def tst_01():
print "Comparing mixed model with target..."
import iotbx.pdb
from cctbx.array_family import flex
model_pdb_inp=iotbx.pdb.input(source_info='model',
lines=flex.split_lines(model))
crystal_symmetry=model_pdb_inp.crystal_symmetry()
model_hierarchy=model_pdb_inp.construct_hierarchy()
query_hierarchy=iotbx.pdb.input(source_info='query',
lines=flex.split_lines(query)).construct_hierarchy()
f=StringIO()
r=run(crystal_symmetry=crystal_symmetry,
chain_hierarchy=query_hierarchy,target_hierarchy=model_hierarchy,out=f)
expected_text="""
Residues matching in forward direction: 16 RMSD: 1.45
Residues matching in reverse direction: 31 RMSD: 1.40
Residues near but not matching one-to-one: 12 RMSD: 1.87
Residues far from target: 2 RMSD: 2.04
"""
found_text="\n".join(f.getvalue().splitlines()[-4:])
if remove_blank(found_text)!=remove_blank(expected_text):
print "Expected: \n%s \nFound: \n%s" %(expected_text,found_text)
raise AssertionError, "FAILED"
print "OK"
def tst_02():
print("Comparing mixed model with target with 2 chains...")
import iotbx.pdb
from cctbx.array_family import flex
model_pdb_inp = iotbx.pdb.input(source_info='model',
lines=flex.split_lines(model1))
crystal_symmetry = model_pdb_inp.crystal_symmetry()
model_hierarchy = model_pdb_inp.construct_hierarchy()
query_hierarchy = iotbx.pdb.input(
source_info='query',
lines=flex.split_lines(query)).construct_hierarchy()
f = StringIO()
r = run(crystal_symmetry=crystal_symmetry,
chain_hierarchy=query_hierarchy,
target_hierarchy=model_hierarchy,
out=f)
expected_text = """
SEQ SCORE is fraction (close and matching target sequence).
MEAN LENGTH is the mean length of contiguous segments in the match with target sequence. (Each gap/reverse of direction starts new segment).
----ALL RESIDUES--- CLOSE RESIDUES ONLY %
MODEL --CLOSE- --FAR-- FORWARD REVERSE MIXED FOUND CA SEQ
RMSD N N N N N SCORE SEQ MATCH(%) SCORE MEAN LENGTH
Unique_target 1.55 54 7 14 29 11 39.7 0.26 9.3 0.04 6.0"""
found_text = "\n".join(f.getvalue().splitlines()[-10:])
if remove_blank(found_text) != remove_blank(expected_text):
print("\n\nExpected: \n%s \n\nFound: \n%s" %
(expected_text, found_text))
raise AssertionError("FAILED")
from libtbx.test_utils import approx_equal
print(r.get_values("forward"))
assert approx_equal(r.get_values("forward"), (1.6751069901864204, 14))
print(r.get_values("reverse"))
assert approx_equal(r.get_values("reverse"), (1.388466550576198, 29))
print(r.get_values("close"))
assert approx_equal(r.get_values("close"), (1.545835235099158, 54))
print(r.get_values("all_far"))
assert approx_equal(r.get_values("all_far"), (0, 0))
print("OK")
def tst_03():
print("Comparing mixed model with target with 2 chains...as group")
import iotbx.pdb
from cctbx.array_family import flex
model_pdb_inp = iotbx.pdb.input(source_info='model',
lines=flex.split_lines(model1))
crystal_symmetry = model_pdb_inp.crystal_symmetry()
model_hierarchy = model_pdb_inp.construct_hierarchy()
query_hierarchy = iotbx.pdb.input(
source_info='query',
lines=flex.split_lines(query)).construct_hierarchy()
import os
if not os.path.isdir("files"):
os.mkdir("files")
ff = open(os.path.join("files", "query.pdb"), 'w')
print("CRYST1 113.949 113.949 32.474 90.00 90.00 90.00 I 4",
file=ff)
print(query_hierarchy.as_pdb_string(), file=ff)
ff.close()
ff = open("model.pdb", 'w')
print(model_hierarchy.as_pdb_string(), file=ff)
ff.close()
f = StringIO()
args = ["query_dir=files", "model.pdb"]
r = run(args, out=f)
expected_text = """
SEQ SCORE is fraction (close and matching target sequence).
MEAN LENGTH is the mean length of contiguous segments in the match with target sequence. (Each gap/reverse of direction starts new segment).
----ALL RESIDUES--- CLOSE RESIDUES ONLY %
MODEL --CLOSE- --FAR-- FORWARD REVERSE MIXED FOUND CA SEQ
RMSD N N N N N SCORE SEQ MATCH(%) SCORE MEAN LENGTH
query.pdb 1.55 54 7 14 29 11 39.7 0.26 9.3 0.04 6.0"""
found_text = "\n".join(f.getvalue().splitlines()[-10:])
if remove_blank(found_text) != remove_blank(expected_text):
print("Expected: \n%s \nFound: \n%s" % (expected_text, found_text))
raise AssertionError("FAILED")
print("OK")
def tst_02():
print "Comparing mixed model with target with 2 chains..."
import iotbx.pdb
from cctbx.array_family import flex
model_pdb_inp=iotbx.pdb.input(source_info='model',
lines=flex.split_lines(model1))
crystal_symmetry=model_pdb_inp.crystal_symmetry()
model_hierarchy=model_pdb_inp.construct_hierarchy()
query_hierarchy=iotbx.pdb.input(source_info='query',
lines=flex.split_lines(query)).construct_hierarchy()
f=StringIO()
r=run(crystal_symmetry=crystal_symmetry,
chain_hierarchy=query_hierarchy,target_hierarchy=model_hierarchy,out=f)
expected_text="""
Space group: I 4 Unit cell: 113.95 113.95 32.47 90.00 90.00 90.00
Looking for chain similarity for None (61 residues) in the model None (272 residues)
Residues matching in forward direction: 16 RMSD: 1.45
Residues matching in reverse direction: 31 RMSD: 1.40
Residues near but not matching one-to-one: 12 RMSD: 1.87
All residues near target: 59 RMSD: 1.52 Seq match (%): 6.8 % Found: 43.4
Residues far from target: 2 RMSD: 3.31
"""
found_text="\n".join(f.getvalue().splitlines()[-10:])
if remove_blank(found_text)!=remove_blank(expected_text):
print "Expected: \n%s \nFound: \n%s" %(expected_text,found_text)
raise AssertionError, "FAILED"
from libtbx.test_utils import approx_equal
print r.get_values("forward")
assert approx_equal(r.get_values("forward"),(1.4473857036049544, 16))
print r.get_values("reverse")
assert approx_equal(r.get_values("reverse"),(1.3969610738798282, 31))
print r.get_values("close")
assert approx_equal(r.get_values("close"),(1.5184018499613678, 59))
print r.get_values("all_far")
assert approx_equal(r.get_values("all_far"),(0,0))
print "OK"
def tst_03():
print "Comparing mixed model with target with 2 chains...as group"
import iotbx.pdb
from cctbx.array_family import flex
model_pdb_inp=iotbx.pdb.input(source_info='model',
lines=flex.split_lines(model1))
crystal_symmetry=model_pdb_inp.crystal_symmetry()
model_hierarchy=model_pdb_inp.construct_hierarchy()
query_hierarchy=iotbx.pdb.input(source_info='query',
lines=flex.split_lines(query)).construct_hierarchy()
import os,shutil
if not os.path.isdir("files"):
os.mkdir("files")
ff=open(os.path.join("files","query.pdb"),'w')
print >>ff,"CRYST1 113.949 113.949 32.474 90.00 90.00 90.00 I 4"
print >>ff,query_hierarchy.as_pdb_string()
ff.close()
ff=open("model.pdb",'w')
print >>ff,model_hierarchy.as_pdb_string()
ff.close()
f=StringIO()
args=["query_dir=files","model.pdb"]
r=run(args,out=f)
expected_text="""
SEQ SCORE is fraction (close and matching target sequence).
----ALL RESIDUES---- CLOSE RESIDUES ONLY %
MODEL --CLOSE- ---FAR-- FORWARD REVERSE MIXED FOUND CA SEQ
RMSD N RMSD N N N N SCORE SEQ MATCH(%) SCORE
query.pdb 1.52 59 3.3 2 16 31 12 43.4 0.29 6.8 0.03
"""
found_text="\n".join(f.getvalue().splitlines()[-10:])
if remove_blank(found_text)!=remove_blank(expected_text):
print "Expected: \n%s \nFound: \n%s" %(expected_text,found_text)
raise AssertionError, "FAILED"
print "OK"
def tst_06():
print("Comparing mixed model with target with 2 chains...using ncs")
import iotbx.pdb
from cctbx.array_family import flex
model_pdb_inp = iotbx.pdb.input(source_info='model',
lines=flex.split_lines(model1))
crystal_symmetry = model_pdb_inp.crystal_symmetry()
f = open('ncs.ncs_spec', 'w')
print(ncs_spec, file=f)
f.close()
f = open('model.pdb', 'w')
print(model1, file=f) #model_hierarchy.as_pdb_string()
f.close()
f = open('query.pdb', 'w')
print(query, file=f) #query_hierarchy.as_pdb_string()
f.close()
f = StringIO()
args = ['model.pdb', 'query.pdb', 'ncs_file=ncs.ncs_spec']
r = run(args, out=f)
expected_text = """
SEQ SCORE is fraction (close and matching target sequence).
MEAN LENGTH is the mean length of contiguous segments in the match with target sequence. (Each gap/reverse of direction starts new segment).
----ALL RESIDUES--- CLOSE RESIDUES ONLY %
MODEL --CLOSE- --FAR-- FORWARD REVERSE MIXED FOUND CA SEQ
RMSD N N N N N SCORE SEQ MATCH(%) SCORE MEAN LENGTH
Unique_target 1.67 58 64 15 29 14 42.6 0.25 8.6 0.04 4.5"""
found_text = "\n".join(f.getvalue().splitlines()[-10:])
if remove_blank(found_text) != remove_blank(expected_text):
print("\n\nExpected: \n%s \n\nFound: \n%s" %
(expected_text, found_text))
raise AssertionError("FAILED")
print("OK")
def tst_06():
print "Comparing mixed model with target with 2 chains...using ncs"
import iotbx.pdb
from cctbx.array_family import flex
model_pdb_inp = iotbx.pdb.input(source_info='model',
lines=flex.split_lines(model1))
crystal_symmetry = model_pdb_inp.crystal_symmetry()
f = open('ncs.ncs_spec', 'w')
print >> f, ncs_spec
f.close()
f = open('model.pdb', 'w')
print >> f, model1 #model_hierarchy.as_pdb_string()
f.close()
f = open('query.pdb', 'w')
print >> f, query #query_hierarchy.as_pdb_string()
f.close()
f = StringIO()
args = ['model.pdb', 'query.pdb', 'ncs_file=ncs.ncs_spec']
r = run(args, out=f)
expected_text = """
SEQ SCORE is fraction (close and matching target sequence).
----ALL RESIDUES--- CLOSE RESIDUES ONLY %
MODEL --CLOSE- --FAR-- FORWARD REVERSE MIXED FOUND CA SEQ
RMSD N N N N N SCORE SEQ MATCH(%) SCORE
Unique_target 1.67 58 64 15 29 14 42.6 0.25 8.6 0.04
"""
found_text = "\n".join(f.getvalue().splitlines()[-10:])
if remove_blank(found_text) != remove_blank(expected_text):
print "\n\nExpected: \n%s \n\nFound: \n%s" % (expected_text,
found_text)
raise AssertionError, "FAILED"
print "OK"
