def listDihedrals(filename):
# This routine gets the names of the atoms in the soft dihedrals
# It's so horrible, since we have to jump through hoops to
# set up the input for gen_soft_list
ll1 = []
ll2 = []
env = Parameterization._preflight_test(None)
mol = Molecule(filename)
mol = Parameterization._rename_mol(mol)
mol.bonds = mol._guessBonds()
# make a tempdir
with tempfile.TemporaryDirectory() as td:
# td=tempfile.mkdtemp()
# print(td)
pwd = os.getcwd()
os.chdir(td)
f = open("mol.prm", "w")
f.close()
mol.write("mol.pdb")
mol.write("mol-opt.xyz")
mol.write("mol.xpsf", type="psf")
for charge in range(-1, 2):
subprocess.check_output([
env['BIN_MATCH'], "-charge",
str(charge), "-forcefield", "top_all36_cgenff_new",
"mol.pdb"
],
stderr=subprocess.STDOUT,
shell=False,
stdin=None)
subprocess.check_output(
[env['BIN_GEN_XPSF'], "mol.rtf", "mol.xpsf", "MOL"],
stderr=subprocess.STDOUT,
shell=False,
stdin=None)
subprocess.check_output([env['BIN_GEN_SOFT_LIST']],
stderr=subprocess.STDOUT,
shell=False,
stdin=None)
f = open("soft-dih-list.txt", "r")
ff = f.readlines()
for l in ff:
ss = []
tt = []
for m in l.split():
tt.append(int(m))
ss.append(mol.name[int(m) - 1].strip().upper())
ll1.append(tt)
ll2.append(ss)
f.close()
os.chdir(pwd)
return ll1, ll2
def to_molecule(self):
from htmd.molecule.molecule import Molecule
coords = self.get_coords()
elements = self.get_elements()
mol = Molecule()
mol.empty(self.get_natoms())
mol.resname[:] = self.get_name()[:3]
mol.resid[:] = 1
mol.name[:] = elements
mol.element[:] = elements
mol.charge[:] = self.get_charges()
mol.coords[:, :, 0] = coords
mol.viewname = self.get_name()
mol.bonds, mol.bondtype = self.get_bonds()
return mol
def build(mol,
ff=None,
topo=None,
param=None,
prefix='structure',
outdir='./build',
caps=None,
ionize=True,
saltconc=0,
saltanion=None,
saltcation=None,
disulfide=None,
tleap='tleap',
execute=True,
atomtypes=None,
offlibraries=None):
""" Builds a system for AMBER
Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The Molecule object containing the system
ff : list of str
A list of leaprc forcefield files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available forcefield files.
Default: :func:`amber.defaultFf <htmd.builder.amber.defaultFf>`
topo : list of str
A list of topology `prepi` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available topology files.
Default: :func:`amber.defaultTopo <htmd.builder.amber.defaultTopo>`
param : list of str
A list of parameter `frcmod` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available parameter files.
Default: :func:`amber.defaultParam <htmd.builder.amber.defaultParam>`
prefix : str
The prefix for the generated pdb and psf files
outdir : str
The path to the output directory
Default: './build'
caps : dict
A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment.
e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. Default: will apply ACE and NME caps to every
protein segment.
ionize : bool
Enable or disable ionization
saltconc : float
Salt concentration to add to the system after neutralization.
saltanion : {'Cl-'}
The anion type. Please use only AMBER ion atom names.
saltcation : {'Na+', 'K+', 'Cs+'}
The cation type. Please use only AMBER ion atom names.
disulfide : list of :class:`DisulfideBridge <htmd.builder.builder.DisulfideBridge>` objects
If None it will guess disulfide bonds. Otherwise provide a list of `DisulfideBridge` objects.
tleap : str
Path to tleap executable used to build the system for AMBER
execute : bool
Disable building. Will only write out the input script needed by tleap. Does not include ionization.
atomtypes : list of triplets
Custom atom types defined by the user as ('type', 'element', 'hybrid') triplets
e.g. (('C1', 'C', 'sp2'), ('CI', 'C', 'sp3')). Check `addAtomTypes` in AmberTools docs.
offlibraries : str or list
A path or a list of paths to OFF library files. Check `loadOFF` in AmberTools docs.
Returns
-------
molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The built system in a Molecule object
Example
-------
>>> from htmd.ui import *
>>> mol = Molecule("3PTB")
>>> molbuilt = amber.build(mol, outdir='/tmp/build') # doctest: +SKIP
...
>>> # More complex example
>>> disu = [DisulfideBridge('P', 157, 'P', 13), DisulfideBridge('K', 1, 'K', 25)]
>>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu) # doctest: +SKIP
"""
# Remove pdb protein bonds as they can be regenerated by tleap. Keep non-protein bonds i.e. for ligands
mol = mol.copy()
_removeProteinBonds(mol)
if shutil.which(tleap) is None:
raise NameError(
'Could not find executable: `{}` in the PATH. Cannot build for AMBER.'
.format(tleap))
if not os.path.isdir(outdir):
os.makedirs(outdir)
_cleanOutDir(outdir)
if ff is None:
ff = defaultFf()
if topo is None:
topo = defaultTopo()
if param is None:
param = defaultParam()
if caps is None:
caps = _defaultProteinCaps(mol)
_missingSegID(mol)
_checkMixedSegment(mol)
_checkResidueInsertions(mol)
mol = _charmmLipid2Amber(mol)
_applyProteinCaps(mol, caps)
f = open(os.path.join(outdir, 'tleap.in'), 'w')
f.write('# tleap file generated by amber.build\n')
# Printing out the forcefields
if isinstance(ff, str):
ff = [ff]
for force in ff:
f.write('source ' + force + '\n')
f.write('\n')
# Adding custom atom types
if atomtypes is not None:
atomtypes = ensurelist(tocheck=atomtypes[0], tomod=atomtypes)
f.write('addAtomTypes {\n')
for at in atomtypes:
if len(at) != 3:
raise RuntimeError(
'Atom type definitions have to be triplets. Check the AMBER documentation.'
)
f.write(' {{ "{}" "{}" "{}" }}\n'.format(at[0], at[1], at[2]))
f.write('}\n\n')
# Loading OFF libraries
if offlibraries is not None:
if not isinstance(offlibraries, list) and not isinstance(
offlibraries, tuple):
offlibraries = [
offlibraries,
]
for off in offlibraries:
f.write('loadoff {}\n\n'.format(off))
# Loading frcmod parameters
f.write('# Loading parameter files\n')
for p in param:
try:
shutil.copy(p, outdir)
f.write('loadamberparams ' + os.path.basename(p) + '\n')
except:
f.write('loadamberparams ' + p + '\n')
logger.info(
"File {:s} not found, assuming its present on the standard Amber location"
.format(p))
f.write('\n')
# Loading prepi topologies
f.write('# Loading prepi topologies\n')
for t in topo:
shutil.copy(t, outdir)
f.write('loadamberprep ' + os.path.basename(t) + '\n')
f.write('\n')
# Detect disulfide bridges if not defined by user
if disulfide is None and not ionize:
logger.info('Detecting disulfide bonds.')
disulfide = detectDisulfideBonds(mol)
# Fix structure to match the disulfide patching
if not ionize and len(disulfide) != 0:
for d in disulfide:
# Rename the residues to CYX if there is a disulfide bond
atoms1 = (mol.segid == d.segid1) & (mol.resid == d.resid1)
atoms2 = (mol.segid == d.segid2) & (mol.resid == d.resid2)
mol.resname[atoms1] = 'CYX'
mol.resname[atoms2] = 'CYX'
# Remove (eventual) HG hydrogens on these CYS (from proteinPrepare)
mol.remove(atoms1 & (mol.name == 'HG'), _logger=False)
mol.remove(atoms2 & (mol.name == 'HG'), _logger=False)
# Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
logger.debug('Writing PDB file for input to tleap.')
pdbname = os.path.join(outdir, 'input.pdb')
# mol2 files have atomtype, here we only write parts not coming from mol2
mol.write(pdbname, mol.atomtype == '')
if not os.path.isfile(pdbname):
raise NameError(
'Could not write a PDB file out of the given Molecule.')
f.write('# Loading the system\n')
f.write('mol = loadpdb input.pdb\n\n')
if np.sum(mol.atomtype != '') != 0:
logger.debug('Writing mol2 files for input to tleap.')
segs = np.unique(mol.segid[mol.atomtype != ''])
combstr = 'mol = combine {mol'
for s in segs:
name = 'segment{}'.format(s)
mol2name = os.path.join(outdir, '{}.mol2'.format(name))
mol.write(mol2name, (mol.atomtype != '') & (mol.segid == s))
if not os.path.isfile(mol2name):
raise NameError(
'Could not write a mol2 file out of the given Molecule.')
f.write('# Loading the rest of the system\n')
f.write('{} = loadmol2 {}.mol2\n\n'.format(name, name))
combstr += ' {}'.format(name)
combstr += '}\n\n'
f.write(combstr)
# Write patches for disulfide bonds (only after ionizing)
if not ionize and len(disulfide) != 0:
f.write('# Adding disulfide bonds\n')
for d in disulfide:
# Convert to stupid amber residue numbering
uqseqid = sequenceID(
(mol.resid, mol.insertion, mol.segid)) + mol.resid[0]
uqres1 = int(
np.unique(uqseqid[(mol.segid == d.segid1)
& (mol.resid == d.resid1)]))
uqres2 = int(
np.unique(uqseqid[(mol.segid == d.segid2)
& (mol.resid == d.resid2)]))
f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
f.write('\n')
f.write('# Writing out the results\n')
f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
f.write('quit')
f.close()
molbuilt = None
if execute:
# Source paths of extra dirs (our dirs, not amber default)
htmdamberdir = os.path.abspath(
os.path.join(home(), 'builder', 'amberfiles'))
sourcepaths = [htmdamberdir]
sourcepaths += [
os.path.join(htmdamberdir, os.path.dirname(f)) for f in ff
if os.path.isfile(os.path.join(htmdamberdir, f))
]
extrasource = []
for p in sourcepaths:
extrasource.append('-I')
extrasource.append('{}'.format(p))
logpath = os.path.abspath(os.path.join(outdir, 'log.txt'))
logger.info('Starting the build.')
currdir = os.getcwd()
os.chdir(outdir)
f = open(logpath, 'w')
try:
cmd = [tleap, '-f', './tleap.in']
cmd[1:1] = extrasource
call(cmd, stdout=f)
except:
raise NameError('tleap failed at execution')
f.close()
os.chdir(currdir)
logger.info('Finished building.')
if os.path.exists(os.path.join(outdir, 'structure.crd')) and \
os.path.getsize(os.path.join(outdir, 'structure.crd')) != 0 and \
os.path.getsize(os.path.join(outdir, 'structure.prmtop')) != 0:
molbuilt = Molecule(os.path.join(outdir, 'structure.prmtop'))
molbuilt.read(os.path.join(outdir, 'structure.crd'))
else:
raise NameError(
'No structure pdb/prmtop file was generated. Check {} for errors in building.'
.format(logpath))
if ionize:
shutil.move(os.path.join(outdir, 'structure.crd'),
os.path.join(outdir, 'structure.noions.crd'))
shutil.move(os.path.join(outdir, 'structure.prmtop'),
os.path.join(outdir, 'structure.noions.prmtop'))
totalcharge = np.sum(molbuilt.charge)
nwater = np.sum(molbuilt.atomselect('water and noh'))
anion, cation, anionatom, cationatom, nanion, ncation = ionizef(
totalcharge,
nwater,
saltconc=saltconc,
ff='amber',
anion=saltanion,
cation=saltcation)
newmol = ionizePlace(mol, anion, cation, anionatom, cationatom,
nanion, ncation)
# Redo the whole build but now with ions included
return build(newmol,
ff=ff,
topo=topo,
param=param,
prefix=prefix,
outdir=outdir,
caps={},
ionize=False,
execute=execute,
saltconc=saltconc,
disulfide=disulfide,
tleap=tleap,
atomtypes=atomtypes,
offlibraries=offlibraries)
tmpbonds = molbuilt.bonds
molbuilt.bonds = [] # Removing the bonds to speed up writing
molbuilt.write(os.path.join(outdir, 'structure.pdb'))
molbuilt.bonds = tmpbonds # Restoring the bonds
return molbuilt
def build(mol,
ff=None,
topo=None,
param=None,
prefix='structure',
outdir='./build',
caps=None,
ionize=True,
saltconc=0,
saltanion=None,
saltcation=None,
disulfide=None,
tleap=None,
execute=True,
atomtypes=None,
offlibraries=None,
gbsa=False,
igb=2):
""" Builds a system for AMBER
Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The Molecule object containing the system
ff : list of str
A list of leaprc forcefield files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available forcefield files.
Default: :func:`amber.defaultFf <htmd.builder.amber.defaultFf>`
topo : list of str
A list of topology `prepi/prep/in` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available topology files.
Default: :func:`amber.defaultTopo <htmd.builder.amber.defaultTopo>`
param : list of str
A list of parameter `frcmod` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available parameter files.
Default: :func:`amber.defaultParam <htmd.builder.amber.defaultParam>`
prefix : str
The prefix for the generated pdb and psf files
outdir : str
The path to the output directory
Default: './build'
caps : dict
A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment.
e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. Default: will apply ACE and NME caps to every
protein segment.
ionize : bool
Enable or disable ionization
saltconc : float
Salt concentration to add to the system after neutralization.
saltanion : {'Cl-'}
The anion type. Please use only AMBER ion atom names.
saltcation : {'Na+', 'K+', 'Cs+'}
The cation type. Please use only AMBER ion atom names.
disulfide : list of pairs of atomselection strings
If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of
residues forming the disulfide bridge.
tleap : str
Path to tleap executable used to build the system for AMBER
execute : bool
Disable building. Will only write out the input script needed by tleap. Does not include ionization.
atomtypes : list of triplets
Custom atom types defined by the user as ('type', 'element', 'hybrid') triplets
e.g. (('C1', 'C', 'sp2'), ('CI', 'C', 'sp3')). Check `addAtomTypes` in AmberTools docs.
offlibraries : str or list
A path or a list of paths to OFF library files. Check `loadOFF` in AmberTools docs.
gbsa : bool
Modify radii for GBSA implicit water model
igb : int
GB model. Select: 1 for mbondi, 2 and 5 for mbondi2, 7 for bondi and 8 for mbondi3.
Check section 4. The Generalized Born/Surface Area Model of the AMBER manual.
Returns
-------
molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The built system in a Molecule object
Example
-------
>>> from htmd.ui import * # doctest: +SKIP
>>> mol = Molecule("3PTB")
>>> molbuilt = amber.build(mol, outdir='/tmp/build') # doctest: +SKIP
>>> # More complex example
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu) # doctest: +SKIP
"""
# Remove pdb protein bonds as they can be regenerated by tleap. Keep non-protein bonds i.e. for ligands
mol = mol.copy()
_removeProteinBonds(mol)
if tleap is None:
tleap = _findTleap()
else:
if shutil.which(tleap) is None:
raise NameError(
'Could not find executable: `{}` in the PATH. Cannot build for AMBER.'
.format(tleap))
if not os.path.isdir(outdir):
os.makedirs(outdir)
_cleanOutDir(outdir)
if ff is None:
ff = defaultFf()
if topo is None:
topo = defaultTopo()
if param is None:
param = defaultParam()
if caps is None:
caps = _defaultProteinCaps(mol)
_missingSegID(mol)
_checkMixedSegment(mol)
mol = _charmmLipid2Amber(mol)
_applyProteinCaps(mol, caps)
f = open(os.path.join(outdir, 'tleap.in'), 'w')
f.write('# tleap file generated by amber.build\n')
# Printing out the forcefields
if isinstance(ff, str):
ff = [ff]
for i, force in enumerate(ff):
if not os.path.isfile(force):
force = _locateFile(force, 'ff', tleap)
if force is None:
continue
newname = 'ff{}_{}'.format(i, os.path.basename(force))
shutil.copy(force, os.path.join(outdir, newname))
f.write('source {}\n'.format(newname))
f.write('\n')
if gbsa:
gbmodels = {
1: 'mbondi',
2: 'mbondi2',
5: 'mbondi2',
7: 'bondi',
8: 'mbondi3'
}
f.write('set default PBradii {}\n\n'.format(gbmodels[igb]))
# Adding custom atom types
if atomtypes is not None:
atomtypes = ensurelist(tocheck=atomtypes[0], tomod=atomtypes)
f.write('addAtomTypes {\n')
for at in atomtypes:
if len(at) != 3:
raise RuntimeError(
'Atom type definitions have to be triplets. Check the AMBER documentation.'
)
f.write(' {{ "{}" "{}" "{}" }}\n'.format(at[0], at[1], at[2]))
f.write('}\n\n')
# Loading OFF libraries
if offlibraries is not None:
offlibraries = ensurelist(offlibraries)
for off in offlibraries:
if not os.path.isfile(off):
raise RuntimeError(
'Could not find off-library in location {}'.format(off))
newname = 'offlib{}_{}'.format(i, os.path.basename(off))
shutil.copy(off, os.path.join(outdir, newname))
f.write('loadoff {}\n'.format(newname))
# Loading frcmod parameters
f.write('# Loading parameter files\n')
for i, p in enumerate(param):
if not os.path.isfile(p):
p = _locateFile(p, 'param', tleap)
if p is None:
continue
newname = 'param{}_{}'.format(i, os.path.basename(p))
shutil.copy(p, os.path.join(outdir, newname))
f.write('loadamberparams {}\n'.format(newname))
f.write('\n')
# Loading prepi topologies
f.write('# Loading prepi topologies\n')
for i, t in enumerate(topo):
if not os.path.isfile(t):
t = _locateFile(t, 'topo', tleap)
if t is None:
continue
newname = 'topo{}_{}'.format(i, os.path.basename(t))
shutil.copy(t, os.path.join(outdir, newname))
f.write('loadamberprep {}\n'.format(newname))
f.write('\n')
f.write('# Loading the system\n')
f.write('mol = loadpdb input.pdb\n\n')
if np.sum(mol.atomtype != '') != 0:
logger.debug('Writing mol2 files for input to tleap.')
segs = np.unique(mol.segid[mol.atomtype != ''])
combstr = 'mol = combine {mol'
for s in segs:
name = 'segment{}'.format(s)
mol2name = os.path.join(outdir, '{}.mol2'.format(name))
mol.write(mol2name, (mol.atomtype != '') & (mol.segid == s))
if not os.path.isfile(mol2name):
raise NameError(
'Could not write a mol2 file out of the given Molecule.')
f.write('# Loading the rest of the system\n')
f.write('{} = loadmol2 {}.mol2\n\n'.format(name, name))
combstr += ' {}'.format(name)
combstr += '}\n\n'
f.write(combstr)
# Write patches for disulfide bonds (only after ionizing)
if not ionize:
# TODO: Remove this once we deprecate the class
from htmd.builder.builder import DisulfideBridge
from htmd.molecule.molecule import UniqueResidueID
if disulfide is not None and len(disulfide) != 0 and isinstance(
disulfide[0], DisulfideBridge):
newdisu = []
for d in disulfide:
r1 = UniqueResidueID.fromMolecule(
mol, 'resid {} and segname {}'.format(d.resid1, d.segid1))
r2 = UniqueResidueID.fromMolecule(
mol, 'resid {} and segname {}'.format(d.resid2, d.segid2))
newdisu.append([r1, r2])
disulfide = newdisu
# TODO: Remove up to here ----------------------
if disulfide is not None and len(disulfide) != 0 and isinstance(
disulfide[0][0], str):
disulfide = convertDisulfide(mol, disulfide)
if disulfide is None:
logger.info('Detecting disulfide bonds.')
disulfide = detectDisulfideBonds(mol)
# Fix structure to match the disulfide patching
if len(disulfide) != 0:
torem = np.zeros(mol.numAtoms, dtype=bool)
f.write('# Adding disulfide bonds\n')
for d in disulfide:
# Rename the residues to CYX if there is a disulfide bond
atoms1 = d[0].selectAtoms(mol, indexes=False)
atoms2 = d[1].selectAtoms(mol, indexes=False)
mol.resname[atoms1] = 'CYX'
mol.resname[atoms2] = 'CYX'
# Remove (eventual) HG hydrogens on these CYS (from proteinPrepare)
torem |= (atoms1 & (mol.name == 'HG')) | (atoms2 &
(mol.name == 'HG'))
# Convert to stupid amber residue numbering
uqseqid = sequenceID(
(mol.resid, mol.insertion, mol.segid)) + mol.resid[0]
uqres1 = int(np.unique(uqseqid[atoms1]))
uqres2 = int(np.unique(uqseqid[atoms2]))
f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
f.write('\n')
mol.remove(torem, _logger=False)
f.write('# Writing out the results\n')
f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
f.write('quit')
f.close()
# Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
logger.debug('Writing PDB file for input to tleap.')
pdbname = os.path.join(outdir, 'input.pdb')
# mol2 files have atomtype, here we only write parts not coming from mol2
# We need to write the input.pdb at the end since we modify the resname for disulfide bridges in mol
mol.write(pdbname, mol.atomtype == '')
if not os.path.isfile(pdbname):
raise NameError(
'Could not write a PDB file out of the given Molecule.')
molbuilt = None
if execute:
# Source paths of extra dirs (our dirs, not amber default)
htmdamberdir = os.path.abspath(
os.path.join(home(), 'builder', 'amberfiles'))
sourcepaths = [htmdamberdir]
sourcepaths += [
os.path.join(htmdamberdir, os.path.dirname(f)) for f in ff
if os.path.isfile(os.path.join(htmdamberdir, f))
]
extrasource = []
for p in sourcepaths:
extrasource.append('-I')
extrasource.append('{}'.format(p))
logpath = os.path.abspath(os.path.join(outdir, 'log.txt'))
logger.info('Starting the build.')
currdir = os.getcwd()
os.chdir(outdir)
f = open(logpath, 'w')
try:
cmd = [tleap, '-f', './tleap.in']
cmd[1:1] = extrasource
call(cmd, stdout=f)
except:
raise NameError('tleap failed at execution')
f.close()
errors = _logParser(logpath)
os.chdir(currdir)
if errors:
raise BuildError(errors + [
'Check {} for further information on errors in building.'.
format(logpath)
])
logger.info('Finished building.')
if os.path.exists(os.path.join(outdir, 'structure.crd')) and \
os.path.getsize(os.path.join(outdir, 'structure.crd')) != 0 and \
os.path.getsize(os.path.join(outdir, 'structure.prmtop')) != 0:
molbuilt = Molecule(os.path.join(outdir, 'structure.prmtop'))
molbuilt.read(os.path.join(outdir, 'structure.crd'))
else:
raise BuildError(
'No structure pdb/prmtop file was generated. Check {} for errors in building.'
.format(logpath))
if ionize:
shutil.move(os.path.join(outdir, 'structure.crd'),
os.path.join(outdir, 'structure.noions.crd'))
shutil.move(os.path.join(outdir, 'structure.prmtop'),
os.path.join(outdir, 'structure.noions.prmtop'))
totalcharge = np.sum(molbuilt.charge)
nwater = np.sum(molbuilt.atomselect('water and noh'))
anion, cation, anionatom, cationatom, nanion, ncation = ionizef(
totalcharge,
nwater,
saltconc=saltconc,
anion=saltanion,
cation=saltcation)
newmol = ionizePlace(mol, anion, cation, anionatom, cationatom,
nanion, ncation)
# Redo the whole build but now with ions included
return build(newmol,
ff=ff,
topo=topo,
param=param,
prefix=prefix,
outdir=outdir,
caps={},
ionize=False,
execute=execute,
saltconc=saltconc,
disulfide=disulfide,
tleap=tleap,
atomtypes=atomtypes,
offlibraries=offlibraries)
tmpbonds = molbuilt.bonds
molbuilt.bonds = [] # Removing the bonds to speed up writing
molbuilt.write(os.path.join(outdir, 'structure.pdb'))
molbuilt.bonds = tmpbonds # Restoring the bonds
return molbuilt
def build(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./', caps=None, ionize=True, saltconc=0,
saltanion=None, saltcation=None, disulfide=None, tleap='tleap', execute=True):
""" Builds a system for AMBER
Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The Molecule object containing the system
ff : list of str
A list of leaprc forcefield files. Default: ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
topo : list of str
A list of topology `prepi` files.
param : list of str
A list of parameter `frcmod` files.
prefix : str
The prefix for the generated pdb and psf files
outdir : str
The path to the output directory
caps : dict
A dictionary with keys segids and values lists of strings describing the caps of that segment.
e.g. caps['P'] = ['ACE', 'NME']. Default: will apply ACE and NME caps to proteins and no caps
to the rest.
ionize : bool
Enable or disable ionization
saltconc : float
Salt concentration to add to the system after neutralization.
saltanion : {'Cl-'}
The anion type. Please use only AMBER ion atom names.
saltcation : {'Na+', 'K+', 'Cs+'}
The cation type. Please use only AMBER ion atom names.
disulfide : np.ndarray
If None it will guess disulfide bonds. Otherwise provide a 2D array where each row is a pair of atom indexes that makes a disulfide bond
tleap : str
Path to tleap executable used to build the system for AMBER
execute : bool
Disable building. Will only write out the input script needed by tleap. Does not include ionization.
Returns
-------
molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The built system in a Molecule object
Example
-------
>>> ffs = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
>>> molbuilt = amber.build(mol, ff=ffs, outdir='/tmp/build', saltconc=0.15)
"""
# Remove pdb bonds!
mol = mol.copy()
mol.bonds = []
if shutil.which(tleap) is None:
raise NameError('Could not find executable: `' + tleap + '` in the PATH. Cannot build for AMBER.')
if not os.path.isdir(outdir):
os.makedirs(outdir)
_cleanOutDir(outdir)
if ff is None:
ff = ['leaprc.lipid14', 'leaprc.ff14SB', 'leaprc.gaff']
if topo is None:
topo = []
if param is None:
param = []
if caps is None:
caps = _defaultCaps(mol)
_missingSegID(mol)
_checkMixedSegment(mol)
logger.info('Converting CHARMM membranes to AMBER.')
mol = _charmmLipid2Amber(mol)
#_checkProteinGaps(mol)
_applyCaps(mol, caps)
f = open(path.join(outdir, 'tleap.in'), 'w')
f.write('# tleap file generated by amber.build\n')
# Printing out the forcefields
for force in ff:
f.write('source ' + force + '\n')
f.write('\n')
# Loading TIP3P water parameters
f.write('# Loading ions and TIP3P water parameters\n')
f.write('loadamberparams frcmod.ionsjc_tip3p\n\n')
# Printing out topologies
logger.info('Writing prepi files.')
f.write('# Loading prepi topologies\n')
for t in topo:
shutil.copy(t, outdir)
f.write('loadamberprep ' + path.basename(t) + '\n')
f.write('\n')
# Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
logger.info('Writing PDB file for input to tleap.')
pdbname = path.join(outdir, 'input.pdb')
mol.write(pdbname)
if not os.path.isfile(pdbname):
raise NameError('Could not write a PDB file out of the given Molecule.')
f.write('# Loading the system\n')
f.write('mol = loadpdb input.pdb\n\n')
# Printing out patches for the disulfide bridges
'''if disulfide is None and not ionize:
logger.info('Detecting disulfide bonds.')
disulfide = detectDisulfideBonds(mol)
if not ionize and len(disulfide) != 0: # Only make disu bonds after ionizing!
f.write('# Adding disulfide bonds\n')
for d in disulfide:
# Convert to stupid amber residue numbering
uqseqid = sequenceID(mol.resid)
uqres1 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid1, d.resid1))]))
uqres2 = int(np.unique(uqseqid[mol.atomselect('segid {} and resid {}'.format(d.segid2, d.resid2))]))
# Rename the CYS to CYX if there is a disulfide bond
mol.set('resname', 'CYX', sel='segid {} and resid {}'.format(d.segid1, d.resid1))
mol.set('resname', 'CYX', sel='segid {} and resid {}'.format(d.segid2, d.resid2))
f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
f.write('\n')'''
f.write('# Writing out the results\n')
f.write('savepdb mol ' + prefix + '.pdb\n')
f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
f.write('quit')
f.close()
molbuilt = None
if execute:
logpath = os.path.abspath('{}/log.txt'.format(outdir))
logger.info('Starting the build.')
currdir = os.getcwd()
os.chdir(outdir)
f = open(logpath, 'w')
try:
call([tleap, '-f', './tleap.in'], stdout=f)
except:
raise NameError('tleap failed at execution')
f.close()
os.chdir(currdir)
logger.info('Finished building.')
if path.getsize(path.join(outdir, 'structure.pdb')) != 0 and path.getsize(path.join(outdir, 'structure.prmtop')) != 0:
molbuilt = Molecule(path.join(outdir, 'structure.pdb'))
molbuilt.read(path.join(outdir, 'structure.prmtop'))
molbuilt.bonds = [] # Causes problems in ionization mol.remove and mol._removeBonds
else:
raise NameError('No structure pdb/prmtop file was generated. Check {} for errors in building.'.format(logpath))
if ionize:
shutil.move(path.join(outdir, 'structure.pdb'), path.join(outdir, 'structure.noions.pdb'))
shutil.move(path.join(outdir, 'structure.crd'), path.join(outdir, 'structure.noions.crd'))
shutil.move(path.join(outdir, 'structure.prmtop'), path.join(outdir, 'structure.noions.prmtop'))
totalcharge = np.sum(molbuilt.charge)
nwater = np.sum(molbuilt.atomselect('water and noh'))
anion, cation, anionatom, cationatom, nanion, ncation = ionizef(totalcharge, nwater, saltconc=saltconc, ff='amber', anion=saltanion, cation=saltcation)
newmol = ionizePlace(molbuilt, anion, cation, anionatom, cationatom, nanion, ncation)
# Redo the whole build but now with ions included
return build(newmol, ff=ff, topo=topo, param=param, prefix=prefix, outdir=outdir, caps={}, ionize=False,
execute=execute, saltconc=saltconc, disulfide=disulfide, tleap=tleap)
return molbuilt
def build(mol, ff=None, topo=None, param=None, prefix='structure', outdir='./build', caps=None, ionize=True, saltconc=0,
saltanion=None, saltcation=None, disulfide=None, tleap=None, execute=True, atomtypes=None,
offlibraries=None, gbsa=False, igb=2):
""" Builds a system for AMBER
Uses tleap to build a system for AMBER. Additionally it allows the user to ionize and add disulfide bridges.
Parameters
----------
mol : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The Molecule object containing the system
ff : list of str
A list of leaprc forcefield files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available forcefield files.
Default: :func:`amber.defaultFf <htmd.builder.amber.defaultFf>`
topo : list of str
A list of topology `prepi/prep/in` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available topology files.
Default: :func:`amber.defaultTopo <htmd.builder.amber.defaultTopo>`
param : list of str
A list of parameter `frcmod` files.
Use :func:`amber.listFiles <htmd.builder.amber.listFiles>` to get a list of available parameter files.
Default: :func:`amber.defaultParam <htmd.builder.amber.defaultParam>`
prefix : str
The prefix for the generated pdb and psf files
outdir : str
The path to the output directory
Default: './build'
caps : dict
A dictionary with keys segids and values lists of strings describing the caps for a particular protein segment.
e.g. caps['P'] = ['ACE', 'NME'] or caps['P'] = ['none', 'none']. Default: will apply ACE and NME caps to every
protein segment.
ionize : bool
Enable or disable ionization
saltconc : float
Salt concentration to add to the system after neutralization.
saltanion : {'Cl-'}
The anion type. Please use only AMBER ion atom names.
saltcation : {'Na+', 'K+', 'Cs+'}
The cation type. Please use only AMBER ion atom names.
disulfide : list of pairs of atomselection strings
If None it will guess disulfide bonds. Otherwise provide a list pairs of atomselection strings for each pair of
residues forming the disulfide bridge.
tleap : str
Path to tleap executable used to build the system for AMBER
execute : bool
Disable building. Will only write out the input script needed by tleap. Does not include ionization.
atomtypes : list of triplets
Custom atom types defined by the user as ('type', 'element', 'hybrid') triplets
e.g. (('C1', 'C', 'sp2'), ('CI', 'C', 'sp3')). Check `addAtomTypes` in AmberTools docs.
offlibraries : str or list
A path or a list of paths to OFF library files. Check `loadOFF` in AmberTools docs.
gbsa : bool
Modify radii for GBSA implicit water model
igb : int
GB model. Select: 1 for mbondi, 2 and 5 for mbondi2, 7 for bondi and 8 for mbondi3.
Check section 4. The Generalized Born/Surface Area Model of the AMBER manual.
Returns
-------
molbuilt : :class:`Molecule <htmd.molecule.molecule.Molecule>` object
The built system in a Molecule object
Example
-------
>>> from htmd.ui import * # doctest: +SKIP
>>> mol = Molecule("3PTB")
>>> molbuilt = amber.build(mol, outdir='/tmp/build') # doctest: +SKIP
>>> # More complex example
>>> disu = [['segid P and resid 157', 'segid P and resid 13'], ['segid K and resid 1', 'segid K and resid 25']]
>>> molbuilt = amber.build(mol, outdir='/tmp/build', saltconc=0.15, disulfide=disu) # doctest: +SKIP
"""
# Remove pdb protein bonds as they can be regenerated by tleap. Keep non-protein bonds i.e. for ligands
mol = mol.copy()
_removeProteinBonds(mol)
if tleap is None:
tleap = _findTleap()
else:
if shutil.which(tleap) is None:
raise NameError('Could not find executable: `{}` in the PATH. Cannot build for AMBER.'.format(tleap))
if not os.path.isdir(outdir):
os.makedirs(outdir)
_cleanOutDir(outdir)
if ff is None:
ff = defaultFf()
if topo is None:
topo = defaultTopo()
if param is None:
param = defaultParam()
if caps is None:
caps = _defaultProteinCaps(mol)
_missingSegID(mol)
_checkMixedSegment(mol)
mol = _charmmLipid2Amber(mol)
_applyProteinCaps(mol, caps)
f = open(os.path.join(outdir, 'tleap.in'), 'w')
f.write('# tleap file generated by amber.build\n')
# Printing out the forcefields
if isinstance(ff, str):
ff = [ff]
for i, force in enumerate(ff):
if not os.path.isfile(force):
force = _locateFile(force, 'ff', tleap)
if force is None:
continue
newname = 'ff{}_{}'.format(i, os.path.basename(force))
shutil.copy(force, os.path.join(outdir, newname))
f.write('source {}\n'.format(newname))
f.write('\n')
if gbsa:
gbmodels = {1: 'mbondi', 2: 'mbondi2', 5: 'mbondi2', 7: 'bondi', 8: 'mbondi3'}
f.write('set default PBradii {}\n\n'.format(gbmodels[igb]))
# Adding custom atom types
if atomtypes is not None:
atomtypes = ensurelist(tocheck=atomtypes[0], tomod=atomtypes)
f.write('addAtomTypes {\n')
for at in atomtypes:
if len(at) != 3:
raise RuntimeError('Atom type definitions have to be triplets. Check the AMBER documentation.')
f.write(' {{ "{}" "{}" "{}" }}\n'.format(at[0], at[1], at[2]))
f.write('}\n\n')
# Loading OFF libraries
if offlibraries is not None:
offlibraries = ensurelist(offlibraries)
for off in offlibraries:
if not os.path.isfile(off):
raise RuntimeError('Could not find off-library in location {}'.format(off))
newname = 'offlib{}_{}'.format(i, os.path.basename(off))
shutil.copy(off, os.path.join(outdir, newname))
f.write('loadoff {}\n'.format(newname))
# Loading frcmod parameters
f.write('# Loading parameter files\n')
for i, p in enumerate(param):
if not os.path.isfile(p):
p = _locateFile(p, 'param', tleap)
if p is None:
continue
newname = 'param{}_{}'.format(i, os.path.basename(p))
shutil.copy(p, os.path.join(outdir, newname))
f.write('loadamberparams {}\n'.format(newname))
f.write('\n')
# Loading prepi topologies
f.write('# Loading prepi topologies\n')
for i, t in enumerate(topo):
if not os.path.isfile(t):
t = _locateFile(t, 'topo', tleap)
if t is None:
continue
newname = 'topo{}_{}'.format(i, os.path.basename(t))
shutil.copy(t, os.path.join(outdir, newname))
f.write('loadamberprep {}\n'.format(newname))
f.write('\n')
f.write('# Loading the system\n')
f.write('mol = loadpdb input.pdb\n\n')
if np.sum(mol.atomtype != '') != 0:
logger.debug('Writing mol2 files for input to tleap.')
segs = np.unique(mol.segid[mol.atomtype != ''])
combstr = 'mol = combine {mol'
for s in segs:
name = 'segment{}'.format(s)
mol2name = os.path.join(outdir, '{}.mol2'.format(name))
mol.write(mol2name, (mol.atomtype != '') & (mol.segid == s))
if not os.path.isfile(mol2name):
raise NameError('Could not write a mol2 file out of the given Molecule.')
f.write('# Loading the rest of the system\n')
f.write('{} = loadmol2 {}.mol2\n\n'.format(name, name))
combstr += ' {}'.format(name)
combstr += '}\n\n'
f.write(combstr)
# Write patches for disulfide bonds (only after ionizing)
if not ionize:
# TODO: Remove this once we deprecate the class
from htmd.builder.builder import DisulfideBridge
from htmd.molecule.molecule import UniqueResidueID
if disulfide is not None and len(disulfide) != 0 and isinstance(disulfide[0], DisulfideBridge):
newdisu = []
for d in disulfide:
r1 = UniqueResidueID.fromMolecule(mol, 'resid {} and segname {}'.format(d.resid1, d.segid1))
r2 = UniqueResidueID.fromMolecule(mol, 'resid {} and segname {}'.format(d.resid2, d.segid2))
newdisu.append([r1, r2])
disulfide = newdisu
# TODO: Remove up to here ----------------------
if disulfide is not None and len(disulfide) != 0 and isinstance(disulfide[0][0], str):
disulfide = convertDisulfide(mol, disulfide)
if disulfide is None:
logger.info('Detecting disulfide bonds.')
disulfide = detectDisulfideBonds(mol)
# Fix structure to match the disulfide patching
if len(disulfide) != 0:
torem = np.zeros(mol.numAtoms, dtype=bool)
f.write('# Adding disulfide bonds\n')
for d in disulfide:
# Rename the residues to CYX if there is a disulfide bond
atoms1 = d[0].selectAtoms(mol, indexes=False)
atoms2 = d[1].selectAtoms(mol, indexes=False)
mol.resname[atoms1] = 'CYX'
mol.resname[atoms2] = 'CYX'
# Remove (eventual) HG hydrogens on these CYS (from proteinPrepare)
torem |= (atoms1 & (mol.name == 'HG')) | (atoms2 & (mol.name == 'HG'))
# Convert to stupid amber residue numbering
uqseqid = sequenceID((mol.resid, mol.insertion, mol.segid)) + mol.resid[0]
uqres1 = int(np.unique(uqseqid[atoms1]))
uqres2 = int(np.unique(uqseqid[atoms2]))
f.write('bond mol.{}.SG mol.{}.SG\n'.format(uqres1, uqres2))
f.write('\n')
mol.remove(torem, _logger=False)
f.write('# Writing out the results\n')
f.write('saveamberparm mol ' + prefix + '.prmtop ' + prefix + '.crd\n')
f.write('quit')
f.close()
# Printing and loading the PDB file. AMBER can work with a single PDB file if the segments are separate by TER
logger.debug('Writing PDB file for input to tleap.')
pdbname = os.path.join(outdir, 'input.pdb')
# mol2 files have atomtype, here we only write parts not coming from mol2
# We need to write the input.pdb at the end since we modify the resname for disulfide bridges in mol
mol.write(pdbname, mol.atomtype == '')
if not os.path.isfile(pdbname):
raise NameError('Could not write a PDB file out of the given Molecule.')
molbuilt = None
if execute:
# Source paths of extra dirs (our dirs, not amber default)
htmdamberdir = os.path.abspath(os.path.join(home(), 'builder', 'amberfiles'))
sourcepaths = [htmdamberdir]
sourcepaths += [os.path.join(htmdamberdir, os.path.dirname(f))
for f in ff if os.path.isfile(os.path.join(htmdamberdir, f))]
extrasource = []
for p in sourcepaths:
extrasource.append('-I')
extrasource.append('{}'.format(p))
logpath = os.path.abspath(os.path.join(outdir, 'log.txt'))
logger.info('Starting the build.')
currdir = os.getcwd()
os.chdir(outdir)
f = open(logpath, 'w')
try:
cmd = [tleap, '-f', './tleap.in']
cmd[1:1] = extrasource
call(cmd, stdout=f)
except:
raise NameError('tleap failed at execution')
f.close()
errors = _logParser(logpath)
os.chdir(currdir)
if errors:
raise BuildError(errors + ['Check {} for further information on errors in building.'.format(logpath)])
logger.info('Finished building.')
if os.path.exists(os.path.join(outdir, 'structure.crd')) and \
os.path.getsize(os.path.join(outdir, 'structure.crd')) != 0 and \
os.path.getsize(os.path.join(outdir, 'structure.prmtop')) != 0:
molbuilt = Molecule(os.path.join(outdir, 'structure.prmtop'))
molbuilt.read(os.path.join(outdir, 'structure.crd'))
else:
raise BuildError('No structure pdb/prmtop file was generated. Check {} for errors in building.'.format(logpath))
if ionize:
shutil.move(os.path.join(outdir, 'structure.crd'), os.path.join(outdir, 'structure.noions.crd'))
shutil.move(os.path.join(outdir, 'structure.prmtop'), os.path.join(outdir, 'structure.noions.prmtop'))
totalcharge = np.sum(molbuilt.charge)
nwater = np.sum(molbuilt.atomselect('water and noh'))
anion, cation, anionatom, cationatom, nanion, ncation = ionizef(totalcharge, nwater, saltconc=saltconc,
anion=saltanion, cation=saltcation)
newmol = ionizePlace(mol, anion, cation, anionatom, cationatom, nanion, ncation)
# Redo the whole build but now with ions included
return build(newmol, ff=ff, topo=topo, param=param, prefix=prefix, outdir=outdir, caps={}, ionize=False,
execute=execute, saltconc=saltconc, disulfide=disulfide, tleap=tleap, atomtypes=atomtypes,
offlibraries=offlibraries)
tmpbonds = molbuilt.bonds
molbuilt.bonds = [] # Removing the bonds to speed up writing
molbuilt.write(os.path.join(outdir, 'structure.pdb'))
molbuilt.bonds = tmpbonds # Restoring the bonds
return molbuilt
