chemfp.com

dalkescientific.com

The origin of the connection table

http://www.dalkescientific.com/writings/diary/archive/2014/07/06/connection_table_origin.html

The origin of the connection table. Instead of doing real work over the last month, I ended up trying to understand more about the origin of the connection table, and the origin of the phrase "connection table.". Regarding real work, chemfp-1.2. Importance of Calvin Mooers' connection table. In my previous essay. Here are examples from the literature which support my belief:. Ray and Kirsch, "Finding Chemical Records by Digital Computers", Science 25 October 1957:. An example of a code suitable for machi...

rdkit.blogspot.com

RDKit: December 2013

http://rdkit.blogspot.com/2013_12_01_archive.html

RDKit experiments and tutorials. Wednesday, December 18, 2013. Optimizing cleanup of stereochemistry. A fair amount of the time spent in constructing molecules using the RDKit goes to the assignment/cleanup of stereochemistry. I did an analysis for the 2012 UGM where I found that 27% of the time spent parsing 100K drug-like molecules from the ZINC set was in the. Egrep '@ /' chembl16 2010-2012.smi chembl16 2010-2012.chiral.smi. That gives 81030 molecules that contain at least one specified chiral center ...

chembioinfo.com

Java | Asad's Blog

https://chembioinfo.com/category/work/java

Man and his will to survive! ChemBLAST: Old dog new tricks. Asymp; 6 Comments. Has a rich page dedicate to the BLAST Tool. Bringing Chemistry in the BLAST. Calculate chemical fingerprints (binary:. For a given molecule for size length L. Choose the indexes in the L which are set to. For example, if bits 1, 10, 30, …. Are set as ‘. Now transform the indexes to char terminated by ‘$’ sign ( i.e 1- B$, 10- BA$, 30- DA$ …). Concatenate the patterns to form a sequence (B$BA$DA$…). I have used ECFP4. I have ch...

chembioinfo.com

Enzymes | Asad's Blog

https://chembioinfo.com/category/work/enzymes

Man and his will to survive! ChemBLAST: Old dog new tricks. Asymp; 6 Comments. Has a rich page dedicate to the BLAST Tool. Bringing Chemistry in the BLAST. Calculate chemical fingerprints (binary:. For a given molecule for size length L. Choose the indexes in the L which are set to. For example, if bits 1, 10, 30, …. Are set as ‘. Now transform the indexes to char terminated by ‘$’ sign ( i.e 1- B$, 10- BA$, 30- DA$ …). Concatenate the patterns to form a sequence (B$BA$DA$…). I have used ECFP4. I have ch...

chembioinfo.com

EMBL | Asad's Blog

https://chembioinfo.com/tag/embl

Man and his will to survive! ChemBLAST: Old dog new tricks. Asymp; 6 Comments. Has a rich page dedicate to the BLAST Tool. Bringing Chemistry in the BLAST. Calculate chemical fingerprints (binary:. For a given molecule for size length L. Choose the indexes in the L which are set to. For example, if bits 1, 10, 30, …. Are set as ‘. Now transform the indexes to char terminated by ‘$’ sign ( i.e 1- B$, 10- BA$, 30- DA$ …). Concatenate the patterns to form a sequence (B$BA$DA$…). I have used ECFP4. I have ch...

chembioinfo.com

chemaxon | Asad's Blog

https://chembioinfo.com/tag/chemaxon

Man and his will to survive! ChemBLAST: Old dog new tricks. Asymp; 6 Comments. Has a rich page dedicate to the BLAST Tool. Bringing Chemistry in the BLAST. Calculate chemical fingerprints (binary:. For a given molecule for size length L. Choose the indexes in the L which are set to. For example, if bits 1, 10, 30, …. Are set as ‘. Now transform the indexes to char terminated by ‘$’ sign ( i.e 1- B$, 10- BA$, 30- DA$ …). Concatenate the patterns to form a sequence (B$BA$DA$…). I have used ECFP4. I have ch...

dalkescientific.com

Indexing ChEMBL for chemistry search

http://www.dalkescientific.com/writings/diary/archive/2014/11/28/indexing_chembl.html

Indexing ChEMBL for chemistry search. I've just downloaded the SD file for ChEMBL-19. I'm happy that after many years they have finally placed the record identifier in the title line of each record! It used to contain either a blank line, or occasionally text that was essentially junk. Now I want to be able to work with the data in the file. More specifically, I want a simple cheminformatics system where I can:. Get the original SD record given its identifier. Search for records similar to a given query.

chembioinfo.com

CDK | Asad's Blog

https://chembioinfo.com/tag/cdk

Man and his will to survive! ChemBLAST: Old dog new tricks. Asymp; 6 Comments. Has a rich page dedicate to the BLAST Tool. Bringing Chemistry in the BLAST. Calculate chemical fingerprints (binary:. For a given molecule for size length L. Choose the indexes in the L which are set to. For example, if bits 1, 10, 30, …. Are set as ‘. Now transform the indexes to char terminated by ‘$’ sign ( i.e 1- B$, 10- BA$, 30- DA$ …). Concatenate the patterns to form a sequence (B$BA$DA$…). I have used ECFP4. I have ch...

chembioinfo.com

ChemBLAST: Old dog new tricks | Asad's Blog

https://chembioinfo.com/2014/12/31/chemblast-old-dog-new-tricks

Man and his will to survive! ChemBLAST: Old dog new tricks. Asymp; 6 Comments. Has a rich page dedicate to the BLAST Tool. Bringing Chemistry in the BLAST. Calculate chemical fingerprints (binary:. For a given molecule for size length L. Choose the indexes in the L which are set to. For example, if bits 1, 10, 30, …. Are set as ‘. Now transform the indexes to char terminated by ‘$’ sign ( i.e 1- B$, 10- BA$, 30- DA$ …). Concatenate the patterns to form a sequence (B$BA$DA$…). I have used ECFP4. I have ch...

chembioinfo.com

atoms | Asad's Blog

https://chembioinfo.com/tag/atoms

Man and his will to survive! ChemBLAST: Old dog new tricks. Asymp; 6 Comments. Has a rich page dedicate to the BLAST Tool. Bringing Chemistry in the BLAST. Calculate chemical fingerprints (binary:. For a given molecule for size length L. Choose the indexes in the L which are set to. For example, if bits 1, 10, 30, …. Are set as ‘. Now transform the indexes to char terminated by ‘$’ sign ( i.e 1- B$, 10- BA$, 30- DA$ …). Concatenate the patterns to form a sequence (B$BA$DA$…). I have used ECFP4. I have ch...