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faq [2018/12/19 11:14]
flack
faq [2020/07/30 15:46]
flack
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 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 <code>sudo apt install pigz</code> or a similar command. 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 <code>sudo apt install pigz</code> or a similar command.
 +
 +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://docs.microsoft.com/en-us/windows/wsl/install-win10]]
  
  
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 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 **uncompressed chunks**, use a command like this:
 <code> <code>
 gzip -dc your.sdf.gz | awk -v name=<chunk_name> -v ext=sdf -v size=<size> 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 > file1}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close(file1);file1=file2}}}}' gzip -dc your.sdf.gz | awk -v name=<chunk_name> -v ext=sdf -v size=<size> 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 > file1}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close(file1);file1=file2}}}}'
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 Just replace your.sdf.gz with your filename, <chunk_name> with the name of the files you want and <size> with the intended chunk size. Just replace your.sdf.gz with your filename, <chunk_name> with the name of the files you want and <size> with the intended chunk size.
  
-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:
 <code> <code>
 gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf -v size=1000000 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 > file1}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close(file1);file1=file2}}}}' gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf -v size=1000000 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 > file1}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close(file1);file1=file2}}}}'
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-To split an sdf.gz file into multiple gzip compressed chunks, use a command like this:+To split an sdf.gz file into multiple **gzip compressed chunks**, use a command like this:
 <code> <code>
 gzip -dc your.sdf.gz | awk -v name=<chunk_name> -v ext=sdf.gz -v size=<size> 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 | "gzip -9 > "file1""}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close("gzip -9 > "file1"");file1=file2}}}}' gzip -dc your.sdf.gz | awk -v name=<chunk_name> -v ext=sdf.gz -v size=<size> 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 | "gzip -9 > "file1""}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close("gzip -9 > "file1"");file1=file2}}}}'
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 Just replace your.sdf.gz with your filename, <chunk_name> with the name of the files you want and <size> with the intended chunk size. Just replace your.sdf.gz with your filename, <chunk_name> with the name of the files you want and <size> with the intended chunk size.
  
-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:
 <code> <code>
 gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf.gz -v size=1000000 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 | "gzip -9 > "file1""}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close("gzip -9 > "file1"");file1=file2}}}}' gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf.gz -v size=1000000 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 | "gzip -9 > "file1""}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close("gzip -9 > "file1"");file1=file2}}}}'
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 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://docs.microsoft.com/en-us/windows/wsl/install-win10]]
  
  
faq.txt ยท Last modified: 2020/07/30 15:46 by flack