v1.3

This version allows use of DSSP 4.0 (https://github.com/PDB-REDO/dssp) by "-t dssp4" which runs mkdssp with option --output-format=dssp instead of the old dsspcmbi.

Full Changelog: v1.2...v1.3

This version allows multiple query structures on input

This version allows multiple query structures on input (in default mode, not -q mode), so that instead of having to load database and initialize GPU for just one query, this can be done just once for a large set of query structures (from stdin).

Also fixed some error messages so that if a structure (tableau and distance matrix) is larger than the maximum (MAXDIM in saparams.h) a better warning message is issued (with name and size) and structure (database or query) skipped, rather than triggering a misleading "bad helix type" error (caused by parsing following distance matrix with wrong size) and exiting.

Also output more CUDA GPU device information to stderr, as well as value of MAXDIM to make it clearer what the limits are.

Update for modern CUDA (11.1) and fix bug with -q mode

Update to work with modern NVIDIA CUDA versions (tested on NVIDIA nvcc compiler and CUDA SDK release 11.1, V11.1.74 on a 64-bit Linux system and a NVIDIA GeForce GTX 1080 (Founders Edition 8GB GDDR5X 2560 CUDA cores).

Fixed bug with query list mode (-q ) with getting 'ERROR: query not found' due to bug in code for building the query list index from the list of identifiers read on stdin.

Initial release as used in paper and PhD thesis (2010)

Includes 2013 update for CUDA 5.0 (original CUDA 2.3)