_fraction() == (1, 1./numtotal)
assert r.get_favored_count_and_fraction() == (47, 47./numtotal)
assert r.get_general_count_and_fraction() == (27, 27./numtotal)
assert r.get_gly_count_and_fraction() == (4, 4./numtotal)
assert r.get_trans_pro_count_and_fraction() == (4, 4./numtotal)
assert r.get_cis_pro_count_and_fraction() == (0, 0./numtotal)
assert r.get_prepro_count_and_fraction() == (5, 5./numtotal)
assert r.get_ileval_count_and_fraction() == (8, 8./numtotal)
output_lines = output.splitlines()
assert len(output_lines) == 48
selected_lines = []
for x in [0, 1, 6, 7, 8, 9, 10, 44, 45, 46, 47]:
selected_lines.append(output_lines[x])
assert not show_diff("\n".join(selected_lines), """\
A 2 ATHR:33.85:-106.92:144.23:Favored:General
A 2 BTHR:37.07:-97.44:137.00:Favored:General
A 7 AILE:98.76:-61.91:-44.35:Favored:Isoleucine or valine
A 7 BILE:61.50:-56.21:-51.56:Favored:Isoleucine or valine
A 8 AVAL:23.11:-50.35:-49.64:Favored:Isoleucine or valine
A 8 BVAL:12.01:-83.20:-12.14:Favored:Isoleucine or valine
A 8 CVAL:73.11:-61.22:-36.49:Favored:Isoleucine or valine
A 43 AASP:51.81:-94.64:5.45:Favored:General
A 43 BASP:56.98:-88.69:-0.12:Favored:General
A 44 TYR:1.76:-133.10:58.75:Allowed:General
A 45 ALA:57.37:-86.61:-8.57:Favored:General""")
# Exercise 3: 2plx excerpt (unusual icode usage)
import iotbx.pdb.hierarchy
pdb_io = iotbx.pdb.hierarchy.input(pdb_string="""\
ATOM 1468 N GLY A 219 3.721 21.322 10.752 1.00 14.12 N
ATOM 1469 CA GLY A 219 3.586 21.486 12.188 1.00 14.85 C
ATOM 1470 C GLY A 219 4.462 20.538 12.995 1.00 15.63 C
ATOM 1471 O GLY A 219 5.513 20.090 12.512 1.00 14.55 O
ATOM 1472 N CYS A 220 4.036 20.213 14.235 1.00 15.02 N
ATOM 1473 CA CYS A 220 4.776 19.228 15.068 1.00 15.56 C
ATOM 1474 C CYS A 220 3.773 18.322 15.741 1.00 14.69 C
ATOM 1475 O CYS A 220 2.799 18.828 16.338 1.00 15.54 O
ATOM 1476 CB CYS A 220 5.620 19.906 16.174 1.00 15.72 C
ATOM 1477 SG CYS A 220 6.762 21.133 15.448 1.00 15.45 S
ATOM 1478 N ALA A 221A 4.054 17.017 15.707 1.00 14.77 N
ATOM 1479 CA ALA A 221A 3.274 16.015 16.507 1.00 14.01 C
ATOM 1480 C ALA A 221A 1.774 15.992 16.099 1.00 14.50 C
ATOM 1481 O ALA A 221A 0.875 15.575 16.881 1.00 14.46 O
ATOM 1482 CB ALA A 221A 3.440 16.318 17.935 1.00 12.28 C
ATOM 1483 N GLN A 221 1.523 16.390 14.848 1.00 14.52 N
ATOM 1484 CA GLN A 221 0.159 16.391 14.325 1.00 15.19 C
ATOM 1485 C GLN A 221 -0.229 15.044 13.717 1.00 14.43 C
ATOM 1486 O GLN A 221 0.641 14.280 13.307 1.00 16.88 O
ATOM 1487 CB GLN A 221 0.002 17.491 13.272 1.00 16.41 C
ATOM 1488 CG GLN A 221 0.253 18.906 13.805 1.00 16.52 C
ATOM 1489 CD GLN A 221 -0.640 19.181 14.995 1.00 17.87 C
ATOM 1490 OE1 GLN A 221 -1.857 19.399 14.826 1.00 13.54 O
ATOM 1491 NE2 GLN A 221 -0.050 19.149 16.228 1.00 16.18 N
ATOM 1492 N LYS A 222 -1.537 14.773 13.694 1.00 14.34 N
ATOM 1493 CA LYS A 222 -2.053 13.536 13.125 1.00 15.07 C
ATOM 1494 C LYS A 222 -1.679 13.455 11.655 1.00 14.88 C
ATOM 1495 O LYS A 222 -1.856 14.424 10.883 1.00 14.32 O
""")
r = ramalyze.ramalyze(
pdb_hierarchy=pdb_io.hierarchy,
outliers_only=False)
assert (len(r.results) == 3)
def exercise_rotalyze():
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/jcm.pdb",
test=os.path.isfile)
if (regression_pdb is None):
print "Skipping exercise_rotalyze(): input pdb (jcm.pdb) not available"
return
if (find_rotarama_data_dir(optional=True) is None):
print "Skipping exercise_rotalyze(): rotarama_data directory not available"
return
pdb_in = file_reader.any_file(file_name=regression_pdb)
hierarchy = pdb_in.file_object.hierarchy
pdb_io = pdb.input(file_name=regression_pdb)
r = rotalyze.rotalyze(
pdb_hierarchy=hierarchy,
outliers_only=True)
out = StringIO()
r.show_old_output(out=out, verbose=False)
output = out.getvalue()
assert output.count("OUTLIER") == 246, output.count("OUTLIER")
assert output.count(":") == 984, output.count(":")
output_lines = output.splitlines()
assert len(output_lines) == 123
for lines in output_lines:
assert float(lines[12:15]) <= 1.0
r = rotalyze.rotalyze(
pdb_hierarchy=hierarchy,
outliers_only=False)
for unpickle in [False, True] :
if unpickle :
r = loads(dumps(r))
out = StringIO()
r.show_old_output(out=out, verbose=False)
for outlier in r.results :
assert (len(outlier.xyz) == 3)
output = out.getvalue()
assert output.count("OUTLIER") == 246
assert output.count(":") == 5144, output.count(":")
assert output.count("p") == 120
assert output.count("m") == 324
assert output.count("t") == 486
output_lines = output.splitlines()
#for line in output_lines:
# print line
#STOP()
assert len(output_lines) == 643
line_indices = [0,1,2,42,43,168,169,450,587,394,641,642]
# top500 version
line_values = [
" A 14 MET:1.00:3.3:29.2:173.3:287.9::Favored:ptm",
" A 15 SER:1.00:0.1:229.0::::OUTLIER:OUTLIER",
" A 16 SER:1.00:4.2:277.9::::Favored:m",
" A 58 ASN:1.00:2.0:252.4:343.6:::Favored:m-20",
" A 59 ILE:1.00:2.0:84.2:186.7:::Allowed:pt",
" A 202 GLU:1.00:0.4:272.7:65.9:287.8::OUTLIER:OUTLIER",
" A 203 ILE:1.00:5.0:292.9:199.6:::Favored:mt",
" B 154 THR:1.00:0.1:356.0::::OUTLIER:OUTLIER",
" B 316 TYR:1.00:5.4:153.7:68.6:::Favored:t80",
" B 86 ASP:1.00:2.2:321.4:145.1:::Favored:m-20",
" B 377 GLU:1.00:45.3:311.7:166.2:160.1::Favored:mt-10",
" B 378 THR:1.00:23.5:309.4::::Favored:m"]
# top8000 version
line_values = [
" A 14 MET:1.00:1.3:29.2:173.3:287.9::Allowed:ptm",
" A 15 SER:1.00:0.1:229.0::::OUTLIER:OUTLIER",
" A 16 SER:1.00:3.0:277.9::::Favored:m",
" A 58 ASN:1.00:1.0:252.4:343.6:::Allowed:m-40",
" A 59 ILE:1.00:0.5:84.2:186.7:::Allowed:pt",
" A 202 GLU:1.00:0.0:272.7:65.9:287.8::OUTLIER:OUTLIER",
" A 203 ILE:1.00:1.0:292.9:199.6:::Allowed:mt",
" B 154 THR:1.00:0.0:356.0::::OUTLIER:OUTLIER",
" B 316 TYR:1.00:4.1:153.7:68.6:::Favored:t80",
" B 86 ASP:1.00:0.4:321.4:145.1:::Allowed:m-30",
" B 377 GLU:1.00:15.0:311.7:166.2:160.1::Favored:mt-10",
" B 378 THR:1.00:17.0:309.4::::Favored:m",
]
for idx, val in zip(line_indices, line_values) :
assert (output_lines[idx] == val), (idx, output_lines[idx])
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/pdb1jxt.ent",
test=os.path.isfile)
if (regression_pdb is None):
print "Skipping exercise_ramalyze(): input pdb (pdb1jxt.ent) not available"
return
pdb_in = file_reader.any_file(file_name=regression_pdb)
hierarchy = pdb_in.file_object.hierarchy
pdb_io = pdb.input(file_name=regression_pdb)
r = rotalyze.rotalyze(
pdb_hierarchy=hierarchy,
outliers_only=True)
out = StringIO()
r.show_old_output(out=out, verbose=False)
output = out.getvalue().strip()
assert output == ""
r = rotalyze.rotalyze(
pdb_hierarchy=hierarchy,
outliers_only=False)
for unpickle in [False, True] :
if unpickle :
r = loads(dumps(r))
out = StringIO()
r.show_old_output(out=out, verbose=False)
output = out.getvalue()
assert not show_diff(output,"""\
A 1 THR:1.00:95.4:299.5::::Favored:m
A 2 ATHR:0.67:49.5:56.1::::Favored:p
A 2 BTHR:0.33:90.4:298.1::::Favored:m
A 3 CYS:1.00:12.9:310.5::::Favored:m
A 4 CYS:1.00:91.6:293.1::::Favored:m
A 5 PRO:1.00:78.8:30.2:319.7:33.8::Favored:Cg_endo
A 6 SER:1.00:90.1:68.4::::Favored:p
A 7 AILE:0.45:49.6:290.8:178.2:::Favored:mt
A 7 BILE:0.55:6.5:284.4:298.4:::Favored:mm
A 8 AVAL:0.50:1.1:156.7::::Allowed:t
A 8 BVAL:0.30:5.1:71.3::::Favored:p
A 8 CVAL:0.20:69.8:172.1::::Favored:t
A 10 AARG:0.65:24.7:176.8:66.5:63.9:180.0:Favored:tpp-160
A 10 BARG:0.35:17.5:176.8:72.8:66.4:171.9:Favored:tpp-160
A 11 SER:1.00:51.6:300.9::::Favored:m
A 12 AASN:0.50:93.9:286.1:343.8:::Favored:m-40
A 12 BASN:0.50:98.9:288.4:337.6:::Favored:m-40
A 13 APHE:0.65:45.1:187.2:276.4:::Favored:t80
A 13 BPHE:0.35:86.1:179.6:263.1:::Favored:t80
A 14 ASN:1.00:95.2:289.6:333.0:::Favored:m-40
A 15 VAL:1.00:42.3:168.2::::Favored:t
A 16 CYS:1.00:40.8:176.5::::Favored:t
A 17 ARG:1.00:21.4:289.7:282.8:288.6:158.7:Favored:mmm160
A 18 LEU:1.00:65.0:287.2:173.3:::Favored:mt
A 19 PRO:1.00:43.6:24.4:324.8:31.6::Favored:Cg_endo
A 21 THR:1.00:5.7:314.0::::Favored:m
A 22 APRO:0.55:87.5:333.5:34.0:333.8::Favored:Cg_exo
A 23 AGLU:0.50:86.9:290.9:187.1:341.8::Favored:mt-10
A 23 BGLU:0.50:91.7:292.0:183.8:339.2::Favored:mt-10
A 25 ALEU:0.50:95.7:294.4:173.6:::Favored:mt
A 26 CYS:1.00:83.0:295.0::::Favored:m
A 28 THR:1.00:29.6:52.9::::Favored:p
A 29 ATYR:0.65:18.5:161.8:67.8:::Favored:t80
A 29 BTYR:0.35:0.4:191.3:322.7:::Allowed:t80
A 30 ATHR:0.70:60.8:57.4::::Favored:p
A 30 BTHR:0.30:6.6:78.1::::Favored:p
A 32 CYS:1.00:61.4:301.7::::Favored:m
A 33 ILE:1.00:36.6:66.5:173.4:::Favored:pt
A 34 AILE:0.70:60.9:303.6:167.6:::Favored:mt
A 34 BILE:0.30:31.4:308.5:296.8:::Favored:mm
A 35 ILE:1.00:45.6:62.4:170.0:::Favored:pt
A 36 PRO:1.00:36.2:22.5:330.5:24.8::Favored:Cg_endo
A 39 ATHR:0.70:14.0:311.0::::Favored:m
A 39 BTHR:0.30:13.1:288.8::::Favored:m
A 40 CYS:1.00:81.4:294.4::::Favored:m
A 41 PRO:1.00:35.4:34.4:317.5:33.1::Favored:Cg_endo
A 43 AASP:0.75:24.8:56.5:340.3:::Favored:p0
A 43 BASP:0.25:43.2:59.6:349.3:::Favored:p0
A 44 TYR:1.00:85.3:290.9:85.1:::Favored:m-80
A 46 ASN:1.00:38.7:301.6:117.9:::Favored:m110
""")
