<tt>PoreMatMod.jl</tt> : Julia Package for <i>in Silico</i> Postsynthetic Modification of Crystal Structure Models
E. Adrian Henle, Nickolas Gantzler, Praveen K. Thallapally, Xiaoli Z. Fern, Cory M. Simon
Abstract
PoreMatMod.jl is a free, open-source, user-friendly, and documented Julia package for modifying crystal structure models of porous materials such as metal–organic frameworks (MOFs). PoreMatMod.jl functions as a find-and-replace algorithm on crystal structures by leveraging (i) Ullmann’s algorithm to search for subgraphs of the crystal structure graph that are isomorphic to the graph of a query fragment and (ii) the orthogonal Procrustes algorithm to align a replacement fragment with a targeted substructure of the crystal structure for installation. The prominent application of PoreMatMod.jl is to generate libraries of hypothetical structures for virtual screenings. For example, one can install functional groups on the linkers of a parent MOF, mimicking postsynthetic modification. Other applications of PoreMatMod.jl to modify crystal structure models include introducing defects with precision and correcting artifacts of X-ray structure determination (adding missing hydrogen atoms, resolving disorder, and removing guest molecules). The find-and-replace operations implemented by PoreMatMod.jl can be applied broadly to diverse atomistic systems for various in silico structural modification tasks.