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Hi,
I am new to pytraj. I dnt know if there is any discussion forum available, so i am posting my issues here.
I cloned pytraj and cpptraj from github. I have been successful in compiling cpptraj wit…
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I love how data.table by default only prints the first and last 5 rows of a long table.
However I often encounter data with columns with very long strings, which destroys the whole effect.
best- Jan…
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A specific consequence of enabling mix-and-match `ffxml` files (#1298) is that we can run into situations where later `ffxml` files might need to overwrite earlier atom types and parameter definitions…
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```
Need to be split to separate issues of course:
- reformat: whatif.RAMCHK.valueList: 0.17999999999999999 (+- .)
- link to residues should not have #top in url because it obscures the header
which…
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should parmed add this function to `parmed.tools`?
(below is how I get 1 letter code for RNA to feed to Curve+ program; of course this not a general solution).
``` python
In [22]: "".join([res.name[…
hainm updated
9 years ago
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See pandegroup/openmm#1281
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It is refreshing to see pv. Reading through the doc, I found that "In case multiple models are present in the file (as designated by MODEL/ENDMDL), only the first is read." Would it be possible for pv…
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Easy change from BMRB according to:
t is probably a good idea to have the cing internal nomenclature adhere to
IUPAC defs as much as we can (soem residues to not exists in IUPAC) before
we releas…
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```
even though the check is meant for nucleic acids only:
From check.db:
ID : model_000.pdb
CheckID : PL3CHK
Program : WHAT IF
Version : 6.0 (20080412-0930)
Text : Side chain planar…
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I just pushed on master an implementation of special symbols for rna and dna. They work properly. Not only backbone angles are defined, but also many other useful names (e.g. sugar, base, ...).
Howev…