The PDBPartMap module provides functions to prepare, check and process models from PDB files. This module is located in Yup/Models/Null/, which contains other modules that may be used to construct parts of a full-featured force field assembler. The import statement is some variant of: from Yup.Models.Null.PDBPartMap import *. Introduction The PDBPartMap module provides a link between PDB files and YUP models. A common work flow is as follows: One or more PDB files are converted into a PDB Partition Map using makepartmap(). This is a Python program that constructs two tuples that together define a hierarchy. This partition map is heavily annotated. It can be manually revised, to alter the hierarchy, to change the (all-atom to coarse-grained) representation and to designate rigid units for the Rigid Body Monte Carlo simulation method. The function checkpartmap() can be used to catch errors introduced by a manual revision of the partition map. The function readpartmap() processes a partition map to populate a YUP Model object. The model can then be used in simulations. The function rigidunits() can be called to obtain a list of groups that are to be treated as rigid bodies. The list is required to set up the Monte Carlo method. The function writepdb() can be used to convert a YUP Model object to one or more PDB files. Only the atoms that have the proper PDB hierarchy encoded in their names will appear in the output files. The PDB hierarchy (model>chain>residue>atom) is encoded in the nodename of the atom AtomMaps that make up the YUP Model object. Normally, these functions are used to construct a force field assembler. Users should not need to use this module directly. Constants The ATOM GROUP TRACT HELIX TRASH VERBATIM BACKBONE GEOMCENTER MASSCENTER KEY_CHARGE KEY_ITYPE KEY_XTYPE KEY_MASS KEY_MASK RIGID_NONE RIGID_FILE RIGID_CHAIN RIGID_RESIDUE RIGID_TRIPLET RIGIDBODYPATTERN Partition Maps A partition map file consists of a Python program in which is defined two tuples named PDBFILES and ATOMMAP. The PDBFILES tuple contains an ordered list of the names of the PDB files that were used to create the partition map. The ATOMMAP tuple contains three items. Atom or group... Three items... Deeply nested... Defined in stages, one level at a time... To make it easy to modify... Can add new levels or collapse some levels... Designate rigid units by negating symbol... Default is each chain is a rigid unit, unlabeled chains grouped into one... Functions Creating Partition Maps The function makepartmap() converts one or a number of PDB files into a Python program that defines two tuples that together defines a YUP hierarchy: Name Arguments Return makepartmap required: pdbfiles, partmap, option - Argument Type Preset pdbfiles tuple of strings - partmap pdbfiles - option pdbfiles - rigidity rigidity - The Processing Partition Maps The function readpartmap() : Name Arguments Return readpartmap required: partmap, home, atoms, coords, params - Argument Type Preset partmap Tuple of energy constructor function-label pairs - home partmap - atoms partmap - coords partmap - params partmap - The Collecting Rigid Units The function rigidunits() collects : Name Arguments Return rigidunits required: root Tuple of Group AtomMaps Argument Type Preset root Group AtomMap - The Checking Partition Maps The function checkpartmap() can be used to check a partition map file: Name Arguments Return checkpartmap required: partmap - Argument Type Preset partmap Name of a partition map file. - This function is under development. Writing PDB Files The function writepdb() converts a YUP Model object to one or more PDB files: Name Arguments Return writepdb required: model; optional: prefix, suffix - Argument Type Preset model A YUP Model object - prefix prefix for the file name 'YUPDB' suffix file name suffix '.pdb' It is assumed that the YUP Model had been created to be compatible with one or more PDB files, although the model need not be created specifically with readpartmap(). This means that the original PDB hierarchy is encoded in the names of the atoms which must be at least 23 characters wide and which can be parsed to yield the following fields: Index or Slice Type Content 0:5 integer atom serial number 5:9 string atom label 9 character alternate location indicator 10:13 string residue label 13:17 integer residue sequence number 17 character residue insertion code 18 character chain label 19:23 string zero filled file number Trailing characters are ignored. Atoms whose names are not formatted as the above are silently ignored. The output will consist of as many files as were originally used to create the model. File names are formed from the prefix, the file number and the suffix. Development FFA HookeFFA NonbondXFFA PDBPartMap Chains Worm Environment