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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. |
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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)) |
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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:] |
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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 |
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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 |
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#include <windows.h> | |
#include <stdlib.h> | |
#include <stdio.h> | |
#include <process.h> | |
#ifdef WIN32 | |
#define USING_OBDLL | |
#endif | |
#include <openbabel/babelconfig.h> |
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#include <windows.h> | |
#include <stdlib.h> | |
#include <stdio.h> | |
#include <process.h> | |
#ifdef WIN32 | |
#define USING_OBDLL | |
#endif | |
#include <openbabel/babelconfig.h> |
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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 |
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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 |
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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: |