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Currently, to construct the dynamical matrix one needs to assign orbitals to each atom to represent the spatial degrees of freedom. Here a simple example
```python
import sisl
c = sisl.Atom("C", …
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I tried run "atom reachables -o app.atom -s reachables.json -l c ." on [tarantool](https://github.com/tarantool/tarantool) repo to test C lang. Then it's printed: "Exception in thread "" java.lang.Ou…
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With GNU Prolog 1.5.0 (64 bits) on Win 10 with 16GB RAM, and the somewhat maximized settings (i.e. anything I try and increment further just makes gprolog fail at launch):
```
TRAILSZ = 262144 (0x…
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Hi There,
I first want to say that for my cases PDBFixer is superior to other methods. For the case of 7zaw.pdb - Human GPC3 having missing atoms and residues (many) - PDBFixer is able to add the m…
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I've tried to test depscan on https://github.com/grpc/grpc by next command:
> atom reachables -o app.atom -s reachables.json -l c .
p.s. bom.json is exist
And got next error:
```
Generati…
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Currently I'm getting the same output between `lynx -dump` and wp2text:
```
$ /usr/bin/lynx -dump http://en.wikipedia.org/wiki/Poitiers | head
#[1]alternate [2]Edit this page [3]Wikipedia (en)…
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It is well-known that preparing the files for molecular dynamic (MD) simulation of protein-ligand complex is a tedious process, which includes preparing ligand topology, solvation, adding ions, energ…
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How to do $$matmul(A, B^T)$$?
I was trying to modify this sycl/pvc [example](https://github.com/codeplaysoftware/cutlass-fork/blob/sycl-develop/examples/sycl/pvc/pvc_gemm.cpp), which I believe does…
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**Describe the bug**
So it appears, that the reader just skips over the lines he cant read. The Bromine atom is not read. So are Cl atoms and i suppose all other atom types that have two letters …
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Hi all,
I'm trying to perform a covalent docking on a LYS using as worhead a benzenesulfonyl fluoride in which the LYS should do a SN2 on the fluoride bonding with the S (e.g. `FS(=O)(=O)[#6]-1=[#6]-…