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Noel O'Boyle baoilleach

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baoilleach / 11thICCS_Noordwijkerhout.txt
Last active June 7, 2018 00:22
My notes from the 11th International Conference on Chemical Structures 2018
https://twitter.com/baoilleach/status/1000988779287629824
=========================================================
#11thICCS Hitesh Patel presents SAVI - Synthetically accessible virtual inventory
Q: What can I make easily, reliably, safely and cheaply? Make a db of 1 billion mols where you know that this is the case. 1-step rxns. Freely available db.
Building blocks (Sigma) + transforms (LHASA) + cheminformatics engine (Xemistry) = SAVI.
Use some of the transforms used in LHASA (written in CHMTRN/PATRAN) but additional ones also.
Related: Enamine REAL db; CHIPMUNK db (TU Dortmund), ChemPass, ChemAxon Reactor, Proximal Lilly, Pfizer GVL, BI CLAIM
"CHMTRN/PATRAN transforms are smarter than SMARTS" - uses scores - if this, then dec score by 10, if that, then inc score; if the other, then kill the reaction
I think this is from the Corey group. Not sure of the details.
Original run (2016) resulted in 283M unique products from 14 transforms.
@baoilleach
baoilleach / geneticalgo.py
Last active May 24, 2018 08:18
Very simple genetic algorithm that manipulates SMILES
import random
random.seed(1)
from collections import defaultdict
import pybel
ob = pybel.ob
ob.obErrorLog.StopLogging()
def CreateValencyTable(mol):
common_valencies = defaultdict(lambda:defaultdict(set))
@baoilleach
baoilleach / randomsmiles.py
Last active April 26, 2018 20:53
Create random smiles
import random
import pybel
def create_mutants(A, B):
# Let's randomly choose a cross-over point in both A and B
# and generate four possible combinations
c1 = random.randint(0, len(A))
c2 = random.randint(0, len(B))
startA, endA = A[:c1], A[c1:]
startB, endB = B[:c2], B[c2:]
@baoilleach
baoilleach / test.cif
Created October 23, 2017 06:30
Test cif
data_Ca2Al2SiO7
_cell_length_a 7.716
_cell_length_b 7.716
_cell_length_c 5.089
_cell_angle_alpha 90
_cell_angle_beta 90
_cell_angle_gamma 90
_cell_volume 302.982
_symmetry_space_group_name_H-M 'P -4 21 m'
_symmetry_int_tables_number 113
@baoilleach
baoilleach / aromaticity.txt
Created June 13, 2017 09:17
Aromaticity examples
These are not all necessarily aromatic:
[nH]1[nH][nH][nH][nH]1
[bH]1cccc1
b1nbnbn1
c1c(=O)
c1c(=O)c(=O)c(=O)c(=O)c(=O)c(=O)c(=O)c(=O)c(=O)c(=O)c(=O)c(=O)c(=O)c(=O)c(=O)c1
@baoilleach
baoilleach / multithread_simple.cpp
Created February 19, 2017 11:10
Test multithreading with a simple example
#include <windows.h>
#include <stdlib.h>
#include <stdio.h>
#include <process.h>
#ifdef WIN32
#define USING_OBDLL
#endif
#include <openbabel/babelconfig.h>
@baoilleach
baoilleach / multithread.cpp
Last active February 21, 2017 20:00
Test multithreaded Open Babel application
#include <windows.h>
#include <stdlib.h>
#include <stdio.h>
#include <process.h>
#ifdef WIN32
#define USING_OBDLL
#endif
#include <openbabel/babelconfig.h>
@baoilleach
baoilleach / linuxmint.txt
Last active May 18, 2020 21:14
Linux Mint Cinnamon 17.2 installing Open Babel
sudo apt install cmake g++ libwxgtk3.0-dev
wget http://prdownloads.sf.net/openbabel/openbabel-2.4.1.tar.gz
tar zxf openbabel-2.4.1.tar.gz
cd openbabel-2.4.1
mkdir build
cd build
cmake .. -DENABLE_TESTS=OFF -DBUILD_GUI=ON
make -j3
@baoilleach
baoilleach / gcc2016fulda.txt
Created November 9, 2016 11:24
Tweets from GCC 2016 Fulda
WendyAnneW #gcc2016Fulda Looking forward to GCC meeting on Sunday
cdsouthan . @WendyAnneWarr #gcc2016Fulda Ich auch
GDCh_CIC @dr_greg_landrum Hi Greg, we decided to take #gcc2016Fulda pls RT
GDCh_CIC @WendyAnneWarr Hi Wendy, please use #gcc2016Fulda
GDCh_CIC Follow the 12. German Conference on Chemoinformatics in Fulda, (GCC2016) via hashtag #gcc2016Fulda https://www.gdch.de/index.php?id=3089 …
dr_greg_la [] #RDKitUGM2016
[] http://compchemkitchen.org/2016/10/25/cck-5-including-rdkit-workshop/ …
[] Chemistry in @knime training at #gcc2016Fulda
cdsouthan So #gcc2016Fulda it is then, might even pop a few comments myself https://twitter.com/GDCh_CIC/status/794126214227169281 …
FOellien Just packing my backs for #gcc2016fulda * will meet the board at 7pm for dinner and last preparations
@baoilleach
baoilleach / snapcraft.yaml
Last active October 9, 2016 16:12
Open Babel snapcraft file
name: openbabel
version: "2.4.0"
summary: Open Babel, the Open Source chemistry toolbox
description: Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas.
confinement: strict
apps:
babel:
command: babel
obabel: