def generate_gaff_xml(): """ Return a file-like object for `gaff.xml` """ from openmoltools import amber gaff_dat_filename = amber.find_gaff_dat() # Generate ffxml file contents for parmchk-generated frcmod output. leaprc = StringIO("parm = loadamberparams %s" % gaff_dat_filename) import parmed params = parmed.amber.AmberParameterSet.from_leaprc(leaprc) params = parmed.openmm.OpenMMParameterSet.from_parameterset(params) citations = """\ Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and bond type perception in molecular mechanical calculations". Journal of Molecular Graphics and Modelling , 25, 2006, 247260. Wang, J., Wolf, R. M.; Caldwell, J. W.;Kollman, P. A.; Case, D. A. "Development and testing of a general AMBER force field". Journal of Computational Chemistry, 25, 2004, 1157-1174. """ ffxml = str() gaff_xml = StringIO(ffxml) provenance=dict(OriginalFile='gaff.dat', Reference=citations) params.write(gaff_xml, provenance=provenance) return gaff_xml
def generate_gaff_xml(): """ Return a file-like object for `gaff.xml` """ from openmoltools import amber gaff_dat_filename = amber.find_gaff_dat() # Generate ffxml file contents for parmchk-generated frcmod output. leaprc = StringIO("parm = loadamberparams %s" % gaff_dat_filename) import parmed params = parmed.amber.AmberParameterSet.from_leaprc(leaprc) params = parmed.openmm.OpenMMParameterSet.from_parameterset(params) citations = """\ Wang, J., Wang, W., Kollman P. A.; Case, D. A. "Automatic atom type and bond type perception in molecular mechanical calculations". Journal of Molecular Graphics and Modelling , 25, 2006, 247260. Wang, J., Wolf, R. M.; Caldwell, J. W.;Kollman, P. A.; Case, D. A. "Development and testing of a general AMBER force field". Journal of Computational Chemistry, 25, 2004, 1157-1174. """ ffxml = str() gaff_xml = StringIO(ffxml) provenance=dict(OriginalFile='gaff.dat', Reference=citations) params.write(gaff_xml, provenance=provenance) return gaff_xml
from protons.ligutils import parametrize_ligand, MultiIsomerResidue from . import get_data from openmoltools.schrodinger import is_schrodinger_suite_installed from openmoltools.amber import find_gaff_dat try: find_gaff_dat() found_gaff = True except ValueError: found_gaff = False from unittest import skipIf, TestCase class LigandXmlTestCase(TestCase): @skipIf(not is_schrodinger_suite_installed() or not found_gaff, "This test requires Schrodinger's suite and gaff") def test_ligand_cphxml(self): """ Run epik on a ligand and parametrize its isomers """ parametrize_ligand(get_data("ligand_allH.mol2", "testsystems"), "/tmp/ligand-isomers.xml", pH=4.5) def test_xml_compilation(self): """ Compile an xml file for the isomers """ xmlfile = get_data("isomers.xml", "testsystems/ligand_xml") m = MultiIsomerResidue(xmlfile)
from constph.ligutils import parametrize_ligand, MultiIsomerResidue from . import get_data from openmoltools.schrodinger import is_schrodinger_suite_installed from openmoltools.amber import find_gaff_dat try: find_gaff_dat() found_gaff = True except ValueError: found_gaff = False from unittest import skipIf, TestCase class LigandXmlTestCase(TestCase): @skipIf(not is_schrodinger_suite_installed() or not found_gaff, "This test requires Schrodinger's suite and gaff") def test_ligand_cphxml(self): """ Run epik on a ligand and parametrize its isomers """ parametrize_ligand(get_data("ligand_allH.mol2", "testsystems"), "/tmp/ligand-isomers.xml", pH=4.5) def test_xml_compilation(self): """ Compile an xml file for the isomers """ xmlfile = get_data("isomers.xml", "testsystems/ligand_xml") m = MultiIsomerResidue(xmlfile) m.write('/tmp/isomers.cph.xml')