class HartreeMoleculeComparator(object):
def __init__(self):
for key, value in locals().items():
if key != self:
setattr(self, key, value)
self.logger = logging.getLogger('hartree_comparator')
self.loader = SnapshotLoader()
def get_atoms(self, fname):
"Pulls the atoms data structure from the given file"
result = self.loader.load(fname, FileReader(fname))
return result.getAtoms()
def compare(self, first, second):
try:
first_atoms = self.get_atoms(first)
except ValueError:
self.logger.exception("Problems parsing first file %s" % first)
raise
try:
second_atoms = self.get_atoms(second)
except ValueError:
self.logger.exception("Problems parsing second file %s" % second)
raise
if first_atoms == second_atoms:
return True
self.logger.error("Atoms for files %s and %s do not match" % (first,
second,))
self.logger.error("%s: %s" % (first, first_atoms))
self.logger.error("%s: %s" % (second, second_atoms))
return False
def __init__(self):
jar_path = Path(__file__).parent / "hartree"
found_jars = sorted(jar_path.glob('*.jar'))
if len(found_jars) == 0:
raise Exception(
"Could not find any JARs in dir {}".format(jar_path))
for found_jar in found_jars:
jpype.addClassPath(found_jar)
print("Classpath: ", jpype.getClassPath())
jpype.startJVM(convertStrings=False)
# TODO: Figure out how to scope these imports for the class
# noinspection PyUnresolvedReferences
from org.cmayes.hartree.loader.gaussian import SnapshotLoader
self.loader = SnapshotLoader()
class HartreeWrapper:
def __init__(self):
jar_path = Path(__file__).parent / "hartree"
found_jars = sorted(jar_path.glob('*.jar'))
if len(found_jars) == 0:
raise Exception(
"Could not find any JARs in dir {}".format(jar_path))
for found_jar in found_jars:
jpype.addClassPath(found_jar)
print("Classpath: ", jpype.getClassPath())
jpype.startJVM(convertStrings=False)
# TODO: Figure out how to scope these imports for the class
# noinspection PyUnresolvedReferences
from org.cmayes.hartree.loader.gaussian import SnapshotLoader
self.loader = SnapshotLoader()
def read_all_gaussian(self, files):
# noinspection PyUnresolvedReferences
from java.io import FileReader
mapped_results = {}
for cur_file in files:
mapped_results[cur_file] = self.loader.load(
cur_file, FileReader(cur_file))
return mapped_results
def read_gaussian(self, tgt_file):
# noinspection PyUnresolvedReferences
from java.io import FileReader
return self.loader.load(tgt_file, FileReader(tgt_file))
def __del__(self):
if jpype.isJVMStarted():
jpype.shutdownJVM()
def __init__(self):
for key, value in locals().items():
if key != self:
setattr(self, key, value)
self.logger = logging.getLogger('hartree_comparator')
self.loader = SnapshotLoader()
