I need to **pairwise align protein structures**. 

Specifically, my task requires 

 - alignment of structure predictions in PDB format, for EACH of ~1000
   full length proteins

**versus** 

 - X-ray crystallography based structure PDB files for Pfam/hmmsearch
   delimited domain only regions of EACH of these 6 (shorter domain)
   sequences.

This means **~1000*6 = 6,000 pairwise structure alignment runs**.

Which software do you recommend from  [Wiki][1] or elsewhere, with my following requirements:

 1. I should be able to download and run on my local laptop or
    university HPC, and not on a webserver (unless batch submission and
    download are allowed).
 2. The runtime, diskspace and RAM needed for each of my 6,000 pairwise
    alignment need to be reasonable for either my local laptop or on my univ's
    HPC (with ~2GB RAM nodes and 12cpu limit on my user account)
 3. I need to be able to parse the alignment results programmatically
    (using Perl or Python scripting...)

**FINAL GOAL** = Classify and/or rank each of the full-length proteins based on likelihood of domain of interest being "present", **not** using pairwise **sequence alignments**, **but** from reported metrics of pairwise **structure alignments** (rather than my arbitrary yes/no/maybe classification)

If your suggested bioinformatics pipeline has been published, better yet! 

Thank you all, in advance. Cheers!


  [1]: https://en.wikipedia.org/wiki/Structural_alignment_software
These links will hopefully be useful as references:

 - https://en.wikipedia.org/wiki/Structural_alignment_software
 - https://en.wikipedia.org/wiki/Structural_alignment
 - https://proteopedia.org/wiki/index.php/Structure_superposition_tools

I have tried locally TM-align, Fr-TM-align, Matt, FATCAT, MAMMOTH, SSAP, FAST, THESEUS, and probably couple of others that I have forgotten. All of them used to be available as independent binaries, but for some of them that may not be the case due to age or general lack of support. All of them are reasonably fast, so I don't think that would be a limiting factor for you no matter what you choose. They have various advantages and disadvantages, and also their outputs are different in terms of information provided. I suggest you try several programs and see what functionality is most useful for your purpose.