GLYCAM-Web gmml issues - Githubissues

GLYCAM-Web / gmml

Glycam Molecular Modeling Library

GNU Lesser General Public License v3.0

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DFrupa2-1DFrupa2-OH breaks gmml.

#171 gitoliver opened 3 weeks ago
0
KDO derivatives not working on test swarm

#170 gitoliver opened 4 months ago
1
Test 019 segfaults sometimes

#169 gitoliver opened 6 months ago
2
Branches that include a 1-5 do not build.

#168 gitoliver closed 5 months ago
2
CONECT Cards in output pdb file are not in a good order

#167 gitoliver closed 5 months ago
2
Deoxy results in skipped numbers in output files.

#166 gitoliver closed 5 months ago
2
Our approach to labelling residues and linkages doesn't work for ano-ano linkages

#165 gitoliver opened 7 months ago
4
It's possible to build and get a minimized structure of DGlcpa1-1DGlcpa1-OH

#164 gitoliver opened 7 months ago
0
DGlcpa1-1DGlcpa becomes DGlcpa1-1DGlcp when "ordered" in gmml.

#163 gitoliver closed 5 months ago
2
Carbohydrate builder tests do not mirror gems enough.

#162 gitoliver closed 5 months ago
2
Feature request: GMML error generator

#161 danwentworthart opened 11 months ago
1
Substituted KDO/KDN is not working

#160 gitoliver closed 5 months ago
1
Read/Write mmcif/pdbx files

#159 gitoliver opened 1 year ago
0
Read/Write mol2 format files

#158 gitoliver opened 1 year ago
0
Tests are taking too long

#157 gitoliver closed 7 months ago
1
Anomer-Anomer bug for DNeup5Aca (and others)

#156 gitoliver closed 5 months ago
2
Test number 016 fails to remain consistent between container and bare metal

#155 Pshepp opened 1 year ago
1
GEMSHOME removal

#154 Pshepp opened 1 year ago
4
hooks wont run the most recent version

#153 Pshepp opened 1 year ago
0
Clean Up Includes

#152 Pshepp opened 1 year ago
0
Version File Cruft Removal

#151 Pshepp closed 1 year ago
3
KDNpa2-6 linkage bug.

#150 gitoliver closed 1 year ago
0
Wrong error when C1 requested, but anomer is C2.

#149 gitoliver opened 1 year ago
0
Some sequences silently don't work

#148 gitoliver closed 11 months ago
4
response.json in the build directory of a carbohydrate has a lot of null values

#147 gitoliver opened 1 year ago
0
Derivatives to a 6 branch should remain rotatable when resolving overlaps, but should not show up as possible rotamers to user

#146 gitoliver opened 1 year ago
1
Compiler segfaulting when compiling gmml

#145 gitoliver opened 1 year ago
5
Missing prep entries for metadata.

#144 gitoliver opened 1 year ago
0
1-8 linkages do not have metadata

#143 gitoliver closed 1 year ago
1
Long sequences cause negative numbers for number of rotamers

#142 gitoliver closed 1 year ago
2
Add test that takes sequences, builds 3D structures, runs sugar ID and checks the sequences match the inputs.

#141 gitoliver opened 2 years ago
0
Prep entries for L sugars not being found, D versions silently found and used instead

#140 gitoliver closed 11 months ago
2
ROH hydrogen default position looks odd

#139 gitoliver closed 1 year ago
1
Sequences with dUA when entered via the website cause a prep entry not found error

#138 gitoliver closed 2 years ago
1
Sequences with dUA cause segfaults

#137 gitoliver closed 1 year ago
1
Gmml dev

#136 Lachele closed 1 year ago
0
Sequences with unnecessary brackets do not fail well e.g. [LFucp[2Me,4A]a1-2]DGalpb1-OH

#135 gitoliver opened 2 years ago
2
Acetyl derivatives get bonded via the wrong atom.

#134 gitoliver closed 2 years ago
1
TBT aka -OtBu terminal is borked

#133 gitoliver closed 2 years ago
1
Both shapes for 2-3 linkages are the same

#132 gitoliver closed 2 years ago
1
TER cards missing for pdb files with branches

#131 gitoliver closed 11 months ago
1
PDBPreprocessor CONECT cards can be either duplicated or incomplete.

#130 gitoliver closed 11 months ago
1
PDBPreprocessor reduce does not add hydrogens to N terminal (or OXT to C). So preprocessor should do it.

#129 gitoliver closed 1 year ago
1
PDBPreprocessor: The added ACE NME residues overlap if there is a 1 residue gap.

#128 gitoliver closed 6 months ago
1
PDBPreprocessor will only take alternative coordinates labeled A. If there are only B and C, it doesn't chose between them.

#127 gitoliver closed 2 years ago
1
broken links in README.md

#126 sbrozell closed 2 years ago
3
GAG builder with Xyl, the lookup code is incorrect.

#125 gitoliver closed 2 years ago
1
PDB2glycam formatted files available as an option from GlyFinder.

#124 gitoliver opened 2 years ago
0
PDB2Glycam segfaulting

#123 gitoliver closed 2 years ago
1
Add Link and Connect cards in carbohydrate builder output PDB files.

#122 gitoliver closed 11 months ago
1