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faq [2018/12/19 01:16] flackfaq [2022/06/29 14:56] (current) flack
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 ====== Frequently asked questions (FAQ) ====== ====== Frequently asked questions (FAQ) ======
 +
 +====I get an error message "invalid file" when I upload a docking target file. What can I do?====
 +
 +Please check if you have uploaded a valid PDB file. If so please try to remove any excess lines NOT starting with "ATOM" or "TER" or "END" expressions. On Linux bash this command will do the trick:
 +<code>
 +cat input.pdb | grep -E "^ATOM|^TER|^END" > fixed.pdb
 +</code>
 +
 +
 +====How can I get access to a Linux system if my operating system is Windows?====
 +
 +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]]
  
 ====Can I get a Mcule database SMILES file in smaller chunks?==== ====Can I get a Mcule database SMILES file in smaller chunks?====
  
-If you have access to a unix based system and the split command you can use the below commands to split large files into smaller chunks.+If you have access to a Linux system and the split command you can use the below commands to split large files into smaller chunks.
  
 To split a smi.gz / smiles.gz file into multiple **uncompressed chunks** use a command like this: To split a smi.gz / smiles.gz file into multiple **uncompressed chunks** use a command like this:
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 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:
 <code> <code>
-gzip -dc your.smi.gz | split --verbose --lines=<size> --numeric-suffixes --suffix-length=<suffix_length> --additional-suffix='.smi' --filter='gzip -9> $FILE' - your__+gzip -dc your.smi.gz | split --verbose --lines=<size> --numeric-suffixes --suffix-length=<suffix_length> --additional-suffix='.smi.gz' --filter='gzip -9> $FILE' - your__
 </code> </code>
  
 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:
 <code> <code>
-gzip -dc mcule_purchasable_full_180817.smi.gz | split --verbose --lines=1000000 --numeric-suffixes --suffix-length=10 --additional-suffix='.smi' --filter='gzip -9> $FILE' - mcule_purchasable_full_180817__+gzip -dc mcule_purchasable_full_180817.smi.gz | split --verbose --lines=1000000 --numeric-suffixes --suffix-length=10 --additional-suffix='.smi.gz' --filter='gzip -9> $FILE' - mcule_purchasable_full_180817__
 </code> </code>
  
-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.+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]] 
 + 
 + 
 +====Can I get a Mcule database SDF file in smaller chunks?==== 
 + 
 +If you have access to a Linux 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: 
 +<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=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close(file1);file1=file2}}}}' 
 +</code> 
 + 
 +Just replace your.sdf.gz with your filename, <chunk_name> with the name of the files you want and <size> with the intended chunk size. 
 + 
 +For example to split the Mcule Purchasable (Full) sdf.gz file into 1M **uncompressed chunks** use: 
 +<code> 
 +gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf -v size=1000000 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 > file1}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close(file1);file1=file2}}}}' 
 +</code> 
 + 
 + 
 +To split an sdf.gz file into multiple **gzip compressed chunks**, use a command like this: 
 +<code> 
 +gzip -dc your.sdf.gz | awk -v name=<chunk_name> -v ext=sdf.gz -v size=<size> 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 | "gzip -9 > "file1""}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close("gzip -9 > "file1"");file1=file2}}}}' 
 +</code> 
 + 
 +Just replace your.sdf.gz with your filename, <chunk_name> with the name of the files you want and <size> with the intended chunk size. 
 + 
 +For example to split the Mcule Purchasable (Full) sdf.gz file into 1M **gzip compressed chunks** use: 
 +<code> 
 +gzip -dc mcule_purchasable_full_180817.sdf.gz | awk -v name=mcule_purchasable_full_180817__ -v ext=sdf.gz -v size=1000000 'BEGIN{size=size}(NR==1){file1=sprintf("%s%0.10d.%s",name,counter,ext)}{print $0 | "gzip -9 > "file1""}{if($0=="$$$$"){file2=sprintf("%s%0.10d.%s",name,int(++counter/size),ext);{if(file1!=file2){close("gzip -9 > "file1"");file1=file2}}}}' 
 +</code> 
 + 
 +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. 
 + 
 +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]]
  
  
 ====Will my previous searches deleted?==== ====Will my previous searches deleted?====
  
-We won’t delete any of your search/screen results. However, you can delete them if you’d like by selecting the collection under the "collectionstab and clicking on Delete.+Searches created by anonymous users (not authenticated users) get deleted after some time, but if you registered an Mcule user account and perform searches workflows while you are signed in (as an authenticated user)those searches / workflow results will remain until you delete them. You can delete them by selecting the collection(s) on the  "Collectionspage and clicking on "Delete".
  
 ====Where can I access my previous search results?==== ====Where can I access my previous search results?====
  
-Under the Collections” tab. All your previous search/screen results are listed here ranked by their date of creation.+On the "Collections" page. All your previous search/workflow results are listed here sorted by their date of creation.
  
 ====How many searches and screens can I run?==== ====How many searches and screens can I run?====
faq.1545182174.txt.gz · Last modified: 2018/12/19 01:16 by flack