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UCL-CCS
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TIES
Topology Superimposition based on joint graph traversal
MIT License
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Analysis: Create summary in columns showing that vdw and ele differ across
#232
bieniekmateusz
closed
2 years ago
0
Ensure that the correction CD-CC / CC-CD is applied on within rings for now.
#231
bieniekmateusz
closed
2 years ago
0
Correction for the arbitrary direction in double bond atoms (CC-CD and CD-CC atom types)
#230
bieniekmateusz
closed
3 years ago
1
Add a small version counter
#229
bieniekmateusz
closed
2 years ago
0
GAFF picks arbitrarily cc-cd or cd-cc depending on the order of the atoms. Treat these as the same atoms.
#228
bieniekmateusz
closed
3 years ago
1
GAFF2 atom type support and others
#227
bieniekmateusz
closed
3 years ago
0
+ The test case was comparing list (and order) rather than sets
#226
bieniekmateusz
closed
3 years ago
0
Prechecks: Check if the molecules are strongly connected, otherwise the molecule is broken.
#225
bieniekmateusz
closed
2 years ago
0
Moving away from removing dangling hydrogens when accounting for pair charges
#224
bieniekmateusz
closed
3 years ago
0
Add a simple check early to see if the atoms used in superimposition have a simplified atom type mapping.
#223
bieniekmateusz
closed
2 years ago
0
Separate the mapping about GAFF2 and other atom types so that the user can use their own too etc.
#222
bieniekmateusz
closed
2 years ago
0
Add badges: Codecov, use travis?
#221
bieniekmateusz
closed
2 years ago
0
Create a file that contains all the antechamber calling code
#220
bieniekmateusz
closed
2 years ago
0
Log the user's input settings into a YAML input file
#219
bieniekmateusz
closed
2 years ago
0
Record specific information about the q imbalance and redistribution
#218
bieniekmateusz
closed
2 years ago
0
Two matched atom-pairs connected via different bond types (- and =)
#217
bieniekmateusz
closed
3 years ago
3
Output superimposing at each stage to make it easier to reconstruct the story
#216
bieniekmateusz
closed
2 years ago
0
By default use -ant-dr when charges are reused
#215
bieniekmateusz
closed
2 years ago
0
Separate the ambertools output into a file rather than polluting the general space
#214
bieniekmateusz
closed
3 years ago
0
Argument -namd_prod should first search the current directory and only then internal files
#213
bieniekmateusz
closed
2 years ago
0
Investigate restraints for keeping matched atoms together if hybrid single-dual topology does not work
#212
bieniekmateusz
closed
2 years ago
0
Decrease the alchemical region - Avoid mutating bridges/bottlenecks which eliminate entire areas
#211
bieniekmateusz
closed
2 years ago
0
Check the areas probed by appearing/disappearing molecule part and see how far they are from each other
#210
bieniekmateusz
closed
2 years ago
0
Rings Mutations and Partial Rings - ensure that rings cannot change their dimensions
#209
bieniekmateusz
closed
2 years ago
0
Partial Rings - ensure that the matched partial rings use the same bond types
#208
bieniekmateusz
closed
2 years ago
0
Support .prep and .ac file as source of the charges
#207
bieniekmateusz
closed
3 years ago
1
Further morphing due to q-tot should be linked to the place where the mutation takes place directly?
#206
bieniekmateusz
closed
2 years ago
0
Check why ester disappearing in mcl1 l1-l8 in resp - is it the bridge issue?
#205
bieniekmateusz
closed
2 years ago
0
Use JSON output to print the full summary
#204
bieniekmateusz
closed
2 years ago
0
Consider adapting the "analysis" system as part of the standard ties classes.
#203
bieniekmateusz
closed
4 years ago
3
Read about "disconnected components" and check if it is possible to use them
#202
bieniekmateusz
closed
2 years ago
0
Check which MCS suffer from "junctions have been removed" and compare their errors
#201
bieniekmateusz
closed
2 years ago
0
Check which mutated areas do not have a net charge, and check their average value to the experiments
#200
bieniekmateusz
closed
2 years ago
0
Add checks if the mutated areas have the same "net charge" as asked for by NAMD
#199
bieniekmateusz
closed
2 years ago
0
Improving "disconnected components" by choosing atoms that do not break the molecule.
#198
bieniekmateusz
closed
2 years ago
0
Compare our superimposition against ChemAxon
#197
bieniekmateusz
closed
2 years ago
0
Renaming atoms: it seems that the digits are larger than they should be
#196
bieniekmateusz
closed
2 years ago
0
.frcmod: negative periodicity and possible problem with merging .frcmod
#195
bieniekmateusz
closed
2 years ago
0
Should ddG use median instead of the average?
#194
bieniekmateusz
closed
2 years ago
0
Rewrite analysis with OOP
#193
bieniekmateusz
closed
2 years ago
0
Use order for replicas to make them tracable
#192
bieniekmateusz
closed
4 years ago
0
Single topology: in the case of l6 l14, two hydrogens are not booked when mismatched
#191
bieniekmateusz
closed
2 years ago
0
Use the same standard for charge limit handling, and move away from assertions
#190
bieniekmateusz
closed
2 years ago
0
The net charges of the appearing and disappearing group need to be the same - add check
#189
bieniekmateusz
closed
2 years ago
0
Avoid changing ring charges in redistribution
#188
bieniekmateusz
closed
2 years ago
0
Allow to pack multiple ligand simulation onto a single node
#187
bieniekmateusz
closed
2 years ago
1
Attempt to use the hybrid single topology in NAMD
#186
bieniekmateusz
closed
4 years ago
0
Add a Check: q of app/dis atoms is never modified and should remain the same.
#185
bieniekmateusz
closed
4 years ago
1
UI: Print all relevant config info after the args are parsed
#184
bieniekmateusz
closed
2 years ago
0
Argparse: transition to --feature and --no-feature
#183
bieniekmateusz
closed
2 years ago
0
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