def test_write_model():
orig_parm = pmd.download_PDB('1l2y')
pdb_out = 'out.pdb'
# default
with tempfolder():
pdb4amber.main(['1l2y', '--pdbid', '-o', pdb_out])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (1, 304, 3)
# model 1
with tempfolder():
pdb4amber.main(['1l2y', '--pdbid', '-o', pdb_out, '--model', '1'])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (1, 304, 3)
np.testing.assert_almost_equal(parm.coordinates,
orig_parm.get_coordinates()[0])
# model 2
model = 2
with tempfolder():
pdb4amber.main(['1l2y', '--pdbid', '-o', pdb_out, '--model',
str(model)
])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (1, 304, 3)
np.testing.assert_almost_equal(parm.coordinates,
orig_parm.get_coordinates()[model - 1])
def test_keep_all_model():
orig_parm = pmd.download_PDB('1l2y')
pdb_out = 'out.pdb'
# default
with tempfolder():
pdb4amber.main(['1l2y', '--pdbid', '-o', pdb_out, '--model', '-1'])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (38, 304, 3)
def testModifiedDNARNA(self):
""" Tests that modified DNA/RNA residue names are properly recognized"""
def count_nures(parm):
nnuc = 0
for res in parm.residues:
if RNAResidue.has(res.name) or DNAResidue.has(res.name):
nnuc += 1
return nnuc
pdb_with_nnures = [('1EHZ', 76), ('3p4a', 48), ('3p4b', 48), ('3p4d', 16)]
for pdbid, correct_nres in pdb_with_nnures:
pdb = pmd.download_PDB(pdbid)
nres = count_nures(pdb)
self.assertEqual(correct_nres, nres)
def test_modified_dna_rna(self):
""" Tests that modified DNA/RNA residue names are properly recognized"""
def count_nures(parm):
nnuc = 0
for res in parm.residues:
if RNAResidue.has(res.name) or DNAResidue.has(res.name):
nnuc += 1
return nnuc
pdb_with_nnures = [('1EHZ', 76), ('3p4a', 48), ('3p4b', 48),
('3p4d', 16)]
for pdbid, correct_nres in pdb_with_nnures:
pdb = pmd.download_PDB(pdbid)
nres = count_nures(pdb)
self.assertEqual(correct_nres, nres)
def test_structure_box_and_space_group_and_symmetry(self):
""" Test correctly copying box, space group and symmetry """
def assert_correctly_copy(parm):
sliced_parm = parm['@1-3']
if parm.box is None:
self.assertIs(sliced_parm.box, None)
else:
np.testing.assert_equal(parm.box, sliced_parm.box)
if parm.symmetry is None:
self.assertIs(sliced_parm.symmetry, None)
else:
np.testing.assert_equal(parm.symmetry.data, sliced_parm.symmetry.data)
self.assertEqual(parm.space_group, sliced_parm.space_group)
# pdb
parm = pmd.load_file(get_fn('4lzt.pdb'))
assert_correctly_copy(parm)
# pdb from rcsb
parm = pmd.download_PDB('2igd')
assert_correctly_copy(parm)
# cif
parm = pmd.load_file(get_fn('sample.cif'))
assert_correctly_copy(parm)
# LES parm7, no rst7
parm = pmd.load_file(get_fn('4lzt.les.parm7'))
assert_correctly_copy(parm)
# LES parm7, with rst7
parm = pmd.load_file(get_fn('4lzt.les.parm7'), xyz=get_fn('4lzt.les.rst7'))
assert_correctly_copy(parm)
# parm7, no box
parm = pmd.load_file(get_fn('ash.parm7'))
assert_correctly_copy(parm)
# gro
parm = pmd.load_file(get_fn('1aki.charmm27.solv.gro'))
assert_correctly_copy(parm)
# psf
parm = pmd.load_file(get_fn('4TVP-dmj_wat-ion.psf'))
assert_correctly_copy(parm)
# mol2
parm = pmd.load_file(get_fn('m2-c1_f3.mol2'), structure=True)
assert_correctly_copy(parm)
# pqr
parm = pmd.load_file(get_fn('adk_open.pqr'))
assert_correctly_copy(parm)
# chamber parm
parm = pmd.load_file(get_fn('ala_ala_ala.parm7'))
assert_correctly_copy(parm)
def main(argv=None):
parser = argparse.ArgumentParser()
parser.add_argument(
"input",
nargs='?',
help="PDB input file (default: stdin)",
)
parser.add_argument("-i",
"--in",
metavar="FILE",
dest="pdbin",
help="PDB input file (default: stdin)",
default='stdin')
parser.add_argument("-o",
"--out",
metavar="FILE",
dest="pdbout",
help="PDB output file (default: stdout)",
default='stdout')
parser.add_argument("-y",
"--nohyd",
action="store_true",
dest="nohyd",
help="remove all hydrogen atoms (default: no)")
parser.add_argument("-d",
"--dry",
action="store_true",
dest="dry",
help="remove all water molecules (default: no)")
parser.add_argument("-s",
"--strip",
dest="strip_atom_mask",
default=None,
help="Strip given atom mask, (default: no)")
parser.add_argument("-m",
"--mutate",
dest="mutation_string",
default=None,
help="Mutate residue")
parser.add_argument(
"-p",
"--prot",
action="store_true",
dest="prot",
help="keep only Amber-compatible residues (default: no)")
parser.add_argument("--constantph",
action="store_true",
dest="constantph",
help="rename GLU,ASP,HIS for constant pH simulation")
parser.add_argument(
"--most-populous",
action="store_true",
dest="mostpop",
help="keep most populous alt. conf. (default is to keep 'A')")
parser.add_argument("--keep-altlocs",
action="store_true",
dest="keep_altlocs",
help="Keep alternative conformations")
parser.add_argument(
"--reduce",
action="store_true",
dest="reduce",
help="Run Reduce first to add hydrogens. (default: no)")
parser.add_argument(
"--no-reduce-db",
action="store_true",
dest="no_reduce_db",
help=
"If reduce is on, skip using it for hetatoms. (default: usual reduce behavior for hetatoms)"
)
parser.add_argument("--pdbid",
action="store_true",
dest="pdbid",
help="fetch structure with given pdbid, "
"should combined with -i option.\n"
"Subjected to change")
parser.add_argument("--add-missing-atoms",
action="store_true",
dest="add_missing_atoms",
help="Use tleap to add missing atoms")
parser.add_argument(
"--model",
type=int,
dest="model",
default=1,
help=
"Model to use from a multi-model pdb file (integer). (default: use 1st model). "
"Use a negative number to keep all models")
parser.add_argument("-l",
"--logfile",
metavar="FILE",
dest="logfile",
help="log filename",
default='stderr')
parser.add_argument("-v",
"--version",
action="store_true",
dest="version",
help="version")
parser.add_argument(
"--leap-template",
action='store_true',
dest="leap_template",
help="write a leap template for easy adaption\n(EXPERIMENTAL)")
parser.add_argument("--no-conect",
action='store_true',
dest="no_conect",
help="Not write S-S conect record")
parser.add_argument("--noter",
action='store_true',
dest="noter",
help="Not writing TER")
opt = parser.parse_args(argv)
# pdbin : {str, file object, parmed.Structure}
if opt.version:
print(__version__)
if opt.input is not None:
pdbin = opt.input
else:
pdbin = opt.pdbin
if opt.pdbid:
pdbin = parmed.download_PDB(pdbin)
if opt.pdbin == 'stdin' and opt.input is None:
if os.isatty(sys.stdin.fileno()):
parser.print_help()
sys.exit(0)
if opt.logfile == 'stderr':
logfile = sys.stderr
elif opt.logfile == 'stdout':
logfile = sys.stdout
else:
logfile = opt.logfile
run(arg_pdbout=opt.pdbout,
arg_pdbin=pdbin,
arg_nohyd=opt.nohyd,
arg_dry=opt.dry,
arg_strip_atom_mask=opt.strip_atom_mask,
arg_mutate_string=opt.mutation_string,
arg_prot=opt.prot,
arg_constph=opt.constantph,
arg_mostpop=opt.mostpop,
arg_reduce=opt.reduce,
arg_no_reduce_db=opt.no_reduce_db,
arg_model=opt.model - 1,
arg_keep_altlocs=opt.keep_altlocs,
arg_add_missing_atoms=opt.add_missing_atoms,
arg_logfile=logfile,
arg_leap_template=opt.leap_template,
arg_conect=not opt.no_conect,
arg_noter=opt.noter)
from parmed.residue import WATER_NAMES
import pytest
try:
from io import StringIO
except ImportError:
from cStringIO import StringIO
from pdb4amber import pdb4amber
# local
from utils import tempfolder, get_fn, _has_program
pdb_fn = get_fn('4lzt/4lzt_h.pdb')
try:
# check internet
pmd.download_PDB('1l2y')
internet_ok = True
except IOError:
internet_ok = False
@unittest.skipUnless(internet_ok, 'must have internet connection to rcsb')
def test_write_model():
orig_parm = pmd.download_PDB('1l2y')
pdb_out = 'out.pdb'
# default
with tempfolder():
pdb4amber.main(['1l2y', '--pdbid', '-o', pdb_out])
parm = pmd.load_file(pdb_out)
assert parm.get_coordinates().shape == (1, 304, 3)
def testDownloadSave(self):
""" Tests downloading PDB files and saving a copy """
fname = get_fn('downloaded.pdb', written=True)
self._check4lzt(download_PDB('4lzt', saveto=fname))
self._check4lzt(read_PDB(fname))
def testDownload(self):
""" Tests downloading PDB files """
self._check4lzt(download_PDB('4lzt'))
def test_space_group(self):
parm_from_cif = pmd.download_CIF('2igd')
parm_from_pdb = pmd.download_PDB('2igd')
self.assertEqual(parm_from_cif.space_group, 'P 21 21 21')
self.assertEqual(parm_from_pdb.space_group, 'P 21 21 21')
def test_space_group(self):
parm_from_cif = pmd.download_CIF('2igd')
parm_from_pdb = pmd.download_PDB('2igd')
self.assertEqual(parm_from_cif.space_group, 'P 21 21 21')
self.assertEqual(parm_from_pdb.space_group, 'P 21 21 21')
import parmed as pmd
p = pmd.download_PDB('3gx5')
p[':SAM'].save('SAM.pdb')