spliting sdf file
Is there any python script to separate/split sdf file(having more than lakhs of compound structure) into smaller size(1000 structure per file))
software error
drug discivery
python
• 3,941 views
•
link
updated
by
WouterDeCoster
•
written
by
jonupk6 •
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
(Nextflow) Having trouble with a generic process to stitch together files that were split and then …
written by sodiumnitrate •I'm new to nextflow and I'm trying to figure out how to: 1. Get a large `.fasta` file, split it into pieces of size `1000` …
-
Help regarding vina split
written by Sharon •Hi, I am using structure data of (approved only) drugs which is available in sdf format. I have converted this single sdf file into pdbqt …
-
how to separate a large matrix into different small matrix with different rows?
written by ROSE •Hi, I have a big matrix (peak by cell) that is more than 75Gb, and I could not open it by Scanpy or in R …
-
Splitting a fasta file based on the number of headers.
written by sicat.paolo20 •I have a fasta files that has more than 2.7 million headers. I want to break it into chunks. >gene1 ACTG... >gene2 ATTT... ... >gene2,700,000 …
-
splitting Multifasta File Into A *Smaller Multifasta File containing few sequence
written by kabir.deb •I am trying to split a large multifasta file into several smaller mutlifasta files. I have seen several examples of being used to split multifasta …
-
How to split fasta into seperate files by chromosome (in the header)
written by ethanagbaker •<p>I have 1000 fasta files that have simulated reads, and I want to split each of these 1000 files into separate files (one per chromosome) …
-
all unique compound structure (SMILES) of PubChem Database
written by ajingnkHi everyone, I want to get all unique compound structures of PubChem Database. I have download SDF file for PubChem, but it is 45G after …
-
Split Super Large Files
written by Bioscientist<p>I think we always could come arcoss large files, say, fastq files. Now I have really super large fastq files, around 10GB. I need to …
-
How To Split A .Vcf.Gz File
written by Jorge Amigo<p>I am currently working with 1000 Genomes latest released data, which is a large >60GB .vcf.gz file. I am having difficulties to process it as …
-
How To Split A Multiple Fasta
written by Gvj<p>How to split a Multiple fasta file into separate files having almost similar file size as specified? Do you have any tool for that? But …
It would be definitely helpful if you show a snippet of how your file looks like - you can't expect us to know an sdf file by heart.
Check this toolkit out. Otherwise use the suggestion in this thread to convert to PDB format.