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')