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Molprobity2
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Fix bogus unit cell volume when creating restraints manager
#127
russell-taylor
closed
3 years ago
1
Fix PDB version naming in type_energy dictionary
#126
russell-taylor
opened
3 years ago
1
Unit tests for CCTBX/Probe/AtomTypes.py
#125
russell-taylor
closed
2 years ago
2
Add option to run SuiteName and have it produce three output files.
#124
russell-taylor
opened
3 years ago
2
Merge SuiteName into CCTBX
#123
russell-taylor
closed
2 years ago
4
Try new SuiteName on 1s72
#122
russell-taylor
closed
3 years ago
0
Consider how to handle Phil options in Reduce
#121
russell-taylor
closed
3 years ago
6
Mainchain-mainchain atom interactions should be turned on in Probe
#120
russell-taylor
closed
2 years ago
1
Check Reduce/Probe heavy-atom radii and donor/acceptor against CCTBX
#119
russell-taylor
opened
3 years ago
23
Find the electron cloud and nuclear distances in Probe and Reduce and see if they agree
#118
russell-taylor
closed
3 years ago
1
Add a description of what SuiteName does to the top of the documentation
#117
russell-taylor
closed
3 years ago
2
1Q9A should be parsed to see if SuiteName can handle alternate conformations
#116
russell-taylor
closed
3 years ago
2
Finding type_energy for atoms in PDB and CIF files is failing
#115
russell-taylor
closed
3 years ago
5
Create native-probe branch of cctbx_project and put Probe CCTBX code into it
#114
russell-taylor
closed
3 years ago
2
Investigate change in C=O radius from 1.65 to 1.70 in Reduce
#113
russell-taylor
closed
3 years ago
3
Make sure that CCTBX can load snippet files that are "badly formatted" file inputs
#112
russell-taylor
closed
1 year ago
0
Handle adjustment of NHQ atoms after flips
#111
russell-taylor
closed
3 years ago
1
Continue to support shortest-unique-prefix commands in command-line parsing
#110
russell-taylor
closed
3 years ago
1
Look at Phenix clashcore to see which Probe command-line arguments it uses
#109
russell-taylor
closed
3 years ago
2
Probe AtomVsAtomDotScorer::score_dots() should probably notice co-located atoms
#108
russell-taylor
opened
3 years ago
0
Probe: rawEnumerate() and enumarate() compute essentially the same things
#107
russell-taylor
closed
2 years ago
1
Add additional testing found in Probe beyond what is in Reduce for probe score determination
#106
russell-taylor
closed
3 years ago
17
annularDots code in Reduce should be for overlap cases (including hydrogen bonds) rather than non-overlap cases
#105
russell-taylor
closed
3 years ago
10
In probe.c, a hydrogen can bond to the face of an Aromatic ring
#104
russell-taylor
opened
3 years ago
4
Define how to identify Movers and ranges of motion for each
#103
russell-taylor
closed
3 years ago
1
Probe: Include near contacts in the calculations for both Probe and Reduce
#102
russell-taylor
closed
3 years ago
5
Check and see if the planar or tetrahedral angle for OH have preferences
#101
russell-taylor
closed
3 years ago
1
Unit tests for SuiteName
#100
russell-taylor
closed
3 years ago
4
Send a list of things that SuiteName is checking for to Jane and Dave to help them pick a smaller test set
#99
russell-taylor
closed
3 years ago
1
Comment the 4D calculations to describe why they are there (see notes below)
#98
russell-taylor
closed
3 years ago
0
Make a way to show the version in SuiteName, perhaps --version
#97
russell-taylor
closed
3 years ago
2
Change the SuiteName license to Apache2
#96
russell-taylor
closed
3 years ago
5
Describe the required --pointIDfields argument in the README.md
#95
russell-taylor
closed
3 years ago
0
Make it possible to run 'python suitename.py' on the root-directory file as well as the command_line file
#94
russell-taylor
closed
3 years ago
1
Merge SuiteName into master
#93
russell-taylor
closed
3 years ago
1
Probe: Consider caching a map of weak pointers to dot sets
#92
russell-taylor
closed
3 years ago
1
Deploy cctbx/molprobity on Apple M1 processors
#91
russell-taylor
closed
3 years ago
6
Unit test for Reduce
#90
russell-taylor
closed
1 year ago
11
Ensure that SuiteName '-' command line argument lets it read from standard input
#89
russell-taylor
closed
3 years ago
2
Decide how to determine where to insert rotations and flips
#88
russell-taylor
closed
2 years ago
2
Keep the warning message when it cannot find the ligand -- gets the contacts wrong
#87
russell-taylor
opened
3 years ago
0
Talk with Christopher about how to integrate SuiteName into CCTBX
#86
russell-taylor
closed
3 years ago
0
Find out how Reduce decides if a ring is aromatic in a HET
#85
russell-taylor
closed
3 years ago
2
Look for a library that can be used to do the graph algorithms that are used to speed up Reduce
#84
russell-taylor
closed
3 years ago
7
Set an nonzero exit code if there is no output
#83
russell-taylor
closed
3 years ago
0
Add a comment in the -help that DNA will be skipped
#82
russell-taylor
closed
3 years ago
0
Convert regression tests to Python
#81
russell-taylor
closed
3 years ago
1
Check the list length to make sure its length matches the dimension -- ignore if not
#80
russell-taylor
closed
3 years ago
1
dotlist and balllist should both be accepted
#79
russell-taylor
closed
3 years ago
1
Update the README according to the notes below
#78
russell-taylor
closed
3 years ago
0
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