def testProteinLigand(self):
from htmd.builder.solvate import solvate
from htmd.parameterization.fftype import fftype, FFTypeMethod
from htmd.parameterization.writers import writeFRCMOD
# Test protein ligand building with parametrized ligand
refdir = home(dataDir=join('test-amber-build', 'protLig'))
tmpdir = os.path.join(self.testDir, 'protLig')
os.makedirs(tmpdir)
mol = Molecule(join(refdir, '3ptb_mod.pdb'))
lig = Molecule(join(refdir, 'benzamidine.pdb'),
guess=('bonds', 'angles', 'dihedrals'))
prm, lig = fftype(lig, method=FFTypeMethod.GAFF2)
writeFRCMOD(lig, prm, join(tmpdir, 'mol.frcmod'))
lig.segid[:] = 'L'
# params =
newmol = Molecule()
newmol.append(lig)
newmol.append(mol)
smol = solvate(newmol)
params = defaultParam() + [
join(tmpdir, 'mol.frcmod'),
]
_ = build(smol, outdir=tmpdir, param=params, ionize=False)
refdir = home(dataDir=join('test-amber-build', 'protLig', 'results'))
TestAmberBuild._compareResultFolders(refdir, tmpdir, '3PTB')
def test_build(self):
from htmd.molecule.molecule import Molecule
from htmd.builder.solvate import solvate
from htmd.home import home
from htmd.util import tempname, assertSameAsReferenceDir
import os
import numpy as np
# Use pre-prepared files so we can tell whether the error is in prepare or in build
# Inputs are reference outputs of proteinprepare.
preparedInputDir = home(dataDir='test-proteinprepare')
pdbids = ['3PTB', '1A25', '1GZM', '1U5U']
for pdb in pdbids:
with self.subTest(pdb=pdb):
print('Building {}'.format(pdb))
inFile = os.path.join(preparedInputDir, pdb,
"{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter(
'protein') # Fix for bad proteinPrepare hydrogen placing
np.random.seed(1) # Needed for ions
smol = solvate(mol)
topos = ['top/top_all36_prot.rtf', 'top/top_water_ions.rtf']
params = [
'par/par_all36_prot_mod.prm', 'par/par_water_ions.prm'
]
tmpdir = tempname()
_ = build(smol, topo=topos, param=params, outdir=tmpdir)
compareDir = home(
dataDir=os.path.join('test-charmm-build', pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
def test_customDisulfideBonds(self):
from htmd.builder.solvate import solvate
# Test without proteinPrepare
pdbids = [
"1GZM",
]
for pid in pdbids:
np.random.seed(1)
mol = Molecule(pid)
mol.filter("protein")
smol = solvate(mol)
ffs = defaultFf()
disu = [
["segid 1 and resid 110", "segid 1 and resid 187"],
["segid 0 and resid 110", "segid 0 and resid 187"],
]
tmpdir = os.path.join(self.testDir, "withoutProtPrep", pid)
_ = build(smol, ff=ffs, outdir=tmpdir, disulfide=disu)
refdir = home(dataDir=join("test-amber-build", "nopp", pid))
_TestAmberBuild._compareResultFolders(refdir, tmpdir, pid)
np.random.seed(1)
tmpdir = os.path.join(self.testDir, "withoutProtPrep", pid)
_ = build(smol, ff=ffs, outdir=tmpdir)
refdir = home(dataDir=join("test-amber-build", "nopp", pid))
_TestAmberBuild._compareResultFolders(refdir, tmpdir, pid)
def test_acemd3(self):
from htmd.util import tempname
from htmd.home import home
from glob import glob
import os
eq = Equilibration(_version=3)
eq.runtime = 4
eq.timeunits = 'ns'
eq.temperature = 300
# keep protein on the same place during all equilibration
from htmd.units import convert
eq.constraintsteps = convert(eq.timeunits,
'timesteps',
eq.runtime,
timestep=eq.acemd.timestep)
eq.constraints = {
'protein and name CA': 1,
'protein and noh and not name CA': 0.1
}
eq.fb_reference = 'protein and name CA'
eq.fb_selection = 'resname MOL and noh'
eq.fb_box = [-21, 21, -19, 19, 29, 30]
eq.fb_k = 5
tmpdir = tempname()
eq.write(
home(dataDir=os.path.join('test-protocols', 'build', 'protLig')),
tmpdir)
# Compare with reference
refdir = home(dataDir=os.path.join('test-protocols', 'equilibration',
'acemd3', 'protLig', 'prerun'))
files = [os.path.basename(f) for f in glob(os.path.join(refdir, '*'))]
self._compareResultFolders(refdir, tmpdir, 'protLig')
def test_disulfideWithInsertion(self):
from htmd.molecule.molecule import Molecule
from htmd.builder.solvate import solvate
from htmd.home import home
from htmd.util import tempname, assertSameAsReferenceDir
import os
import numpy as np
# Use pre-prepared files so we can tell whether the error is in prepare or in build
# Inputs are reference outputs of proteinprepare.
preparedInputDir = home(dataDir='test-proteinprepare')
pdb = '3PTB'
print('Building {}'.format(pdb))
inFile = os.path.join(preparedInputDir, pdb,
"{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
np.random.seed(1) # Needed for ions
smol = solvate(mol)
topos = ['top/top_all36_prot.rtf', 'top/top_water_ions.rtf']
params = ['par/par_all36_prot_mod.prm', 'par/par_water_ions.prm']
smol.insertion[
smol.resid ==
42] = 'A' # Adding an insertion to test that disulfide bonds with insertions work
tmpdir = tempname()
_ = build(smol, topo=topos, param=params, outdir=tmpdir)
compareDir = home(
dataDir=os.path.join('test-charmm-build', '3PTB_insertion'))
assertSameAsReferenceDir(compareDir, tmpdir)
def testProteinLigand(self):
from htmd.builder.solvate import solvate
# Test protein ligand building with parametrized ligand
refdir = home(dataDir=join("test-amber-build", "protLig"))
tmpdir = os.path.join(self.testDir, "protLig")
os.makedirs(tmpdir)
mol = Molecule(join(refdir, "3ptb_mod.pdb"))
lig = Molecule(join(refdir, "benzamidine.mol2"))
lig.segid[:] = "L"
# params =
newmol = Molecule()
newmol.append(lig)
newmol.append(mol)
smol = solvate(newmol)
params = defaultParam() + [
join(refdir, "benzamidine.frcmod"),
]
_ = build(smol, outdir=tmpdir, param=params, ionize=False)
refdir = home(dataDir=join("test-amber-build", "protLig", "results"))
_TestAmberBuild._compareResultFolders(refdir, tmpdir, "3PTB")
def setUpClass(self):
from htmd.simlist import simlist, simfilter
from glob import glob
from htmd.projections.metric import Metric
from moleculekit.projections.metricdistance import MetricDistance
from moleculekit.projections.metricdihedral import MetricDihedral
from moleculekit.util import tempname
from htmd.home import home
from os.path import join
sims = simlist(glob(join(home(dataDir='adaptive'), 'data', '*', '')),
glob(join(home(dataDir='adaptive'), 'input', '*')))
fsims = simfilter(sims, tempname(), 'not water')
metr = Metric(fsims)
metr.set(
MetricDistance('protein and resid 10 and name CA',
'resname BEN and noh',
metric='contacts',
groupsel1='residue',
threshold=4))
self.data1 = metr.project()
metr.set(MetricDihedral())
self.data2 = metr.project()
def test_customDisulfideBonds(self):
from moleculekit.molecule import Molecule
from htmd.builder.solvate import solvate
from htmd.home import home
from htmd.util import tempname, assertSameAsReferenceDir
import os
import numpy as np
# Use pre-prepared files so we can tell whether the error is in prepare or in build
# Inputs are reference outputs of proteinprepare.
preparedInputDir = home(dataDir="test-proteinprepare")
pdb = "1GZM"
inFile = os.path.join(preparedInputDir, pdb,
"{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter("protein") # Fix for bad proteinPrepare hydrogen placing
np.random.seed(1) # Needed for ions
smol = solvate(mol)
topos = ["top/top_all36_prot.rtf", "top/top_water_ions.rtf"]
params = ["par/par_all36_prot.prm", "par/par_water_ions.prm"]
disu = [
["segid 1 and resid 110", "segid 1 and resid 187"],
["segid 0 and resid 110", "segid 0 and resid 187"],
]
tmpdir = tempname()
_ = build(smol,
topo=topos,
param=params,
outdir=tmpdir,
disulfide=disu)
compareDir = home(dataDir=os.path.join("test-charmm-build", pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
def test_build(self):
from moleculekit.molecule import Molecule
from htmd.builder.solvate import solvate
from htmd.home import home
from htmd.util import tempname, assertSameAsReferenceDir
import os
import numpy as np
# Use pre-prepared files so we can tell whether the error is in prepare or in build
# Inputs are reference outputs of proteinprepare.
preparedInputDir = home(dataDir="test-proteinprepare")
pdbids = ["3PTB", "1A25", "1GZM", "1U5U"]
for pdb in pdbids:
with self.subTest(pdb=pdb):
print("Building {}".format(pdb))
inFile = os.path.join(preparedInputDir, pdb,
"{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter(
"protein") # Fix for bad proteinPrepare hydrogen placing
np.random.seed(1) # Needed for ions
smol = solvate(mol)
topos = ["top/top_all36_prot.rtf", "top/top_water_ions.rtf"]
params = ["par/par_all36_prot.prm", "par/par_water_ions.prm"]
tmpdir = tempname()
_ = build(smol, topo=topos, param=params, outdir=tmpdir)
compareDir = home(
dataDir=os.path.join("test-charmm-build", pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
def test_build(self):
from htmd.molecule.molecule import Molecule
from htmd.builder.solvate import solvate
from htmd.home import home
from htmd.util import tempname, assertSameAsReferenceDir
import os
import numpy as np
# Use pre-prepared files so we can tell whether the error is in prepare or in build
# Inputs are reference outputs of proteinprepare.
preparedInputDir = home(dataDir='test-proteinprepare')
pdbids = ['3PTB', '1A25', '1GZM', '1U5U']
for pdb in pdbids:
with self.subTest(pdb=pdb):
print('Building {}'.format(pdb))
inFile = os.path.join(preparedInputDir, pdb, "{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
np.random.seed(1) # Needed for ions
smol = solvate(mol)
topos = ['top/top_all36_prot.rtf', 'top/top_water_ions.rtf']
params = ['par/par_all36_prot_mod.prm', 'par/par_water_ions.prm']
tmpdir = tempname()
_ = build(smol, topo=topos, param=params, outdir=tmpdir)
compareDir = home(dataDir=os.path.join('test-charmm-build', pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
def test_disulfideWithInsertion(self):
from htmd.molecule.molecule import Molecule
from htmd.builder.solvate import solvate
from htmd.home import home
from htmd.util import tempname, assertSameAsReferenceDir
import os
import numpy as np
# Use pre-prepared files so we can tell whether the error is in prepare or in build
# Inputs are reference outputs of proteinprepare.
preparedInputDir = home(dataDir='test-proteinprepare')
pdb = '3PTB'
print('Building {}'.format(pdb))
inFile = os.path.join(preparedInputDir, pdb, "{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
np.random.seed(1) # Needed for ions
smol = solvate(mol)
topos = ['top/top_all36_prot.rtf', 'top/top_water_ions.rtf']
params = ['par/par_all36_prot_mod.prm', 'par/par_water_ions.prm']
smol.insertion[smol.resid == 42] = 'A' # Adding an insertion to test that disulfide bonds with insertions work
tmpdir = tempname()
_ = build(smol, topo=topos, param=params, outdir=tmpdir)
compareDir = home(dataDir=os.path.join('test-charmm-build', '3PTB_insertion'))
assertSameAsReferenceDir(compareDir, tmpdir)
def test_acemd3(self):
from htmd.util import tempname
from htmd.home import home
from htmd.units import convert
from glob import glob
import os
from htmd.mdengine.acemd.acemd import GroupRestraint
eq = Equilibration()
eq.runtime = 4
eq.timeunits = "ns"
eq.temperature = 300
eq.restraintsteps = convert(
eq.timeunits, "timesteps", eq.runtime, timestep=eq.acemd.timestep
)
ligres = GroupRestraint(
"resname MOL and noh",
[42, 38, 1],
[(5, 0)],
fbcentre=[-0.178, -0.178, 29.195],
)
eq.restraints = eq.defaultEquilRestraints(1000000) + [ligres]
tmpdir = tempname()
eq.write(
home(dataDir=os.path.join("test-protocols", "build", "protLig")), tmpdir
)
# Compare with reference
refdir = home(
dataDir=os.path.join(
"test-protocols", "equilibration", "acemd3", "protLig", "prerun"
)
)
files = [os.path.basename(f) for f in glob(os.path.join(refdir, "*"))]
self._compareResultFolders(refdir, tmpdir, "protLig")
def testProteinLigand(self):
from htmd.builder.solvate import solvate
from htmd.parameterization.fftype import fftype, FFTypeMethod
from htmd.parameterization.writers import writeFRCMOD
# Test protein ligand building with parametrized ligand
refdir = home(dataDir=join('test-amber-build', 'protLig'))
tmpdir = os.path.join(self.testDir, 'protLig')
os.makedirs(tmpdir)
mol = Molecule(join(refdir, '3ptb_mod.pdb'))
lig = Molecule(join(refdir, 'benzamidine.pdb'), guess=('bonds', 'angles', 'dihedrals'))
prm, lig = fftype(lig, method=FFTypeMethod.GAFF2)
writeFRCMOD(lig, prm, join(tmpdir, 'mol.frcmod'))
lig.segid[:] = 'L'
# params =
newmol = Molecule()
newmol.append(lig)
newmol.append(mol)
smol = solvate(newmol)
params = defaultParam() + [join(tmpdir, 'mol.frcmod'),]
_ = build(smol, outdir=tmpdir, param=params, ionize=False)
refdir = home(dataDir=join('test-amber-build', 'protLig', 'results'))
TestAmberBuild._compareResultFolders(refdir, tmpdir, '3PTB')
def test_production(self):
from htmd.home import home
import filecmp
from htmd.util import tempname
from glob import glob
tmpdir = tempname()
pdbid = "3PTB"
prod = Acemd("production")
prod.run = "2000"
prod.trajectoryperiod = 200
prod.temperature = 300
prod.write(
home(dataDir=os.path.join("test-acemd", pdbid, "equil_out")),
tmpdir)
print(tmpdir)
# Compare with reference
refdir = home(dataDir=os.path.join("test-acemd", pdbid, "prod"))
files = [os.path.basename(f) for f in glob(os.path.join(refdir, "*"))]
match, mismatch, error = filecmp.cmpfiles(refdir,
tmpdir,
files,
shallow=False)
if len(mismatch) != 0 or len(error) != 0 or len(match) != len(files):
raise RuntimeError(
"Different results produced by Acemd production for "
"test {} between {} and {} in files {}.".format(
pdbid, refdir, tmpdir, mismatch))
def test_production(self):
from htmd.home import home
import filecmp
from htmd.util import tempname
from glob import glob
tmpdir = tempname()
pdbid = '3PTB'
prod = Acemd('production')
prod.run = '2000'
prod.trajectoryfreq = 200
prod.temperature = 300
prod.write(
home(dataDir=os.path.join('test-acemd', pdbid, 'equil_out')),
tmpdir)
print(tmpdir)
# Compare with reference
refdir = home(dataDir=os.path.join('test-acemd', pdbid, 'prod'))
files = [os.path.basename(f) for f in glob(os.path.join(refdir, '*'))]
match, mismatch, error = filecmp.cmpfiles(refdir,
tmpdir,
files,
shallow=False)
if len(mismatch) != 0 or len(error) != 0 or len(match) != len(files):
raise RuntimeError(
'Different results produced by Acemd production for '
'test {} between {} and {} in files {}.'.format(
pdbid, refdir, tmpdir, mismatch))
def test_equilibration(self):
from htmd.home import home
import filecmp
from htmd.util import tempname
from glob import glob
from moleculekit.molecule import Molecule
tmpdir = tempname()
pdbid = "3PTB"
builddir = home(dataDir=os.path.join("test-acemd", pdbid, "build"))
equil = Acemd("equilibration")
mol = Molecule(os.path.join(builddir, "structure.pdb"))
celldim = mol.coords.max(axis=0) - mol.coords.min(axis=0)
equil.boxsize = " ".join(
["{:3.1f}".format(val) for val in celldim.squeeze()])
equil.run = "2000"
equil.trajectoryperiod = 200
equil.temperature = 300
equil.write(builddir, tmpdir)
# Compare with reference
refdir = home(dataDir=os.path.join("test-acemd", pdbid, "equil"))
files = [os.path.basename(f) for f in glob(os.path.join(refdir, "*"))]
match, mismatch, error = filecmp.cmpfiles(refdir,
tmpdir,
files,
shallow=False)
if len(mismatch) != 0 or len(error) != 0 or len(match) != len(files):
raise RuntimeError(
"Different results produced by Acemd equilibration for "
"test {} between {} and {} in files {}.".format(
pdbid, refdir, tmpdir, mismatch))
def test_equilibration(self):
from htmd.home import home
import filecmp
from htmd.util import tempname
from glob import glob
from htmd.molecule.molecule import Molecule
tmpdir = tempname()
pdbid = '3PTB'
builddir = home(dataDir=os.path.join('test-acemd', pdbid, 'build'))
equil = Acemd('equilibration')
mol = Molecule(os.path.join(builddir, 'structure.pdb'))
celldim = mol.coords.max(axis=0) - mol.coords.min(axis=0)
equil.celldimension = ' '.join(['{:3.1f}'.format(val) for val in celldim.squeeze()])
equil.run = '2000'
equil.trajectoryfreq = 200
equil.temperature = 300
equil.write(builddir, tmpdir)
# Compare with reference
refdir = home(dataDir=os.path.join('test-acemd', pdbid, 'equil'))
files = [os.path.basename(f) for f in glob(os.path.join(refdir, '*'))]
match, mismatch, error = filecmp.cmpfiles(refdir, tmpdir, files, shallow=False)
if len(mismatch) != 0 or len(error) != 0 or len(match) != len(files):
raise RuntimeError('Different results produced by Acemd equilibration for '
'test {} between {} and {} in files {}.'.format(pdbid, refdir, tmpdir, mismatch))
def test_equilibration(self):
from htmd.home import home
import filecmp
from htmd.util import tempname
from glob import glob
from htmd.molecule.molecule import Molecule
tmpdir = tempname()
pdbid = '3PTB'
builddir = home(dataDir=os.path.join('test-acemd', pdbid, 'build'))
equil = Acemd('equilibration')
mol = Molecule(os.path.join(builddir, 'structure.pdb'))
celldim = mol.coords.max(axis=0) - mol.coords.min(axis=0)
equil.celldimension = ' '.join(
['{:3.1f}'.format(val) for val in celldim.squeeze()])
equil.run = '2000'
equil.trajectoryfreq = 200
equil.temperature = 300
equil.write(builddir, tmpdir)
# Compare with reference
refdir = home(dataDir=os.path.join('test-acemd', pdbid, 'equil'))
files = [os.path.basename(f) for f in glob(os.path.join(refdir, '*'))]
match, mismatch, error = filecmp.cmpfiles(refdir,
tmpdir,
files,
shallow=False)
if len(mismatch) != 0 or len(error) != 0 or len(match) != len(files):
raise RuntimeError(
'Different results produced by Acemd equilibration for '
'test {} between {} and {} in files {}.'.format(
pdbid, refdir, tmpdir, mismatch))
def test_customDisulfideBonds(self):
from htmd.builder.solvate import solvate
# Test without proteinPrepare
pdbids = [
'1GZM',
]
for pid in pdbids:
np.random.seed(1)
mol = Molecule(pid)
mol.filter('protein')
smol = solvate(mol)
ffs = defaultFf()
disu = [['segid 1 and resid 110', 'segid 1 and resid 187'],
['segid 0 and resid 110', 'segid 0 and resid 187']]
tmpdir = os.path.join(self.testDir, 'withoutProtPrep', pid)
_ = build(smol, ff=ffs, outdir=tmpdir, disulfide=disu)
refdir = home(dataDir=join('test-amber-build', 'nopp', pid))
TestAmberBuild._compareResultFolders(refdir, tmpdir, pid)
np.random.seed(1)
tmpdir = os.path.join(self.testDir, 'withoutProtPrep', pid)
_ = build(smol, ff=ffs, outdir=tmpdir)
refdir = home(dataDir=join('test-amber-build', 'nopp', pid))
TestAmberBuild._compareResultFolders(refdir, tmpdir, pid)
def setUpClass(self):
from htmd.simlist import simlist, simfilter
from glob import glob
from htmd.projections.metric import Metric
from moleculekit.projections.metricdistance import MetricDistance
from moleculekit.projections.metricdihedral import MetricDihedral
from moleculekit.util import tempname
from htmd.home import home
from os.path import join
sims = simlist(
glob(join(home(dataDir="adaptive"), "data", "*", "")),
glob(join(home(dataDir="adaptive"), "input", "*")),
)
fsims = simfilter(sims, tempname(), "not water")
metr = Metric(fsims)
metr.set(
MetricDistance(
"protein and resid 10 and name CA",
"resname BEN and noh",
periodic="selections",
metric="contacts",
groupsel1="residue",
threshold=4,
)
)
self.data1 = metr.project()
metr.set(MetricDihedral())
self.data2 = metr.project()
def test_acemd3(self):
from htmd.util import tempname
from htmd.home import home
from glob import glob
import os
pd = Production()
pd.runtime = 4
pd.timeunits = "ns"
pd.temperature = 300
pd.useconstraints = True
pd.constraints = {
"protein and name CA": 1,
"protein and noh and not name CA": 0.1,
}
pd.fb_reference = "protein and name CA"
pd.fb_selection = "resname MOL and noh"
pd.fb_box = [-21, 21, -19, 19, 29, 30]
pd.fb_k = 5
tmpdir = tempname()
pd.write(
home(dataDir=os.path.join("test-protocols", "equilibration",
"acemd3", "protLig", "postrun")),
tmpdir,
)
# Compare with reference
refdir = home(dataDir=os.path.join("test-protocols", "production",
"acemd3", "protLig", "prerun"))
files = [os.path.basename(f) for f in glob(os.path.join(refdir, "*"))]
self._compareResultFolders(refdir, tmpdir, "protLig")
def setUp(self):
self.lfh = sys.stderr
self.verbose = False
self.pathPdbxDataFile = os.path.join(home(dataDir='molecule-readers'),
"1kip.cif")
self.pathBigPdbxDataFile = os.path.join(
home(dataDir='molecule-readers'), "1ffk.cif")
self.pathSFDataFile = os.path.join(home(dataDir='molecule-readers'),
"1kip-sf.cif")
def setUp(self):
self.h2_074_file = os.path.join(home('test-qm'), 'H2-0.74.mol2')
self.h2_074 = FFMolecule(self.h2_074_file, method=FFTypeMethod.NONE)
molFile = os.path.join(home('test-qm'), 'H2-1.00.mol2')
self.h2_100 = FFMolecule(molFile, method=FFTypeMethod.NONE)
molFile = os.path.join(home('test-qm'), 'H2O2-90.mol2')
self.h2o2_90 = FFMolecule(molFile, method=FFTypeMethod.NONE)
def setUp(self):
molFile = os.path.join(home('test-qm'), 'H2-0.74.mol2')
self.h2_074 = Molecule(molFile)
molFile = os.path.join(home('test-qm'), 'H2-1.00.mol2')
self.h2_100 = Molecule(molFile)
molFile = os.path.join(home('test-qm'), 'H2O2-90.mol2')
self.h2o2_90 = Molecule(molFile)
def setUp(self):
molFile = os.path.join(home('test-qm'), 'H2-0.74.mol2')
self.h2_074 = Molecule(molFile)
molFile = os.path.join(home('test-qm'), 'H2-1.00.mol2')
self.h2_100 = Molecule(molFile)
molFile = os.path.join(home('test-qm'), 'H2O2-90.mol2')
self.h2o2_90 = Molecule(molFile)
def setUpClass(self):
from htmd.molecule.molecule import Molecule
from os import path
self.mol = Molecule(
path.join(home(), 'data', 'metricdistance', 'filtered.pdb'))
self.mol_skipped = self.mol.copy()
self.mol.read(path.join(home(), 'data', 'metricdistance', 'traj.xtc'))
self.mol_skipped.read(path.join(home(), 'data', 'metricdistance',
'traj.xtc'),
skip=10)
def test_simlist_auto_structure(self):
from htmd.home import home
from htmd.projections.metric import _singleMolfile
sims = simlist(
glob(path.join(home(dataDir="adaptive"), "data", "*", "")),
glob(path.join(home(dataDir="adaptive"), "input", "*")),
)
x = sims[0].copy()
assert x == sims[0]
assert x != sims[1]
assert len(sims[0].molfile) == 2
assert _singleMolfile(sims)[0]
def test_tmscore(self):
from htmd.molecule.molecule import Molecule
expectedTMscore = np.array([0.21418524, 0.2367377, 0.23433833, 0.21362964, 0.20935164,
0.20279461, 0.27012895, 0.22675238, 0.21230793, 0.2372011])
expectedRMSD = np.array([3.70322128, 3.43637027, 3.188193, 3.84455877, 3.53053882,
3.46781854, 2.93777629, 2.97978692, 2.70792428, 2.63051318])
mol = Molecule(os.path.join(home(dataDir='tmscore'), 'filtered.pdb'))
mol.read(os.path.join(home(dataDir='tmscore'), 'traj.xtc'))
ref = Molecule(os.path.join(home(dataDir='tmscore'), 'ntl9_2hbb.pdb'))
tmscore, rmsd = molTMscore(mol, ref, mol.atomselect('protein'), ref.atomselect('protein'))
self.assertTrue(np.allclose(tmscore, expectedTMscore))
self.assertTrue(np.allclose(rmsd, expectedRMSD))
def test_simlist_single_structure(self):
from htmd.home import home
from htmd.projections.metric import _singleMolfile
sims = simlist(
glob(path.join(home(dataDir="adaptive"), "data", "*", "")),
path.join(home(dataDir="adaptive"), "input", "e1s1_1",
"structure.pdb"),
)
x = sims[0].copy()
assert x == sims[0]
assert x != sims[1]
assert not isinstance(sims[0].molfile, list)
assert _singleMolfile(sims)[0]
def test_customDisulfideBonds(self):
from htmd.molecule.molecule import Molecule
from htmd.builder.solvate import solvate
from htmd.home import home
from htmd.util import tempname, assertSameAsReferenceDir
import os
import numpy as np
# Use pre-prepared files so we can tell whether the error is in prepare or in build
# Inputs are reference outputs of proteinprepare.
preparedInputDir = home(dataDir='test-proteinprepare')
pdb = '1GZM'
inFile = os.path.join(preparedInputDir, pdb,
"{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
np.random.seed(1) # Needed for ions
smol = solvate(mol)
topos = ['top/top_all36_prot.rtf', 'top/top_water_ions.rtf']
params = ['par/par_all36_prot_mod.prm', 'par/par_water_ions.prm']
disu = [['segid 1 and resid 110', 'segid 1 and resid 187'],
['segid 0 and resid 110', 'segid 0 and resid 187']]
tmpdir = tempname()
_ = build(smol,
topo=topos,
param=params,
outdir=tmpdir,
disulfide=disu)
compareDir = home(dataDir=os.path.join('test-charmm-build', pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
# TODO: Remove this after deprecation
from htmd.builder.builder import DisulfideBridge
np.random.seed(1) # Needed for ions
disu = [
DisulfideBridge('1', 110, '1', 187),
DisulfideBridge('0', 110, '0', 187)
]
tmpdir = tempname()
_ = build(smol,
topo=topos,
param=params,
outdir=tmpdir,
disulfide=disu)
compareDir = home(dataDir=os.path.join('test-charmm-build', pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
def compareVersions():
from htmd.home import home
from htmd.version import version
from natsort import natsorted
import os
import time
#t = time.time()
__file = os.path.join(home(), '.latestversion')
if not os.path.isfile(__file) or time.time() > os.path.getmtime(
__file
) + 86400: #86400: # Check if one day has passed since last version check
_writeLatestVersionFile(__file)
f = open(__file, 'r')
latestver = f.read()
f.close()
currver = version()
if currver != 'unpackaged' and natsorted(
(latestver, currver))[1] != currver:
print(
'New HTMD version ({}) is available. You are currently on ({}). Use \'conda update htmd\' to update to the new version.'
.format(latestver, currver))
else:
print('You are on the latest HTMD version ({}).'.format(currver))
def listFiles():
""" Lists all available AMBER forcefield files
"""
try:
tleap = check_output(['which', 'tleap'],
stderr=DEVNULL).decode('UTF-8').rstrip('\n')
except:
raise NameError(
'tleap not found. You should either have AmberTools or ambermini installed '
'(to install ambermini do: conda install ambermini)')
amberhome = path.normpath(path.join(path.dirname(tleap), '../'))
# Original AMBER FFs
amberdir = path.join(amberhome, 'dat', 'leap', 'cmd')
ffs = [
f for f in os.listdir(amberdir) if path.isfile(path.join(amberdir, f))
]
print('---- Forcefield files list: ' + path.join(amberdir, '') + ' ----')
for f in ffs:
print(f)
# Extra AMBER FFs on HTMD
htmdamberdir = path.join(home(), 'builder', 'amberfiles', '')
extraffs = [
f + '/' +
path.basename(glob(os.path.join(htmdamberdir, f) + '/leaprc.*')[0])
for f in os.listdir(htmdamberdir)
if os.path.isdir(os.path.join(htmdamberdir, f))
and len(glob(os.path.join(htmdamberdir, f) + '/leaprc.*')) == 1
]
print('---- Extra forcefield files list: ' + path.join(htmdamberdir, '') +
' ----')
for f in extraffs:
print(f)
def _locateFile(fname, type, tleap):
amberhome = os.path.normpath(os.path.join(os.path.dirname(tleap), '../'))
htmdamberdir = os.path.abspath(os.path.join(home(), 'builder', 'amberfiles', ''))
if type == 'topo':
topodir = os.path.join(amberhome, 'dat', 'leap', 'prep')
foundfile = glob(os.path.join(topodir, fname))
if len(foundfile) != 0:
return foundfile[0]
foundfile = glob(os.path.join(htmdamberdir, fname))
if len(foundfile) != 0:
return foundfile[0]
logger.warning('Was not able to find topology file {}'.format(fname))
elif type == 'param':
parmdir = os.path.join(amberhome, 'dat', 'leap', 'parm')
foundfile = glob(os.path.join(parmdir, fname))
if len(foundfile) != 0:
return foundfile[0]
foundfile = glob(os.path.join(htmdamberdir, fname))
if len(foundfile) != 0:
return foundfile[0]
logger.warning('Was not able to find parameter file {}'.format(fname))
elif type == 'ff':
ffdir = os.path.join(amberhome, 'dat', 'leap', 'cmd')
foundfile = glob(os.path.join(ffdir, fname))
if len(foundfile) != 0:
return foundfile[0]
foundfile = glob(os.path.join(htmdamberdir, fname))
if len(foundfile) != 0:
return foundfile[0]
logger.warning('Was not able to find forcefield file {}'.format(fname))
def listFiles():
""" Lists all available Charmm topologies and parameter files
Examples
--------
>>> from htmd.builder import charmm
>>> charmm.listFiles() # doctest: +ELLIPSIS
---- Topologies files list...
"""
from natsort import natsorted
charmmdir = path.join(home(), 'builder', 'charmmfiles', '') # maybe just lookup current module?
topos = natsorted(glob(path.join(charmmdir, 'top', '*.rtf')))
params = natsorted(glob(path.join(charmmdir, 'par', '*.prm')))
streams = natsorted(glob(path.join(charmmdir, 'str', '*', '*.str')))
print('---- Topologies files list: ' + path.join(charmmdir, 'top', '') + ' ----')
for t in topos:
t = t.replace(charmmdir, '')
print(t)
print('---- Parameters files list: ' + path.join(charmmdir, 'par', '') + ' ----')
for p in params:
p = p.replace(charmmdir, '')
print(p)
print('---- Stream files list: ' + path.join(charmmdir, 'str', '') + ' ----')
for s in streams:
s = s.replace(charmmdir, '')
print(s)
def _locateFile(fname, type, tleap):
amberhome = os.path.normpath(os.path.join(os.path.dirname(tleap), '../'))
htmdamberdir = os.path.abspath(
os.path.join(home(), 'builder', 'amberfiles', ''))
if type == 'topo':
topodir = os.path.join(amberhome, 'dat', 'leap', 'prep')
foundfile = glob(os.path.join(topodir, fname))
if len(foundfile) != 0:
return foundfile[0]
foundfile = glob(os.path.join(htmdamberdir, fname))
if len(foundfile) != 0:
return foundfile[0]
logger.warning('Was not able to find topology file {}'.format(fname))
elif type == 'param':
parmdir = os.path.join(amberhome, 'dat', 'leap', 'parm')
foundfile = glob(os.path.join(parmdir, fname))
if len(foundfile) != 0:
return foundfile[0]
foundfile = glob(os.path.join(htmdamberdir, fname))
if len(foundfile) != 0:
return foundfile[0]
logger.warning('Was not able to find parameter file {}'.format(fname))
elif type == 'ff':
ffdir = os.path.join(amberhome, 'dat', 'leap', 'cmd')
foundfile = glob(os.path.join(ffdir, fname))
if len(foundfile) != 0:
return foundfile[0]
foundfile = glob(os.path.join(htmdamberdir, fname))
if len(foundfile) != 0:
return foundfile[0]
logger.warning('Was not able to find forcefield file {}'.format(fname))
def setUp(self):
self.maxDiff = None
self.dataDir = home(dataDir='test-param')
if os.environ.get('TRAVIS_OS_NAME') == 'osx':
self.skipTest('Mac does not work!')
def licenseEntitlements():
libdir = home(libDir=True)
# No liblicense.so for OS X yet. Need to buy it
if platform.system() == "Darwin":
return dict()
if platform.system() == "Windows":
cdll.LoadLibrary(os.path.join(libdir, "libgcc_s_seh-1.dll"))
if os.path.exists(os.path.join(libdir, "psprolib.dll")):
cdll.LoadLibrary(os.path.join(libdir, "psprolib.dll"))
lib = cdll.LoadLibrary(os.path.join(libdir, "liblicense.so"))
arg1 = create_string_buffer(2048)
arg2 = c_int(2048)
lib.license_check(arg1, arg2)
val = (arg1.value.decode("utf-8")).split(":")
toks = dict()
for v in val:
x = v.split("-")
if len(x) > 1:
if x[0] not in toks:
toks[x[0]] = dict()
if (x[1] not in toks[x[0]]):
toks[x[0]][x[1]] = 0
try:
toks[x[0]][x[1]] = toks[x[0]][x[1]] + int(x[2])
except:
pass
return toks
def test_run_water(self):
from htmd.util import tempname
from htmd.home import home
from glob import glob
from subprocess import check_output
import subprocess
import shutil
import os
acemd3exe = shutil.which('acemd3', mode=os.X_OK)
if not acemd3exe:
raise NameError('Could not find acemd3, or no execute permissions are given')
for system in ['amber-equil-completed', 'charmm-equil-completed']:
pd = Production(_version=3)
pd.runtime = 5
pd.timeunits = 'steps'
pd.temperature = 300
pd.constraints = {}
# Set these down for tiny box size of water
pd.acemd.cutoff = 3
pd.acemd.switchdistance = 2
######
tmpdir = tempname()
pd.write(home(dataDir=os.path.join('test-acemd', 'tiny-water', system)), tmpdir)
try:
res = check_output(['acemd3', '--platform', 'CPU', os.getenv('ACE3ARG')], cwd=tmpdir)
except subprocess.CalledProcessError as exc:
assert False, f'Failed to run due to error: {exc}\n\n ---> Error log:\n\n{exc.output.decode("ascii")}'
res = res.decode('utf-8').strip()
print(res)
assert res.endswith('Completed simulation!'), 'Failed at system ' + system
def _run(self, molName):
self.molName = molName
logger.info('Molecule: {}'.format(self.molName))
molFile = os.path.join(home('test-charge'), self.molName + '.mol2')
self.mol = Molecule(molFile)
self.new_mols = {}
self.extras = {}
self.new_mols['Gasteiger'] = fitGasteigerCharges(self.mol)
try:
self.new_mols['AM1-BCC'] = fitChargesWithAntechamber(self.mol, type='bcc')
except:
pass
qm = Psi4()
qm.theory = 'B3LYP'
qm.basis = '6-311++G**'
workDir = os.path.join('tmp', self.molName)
os.makedirs(workDir, exist_ok=True)
for factor in [-10, -5, -4, -3, -2, -1]:
logger.info('Factor: {}'.format(factor))
key = 'ESP b {}'.format(factor)
np.random.seed(20181114) # Make ESP grid generation deterministic
self.new_mols[key], self.extras[key] = fitESPCharges(self.mol, qm, workDir, restraint_factor=10**factor)
def listFiles():
""" Lists all available Charmm topologies and parameter files
Examples
--------
>>> from htmd.builder import charmm
>>> charmm.listFiles() # doctest: +ELLIPSIS
---- Topologies files list...
"""
from natsort import natsorted
charmmdir = path.join(home(), 'builder', 'charmmfiles',
'') # maybe just lookup current module?
topos = natsorted(glob(path.join(charmmdir, 'top', '*.rtf')))
params = natsorted(glob(path.join(charmmdir, 'par', '*.prm')))
streams = natsorted(glob(path.join(charmmdir, 'str', '*', '*.str')))
print('---- Topologies files list: ' + path.join(charmmdir, 'top', '') +
' ----')
for t in topos:
t = t.replace(charmmdir, '')
print(t)
print('---- Parameters files list: ' + path.join(charmmdir, 'par', '') +
' ----')
for p in params:
p = p.replace(charmmdir, '')
print(p)
print('---- Stream files list: ' + path.join(charmmdir, 'str', '') +
' ----')
for s in streams:
s = s.replace(charmmdir, '')
print(s)
def test_project_align(self):
from htmd.molecule.molecule import Molecule
from htmd.home import home
from os import path
mol = Molecule(path.join(home(), 'data', 'metricdistance', 'filtered.pdb'))
mol.read(path.join(home(), 'data', 'metricdistance', 'traj.xtc'))
ref = mol.copy()
ref.coords = np.atleast_3d(ref.coords[:, :, 0])
metr = MetricCoordinate('protein and name CA', ref)
data = metr.project(mol)
lastcoors = np.array([6.79283285, 5.55226946, 4.49387407, 2.94484425,
5.36937141, 3.18590879, 5.75874281, 5.48864174,
1.69625032, 1.58790839, 0.57877392, -2.66498065,
-3.70919156, -3.33702421, -5.38465405, -8.43286991,
-8.15859032, -7.85062265, -10.92551327, -13.70733166], dtype=np.float32)
assert np.all(np.abs(data[-1, -20:] - lastcoors) < 0.001), 'Coordinates calculation is broken'
def test_project(self):
from htmd.molecule.molecule import Molecule
from htmd.home import home
from os import path
mol = Molecule(path.join(home(), 'data', 'metricdistance', 'filtered.pdb'))
mol.read(path.join(home(), 'data', 'metricdistance', 'traj.xtc'))
ref = mol.copy()
ref.coords = np.atleast_3d(ref.coords[:, :, 0])
metr = MetricCoordinate('protein and name CA')
data = metr.project(mol)
lastcoors = np.array([-24.77000237, -27.76000023, -30.44000244, -33.65000153,
-33.40999985, -36.32000351, -36.02000427, -36.38000107,
-39.61000061, -41.01000214, -43.80000305, -45.56000137,
-45.36000061, -47.13000488, -49.54000473, -50.6000061 ,
-50.11000061, -52.15999985, -55.1400032 , -55.73000336], dtype=np.float32)
assert np.all(np.abs(data[-1, -20:] - lastcoors) < 0.001), 'Coordinates calculation is broken'
def pp_calcMinDistances(mol, sel1, sel2, metric='distances', threshold=8, pbc=True, gap=1, truncate=None):
import os
import ctypes
from htmd.home import home
# Converting non-grouped boolean atomselection to group-style atomselections
if np.ndim(sel1) != 2:
sel1idx = tuple(np.where(sel1)[0])
sel1 = np.zeros((len(sel1idx), len(sel1)), dtype=bool)
sel1[range(sel1.shape[0]), sel1idx] = True
if np.ndim(sel2) != 2:
sel2idx = tuple(np.where(sel2)[0])
sel2 = np.zeros((len(sel2idx), len(sel2)), dtype=bool)
sel2[range(sel2.shape[0]), sel2idx] = True
box = np.array([0, 0, 0], dtype=np.float32)
if pbc:
if mol.box is None or np.sum(mol.box) == 0:
raise NameError('No periodic box dimensions given in the molecule/trajectory. '
'If you want to calculate distance without wrapping, set the pbc option to False')
box = mol.box[:, 0] # TODO: make it work for varying box size
if np.max(mol.box.T - mol.box[:, 0]) != 0:
raise NameError('Different box sizes per frame. Still unsupported by mindist. Contact Stefan Doerr.')
coords = mol.coords
# Converting from 2D boolean atomselect array to 2D int array where each row starts with the indexes of the boolean
groups1 = np.ones((sel1.shape[0], mol.numAtoms), dtype=np.int32) * -1
groups2 = np.ones((sel2.shape[0], mol.numAtoms), dtype=np.int32) * -1
for i in range(sel1.shape[0]):
idx = np.where(sel1[i, :])[0]
groups1[i, 0:len(idx)] = idx
for i in range(sel2.shape[0]):
idx = np.where(sel2[i, :])[0]
groups2[i, 0:len(idx)] = idx
# Running the actual calculations
lib = ctypes.cdll.LoadLibrary(os.path.join(home(libDir=True), 'mindist_ext.so'))
mindist = np.zeros((mol.numFrames, len(groups1) * len(groups2)), dtype=np.float32) # Preparing the return array
lib.mindist_trajectory(coords.ctypes.data_as(ctypes.POINTER(ctypes.c_float)),
box.ctypes.data_as(ctypes.POINTER(ctypes.c_float)),
groups1.ctypes.data_as(ctypes.POINTER(ctypes.c_int)),
groups2.ctypes.data_as(ctypes.POINTER(ctypes.c_int)),
ctypes.c_int(len(groups1)),
ctypes.c_int(len(groups2)),
ctypes.c_int(mol.numAtoms),
ctypes.c_int(mol.numFrames),
ctypes.c_int(int(pbc)),
mindist.ctypes.data_as(ctypes.POINTER(ctypes.c_float)))
if metric == 'contacts':
mindist = mindist <= threshold
elif metric == 'distances':
mindist = mindist.astype(dtype=np.float32)
else:
raise NameError('The metric you asked for is not supported. Check spelling and documentation')
return mindist
def setUp(self):
from htmd.home import home
from htmd.parameterization.ffmolecule import FFMolecule, FFTypeMethod
molFile = os.path.join(home('test-param'), 'H2O2.mol2')
self.mol = FFMolecule(molFile, method=FFTypeMethod.GAFF2)
self.esp = ESP()
self.esp.molecule = self.mol
def test_getEquivalentDihedrals(self):
from htmd.home import home
from htmd.parameterization.ffmolecule import FFMolecule, FFTypeMethod
molFile = os.path.join(home('test-param'), 'glycol.mol2')
self.df.molecule = FFMolecule(molFile, method=FFTypeMethod.GAFF2)
self.assertListEqual(self.df._getEquivalentDihedrals([0, 1, 2, 3]), [[0, 1, 2, 3]])
self.assertListEqual(self.df._getEquivalentDihedrals([4, 0, 1, 2]), [[4, 0, 1, 2]])
self.assertListEqual(self.df._getEquivalentDihedrals([5, 1, 2, 7]), [[5, 1, 2, 7]])
def test_guessAnglesDihedrals(self):
from htmd.home import home
from htmd.molecule.molecule import Molecule
mol = Molecule(os.path.join(home(dataDir='test-molecule-utils'), 'NH4.pdb'))
angles, dihedrals = guessAnglesAndDihedrals(mol.bonds)
self.assertTrue(angles.dtype == np.uint32, 'Returned wrong dtype for angles')
self.assertTrue(dihedrals.dtype == np.uint32, 'Returned wrong dtype for dihedrals')
self.assertTrue(np.all(angles.shape == (6, 3)), 'Returned wrong number of angles')
self.assertTrue(np.all(dihedrals.shape == (0, 4)), 'Returned wrong number of dihedrals')
def setUp(self):
if os.environ.get('TRAVIS_OS_NAME') == 'osx':
self.skipTest('Mac does not work!')
self.maxDiff = None
self.dataDir = home(dataDir='test-param')
if os.environ.get('TESTDIR') is not None:
self.testDir = os.environ['TESTDIR']
else:
self.testDir = tempname()
print('Test dir: {}'.format(self.testDir))
def test_maximalSubstructureAlignment(self):
from htmd.home import home
from htmd.molecule.molecule import Molecule
path = home(dataDir='test-molecule-graphalignment')
ref_lig = Molecule(os.path.join(path, 'ref_lig.pdb'))
lig2align = Molecule(os.path.join(path, 'lig2align.pdb'))
lig_aligned = maximalSubstructureAlignment(ref_lig, lig2align)
lig_reference = Molecule(os.path.join(path, 'lig_aligned.pdb'))
self.assertTrue(np.allclose(lig_aligned.coords, lig_reference.coords, rtol=1e-4),
'maximalSubstructureAlignment produced different coords')
def test_production(self):
from htmd.home import home
import filecmp
from htmd.util import tempname
from glob import glob
tmpdir = tempname()
pdbid = '3PTB'
prod = Acemd('production')
prod.run = '2000'
prod.trajectoryfreq = 200
prod.temperature = 300
prod.write(home(dataDir=os.path.join('test-acemd', pdbid, 'equil_out')), tmpdir)
print(tmpdir)
# Compare with reference
refdir = home(dataDir=os.path.join('test-acemd', pdbid, 'prod'))
files = [os.path.basename(f) for f in glob(os.path.join(refdir, '*'))]
match, mismatch, error = filecmp.cmpfiles(refdir, tmpdir, files, shallow=False)
if len(mismatch) != 0 or len(error) != 0 or len(match) != len(files):
raise RuntimeError('Different results produced by Acemd production for '
'test {} between {} and {} in files {}.'.format(pdbid, refdir, tmpdir, mismatch))
def test_customDisulfideBonds(self):
from htmd.molecule.molecule import Molecule
from htmd.builder.solvate import solvate
from htmd.home import home
from htmd.util import tempname, assertSameAsReferenceDir
import os
import numpy as np
# Use pre-prepared files so we can tell whether the error is in prepare or in build
# Inputs are reference outputs of proteinprepare.
preparedInputDir = home(dataDir='test-proteinprepare')
pdb = '1GZM'
inFile = os.path.join(preparedInputDir, pdb, "{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
np.random.seed(1) # Needed for ions
smol = solvate(mol)
topos = ['top/top_all36_prot.rtf', 'top/top_water_ions.rtf']
params = ['par/par_all36_prot_mod.prm', 'par/par_water_ions.prm']
disu = [['segid 1 and resid 110', 'segid 1 and resid 187'], ['segid 0 and resid 110', 'segid 0 and resid 187']]
tmpdir = tempname()
_ = build(smol, topo=topos, param=params, outdir=tmpdir, disulfide=disu)
compareDir = home(dataDir=os.path.join('test-charmm-build', pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
# TODO: Remove this after deprecation
from htmd.builder.builder import DisulfideBridge
np.random.seed(1) # Needed for ions
disu = [DisulfideBridge('1', 110, '1', 187), DisulfideBridge('0', 110, '0', 187)]
tmpdir = tempname()
_ = build(smol, topo=topos, param=params, outdir=tmpdir, disulfide=disu)
compareDir = home(dataDir=os.path.join('test-charmm-build', pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
def test_customDisulfideBonds(self):
from htmd.builder.solvate import solvate
# Test without proteinPrepare
pdbids = ['1GZM', ]
for pid in pdbids:
np.random.seed(1)
mol = Molecule(pid)
mol.filter('protein')
smol = solvate(mol)
ffs = defaultFf()
disu = [['segid 1 and resid 110', 'segid 1 and resid 187'],
['segid 0 and resid 110', 'segid 0 and resid 187']]
tmpdir = os.path.join(self.testDir, 'withoutProtPrep', pid)
_ = build(smol, ff=ffs, outdir=tmpdir, disulfide=disu)
refdir = home(dataDir=join('test-amber-build', 'nopp', pid))
TestAmberBuild._compareResultFolders(refdir, tmpdir, pid)
np.random.seed(1)
tmpdir = os.path.join(self.testDir, 'withoutProtPrep', pid)
_ = build(smol, ff=ffs, outdir=tmpdir)
refdir = home(dataDir=join('test-amber-build', 'nopp', pid))
TestAmberBuild._compareResultFolders(refdir, tmpdir, pid)
def search(key, name):
""" Searches for CHARMM files containing a given definition.
Parameters
----------
key : str
A key
name : str
The corresponding name
Examples
--------
>>> charmm.search(key='RESI', name = 'CHL1') # doctest: +SKIP
"""
charmmdir = path.join(home(), 'builder', 'charmmfiles', '')
os.system('find {} -type f -exec grep -n "{} {}" {{}} +'.format(charmmdir, key, name))
def setUp(self):
from htmd.home import home
from htmd.parameterization.util import getEquivalentsAndDihedrals
from htmd.molecule.molecule import Molecule
molFile = os.path.join(home('test-param'), 'H2O2.mol2')
mol = Molecule(molFile, guessNE='bonds', guess=('angles', 'dihedrals'))
mol, equivalents, all_dihedrals = getEquivalentsAndDihedrals(mol)
self.mol = mol
self.esp = ESP()
self.esp.molecule = self.mol
# Precalculating here for the tests
equivalents = detectEquivalentAtoms(self.esp.molecule)
self.esp._equivalent_atom_groups = equivalents[0]
self.esp._equivalent_group_by_atom = equivalents[2]
def testWithoutProteinPrepare(self):
from htmd.builder.solvate import solvate
# Test without proteinPrepare
pdbids = ['3PTB']
# pdbids = ['3PTB', '1A25', '1GZM', '1U5U']
for pid in pdbids:
np.random.seed(1)
mol = Molecule(pid)
mol.filter('protein')
smol = solvate(mol)
ffs = defaultFf()
tmpdir = os.path.join(self.testDir, 'withoutProtPrep', pid)
_ = build(smol, ff=ffs, outdir=tmpdir)
refdir = home(dataDir=join('test-amber-build', 'nopp', pid))
TestAmberBuild._compareResultFolders(refdir, tmpdir, pid)
def readConfig(self, configfile):
import json
if not os.path.exists(configfile):
from htmd.home import home
configfile = os.path.join(home(), 'mdengine', 'acemd', 'config', '{}.json'.format(configfile))
with open(configfile, 'r') as f:
config = json.load(f)
for key in config:
if key == 'restraints':
self.restraints = []
for restr in ensurelist(config[key]['value']):
self.restraints.append(_Restraint._fromDict(restr))
else:
setattr(self, key, config[key]['value'])
def listFiles():
""" Lists all available Charmm topologies and parameter files
"""
charmmdir = path.join(home(), 'builder', 'charmmfiles', '') # maybe just lookup current module?
topos = natsorted(glob(path.join(charmmdir, 'top', '*.rtf')))
params = natsorted(glob(path.join(charmmdir, 'par', '*.prm')))
streams = natsorted(glob(path.join(charmmdir, 'str', '*', '*.str')))
print('---- Topologies files list: ' + path.join(charmmdir, 'top', '') + ' ----')
for t in topos:
t = t.replace(charmmdir, '')
print(t)
print('---- Parameters files list: ' + path.join(charmmdir, 'par', '') + ' ----')
for p in params:
p = p.replace(charmmdir, '')
print(p)
print('---- Stream files list: ' + path.join(charmmdir, 'str', '') + ' ----')
for s in streams:
s = s.replace(charmmdir, '')
print(s)
def testWithProteinPrepare(self):
from htmd.builder.preparation import proteinPrepare
from htmd.builder.solvate import solvate
# Test with proteinPrepare
pdbids = ['3PTB']
# pdbids = ['3PTB', '1A25', '1GZM'] # '1U5U' out because it has AR0 (no parameters)
for pid in pdbids:
np.random.seed(1)
mol = Molecule(pid)
mol.filter('protein')
mol = proteinPrepare(mol)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
smol = solvate(mol)
ffs = defaultFf()
tmpdir = os.path.join(self.testDir, 'withProtPrep', pid)
_ = build(smol, ff=ffs, outdir=tmpdir)
refdir = home(dataDir=join('test-amber-build', 'pp', pid))
TestAmberBuild._compareResultFolders(refdir, tmpdir, pid)
def _getPDB(pdbid):
import requests
from htmd.molecule.support import string_to_tempfile
from htmd.home import home
# Try loading it from the pdb data directory
tempfile = False
localpdb = os.path.join(home(dataDir='pdb'), pdbid.lower() + '.pdb')
if os.path.isfile(localpdb):
logger.info('Using local copy for {:s}: {:s}'.format(pdbid, localpdb))
filepath = localpdb
else:
# or the PDB website
logger.info('Attempting PDB query for {:s}'.format(pdbid))
r = requests.get('https://files.rcsb.org/download/{}.pdb'.format(pdbid))
if r.status_code == 200:
filepath = string_to_tempfile(r.content.decode('ascii'), 'pdb')
tempfile = True
else:
raise NameError('Invalid PDB code')
return filepath, tempfile
def listLipids():
""" Lists all available lipids
Examples
--------
>>> from htmd.membranebuilder.build_membrane import buildMembrane
>>> build_membrane.listLipids()
---- Lipids list: ...
"""
from htmd.home import home
import os
from natsort import natsorted
membranebuilderhome = os.path.join( home(), 'membranebuilder', 'lipids', '' )
lipids = natsorted(glob( os.path.join(membranebuilderhome, '*')))
print('---- Lipids list: ' + membranebuilderhome + ' ----')
for l in lipids:
l = os.path.basename(l)
print('- ', l)
def listFiles():
""" Lists all available AMBER forcefield files
"""
tleap = shutil.which("tleap")
if not tleap:
raise NameError('tleap not found. You should either have AmberTools or ambermini installed '
'(to install ambermini do: conda install ambermini -c acellera)')
amberhome = path.normpath(path.join(path.dirname(tleap), '../'))
# Original AMBER FFs
amberdir = path.join(amberhome, 'dat', 'leap', 'cmd')
ffs = [f for f in os.listdir(amberdir) if path.isfile(path.join(amberdir, f))]
print('---- Forcefield files list: ' + path.join(amberdir, '') + ' ----')
for f in ffs:
print(f)
amberdir = path.join(amberhome, 'dat', 'leap', 'cmd', 'oldff')
ffs = [f for f in os.listdir(amberdir) if path.isfile(path.join(amberdir, f))]
print('---- OLD Forcefield files list: ' + path.join(amberdir, '') + ' ----')
for f in ffs:
print(f)
# FRCMOD files
frcmoddir = path.join(amberhome, 'dat', 'leap', 'parm')
ffs = glob(frcmoddir+"/frcmod.*")
print('---- Parameter files list: ' + path.join(frcmoddir, '') + ' ----')
for f in ffs:
print(path.basename(f))
# Extra AMBER FFs on HTMD
htmdamberdir = path.abspath(path.join(home(), 'builder', 'amberfiles', ''))
extraffs = [f + '/' + path.basename(glob(os.path.join(htmdamberdir, f) + '/leaprc.*')[0])
for f in os.listdir(htmdamberdir) if os.path.isdir(os.path.join(htmdamberdir, f))
and len(glob(os.path.join(htmdamberdir, f) + '/leaprc.*')) == 1]
print('---- Extra forcefield files list: ' + path.join(htmdamberdir, '') + ' ----')
for f in extraffs:
print(f)