Values used to compile the firmware for my Ender3v2 with official Sprite extruder, BLtouch and filament sensor. Not a fork because I started off with a Creality fork, then tried the https://github.com/mriscoc/Ender3V2S1 repo. Marlin precompiled does not work with my machine.
platformio run --silent -e STM32F103RE_creality
NB. Firmware build is in .pio/build for reasons mysterious.
| """ | |
| The values from https://towhee.sourceforge.net/forcefields/mmff94.html | |
| were extracted and compared to https://raw.githubusercontent.com/rdkit/rdkit/master/Code/GraphMol/ForceFieldHelpers/MMFF/AtomTyper.cpp | |
| NB. Do not ask ChatGTP4 for the atomtypes as they will be wrong. | |
| """ | |
| atomtype2namedex: Dict[int, str] = {"1": {"CR ": "ALKYL CARBON, SP3"}, "2": {"C=C ": "VINYLIC CARBON, SP2", "CSP2": "GENERIC SP2 CARBON"}, "3": {"C=O ": "GENERAL CARBONYL CARBON", "C=N ": "SP2 CARBON IN C=N", "CGD ": "GUANIDINE CARBON, DOUBLY BONDED TO N", "C=OR": "KETONE OR ALDEHYDE CARBONYL CARBON", "C=ON": "AMIDE CARBONYL CARBON", "CONN": "UREA CARBONYL CARBON", "COO ": "CARBOXYLIC ACID OR ESTER CARBONYL CARBON", "COON": "CARBAMATE CARBONYL CARBON", "COOO": "C ARBONIC ACID OR ESTER CARBONYL CARBON", "C=OS": "THIOESTER CARBONYL CARBON, DOUBLE BONDED TO O", "C=S ": "THIOESTER CARBON, DOUBLY BONDED TO S", "C=SN": "THIOAMIDE, CARBON, DOUBLY BONDED TO S", "CSO2": "CARBON IN >C=SO2", "CS=O": "CARBON IN >C=S=O (SULFINYL GROUP)", "CSS ": |
| """ | |
| Chemical isomorphism refers to the phenomenon where elements of similar electron density, | |
| such as carbon (C), nitrogen (N), and oxygen (O), cannot be easily distinguished in the electron density map. | |
| This is because these atoms scatter X-rays similarly, resulting in overlapping or indistinguishable electron density. | |
| This isomorphism is also called `crystallographic ambiguity`. | |
| .. code-block:: python | |
| isomorphics: List[Chem.Mol] = get_chemical_isomorphisms(hit) |
| # I am sure I have pasted this snippet somewhere, but I always forget where —so may be a duplicate. | |
| wrong_ref: Chem.Mol = ... # the reference mol in former frame/location/crystal | |
| right_ref: Chem.Mol = ... # the reference mol in desired frame | |
| wrong: Chem.Mol = ... # the target | |
| affine_matrix = AllChem.GetAlignmentTransform(wrong_ref, right_ref)[1] | |
| AllChem.TransformConformer(wrong.GetConformer(), affine_matrix) # this is in place |
| import numpy as np | |
| import pymol2 | |
| token_resi = 25 # this present in all chains | |
| filename = '👾👾👾.pse' | |
| coords = {} | |
| with pymol2.PyMOL() as pymol: | |
| pymol.cmd.load('crysalin_lattice.pse') | |
| for name in pymol.cmd.get_object_list(): | |
| for chain in pymol.cmd.get_chains(name): |
I want Pytorch, Jax and Tensorflow.
Check: nvidia-smi still gives 'NVIDIA-SMI 510.85.02 Driver Version: 510.85.02 CUDA Version: 11.6 '
conda activate base
unset LD_LIBRARY_PATH
unset CUDA_HOME
export NEW_ENV='cuda118redux'
export CONDA_ALWAYS_YES=yes
| // In NGL it may be handy to show an XYZ system axes / caltrop / cube edge | |
| // the following is called via `addAxis(stage)` | |
| const addAxis = (stage) => { | |
| let shape = new NGL.Shape("shape", { dashedCylinder: true }) | |
| shape.addArrow([ 0, 0, 0 ], [ 10, 0, 0 ], [ 1, 0, 0 ], 1.0); | |
| shape.addText([ 12, 0, 0 ], [ 1, 0, 0 ], 2.5, "x"); | |
| shape.addArrow([ 0, 0, 0 ], [ 0, 10, 0 ], [ 0, 1, 0 ], 1.0); | |
| shape.addText([ 0, 12, 0 ], [ 0, 1, 0 ], 2.5, "y"); | |
| shape.addArrow([ 0, 0, 0 ], [ 0, 0, 10 ], [ 0, 0, 1 ], 1.0); |
I wanted to get the void volume with OpenEye Spicoli for use in OERocs.
But it did not create a usable surface.
This here is for my reference as I am missing something.
Standard reading:
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