RDS instances are managed by Amazon, so they do not provide access to the underlying operating system.
An alternative is to host your database in an EC2 instance. I discourage this thought, as you lose real benefit of cloud such as operational overhead moved over to AWS rather than your team, so you do not have to maintain and patch. Nevertheless you ll have access to OS and may be able to customize as you wish.
An alternative approach would be to use a service such as Amazon CloudSearch or Amazon Elasticsearch Service to perform full-text search on PDFs. You may integrate RDS with those services so you exploit what they are meant to be, exactly full-text-search.
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