def getCovalentlyBoundFragments(self, idx):
""" Returns list of fragments that are covalently connected to the idx fragment
Arguments:
----------
idx : the fragment index to use when looking for other covalently bound fragments
Returns:
--------
A list of fragments covalently bound to the idx'th fragment.
"""
atomids = self._fragments[idx]
bonds = self._fragmentation.getExplicitlyBreakAtomPairs()
other_fragment_atomids = []
other_fragments = []
if not self._fragmentation.doQMMMIncludeCovalent():
return other_fragments
print("Info: FragIt will include all fragments covalently bound in the QM region.")
# let us find the nearby fragments that are covalently connected
# currently, this only works with nearest neighbours
for (l,r) in bonds:
if l in atomids:
other_fragment_atomids.append(r)
if r in atomids:
other_fragment_atomids.append(l)
# lets find the associated fragments
for ifg,atoms in enumerate(self._fragments):
if len(atoms) > len(listDiff(atoms, other_fragment_atomids)):
other_fragments.append(ifg)
return other_fragments
def pop_qm_fragment(self):
""" Remove the qm fragments from the fragmentation. Adds hydrogens to both the
qm-fragment that is returned and to the neighbouring fragments if bonds were cut.
"""
# at this point, fragments have been generated
fragments = self._fragmentation.getFragments()
# investigate which fragments should be included in the QM-region
qmfrags = self._qmfrags[:]
distance = self._fragmentation.getActiveAtomsDistance()
qmfrags = Uniqify(self._add_fragments_to_QM(qmfrags))
qmfrags.sort()
qmfrags.reverse()
qm_region_charge = 0
fragments_for_qm_no_hydrogens = []
# instead of removing the qm-fragment, we rather adopt a quite novel approach
# in which we signal to the user of the API that the fragment is not to be used
# further by setting its original atom numbers to -1
for idx in qmfrags:
qm_region_charge += self._qm_charges[idx]
old_fragment = fragments.pop(idx)
fragments.insert(idx, [-1 for i in old_fragment])
fragments_for_qm_no_hydrogens.insert(0,old_fragment[:])
# for simplicity, let us just squash the qm fragments into one big fragment
fragments_for_qm_no_hydrogens = ravel2D(fragments_for_qm_no_hydrogens)
breaks = self._fragmentation.getExplicitlyBreakAtomPairs()
if len(breaks) == 0:
return (fragments_for_qm_no_hydrogens, qm_region_charge)
# below here: add hydrogens to qm-fragment and to the rest of the capped structure
fragment_for_qm = fragments_for_qm_no_hydrogens[:]
# first, fix the QM-fragment, removing any bond-breaks that reside
# inside (or bordering) the qm-fragment. if breaks are bordering,
# add appropriate hydrogen atoms.
lenqmfrags = len(fragments_for_qm_no_hydrogens)
remove_breaks = []
for ibreak, bbreak in enumerate(breaks):
lendiff = len(listDiff(fragments_for_qm_no_hydrogens, list(bbreak)))
difflen = lenqmfrags - lendiff
# the break is not present in the qm-region, leave it
if difflen == 0: continue
# mark the ibreak'th item for removal. no hydrogens to be added
if difflen == 2: remove_breaks.append(ibreak)
# the break is bordering the qm-region and the mm-region
if difflen == 1:
for iibreak in bbreak:
# fix the qm-fragment first
if iibreak in fragments_for_qm_no_hydrogens:
new_atoms = self.satisfyValency(fragments_for_qm_no_hydrogens, iibreak, bbreak)
if len(new_atoms) > 0:
print("Info: FragIt adds", len(new_atoms), "atom(s) to the QM fragment.")
self._fragmentation._atom_names.extend([' H '] * len(new_atoms))
fragment_for_qm.extend(new_atoms)
# then fix the fragments themselves
# INFO/WARNING: this is a lists of lists thing. BE CAREFULL
for ifragment, fragment in enumerate(fragments):
if iibreak in fragment:
new_atoms = self.satisfyValency(fragment, iibreak, bbreak)
print("Info: FragIt adds", len(new_atoms), "atom(s) to MM fragment", ifragment+1)
self._fragmentation._atom_names.extend([' H '] * len(new_atoms))
fragments[ifragment].extend(new_atoms)
# also mark the ibreak'th item for removal
remove_breaks.append(ibreak)
for ibreak in remove_breaks:
self._fragmentation.popExplicitlyBreakAtomPairs(breaks[ibreak])
#print("FRAGIT: [qm] {0}".format(fragment_for_qm))
return (fragment_for_qm, qm_region_charge)
def test_listDiff(self):
test_array1 = range(10)
test_array2 = range(3,7)
self.assertEqual( util.listDiff( test_array1, test_array2 ), [0,1,2,7,8,9] )
self.assertRaises( ValueError, util.listDiff, test_array2, test_array1 )