natedey RINRUS issues - Githubissues

natedey / RINRUS

Residue Interaction Network ResidUe Selector

MIT License

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No option to write FSAPT inputs in write_input.py

#53 dwappett opened 2 months ago
0
how do we safely convert "ligand" in probe/arpeggio output to "seed"?

#52 natedey opened 2 months ago
0
Seed atoms being removed in distance-based trimming

#51 dwappett opened 3 months ago
0
documentation of distance based approach needs to be clarified

#50 natedey opened 3 months ago
0
Can rinrus_trim2_pdb.py flag or recognize redundant models?

#49 natedey opened 3 months ago
0
There are two versions of check_residue_atom.py

#48 dwappett opened 4 months ago
0
Changes to probe2rins.py add pandas package dependency

#47 natedey opened 4 months ago
0
driver is acting funny on bigblue - from pathlib import path in RINRUS_driver.py hanging

#46 natedey opened 4 months ago
2
Gaussian template is adding an extra line between basis set specification and solvation parameters sometimes

#45 natedey opened 4 months ago
0
how does "-pdbfilename res_.pdb" command line argument in pymol_scripts.py work?

#44 natedey opened 6 months ago
0
can't put chain ID into pymol_scripts

#43 natedey opened 6 months ago
1
Have RINRUS throw a warning if canonical amino acids have an atom type not shown in res_atoms.py

#42 natedey opened 7 months ago
0
character justification of element names could be more flexible?

#41 natedey opened 7 months ago
3
adding a header to the RINRUS driver

#40 natedey opened 10 months ago
2
if a lone glycine CA is tagged by probe, we can have a free glycine unit trimmed to CH4?

#39 natedey closed 11 months ago
9
PDB files from MD that are processed through VMD will have water residue IDs written in hexadecimal - crashes RINRUS

#38 natedey closed 11 months ago
1
reduce_het_dict needs to be packaged with the code

#37 natedey closed 11 months ago
0
adding documentation that let the user know what indexes each component of the PDB files need to be.

#36 tsantaloci opened 1 year ago
5
Fixing .split(":") for when the pdb file does not have a chain ID.

#35 tsantaloci closed 11 months ago
5
Update pdb_dist_rank.py new distance method to not split water into SC or MC when the script includes hydrogens

#34 tsantaloci opened 1 year ago
0
Can't have two lines of same residues in res_atoms.dat.

#33 tsantaloci closed 1 year ago
2
documentation update

#32 tsantaloci opened 1 year ago
1
Driver-test

#31 MiloCheng17 closed 7 months ago
2
more flexible distance "center"

#30 natedey opened 1 year ago
2
FSAPT GNMT example needs to be reworked

#29 natedey opened 1 year ago
0
installation instructions need to be improved to eliminate path or pythonpath dependencies

#28 natedey opened 1 year ago
2
Is instruction 6 for probe model creation correct?

#27 natedey opened 1 year ago
3
need consistency with script arguments

#26 natedey opened 1 year ago
1
analyze-FG-SAPT.py "-a" argument not working as intended.

#25 natedey closed 1 year ago
1
how to get probe/RINRUS to consider canonical amino acid as SIF "ligand" type

#24 natedey opened 2 years ago
2
automating the treatment of seed canonical amino acids

#23 natedey opened 2 years ago
1
From all possibilities of backbone atoms in res_atoms.dat - need to include logic for simple trims

#22 natedey opened 2 years ago
3
graphical workflow tree needed to plan driver

#21 natedey closed 11 months ago
1
consistency needed in output file names

#20 natedey opened 2 years ago
1
We need a log file

#19 natedey closed 11 months ago
3
probe / arpeggio file names can be more consistent when providing the same information

#18 Jmller56 closed 2 years ago
1
how to resolve ties from arpeggio (or probe)?

#17 Jmller56 opened 2 years ago
1
GenResAtoms.py should write a model_detail.dat file like v1 probe_freq_2pdb.py

#16 Jmller56 opened 2 years ago
3
need instructions on how to fake out GenResAtoms.py if we need to manually add a residue to seed

#15 Jmller56 opened 2 years ago
5
Two use cases need to be added to /bin/README.md

#14 natedey closed 7 months ago
2
pymol_scripts.py should iterate over all models

#13 natedey closed 10 months ago
2
GenResAtoms.py does not behave at all like description in README.md

#12 natedey closed 2 years ago
1
need permission from Jubb group to package arpeggio

#11 natedey closed 2 years ago
1
need permission from Richardson groups to repackage probe/reduce

#10 natedey closed 2 years ago
1
pymol_scripts.py doesn't work at all

#9 natedey closed 2 years ago
2
probe2rins.py doesn't handle having no chain IDs in pdb in a sensible way

#8 natedey closed 1 year ago
3
Moves notes and example instructions into README

#7 berquist closed 3 years ago
0
Added vec_calc.py

#6 tsmmers1 closed 5 years ago
0
modify sort-residues.py

#5 tsmmers1 closed 5 years ago
0
add sort-residues.py file

#4 tsmmers1 closed 5 years ago
0