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"""
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)

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# 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

matteoferla

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):

matteoferla

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

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matteoferla

// 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);

matteoferla

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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matteoferla

#! bin/bash

# For scripts required see: https://gist.github.com/matteoferla/e0496d5766c12a0ae1738b943b41a536
# A few things don't work in CentOS 7 due to GNU lib C (glibc) 2.17, so it has to be run in a Singularity container

: << USAGE
export JOB_SCRIPT=/data/xchem-fragalysis/shared/singularity.sh;
export APPTAINER_CONTAINER=/data/xchem-fragalysis/shared/singularity/rockyplus.sif;
export JOB_INNER_SCRIPT=/data/xchem-fragalysis/mferla/Zika/job.sh;
condor_submit /data/xchem-fragalysis/shared/target_script.condor

matteoferla

# ========================
# Sets presents...
# tries to source $HOME/.bashrc
# or $HOME2/.bashrc;
# or a fallback
# ========================

# source /data/xchem-fragalysis/shared/bashrc.sh

# universal fixes