Modules The utility modules can be found in Yup.Tools. Name Contents Summary Atoms Functions Find Atom AtomMaps matching one of several criteria. AutoGen Class Generate three-atom and four-atom interactions from two-atom interactions. AVRecords Class Iterate over the records of an AtomVector file. Brookhaven Classes Convert between YUP models and PDB files. Chains Class Template for a force field assembler for models of unbranched chain molecules. Requires the LinSeq module. ChemNames Dictionaries Long and short names of common residues. FFA Class Template for a force field assembler. Groups Functions Find Group AtomMaps matching one of several criteria. LinSeq Functions Utilities for models of unbranched linear and circular chain molecules. MakeGraph Functions Generate graphical displays for a Model object. MakeLine Functions Generate the coordinates of lines of several kinds. misc Functions Generate paths to sub-directories of the Yup package ParmTop Class Translate a YUP Model to an AMBER parmtop file. SwissCheese Classes and Functions Convert, check and analyze Swiss Cheese (SCX) and other density files Topology Functions Calculate topological quantities for closed curves. TraceChain Class Use the path of one chain to trace the path of another. Programs The utility programs can be installed in any directory that is in users' command path. Name Summary Yup.avf Convert an unformatted AtomVector file (used in YUP, hardware specific) to a text dump (useful for storage, hardware-agnostic) or back. Use the --help option to obtain complete documentation. Yup.fpf Convert the parameters of a model type into a number of indexed files. Yup.king Symbolic link to the KiNG molecular display program. Normally invoked from within YUP. Yup.python Symbolic link to the Python interpreter best suited to the YUP package. Especially useful if there are several versions of the interpreter installed. Yup.scx A command-line program to fit a molecular structure into a density map. Use the --help option to obtain complete documentation. Yup.test A command-line program to test an installation of YUP. Also for benchmarking. Use the --help option to obtain complete documentation. Yup.which Report the location of the YUP package. Useful for developers who may have more than one version of the YUP package installed.