frobnitzem / autoqct Goto Github PK

This step involves extracting cluster structures from a trajectory generated elsewhere.

• Implement read_xdr read_cp2k in io.py and test with test_io in simple.py

Implement extract method for the Sys class that takes an (N,3) array and a list of 0-based atom numbers (1 for each molecule) and returns a new, populated Sys instance.

• Implement a read_sys function that takes a .gro file CP2K trajectory frame and creates a Sys class.

Implement a search method for the Sys class that finds the nearest n molecules to a given, central molecule. -- returning an index list usable by extract.

• Implement a check_solvent function that determines whether a solvent conforms to its expected ground-state geometry.

• Implement a check_cluster function that determines whether all solvent molecules are within the prescribed cluster radius.