2 Commits

Author	SHA1	Message	Date
Peter Eastman	fe0550bb7b	Create bonds based on chem_comp_bond records (#4904) ... * Create bonds based on chem_comp_bond records * Fixed a test that assumed bonds would be in a particular order	2025-04-22 08:58:54 -07:00
Stephen Farr	81271f93ab	Add support for writing atom subsets to PDBReporter (#3931) ... * enable atom subset in PDBReporter * adds optional atomSubset argument to PDBReporter * adds functions in PDBReporter which create a new topology and positions with chosen subset of atoms * PDBReporter write PDB files with the subset topology and positions. * refactor PDBReporter * make _createTopologySubset a method that is called only the first time it is needed * more efficient creation of subset positions * check that atomSubset is ordered * refactoring PDBReporter and add PDBx * move checks on atomSubset to _createSubsetTopology * copy periodic box vectors from topology to subsetTopology * add atomSubset to PDBx reporter * add bond subset to createSubsetTopology * formatting changes to pdbreporter * loop over atoms cleaned up * put file opening inside parameter loop in TestPdbReporter::testinvalidSubsets to try and fix failing tests on windows * add thorough tests to TestPdbReporter * spelling changes * Add tests for atom positions, elements, names etc * attempt at fixing PyPy and Windows failing test cases * fix spellings * close output file before raising exceptions * closes output files before raising exception in pdbreporter createSubsetTopology * changes assertVecAlmostEqual from a method to function to avoid repeating	2023-02-28 11:30:10 -08:00