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_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_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_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_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_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_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 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 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 _prep_and_run(self, mol, rtf, prm, outdir, solvated):
from htmd.builder.solvate import solvate
from htmd.apps.acemdlocal import AcemdLocal
# Do a simple solvation then run for 50ns
ionize = True
mol = Molecule(mol)
mol.center()
mol.set("segid", "L")
d = maxDistance(mol, 'all') + 6
if solvated:
mol = solvate(mol, minmax=[[-d, -d, -d], [d, d, d]])
if not solvated:
ionize = False
build_dir = os.path.join(outdir, "build")
equil_dir = os.path.join(outdir, "equil")
rtfs = ['top/top_water_ions.rtf', rtf]
prms = ['par/par_water_ions.prm', prm]
charmm.build(mol, topo=rtfs, param=prms, outdir=build_dir, ionize=ionize)
md = Equilibration()
md.runtime = 50
md.timeunits = 'ns'
md.temperature = 300
md.write(build_dir, equil_dir)
mdx = AcemdLocal()
mdx.submit(equil_dir)
mdx.wait()
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_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 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 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 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 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 test_customTeLeapImports(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)
amberhome = defaultAmberHome()
teleapimports = []
teleapimports.append(
os.path.join(amberhome, _defaultAmberSearchPaths['lib']))
teleapimports.append(
os.path.join(amberhome, _defaultAmberSearchPaths['param']))
_ = build(smol, ff=ffs, outdir=tmpdir, teleapimports=teleapimports)
refdir = home(dataDir=join('test-amber-build', 'nopp', pid))
_TestAmberBuild._compareResultFolders(refdir, tmpdir, pid)
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_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)
if len(mismatch) != 0 or len(error) != 0 or len(match) != len(files):
raise RuntimeError(
'Different results produced by amber.build for test {} between {} and {} in files {}.'.format(pid, compare, tmpdir, mismatch))
for f in deletefiles:
os.remove(f)
# Test with proteinPrepare
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 = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
tmpdir = tempname()
bmol = build(smol, ff=ffs, outdir=tmpdir)
refdir = home(dataDir=os.path.join('test-amber-build', pid))
_compareResultFolders(refdir, tmpdir, pid)
shutil.rmtree(tmpdir)
# Test without proteinPrepare
pdbids = ['3PTB', '1A25', '1GZM', '1U5U']
for pid in pdbids:
np.random.seed(1)
mol = Molecule(pid)
mol.filter('protein')
smol = solvate(mol)
def buildMembrane(xysize, ratioupper, ratiolower, waterbuff=20, minimplatform='CPU', equilibrate=True, equilplatform='CUDA', outdir=None, lipidf=None):
""" Construct a membrane containing arbitrary lipids and ratios of them.
Parameters
----------
xysize : list
A list containing the size in x and y dimensions of the membrane in Angstroms
ratioupper : dict
A dict with keys the molecule names and the ratio of that molecule for the upper layer
ratiolower : dict
Same as ratioupper but for the lower layer
waterbuff : float
The z-dimension size of the water box above and below the membrane
minimplatform : str
The platform on which to run the minimization ('CUDA' or 'CPU')
equilibrate : bool
If True it equilibrates the membrane
equilplatform : str
The platform on which to run the equilibration ('CUDA' or 'CPU')
outdir : str
A folder in which to store the psf and pdb files
lipidf : str
The path to the folder containing the single-lipid PDB structures as well as the lipid DB file
Returns
-------
mol : :class:`Molecule <moleculekit.molecule.Molecule`
The resulting membrane including surrounding waters
Examples
--------
>>> lipidratioupper = {'popc': 10, 'chl1': 1}
>>> lipidratiolower = {'popc': 8, 'chl1': 2}
>>> width = [50, 100]
>>> res = buildMembrane(width, lipidratioupper, lipidratiolower)
"""
from htmd.membranebuilder.ringpenetration import resolveRingPenetrations
from htmd.builder.solvate import solvate
from htmd.builder.charmm import build
from htmd.util import tempname
from moleculekit.molecule import Molecule
from htmd.home import home
import os
import pandas as pd
if lipidf is None:
lipidf = os.path.join(home(shareDir=True), 'membranebuilder', 'lipids')
lipiddb = pd.read_csv(os.path.join(lipidf, 'lipiddb.csv'), index_col='Name')
uqlip = np.unique(list(ratioupper.keys()) + list(ratiolower.keys()))
files = _locateLipidFiles(lipidf, uqlip)
area = np.prod(xysize)
lipids = _createLipids(ratioupper, area, lipiddb, files, leaflet='upper')
lipids += _createLipids(ratiolower, area, lipiddb, files, leaflet='lower')
_setPositionsLJSim(xysize, [l for l in lipids if l.xyz[2] > 0])
_setPositionsLJSim(xysize, [l for l in lipids if l.xyz[2] < 0])
_findNeighbours(lipids, xysize)
_loadMolecules(lipids, files)
# from globalminimization import minimize
# newpos, newrot = minimize(lipids, xysize + [100], stepxy=0.5, steprot=50, contactthresh=1)
# for i in range(len(lipids)):
# lipids[i].xyz[:2] = newpos[i]
# lipids[i].rot = newrot[i]
resolveRingPenetrations(lipids, xysize)
memb = _createMembraneMolecule(lipids)
minc = memb.get('coords', 'name P').min(axis=0) - 5
maxc = memb.get('coords', 'name P').max(axis=0) + 5
mm = [[0, 0, maxc[2] - 2], [xysize[0], xysize[1], maxc[2] + waterbuff]]
smemb = solvate(memb, minmax=mm)
mm = [[0, 0, minc[2] - waterbuff], [xysize[0], xysize[1], minc[2] + 2]]
smemb = solvate(smemb, minmax=mm)
smemb.moveBy([0, 0, -smemb.coords[:, 2, 0].min()])
if outdir is None:
outdir = tempname()
logger.info('Outdir {}'.format(outdir))
res = build(smemb, ionize=False, stream=['str/lipid/toppar_all36_lipid_cholesterol_model_1.str'], outdir=outdir)
if equilibrate:
from htmd.membranebuilder.simulate_openmm import equilibrateSystem
from shutil import copy, move
outpdb = tempname(suffix='.pdb')
charmmf = os.path.join(home(shareDir=True), 'membranebuilder', 'charmm-toppar')
equilibrateSystem(os.path.join(outdir, 'structure.pdb'), os.path.join(outdir, 'structure.psf'), outpdb,
charmmfolder=charmmf, equilplatform=equilplatform, minimplatform=minimplatform)
res = Molecule(outpdb)
res.center()
move(os.path.join(outdir, 'structure.pdb'), os.path.join(outdir, 'starting_structure.pdb'))
copy(outpdb, os.path.join(outdir, 'structure.pdb'))
return res
for f in deletefiles:
os.remove(f)
# 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')
if mol._checkInsertions():
mol.renumberResidues()
mol = proteinPrepare(mol)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
smol = solvate(mol)
ffs = defaultFf()
tmpdir = tempname()
bmol = build(smol, ff=ffs, outdir=tmpdir)
refdir = home(dataDir=join('test-amber-build', pid))
_compareResultFolders(refdir, tmpdir, pid)
shutil.rmtree(tmpdir)
# Test without proteinPrepare
pdbids = ['3PTB']
# pdbids = ['3PTB', '1A25', '1GZM', '1U5U']
for pid in pdbids:
np.random.seed(1)
mol = Molecule(pid)
mol.filter('protein')
def buildMembrane(xysize, ratioupper, ratiolower, waterbuff=20, equilibrate=True, outdir='./buildmemb/', lipidf=None):
""" Construct a membrane containing arbitrary lipids and ratios of them.
Parameters
----------
xysize : list
A list containing the size in x and y dimensions of the membrane in Angstroms
ratioupper : list of lists
A list containing sublists indicating the molecule name and the ratio of that molecule for the upper layer
ratiolower : list of lists
Same as ratioupper but for the lower layer
waterbuff : float
The z-dimension size of the water box above and below the membrane
equilibrate : bool
If True it equilibrates the membrane
outdir : str
A folder in which to store the psf and pdb files
lipidf : str
The path to the starting lipid conformations
Returns
-------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule`
The resulting membrane including surrounding waters
Examples
--------
>>> lipidratioupper = [['popc', 10], ['chl1', 1]]
>>> lipidratiolower = [['popc', 8], ['chl1', 2]]
>>> width = [50, 100]
>>> res = buildMembrane(width, lipidratioupper, lipidratiolower)
"""
from htmd.membranebuilder.ringpenetration import resolveRingPenetrations
from htmd.builder.solvate import solvate
from htmd.builder.charmm import build
from htmd.util import tempname
from htmd.molecule.molecule import Molecule
from htmd.home import home
import os
import pandas as pd
if lipidf is None:
lipidf = os.path.join(home(), 'membranebuilder', 'lipids')
lipiddb = pd.read_csv(os.path.join(home(), 'membranebuilder', 'lipiddb.csv'), index_col='Name')
uqlip = np.unique([x[0] for x in ratioupper] + [x[0] for x in ratiolower])
files = _locateLipidFiles(lipidf, uqlip)
area = np.prod(xysize)
lipids = _createLipids(ratioupper, area, lipiddb, files, leaflet='upper')
lipids += _createLipids(ratiolower, area, lipiddb, files, leaflet='lower')
_setPositionsLJSim(xysize, [l for l in lipids if l.xyz[2] > 0])
_setPositionsLJSim(xysize, [l for l in lipids if l.xyz[2] < 0])
_findNeighbours(lipids, xysize)
_loadMolecules(lipids, files)
resolveRingPenetrations(lipids, xysize)
memb = _createMembraneMolecule(lipids)
# from globalminimization import minimize
# newpos, newrot = minimize(lipids, xysize + [100], stepxy=0.5, steprot=50, contactthresh=1)
# for i in range(len(lipids)):
# lipids[i].xyz[:2] = newpos[i]
# lipids[i].rot = newrot[i]
#
# resolveRingPenetrations(lipids, xysize)
# endmemb = _createMembraneMolecule(lipids)
minc = memb.get('coords', 'name P').min(axis=0) - 5
maxc = memb.get('coords', 'name P').max(axis=0) + 5
mm = [[0, 0, maxc[2] - 2], [xysize[0], xysize[1], maxc[2] + waterbuff]]
smemb = solvate(memb, minmax=mm)
mm = [[0, 0, minc[2] - waterbuff], [xysize[0], xysize[1], minc[2] + 2]]
smemb = solvate(smemb, minmax=mm)
smemb.moveBy([0, 0, -smemb.coords[:, 2, 0].min()])
if outdir is None:
outdir = tempname()
print('Outdir ', outdir)
res = build(smemb, ionize=False, stream=['str/lipid/toppar_all36_lipid_cholesterol_model_1.str'], outdir=outdir)
if equilibrate:
from htmd.membranebuilder.simulate_openmm import equilibrateSystem
from shutil import copy, move
outpdb = tempname(suffix='.pdb')
charmmf = os.path.join(home(), 'membranebuilder', 'charmm-toppar')
equilibrateSystem(os.path.join(outdir, 'structure.pdb'), os.path.join(outdir, 'structure.psf'), outpdb, charmmfolder=charmmf)
res = Molecule(outpdb)
res.center()
move(os.path.join(outdir, 'structure.pdb'), os.path.join(outdir, 'starting_structure.pdb'))
copy(outpdb, os.path.join(outdir, 'structure.pdb'))
return res
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:
inFile = os.path.join(preparedInputDir, pdb,
"{}-prepared.pdb".format(pdb))
mol = Molecule(inFile)
mol.filter('protein') # Fix for bad proteinPrepare hydrogen placing
if mol._checkInsertions():
mol.renumberResidues()
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()
bmol = build(smol, topo=topos, param=params, outdir=tmpdir)
compareDir = home(dataDir=os.path.join('test-charmm-build', pdb))
assertSameAsReferenceDir(compareDir, tmpdir)
# shutil.rmtree(tmpdir)
from htmd.ui import *
import doctest
doctest.testmod()
from htmd.builder.amber import defaultParam, build
# Test protein ligand building with parametrized ligand
refdir = home(dataDir=join('test-amber-build', 'protLig'))
tmpdir = './protLig'
mol = Molecule(join(refdir, '3ptb_mod.pdb'))
mol.center()
lig = Molecule(join(refdir, 'benzamidine.pdb'),
guess=('bonds', 'angles', 'dihedrals'))
prm, lig = fftype(lig, method='GAFF2')
writeFRCMOD(lig, prm, join(tmpdir, 'mol.frcmod'))
lig.segid[:] = 'L'
lig.center()
from moleculekit.util import maxDistance
D = maxDistance(mol, 'all')
D += 6
lig.moveBy([0, 0, D])
newmol = Molecule()
newmol.append(lig)
newmol.append(mol)
smol = solvate(newmol, posz=3)
params = defaultParam() + [
join(tmpdir, 'mol.frcmod'),
]
_ = build(smol, outdir=tmpdir, param=params, ionize=False)