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Sep 5 6 tweets 3 min read Twitter logo Read on Twitter


lets deal with this mf now:
so the code has some functions,classes that do some stuff for us caveman's , Awoooga.

also python strong 💪, java weak ☹️

#StereoEnumerationOptions a class->configs how stereoisomers to be generated (you can pass params) 😇 github.com/rdkit/rdkit/bl…
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then we have some helper classes, these will be called by others to do :

_BondFlipper-> flips the stereochemistry of a bond
_AtomFlipper -> flips the stereochemistry of an atom.
_StereoGroupFlipper-> flips stereochemistry of a group of atoms associated with a StereoGroup. Image
`_getFlippers` Function -> determines which flippers based on structure.
-identifies potential stereocenters

`GetStereoisomerCount` Function -> estimates the total no. of possible stereoisomers

uses info gathered by _getFlippers to calc an uppr bound on no. of stereoisomers. Image
`EnumerateStereoisomers` Function -> this is main boss here 💪.

-takes a molecule (m) and options
-calcs the no. of potential stereocenters and double bonds in the molecule.
-based on centers, decides whether to use a deterministic or random approach to generate combinations. Image
-for each combo: applies the possible stereochemistry changes to make new isomer.

- tryEmbedding` option lets you a generate a 3D conformation , like I showed my vs code.
-if isomer is valid, the code generates each valid stereoisomer one at a time ✌️.
me got low energy now, need to buy some banana's.
I now goes to market and buys banana's then play with ferns , cause I have life outside computer.

mom says too much computer is not good ✌️

shorturl.at/fghzO
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More from @corvus_ikshana

Sep 5
the working of the function- `AllChem.EnumerateStereoisomers(input_molecule)`

input -> a SMILES string()
string is first parsed into a RDKit molecule object.
you also use diff params:

-include_cistrans( for geometric isomer)
-include_optical(enantiomers) shorturl.at/qsxG0
internal working for stereoisomers:
- function generates stereoisomers by trying diff combo's( different stereochemical configurations) with rules followed:

1- Chirality : for those with chiral centers, func try's for two possible configurations: R (right-handed) ,S (left-hnd)
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config is based on-configurations-the Cahn-Ingold-Prelog priority rules(see pics):
chiral center-ranked by ->atomic numbers or mass.

2-Double Bond : those who can exhibit cis-trans isomerism, func tries for two possible config(CIS/TRANS)

func combine diff config of above two 🫠
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Read 5 tweets
Sep 4
yesterday I was able to generate isomer's of some compounds , the input I have 2,3-dichlorobutane in a "SMILE format".
my main focus is on pantoprazole currently.
Those who had GERD or acidic reflux in stomach might have taken this drug.
Its a type of Proton-pump inhibitor.


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it binds and forms a covalent bond with something called a proton pump in your stomach and stops the production of H+.
it works like a key and lock thing.
key: pantop and lock : the pump (👉👌)

pretty sure I will fail cause isomers have diff structure and it won't bind same way
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but I still want to try to see how this whole process works 👍.
Now I will be doing the molecular docking part.
to test if that key will fit the lock, we have some docking software libs, one of them is (AutoDock Vina)

its open source not paid.
Read 5 tweets
Aug 26
wanna know another way to identify viral diseases:
This was used during Covid-19 time , to find what family did Covid came from and if you had it.
remember RT-PCR thing : Image
getting the initial sequence is the tough, time taking costly part, rest is fast.
India didn't had many labs initially for sequencing , and we struggled for testing .
lol my biotech prof struggled to format the RNA sequence to use it in BLAST.
Python came really handy there. Image
the api documentation of NCBI gave me headache Image
Read 4 tweets

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