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marrink-lab
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vermouth-martinize
Describe and apply transformation on molecular structures and topologies
Apache License 2.0
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GitHub Actions not running devs
#387
fgrunewald
closed
1 year ago
2
making cystein bridge with martinizie2
#386
Byun-jinyoung
closed
2 years ago
6
Funny stuff with ifdef/ifndef
#385
fgrunewald
opened
2 years ago
3
modifications parser bug
#384
fgrunewald
closed
2 years ago
0
Missing Atom and PTM_Atom Assignment
#383
mbrosz
closed
2 years ago
5
Dssp error for two peptide system
#382
azadeha83
closed
2 years ago
1
Protonation state of histidine and other (de-)protonable AAs
#381
s-schaef
closed
2 years ago
5
Adding Modifications
#380
lukekruse
closed
2 years ago
5
free speedup: make_residue_graph
#379
fgrunewald
closed
3 years ago
0
Itp reader issues
#378
fgrunewald
closed
3 years ago
3
slow itp parser
#377
fgrunewald
closed
3 years ago
0
modifications (ASP0 and GLU0): not working
#376
tozturkwashu
closed
2 years ago
11
ENH: run_residue method for Processor
#375
pckroon
opened
3 years ago
0
ENH: timeout for repair graph
#374
pckroon
opened
3 years ago
0
Docs
#373
pckroon
closed
3 years ago
0
DOC: add see also references to processors
#372
pckroon
closed
3 years ago
0
non-edge directive
#371
fgrunewald
opened
3 years ago
4
CG DNA
#370
philipford
closed
2 years ago
5
Remove 'HN'/'HN1' from N-terminal modifications for proline
#369
pckroon
closed
3 years ago
1
Add "how to contribute" to the README
#368
jbarnoud
opened
3 years ago
1
-ss input_file.ssd for martinize2
#367
philipford
opened
3 years ago
4
Incorrect residue numbering when merging chains
#366
bisejdiu
closed
2 years ago
5
Add stiff BB-SC1 bond for ALA #ifdef FLEXIBLE
#365
pckroon
closed
3 years ago
0
Which DSSP version does martinize2 expect for -dssp [executable] flag
#364
KasperBuskPedersen
opened
3 years ago
5
No parameters for ALA-SC1 beads when using martini3001
#363
bisejdiu
closed
3 years ago
2
`itp_read.py` doens't handle `#else` lines in `itp`
#362
ricalessandri
closed
3 years ago
0
The file for the formal Martini 3
#361
xiki-tempula
closed
2 years ago
11
Make martinize2 accessible in python
#360
OLaprevote
opened
3 years ago
1
(re-)Implement GMX RTP parser using lark-parser
#359
pckroon
opened
3 years ago
2
Martini 3
#358
pckroon
closed
3 years ago
0
Internal coordinates from molecule
#357
fgrunewald
closed
2 years ago
1
Problem with white-spaces when parsing citations in bibtex format
#356
ricalessandri
opened
3 years ago
3
Fix 354
#355
pckroon
closed
3 years ago
0
`KeyError` in canonicalize_modifications
#354
jbarnoud
closed
3 years ago
1
An ITP file can be included more than once
#353
jbarnoud
opened
3 years ago
0
Missing block for hydroxyproline
#352
jbarnoud
closed
1 year ago
1
Switch PyPI deployment from test to actual
#351
pckroon
closed
3 years ago
0
Make cter and nter residue specifications only match proteins
#350
pckroon
closed
3 years ago
1
Control model parameters for separate system components
#349
pckroon
opened
3 years ago
2
Mis-handling of some insertion codes
#348
jbarnoud
opened
3 years ago
5
Repair graph too thorough in propagating node attributes from blocks?
#347
pckroon
opened
3 years ago
0
propagate edge attributes in res-graph making
#346
fgrunewald
closed
3 years ago
0
Atom names are misaligned in PDB files
#345
jbarnoud
opened
3 years ago
7
Set the warning type when making bonds does not find a block
#344
jbarnoud
closed
3 years ago
1
Emit a warning when a residue is missing
#343
jbarnoud
opened
3 years ago
0
Display doi for citations
#342
jbarnoud
closed
2 years ago
4
Use a different logging type for citations
#341
jbarnoud
opened
3 years ago
1
Remove resid from reference blocks in repair graph
#340
pckroon
closed
3 years ago
1
Fix 317 by ensuring repair_graph prefers matching non-modification atoms
#339
pckroon
closed
3 years ago
2
Identify and fix edge case in ISMAGS symmetry detection
#338
pckroon
closed
3 years ago
5
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