## its license. Please see the LICENSE file that should have been
## included as part of this package.
"""This example uses the Python code profiler to load a file with mmLib.
We use this to help performance tune mmLib.
"""
## Python
import sys
## pymmlib
import test_util
from mmLib import FileIO
def main(path):
print "mmLib.LoadStructure(fil=%s)" % (path)
struct = FileIO.LoadStructure(fil=path)
if __name__ == "__main__":
import os
try:
path = sys.argv[1]
except IndexError:
print "usage: load_test.py <PDB/mmCIF file or directory of files>"
sys.exit(1)
for pathx in test_util.walk_pdb_cif(path):
main(pathx)
## This code is part of the PyMMLib distribution and governed by
## its license. Please see the LICENSE file that should have been
## included as part of this package.
"""This example uses the Python code profiler to load a file with mmLib.
We use this to help performance tune mmLib.
"""
## Python
import sys
## pymmlib
import test_util
from mmLib import FileIO
def main(path):
print "mmLib.LoadStructure(fil=%s)" % (path)
struct = FileIO.LoadStructure(fil=path)
if __name__ == "__main__":
import os
try:
path = sys.argv[1]
except IndexError:
print "usage: load_test.py <PDB/mmCIF file or directory of files>"
sys.exit(1)
for pathx in test_util.walk_pdb_cif(path):
main(pathx)
def main(walk_path, start_path):
print "Running Python Macromolecular Library Test Program"
print "--------------------------------------------------"
print "This program will throw a AssertionError (or worse!) if it"
print "runs into any problems."
print
for path in test_util.walk_pdb_cif(walk_path, start_path):
print "[%s]" % (path)
time1 = time.time()
stats = Stats()
struct = FileIO.LoadStructure(fil=path,
build_properties=("library_bonds", ))
## track memory leaks
sref = weakref.ref(struct, weakref_callback)
WEAKREF_PATH[sref] = path
WEAKREF_LIST.append(sref)
## test the mmLib.Structure object API and
## with massive sanity checking
print "[loaded struct]"
try:
run_structure_tests(struct, stats)
except AssertionError:
print "*** AssertionError while testing: %s ***" % (str(
stats["testing"]))
raise
except:
print "*** Error while testing: %s ***" % (str(stats["testing"]))
raise
stats.print_stats()
## copy the structure and re-run those tests
print "[copy struct]"
struct_cp = copy.deepcopy(struct)
cmp_struct(struct, struct_cp)
## verify the number of atoms in the mmLib.Structure object
## matches the number of atoms in the source file
file_verify(path, struct, stats)
## test file saving
from mmLib.CIF import DataBlock
if (hasattr(struct, "cif_data")
and isinstance(struct.cif_data, DataBlock)):
print "[save verify skipped]"
else:
print "[save verify]"
save_verify(struct, stats)
time2 = time.time()
print "Tests Time (sec)-----:", int(time2 - time1)
## dereference!
struct = None
struct_cp = None
stats = None
stats_cp = None
## force garbage collection
gc.collect()
print
def main(walk_path, start_path):
print "Running Python Macromolecular Library Test Program"
print "--------------------------------------------------"
print "This program will throw a AssertionError (or worse!) if it"
print "runs into any problems."
print
for path in test_util.walk_pdb_cif(walk_path, start_path):
print "[%s]" % (path)
time1 = time.time()
stats = Stats()
struct = FileIO.LoadStructure(
fil = path,
build_properties = ("library_bonds",))
## track memory leaks
sref = weakref.ref(struct, weakref_callback)
WEAKREF_PATH[sref] = path
WEAKREF_LIST.append(sref)
## test the mmLib.Structure object API and
## with massive sanity checking
print "[loaded struct]"
try:
run_structure_tests(struct, stats)
except AssertionError:
print "*** AssertionError while testing: %s ***" % (
str(stats["testing"]))
raise
except:
print "*** Error while testing: %s ***" % (
str(stats["testing"]))
raise
stats.print_stats()
## copy the structure and re-run those tests
print "[copy struct]"
struct_cp = copy.deepcopy(struct)
cmp_struct(struct, struct_cp)
## verify the number of atoms in the mmLib.Structure object
## matches the number of atoms in the source file
file_verify(path, struct, stats)
## test file saving
from mmLib.CIF import DataBlock
if (hasattr(struct, "cif_data")
and isinstance(struct.cif_data, DataBlock)):
print "[save verify skipped]"
else:
print "[save verify]"
save_verify(struct, stats)
time2 = time.time()
print "Tests Time (sec)-----:",int(time2-time1)
## dereference!
struct = None
struct_cp = None
stats = None
stats_cp = None
## force garbage collection
gc.collect()
print
