It is my intention to use protected PDF files on my web journal, the type that does not allow the text to be copied.
I would like to know if this will affect its indexing on Google Scholar, and if there are any alternatives.
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Unless you are password protecting the PDF file in question to prevent it from being read without the password then Google will still be able to crawl and index the PDF files in question.
I don't have the exact reference in front of me but Google has been able to extract text data from PDF files for many years now for indexing purposes and only a password protected PDF file or one protected through a robots.txt exclusion won't be indexed.