GitHub PushEvent at 2014-09-10 22:04:20
Repository: q2mm
Actor: ericchansen
Payload: {"shas":[["0c1905fb27989607ba8d85922b159edda65eae60","87a11d15f1db60bb8a56dc0978efe0a9dbe4089b@gmail.com","Added bonds and angles as data types\n\nModified the Datum class to include str_num. Keeps track of the\nstructure/conformer number for large mae or mmo files. Modified\nthe sorting methods accordingly.\n\nThe previous change was integrated to accomodate the new data\ntypes: bonds and angles. These data types work on files containg\na single structure or many structures. The str_num attribute was\nadded to organize this data. Previously only energies were fully\ncompatible with multiple structures per file. Now, to the best of\nmy current knowledge and testing, everything works with multiple\nstructures per file. For this to work, many adjustments were made\nto the calculate script.\n\nThese new types are accessed via \"-ma\" and \"-mb\" for MacroModel\nangles and bonds, and \"-ja\" and \"-jb\" for Jaguar angles and bonds.\nUnfortunately, these data types are extracted from an mmo file, so\na calculation must be performed even for the reference Jaguar data.\nExtraction from the mae file is possible, but would require a lot\nmore work. Now that I think about it, it also probably couldn't\nfulfill my point in the next paragraph.\n\nCurrently, all bonds and angles are used. However, this should\nbe limited to bonds and angles that are actively being\nparameterized. All other bonds and angles should not be included\nthe data. This change will come soon.\n\nAdded the option \"--norel\" to calculate. This prevents converting\nabsolute energies to relative energies for printing/writing data.\nRelative energies are still used no matter what when calculating\nthe penalty function (that just wouldn't make sense otherwise).\n\nMinor changes were made to the output from calculate to\naccomodate the now longer data labels.\n\nThe calculation indices determined when creating com files in\ncalculate.make_macromodel_coms are now split in two: one for mae\nfiles and one for mmo files.\n\nThe ELST, WRIT, and MINI commands still may be redundant. However,\nthings seem to work now, and I'm tired, so it is what it is for\nnow. Perhaps later someone will optimize this further (if\npossible).\n\nSome changes were made to filetypes.BaseFile.get_data to be more\naccomodating to the multiple structure format that is now assumed.\n\nMinor additions were made to filetypes.MMoFile to finish the data\nextraction.","Eric Hansen",false],["e1e6948954778a11841dc84b7b1fd9f835f8d7d3","87a11d15f1db60bb8a56dc0978efe0a9dbe4089b@gmail.com","Added MM3* Hess. Added Jaguar Hess. mass-weighting\n\nAdded options to calculate.process_args and the rest of the script\nto handle getting the MM3* Hessian. Also modified the Jaguar Hessian\nmethod in calculate.extract_data to account for mass-weighting.\n\nModified the Hessian methods of filetypes.FileType to make them more\nconvenient.\n\nThe current method appears to work, but it feels sloppy. I think that\nwe should make a class for the Hessian that does a better job at\nconverting between mass-weighted versions, inversion, etc.","Eric Hansen",false],["836f6d1a633aa9beafd5b1eea1af0e5e8008317e","87a11d15f1db60bb8a56dc0978efe0a9dbe4089b@gmail.com","Modified bond/angle extraction\n\nBonds and angles are now only included as reference data if there\nis a FF term that directly relates to them. However, this distinction\nrequires the mmo file. Each line pertaining to a bond or angle in the\nmmo file has a comment at the end. For substructures in MM3*, that\ncomment refers to the substructure's name.\n\nRight now, all bonds and angles are eliminated based on the keyword\n\"OPT\", which must appear the in the substructure's name. It would be\nnice to auto-detect the substructure name.","Eric Carl Hansen",false],["52ad9b16a5445021bc217b15ab588c4e45ad03ec","87a11d15f1db60bb8a56dc0978efe0a9dbe4089b@gmail.com","Slightly modified bonds and angles\n\nAdded an option to calculate.process_args to eliminate bonds and\nangles if they are not included in the substructure. This is no\nlonger the default behavior.","Eric Carl Hansen",false],["ed35b3b22495e7bb9318aacbd533c7f93d0bc3a9","87a11d15f1db60bb8a56dc0978efe0a9dbe4089b@gmail.com","Working on improving energy extraction/adding plots\n\nThis is a work in progress! Beware! Very sloppy.","Eric Carl Hansen",false],["8ecd46256e4e1f7e4f106790b7a9418be502c3df","87a11d15f1db60bb8a56dc0978efe0a9dbe4089b@gmail.com","Fixed/finished/modified atom indices for energies\n\nCan now use the scanind argument for calculate.process_args\nto use the user specified scan index.","Eric Carl Hansen",false],["5437fcc2fec8638facbd9ca3f7a8ef91b9516e26","87a11d15f1db60bb8a56dc0978efe0a9dbe4089b@gmail.com","Ignoring files in example_data","Eric Hansen",true]],"size":7,"ref":"refs/heads/master","head":"5437fcc2fec8638facbd9ca3f7a8ef91b9516e26"}