How to export SD files or get SMILES formula ?

This guide aims to explain how to export SD files or get SMILES from commercial or Open Source molecule editor programs.

On this page you will find guidelines:

• How to export SD files from Chemdraw or DataWarrior
• How combine multiple SD Files into One File
  • How to save a chemical spreadsheet in sdf format from Molsoft
  • how to use the “cat” command to combine multiple SD files
  • how to use Open Babel to combine multiple SD files

Here’s a step-by-step guide on how to export SD files from Chemdraw, a popular chemical drawing software:

1. Open Chemdraw and create or open the file containing the molecule you want to export.
2. Select the molecule in the document by clicking on it.
3. From the File menu, select “Save As…”
4. In the Save As dialog box, select “Chemdraw (*.cdx)” as the file type.
5. In the same dialog box, select the “Save as type” as “Chemdraw SD file (*.sdf)”
6. Choose a location to save the file and give it a name, then click “Save”
7. The file will be saved as a SD file, which can be used for in silico screening and other applications
8. Repeat steps 2 to 7 for any other molecules in the document that you want to export.

Please note that this is a general guide for Chemdraw and the steps may be slightly different depending on the version of the software you are using. But the steps are similar for other software like Accelrys Discovery Studio, Open Babel, and others.

How can I combine multiple molecules in 1 SD File ? 

 SD files are a type of text file that can be easily combined into a single file. There are a few ways to combine multiple SD files into one file:

1. Using a text editor: You can use a text editor like Notepad++, Sublime Text or Atom to open the multiple SD files, then copy and paste the contents of each file into a new document. Be sure to save the new document in the SD file format.
2. Using a command line tool: The open-source tool “cat” can be used to combine multiple files in the command line. For example, you can use the command “cat file1.sdf file2.sdf > combined_file.sdf” to combine file1.sdf and file2.sdf into a new file named combined_file.sdf
3. Using a software that allows batch processing: Some software like Open Babel, RDKit and KNIME have a batch processing option that can easily merge multiple SD files into one file.
4. Using a Python script: You can also use a Python script that can read and combine multiple SD files into a single file. You can use the standard library functions like open() and write() to read the content of the files and write it to a new file. You can also use libraries like pandas or rdkit to load and concatenate the files.

Please note that you should double check the compatibility of the software or script you are using, making sure that the files you want to combine are not corrupted, and that the resulting file is still in the correct format and readable.

For imports into the Inospiner platform, we strongly recommend to prepare import batches by type of molecules (Synthetic compounds, fragment-like molecules, etc.)

How to save a chemical spreadsheet in sdf format from Molsoft ?

Export example from Molsoft.

Step-by-step guide on how to use the “cat” command to combine multiple SD files into one file:

1. Open a command prompt or terminal window on your computer.
2. Navigate to the directory where the SD files you want to combine are located. You can use the “cd” command to change directories.
3. Use the “cat” command to combine the files. The basic syntax for the “cat” command is: “cat file1 file2 > combined_file”. For example, if you have two files named “file1.sdf” and “file2.sdf” in the current directory and you want to combine them into a new file named “combined_file.sdf”, you would use the command: “cat file1.sdf file2.sdf > combined_file.sdf”
4. Press enter to run the command. The contents of file1.sdf and file2.sdf will be combined into a new file named combined_file.sdf
5. You can repeat the command to combine more files, for example: “cat file3.sdf file4.sdf >> combined_file.sdf”
6. To verify that the files have been combined, you can use the “less” command to view the contents of the combined_file.sdf

Please keep in mind that the “cat” command can be used with any type of text file, not only SD files. Also, you should double check the compatibility of the files you want to combine, making sure that the files are not corrupted, and that the resulting file is still in the correct format and readable.

Step-by-step guide on how to use Open Babel, a chemical toolbox, to combine multiple SD files into one file:

1. Install Open Babel by visiting the website https://openbabel.org/wiki/Category:Installation and following the instructions for your operating system
2. Open a command prompt or terminal window on your computer
3. Navigate to the directory where the SD files you want to combine are located. You can use the “cd” command to change directories
4. Use the command “babel” to convert the input files into the desired format, you can use the option -i to specify the input format, -o to specify the output format and -m to merge the files, for example, to merge file1.sdf and file2.sdf into a file named combined.sdf you will use the command: babel -i sdf file1.sdf file2.sdf -o sdf -m -x combined.sdf

1. Press enter to run the command. The contents of file1.sdf and file2.sdf will be combined into a new file named combined.sdf
2. You can repeat the command to combine more files, for example: babel -i sdf file3.sdf file4.sdf -o sdf -a -x combined.sdf

Please keep in mind that Open Babel can be used with many other file formats and can also perform other operations like converting, filtering and searching. Also, you should double check the compatibility of the files you want to combine, making sure that the files are not corrupted, and that the resulting file is still in the correct format and readable.