The Molecular Mechanics class (MolMech) is the parent class of the Molecular Dynamics (Motors), Energy Minimization (Minimizers) and Monte Carlo (MonteCarlo) classes. The MolMech class is defined in the MolMech module in Yup.Models. Since the subclass modules are in the same sub-directory of the Yup package, only a local import is necessary: from MolMech import MolMech. If a subclass is outside the package hierarchy then a full import path is required: from Yup.Methods.MolMech import MolMech. Data Attributes Data attribute names are case-sensitive. Most of the data attributes can be assigned new values. However, read-only attributes must not be assigned new values. If you do, the classes will not work. However, it is easy to recover from this stupidity: simply delete the added attribute. Note that each molecular mechanics class inherits the data attributes from this class. Therefore, you have to set these attributes independently for each descendant class. For example, you can set NumberOfPrintDivisions to 25 in the Motors class for molecular dynamics, and 10 in the Minimizers class for energy minimization. If you want to set the same value (that is not the default) in both classes, you will have to set the attribute separately in each class. Attribute Description MODEL This attribute is read-only. Returns the Model object registered when the class was instanced. ArchiveInterval Interval between periodic archives. The default value is 0 which means no periodic archive. Even if set greater than zero, archiving is done only if the appropriate file names (the CoordinateArchive and Motors.VelocityArchive attributes) are not at their default values of blank strings. CoordinateArchive Name of archive into which the Coordinates will be written at intervals defined in the ArchiveInterval attribute. The default value is a blank string which means that this archive is not created. ColumnWidth The width of each column in the printout generated by the molecular mechanic methods. The preset value is 11, where 10 columns are used to print the number and the last column is reserved for a space. This is wide enough to print numbers to only four places of significance in scientific format (allowing room for the signs). If set below 8, number fields are was wide as necessary and are separated by tabs. The columns of numbers will no longer line up for most tab settings but the output is suitable for input to databases or spreadsheets. NumberOfPrintDivisions This is one less than the number of energy output lines from the molecular mechanic methods. The preset value is 5, i.e., there will be 6 lines of output. The starting values (the zeroth step) and the final values (which may be short of the total number of steps requested by the user, e.g., if an energy minimization is terminated prematurely) are always printed. If set to zero, the calculation will be carried out without any print out except for exceptions and error messages. If set to a negative integer, the absolute number will be taken as the print interval. Thus, to print every step of a calculation set this attribute to -1. UpdateInterval The number of steps between updates of the non-bond lists. The preset value is 100. The non-bond list update creates a list of atom pairs whose atoms are within a certain distance of one another. This distance is somewhat larger than a cutoff distance which is the distance at which the magnitude of the non-bond interaction is considered to be insignificant. In between updates, some atom pairs in the list may move further apart from one another and should really be taken off the list. At the same time, atom pairs that are not in the list may move close enough that they should really be considered for calculation. This attribute must be set so that the non-bond lists are accurate and this also depends on the distance settings in the non-bond energy modules. UserAfterInterval If set above 0, this is the interval between calls to the userafter() method (see below). Preset value is 0. UserBeforeInterval If set above 0, this is the interval between calls to the userbefore() method (see below). Preset value is 0. Methods The MolMech class defines only the constructor function and four methods. The constructor function requires one argument, the model on which the molecular mechanics method is to be applied. This is a Model object that is constructed by a force field assembler. Constructor Number of Arguments Return Value MolMech 1 The new MolMech object Argument Purpose Preset Value a Model object the model that is to be subjected to the molecular mechanics calculation - The model object must be complete, i.e., the Map, Energy and Coordinates attributes must all be defined. The Prologue method is called to prepare for a calculation. Method Argument Keywords Return Values Prologue "numsteps", "limit" Tuple of 4 items Argument Type Preset Value numsteps Integer - limit None, a group AtomMap or a list of two integers - Molecular mechanic calculations can be restricted to a portion of a model. Please see the Targeted Simulation section of the Introduction to see how to set this argument. However, the energy is always evaluated for the entire model regardless of this setting. This method will set the column width attribute in the Potential module to the same value as set in the ColumnWidth attribute of this class. The returned tuple contains four items. (1) the coordinate AtomVector of the group specified in limit or of the entire model if limit is None, (2) the corresponding gradient AtomVector, (3) the evaluate() method of the Model object that is registered with this class and (4) the numbers of steps between printing, calculated from the values specified in numsteps and the NumberOfPrintDivisions attribute. The Preface method is called to prepare for a Monte Carlo calculation. Method Argument Keywords Return Values Preface "numsteps" Tuple of 5 items Argument Type Preset Value numsteps Integer - This method will set the column width attribute in the Potential module to the same value as set in the ColumnWidth attribute of this class. The returned tuple contains five items. (1) the mcprep() method, (2) the mcmove() method, (3) the mcpass() method, (4) the mceval() method, all four methods are of the Model object that is registered with this class and (5) the numbers of steps between printing, calculated from the values specified in numsteps and the NumberOfPrintDivisions attribute. The following two methods provide a limited opportunity to customize the molecular mechanics calculations. The userafter method is called every so many steps as defined in the UserAfterInterval attribute immediately after the steps that update the coordinates. The userbefore method is called every so many steps as defined in the UserBeforeInterval attribute immediately before the steps that update the coordinates. These methods are parameter-less (except for self). Note that these methods must be replaced with your own definitions. The methods that are provided in the MolMech class will only raise a Runtime exception. To use this facility: define a class based on the appropriate molecular mechanics class: Motors, Minimizers or Casino. Override the userafter and/or userbefore methods, i.e. by defining these methods in your derived class. For your class, use your initialization function to cache whatever objects that your update methods need. You will have to examine the code for the parent module to see what other (undocumented) attributes and methods that are accessible to you. Once you have a definition, you can create an instance of your class. Then, set values for the UserAfterInterval and/or UserBeforeInterval attributes. You still have the attributes of the parent class that you have to set and methods that you can call. An example can be found in the Calculate module of the rrDNAv1 model. Functions The AVLimits function takes a list of AtomVectors, impose the specified limits and returns a list of restricted AtomVectors. Method Number of Arguments Return Values AVLimits 2 Tuple of restricted AtomVector Argument Type Preset Value AV list of AtomVector - limit None, AtomMap or list of two Integers - Please see the Targeted Simulation section of the Introduction to see how to set limit. Introduction Molecular Mechanics Energy Minimization Molecular Dynamics Monte Carlo