faq
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| Both sides previous revisionPrevious revisionNext revision | Previous revisionNext revisionBoth sides next revision | ||
| faq [2018/12/19 01:40] – flack | faq [2020/07/30 13:46] – flack | ||
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| Line 18: | Line 18: | ||
| To split a smi.gz / smiles.gz file into multiple **gzip compressed chunks** use a command like this: | To split a smi.gz / smiles.gz file into multiple **gzip compressed chunks** use a command like this: | ||
| < | < | ||
| - | gzip -dc your.smi.gz | split --verbose --lines=< | + | gzip -dc your.smi.gz | split --verbose --lines=< |
| </ | </ | ||
| For example to split the Mcule Purchasable (Full) smi.gz file into 1M **gzip compressed chunks** use: | For example to split the Mcule Purchasable (Full) smi.gz file into 1M **gzip compressed chunks** use: | ||
| < | < | ||
| - | gzip -dc mcule_purchasable_full_180817.smi.gz | split --verbose --lines=1000000 --numeric-suffixes --suffix-length=10 --additional-suffix=' | + | gzip -dc mcule_purchasable_full_180817.smi.gz | split --verbose --lines=1000000 --numeric-suffixes --suffix-length=10 --additional-suffix=' |
| </ | </ | ||
| If you have pigz installed on your system you can replace gzip with pigz in the commands above to speed up the process, especially when you want compressed chunks. You can typically install it with < | If you have pigz installed on your system you can replace gzip with pigz in the commands above to speed up the process, especially when you want compressed chunks. You can typically install it with < | ||
| + | |||
| + | If you are on Windows 10, we suggest to install WSL to get access to a Linux distribution (for example Ubuntu). You can find WSL install instructions here: | ||
| + | |||
| + | [[https:// | ||
| Line 33: | Line 37: | ||
| If you have access to a unix based system and awk you can use the below commands to split large, gzipped SDF files into smaller chunks. | If you have access to a unix based system and awk you can use the below commands to split large, gzipped SDF files into smaller chunks. | ||
| - | To split an sdf.gz file into multiple uncompressed chunks, use a command like this: | + | To split an sdf.gz file into multiple |
| < | < | ||
| gzip -dc your.sdf.gz | awk -v name=< | gzip -dc your.sdf.gz | awk -v name=< | ||
| Line 40: | Line 44: | ||
| Just replace your.sdf.gz with your filename, < | Just replace your.sdf.gz with your filename, < | ||
| - | For example to split the Mcule Purchasable (Full) sdf.gz file into 1M uncompressed chunks use: | + | For example to split the Mcule Purchasable (Full) sdf.gz file into 1M **uncompressed chunks** use: |
| < | < | ||
| gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf -v size=1000000 ' | gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf -v size=1000000 ' | ||
| Line 46: | Line 50: | ||
| - | To split an sdf.gz file into multiple gzip compressed chunks, use a command like this: | + | To split an sdf.gz file into multiple |
| < | < | ||
| gzip -dc your.sdf.gz | awk -v name=< | gzip -dc your.sdf.gz | awk -v name=< | ||
| Line 53: | Line 57: | ||
| Just replace your.sdf.gz with your filename, < | Just replace your.sdf.gz with your filename, < | ||
| - | For example to split the Mcule Purchasable (Full) sdf.gz file into 1M gzip compressed chunks use: | + | For example to split the Mcule Purchasable (Full) sdf.gz file into 1M **gzip compressed chunks** use: |
| < | < | ||
| gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf.gz -v size=1000000 ' | gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf.gz -v size=1000000 ' | ||
| Line 61: | Line 65: | ||
| Please note that the process can take a while. | Please note that the process can take a while. | ||
| + | |||
| + | If you are on Windows 10, we suggest to install WSL to get access to a Linux distribution (for example Ubuntu). You can find WSL install instructions here: | ||
| + | |||
| + | [[https:// | ||
faq.txt · Last modified: 2024/04/09 08:33 by rkiss