def _fillMolecule(name, resname, chain, resid, insertion, coords, segid, element,
occupancy, beta, charge, record):
numAtoms = len(name)
mol = Molecule()
mol.empty(numAtoms)
mol.name = np.array(name, dtype=mol._dtypes['name'])
mol.resname = np.array(resname, dtype=mol._dtypes['resname'])
mol.chain = np.array(chain, dtype=mol._dtypes['chain'])
mol.resid = np.array(resid, dtype=mol._dtypes['resid'])
mol.insertion = np.array(insertion, dtype=mol._dtypes['insertion'])
mol.coords = np.array(np.atleast_3d(np.vstack(coords)), dtype=mol._dtypes['coords'])
mol.segid = np.array(segid, dtype=mol._dtypes['segid'])
mol.element = np.array(element, dtype=mol._dtypes['element'])
mol.occupancy = np.array(occupancy, dtype=mol._dtypes['occupancy'])
mol.beta = np.array(beta, dtype=mol._dtypes['beta'])
# mol.charge = np.array(charge, dtype=mol._dtypes['charge'])
# mol.record = np.array(record, dtype=mol._dtypes['record'])
return mol
def _fillMolecule(name, resname, chain, resid, insertion, coords, segid,
element, occupancy, beta, charge, record):
numAtoms = len(name)
mol = Molecule()
mol.empty(numAtoms)
mol.name = np.array(name, dtype=mol._dtypes['name'])
mol.resname = np.array(resname, dtype=mol._dtypes['resname'])
mol.chain = np.array(chain, dtype=mol._dtypes['chain'])
mol.resid = np.array(resid, dtype=mol._dtypes['resid'])
mol.insertion = np.array(insertion, dtype=mol._dtypes['insertion'])
mol.coords = np.array(np.atleast_3d(np.vstack(coords)),
dtype=mol._dtypes['coords'])
mol.segid = np.array(segid, dtype=mol._dtypes['segid'])
mol.element = np.array(element, dtype=mol._dtypes['element'])
mol.occupancy = np.array(occupancy, dtype=mol._dtypes['occupancy'])
mol.beta = np.array(beta, dtype=mol._dtypes['beta'])
# mol.charge = np.array(charge, dtype=mol._dtypes['charge'])
# mol.record = np.array(record, dtype=mol._dtypes['record'])
return mol
def ionizePlace(mol, anion, cation, anionatom, cationatom, nanion, ncation, dfrom=5, dbetween=5, segname=None):
newmol = mol.copy()
logger.info('Min distance of ions from molecule: ' + str(dfrom) + 'A')
logger.info('Min distance between ions: ' + str(dbetween) + 'A')
logger.info('Placing ' + str(nanion+ncation) + ' ions.')
if (nanion + ncation) == 0:
return newmol
segname = _getSegname(newmol, segname)
nions = nanion + ncation
betabackup = newmol.beta
newmol.set('beta', sequenceID((newmol.resid, newmol.segid)))
# Find water oxygens to replace with ions
ntries = 0
maxtries = 10
while True:
ionlist = np.empty(0, dtype=int)
watindex = newmol.atomselect('noh and water and not (within ' + str(dfrom) + ' of not water)', indexes=True)
watsize = len(watindex)
if watsize == 0:
raise NameError('No waters could be found further than ' + str(dfrom) + ' from other molecules to be replaced by ions. You might need to solvate with a bigger box.')
while len(ionlist) < nions:
if len(watindex) == 0:
break
randwat = np.random.randint(len(watindex))
thision = watindex[randwat]
addit = True
if len(ionlist) != 0: # Check for distance from precious ions
ionspos = newmol.get('coords', sel=ionlist)
thispos = newmol.get('coords', sel=thision)
dists = distance.cdist(np.atleast_2d(ionspos), np.atleast_2d(thispos), metric='euclidean')
if np.any(dists < dbetween):
addit = False
if addit:
ionlist = np.append(ionlist, thision)
watindex = np.delete(watindex, randwat)
if len(ionlist) == nions:
break
ntries += 1
if ntries == maxtries:
raise NameError('Failed to add ions after ' + str(maxtries) + ' attempts. Try decreasing the ''from'' and ''between'' parameters, decreasing ion concentration or making a larger water box.')
# Delete waters but keep their coordinates
waterpos = np.atleast_2d(newmol.get('coords', ionlist))
stringsel = 'beta'
for x in newmol.beta[ionlist]:
stringsel += ' ' + str(int(x))
atmrem = np.sum(newmol.atomselect(stringsel))
atmput = 3 * len(ionlist)
# assert atmrem == atmput, 'Removing {} atoms instead of {}. Report this bug.'.format(atmrem, atmput)
sel = newmol.atomselect(stringsel, indexes=True)
newmol.remove(sel, _logger=False)
# assert np.size(sel) == atmput, 'Removed {} atoms instead of {}. Report this bug.'.format(np.size(sel), atmput)
betabackup = np.delete(betabackup, sel)
# Add the ions
randidx = np.random.permutation(np.size(waterpos, 0))
atom = Molecule()
atom.record = 'ATOM'
atom.chain = 'I'
atom.segid = 'I'
atom.occupancy = 0
atom.beta = 0
atom.insertion = ''
atom.element = ''
atom.altloc = ''
for i in range(nanion):
atom.name = anionatom
atom.resname = anion
atom.resid = newmol.resid[-1] + 1
atom.coords = waterpos[randidx[i], :]
newmol.insert(atom, len(newmol.name))
for i in range(ncation):
atom.name = cationatom
atom.resname = cation
atom.resid = newmol.resid[-1] + 1
atom.coords = waterpos[randidx[i+nanion], :]
newmol.insert(atom, len(newmol.name))
# Restoring the original betas
sel = np.ones(len(betabackup) + nions, dtype=bool)
sel[len(betabackup)::] = False
newmol.set('beta', betabackup, sel=sel)
return newmol
def ionizePlace(mol,
anion,
cation,
anionatom,
cationatom,
nanion,
ncation,
dfrom=5,
dbetween=5,
segname=None):
newmol = mol.copy()
logger.info('Min distance of ions from molecule: ' + str(dfrom) + 'A')
logger.info('Min distance between ions: ' + str(dbetween) + 'A')
logger.info('Placing ' + str(nanion + ncation) + ' ions.')
if (nanion + ncation) == 0:
return newmol
segname = _getSegname(newmol, segname)
nions = nanion + ncation
betabackup = newmol.beta
newmol.set('beta', sequenceID((newmol.resid, newmol.segid)))
# Find water oxygens to replace with ions
ntries = 0
maxtries = 10
while True:
ionlist = np.empty(0, dtype=int)
watindex = newmol.atomselect('noh and water and not (within ' +
str(dfrom) + ' of not water)',
indexes=True)
watsize = len(watindex)
if watsize == 0:
raise NameError(
'No waters could be found further than ' + str(dfrom) +
' from other molecules to be replaced by ions. You might need to solvate with a bigger box.'
)
while len(ionlist) < nions:
if len(watindex) == 0:
break
randwat = np.random.randint(len(watindex))
thision = watindex[randwat]
addit = True
if len(ionlist) != 0: # Check for distance from precious ions
ionspos = newmol.get('coords', sel=ionlist)
thispos = newmol.get('coords', sel=thision)
dists = distance.cdist(np.atleast_2d(ionspos),
np.atleast_2d(thispos),
metric='euclidean')
if np.any(dists < dbetween):
addit = False
if addit:
ionlist = np.append(ionlist, thision)
watindex = np.delete(watindex, randwat)
if len(ionlist) == nions:
break
ntries += 1
if ntries == maxtries:
raise NameError(
'Failed to add ions after ' + str(maxtries) +
' attempts. Try decreasing the '
'from'
' and '
'between'
' parameters, decreasing ion concentration or making a larger water box.'
)
# Delete waters but keep their coordinates
waterpos = np.atleast_2d(newmol.get('coords', ionlist))
stringsel = 'beta'
for x in newmol.beta[ionlist]:
stringsel += ' ' + str(int(x))
atmrem = np.sum(newmol.atomselect(stringsel))
atmput = 3 * len(ionlist)
assert atmrem == atmput, 'Removing {} atoms instead of {}. Report this bug.'.format(
atmrem, atmput)
sel = newmol.remove(stringsel, _logger=False)
assert np.size(
sel
) == atmput, 'Removed {} atoms instead of {}. Report this bug.'.format(
np.size(sel), atmput)
betabackup = np.delete(betabackup, sel)
# Add the ions
randidx = np.random.permutation(np.size(waterpos, 0))
atom = Molecule()
atom.record = 'ATOM'
atom.chain = 'I'
atom.segid = 'I'
atom.occupancy = 0
atom.beta = 0
atom.insertion = ''
atom.element = ''
atom.altloc = ''
for i in range(nanion):
atom.name = anionatom
atom.resname = anion
atom.resid = newmol.resid[-1] + 1
atom.coords = waterpos[randidx[i], :]
newmol.insert(atom, len(newmol.name))
for i in range(ncation):
atom.name = cationatom
atom.resname = cation
atom.resid = newmol.resid[-1] + 1
atom.coords = waterpos[randidx[i + nanion], :]
newmol.insert(atom, len(newmol.name))
# Restoring the original betas
sel = np.ones(len(betabackup) + nions, dtype=bool)
sel[len(betabackup)::] = False
newmol.set('beta', betabackup, sel=sel)
return newmol
