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How to use molecule_directory method in molecule

Best Python code snippet using molecule_python

setupBatchResp.py

Source:setupBatchResp.py

1#!/usr/bin/python2#=============================================================================================3# Program to test the Resp.py wrapper for the RESP charge derivation procedure.4#=============================================================================================5# TODO:6# - add command-line arguments7#=============================================================================================8# Version control information9__version__ = "$Revision: 1.1 $"10# $Source: /share_kubo/Storage/cvsroot/pymol-tools/setupBatchResp.py,v $11#=============================================================================================12# Imports13import sys14import os.path15from optparse import OptionParser # For parsing of command line arguments16from openeye.oechem import *       # Use OpenEye OEChem toolkit17from openeye.oeomega import *      # Use OpenEye Omega18import BatchResp # for RESP charge-fitting19import exceptions20#=============================================================================================21# Create command-line argument options.22usage_string = """\23usage: %prog --input INFILE.mol2 --outdir OUTPUT_DIRECTORY24example: %prog --input guthrie.mol2 --outdir molecules/25"""26version_string = "%prog %__version__"27parser = OptionParser(usage=usage_string, version=version_string)28parser.add_option("-i", "--input", metavar='INFILE',29                  action="store", type="string", dest='infile', default='',30                  help="Input mol2 file containing one or more molecules.")31parser.add_option("-o", "--outdir", metavar='OUTPUT_DIRECTORY',32                  action="store", type="string", dest='output_directory', default='.',33                  help="Directory to contain output mol2 files, whose names are extracted from input mol2 file (default '.').")34# Parse command-line arguments.35(options,args) = parser.parse_args()36# Perform minimal error checking.37if not options.infile:38  parser.print_help()39  parser.error("An input file must be specified.")40# Open input mol2 file.41input_molecule_stream = oemolistream()42input_molecule_stream.open(options.infile)43# Create a molecule.44molecule = OEMol()45# Create an instance of Resp, telling it where to find GAMESS and Antechamber.46#resp = Resp(gamess_path = '/Users/jchodera/local/src/gamess', antechamber_path = '/Users/jchodera/local/src/antechamber-1.27')47batch_resp = BatchResp.BatchResp()48# Keep track of number of conformers for each.49molecules = []50# Process all molecules in the input stream51while OEReadMolecule(input_molecule_stream, molecule):52    # Extract name of molecule.53    molecule_name = molecule.GetTitle().split()[0].replace('.xyz','')54    print "\nProcessing '%s'..." % molecule_name55    # Make a directory for this molecule.56    molecule_directory = os.path.join(options.output_directory, molecule_name)57    print "Creating directory '%s'..." % molecule_directory58    os.mkdir(molecule_directory)59    60    # Set up GAMESS directories.61    nconformers = batch_resp.setupJobs(molecule, molecule_name, molecule_directory, generate_conformers = True)62    # Keep track of number of conformers.63    molecules.append( (molecule_name, nconformers) )64# Generate master submission script in order of fewest conformers to most conformers.65outfile = open(os.path.join(options.output_directory,'submit_all.sh'),'w')66import operator67molecules.sort(key = operator.itemgetter(1))68for molecule in molecules:69    print molecule70    outfile.write("cd %s ; qsub run_batch.cmd ; cd .. \n" % molecule[0])71    print "%5d %s" % (molecule[1], molecule[0])72outfile.close()73    74    ...

test_default.py

Source:test_default.py

1from ansible.parsing.dataloader import DataLoader2from ansible.template import Templar3import pytest4import os5import testinfra.utils.ansible_runner6import pprint7pp = pprint.PrettyPrinter()8testinfra_hosts = testinfra.utils.ansible_runner.AnsibleRunner(9    os.environ['MOLECULE_INVENTORY_FILE']).get_hosts('all')10def base_directory():11    cwd = os.getcwd()12    if('group_vars' in os.listdir(cwd)):13        directory = "../.."14        molecule_directory = "."15    else:16        directory = "."17        molecule_directory = "molecule/{}".format(os.environ.get('MOLECULE_SCENARIO_NAME'))18    return directory, molecule_directory19@pytest.fixture()20def get_vars(host):21    """22    """23    base_dir, molecule_dir = base_directory()24    file_defaults = "file={}/defaults/main.yml name=role_defaults".format(base_dir)25    file_vars = "file={}/vars/main.yml name=role_vars".format(base_dir)26    file_molecule = "file={}/group_vars/all/vars.yml name=test_vars".format(molecule_dir)27    defaults_vars = host.ansible("include_vars", file_defaults).get("ansible_facts").get("role_defaults")28    vars_vars = host.ansible("include_vars", file_vars).get("ansible_facts").get("role_vars")29    molecule_vars = host.ansible("include_vars", file_molecule).get("ansible_facts").get("test_vars")30    ansible_vars = defaults_vars31    ansible_vars.update(vars_vars)32    ansible_vars.update(molecule_vars)33    templar = Templar(loader=DataLoader(), variables=ansible_vars)34    result = templar.template(ansible_vars, fail_on_undefined=False)35    return result36def test_packages(host):37    """38    """39    distribution = host.system_info.distribution40    release = host.system_info.release41    pp.pprint(distribution)42    pp.pprint(release)43    packages = []44    packages.append("screen")45    for package in packages:46        p = host.package(package)47        assert p.is_installed48@pytest.mark.parametrize("files", [49    "/etc/screenrc",50])51def test_filess(host, files):52    d = host.file(files)...

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