schrodinger.application.desmond.packages.viparr1.viparr.viparr module

class schrodinger.application.desmond.packages.viparr1.viparr.viparr.Struct

Bases: object

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.packages.viparr1.viparr.viparr', '__dict__': <attribute '__dict__' of 'Struct' objects>, '__weakref__': <attribute '__weakref__' of 'Struct' objects>, '__doc__': None})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.packages.viparr1.viparr.viparr'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

class schrodinger.application.desmond.packages.viparr1.viparr.viparr.Atom

Bases: object

__class__

alias of builtins.type

__delattr__

Implement delattr(self, name).

__dict__ = mappingproxy({'__module__': 'schrodinger.application.desmond.packages.viparr1.viparr.viparr', '__dict__': <attribute '__dict__' of 'Atom' objects>, '__weakref__': <attribute '__weakref__' of 'Atom' objects>, '__doc__': None})

__dir__() → list

default dir() implementation

__eq__

Return self==value.

__format__()

default object formatter

__ge__

Return self>=value.

__getattribute__

Return getattr(self, name).

__gt__

Return self>value.

__hash__

Return hash(self).

__init__

Initialize self. See help(type(self)) for accurate signature.

__init_subclass__()

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__

Return self<=value.

__lt__

Return self<value.

__module__ = 'schrodinger.application.desmond.packages.viparr1.viparr.viparr'

__ne__

Return self!=value.

__new__()

Create and return a new object. See help(type) for accurate signature.

__reduce__()

helper for pickle

__reduce_ex__()

helper for pickle

__repr__

Return repr(self).

__setattr__

Implement setattr(self, name, value).

__sizeof__() → int

size of object in memory, in bytes

__str__

Return str(self).

__subclasshook__()

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

__weakref__

list of weak references to the object (if defined)

schrodinger.application.desmond.packages.viparr1.viparr.viparr.templates_convert(templates)

Convert templates structure to internal data structure.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.compress_residue_list(residue_list)

Compress FF representation if possible

schrodinger.application.desmond.packages.viparr1.viparr.viparr.get_atom_list(atoms, neighbors, templates, residue_list)

Return a list of atoms in the ct structure. Each atom has the following fields: pdbname, pdbres, resnum, atomic number, charge, atomtypes. Also check that all residue and atom names are in the templates data structure.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.get_neighbor_list(atom_list)

Return list of neighbor lists; one neighbor list for each atom, in order. Each neighborlist is guaranteed to be sorted. Entries are 1-based.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.get_bond_list(neighbor_list)

Return list of all bonds (i,j) such that i<j. List will be sorted meaningfully. Entries are 1-based.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.get_angle_list(neighbor_list)

Return list of all angles (i,j,k) such that i<k. List will be sorted meaningfully. Entries are 1-based.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.get_proper_list(neighbor_list, bond_list)

Return list of all propers (i,j,k,l) such that i<l. List will be sorted meaningfully. Entries are 1-based.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.get_bonded_term_list(fieldname, templates, residue_list, sorted)

Return a list of bonded items. Each bonded item is a list, namely: [i,j] when fieldname = ‘bonds’ or ‘exclusions’. if sorted, i<j [i,j,k] when fieldname = ‘angles’. if sorted, i<k [i,j,k,l] when fieldname = ‘propers’ or ‘impropers’. if sorted, i<l The returned list will be sorted in a meaningful way.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.merge(list0, list1)

Merge list1 into list0, as long as there are no entries in common.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.get_pseudo_terms(iffld, pseudo_residue_list, nres, nstart)

Return drude and virtual particle list (numbering starting at nstart) and list of ‘bonds’ between drudes, virtual sites and particles. The pseudo_list can be appended to the atom list.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.update_pseudo_residue_list(iffld, pseudo_residue_list, atoms, templates, residue_list)

pseudo_list is a list of all residues in ct block, and each residue is a list of pseudo particles.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.construct_lists(iffld, atoms, neighbors, rules, templates, residue_list, pseudo_residue_list)

Return lists that describe the structure.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.merge_blocks(first, second)

Merge second block into first; print warning message if element in second block is already in the first block. Assumes blocks themselves hold unique entries. First block is the merged one.

schrodinger.application.desmond.packages.viparr1.viparr.viparr.merge_blocks2(first, second)

Merge first block into second; print warning message if element in first block will override element in second block. Assumes blocks themselves hold unique entries. Second block is the merged one. [NOT THE SAME BEHAVIOR AS ABOVE.]

schrodinger.application.desmond.packages.viparr1.viparr.viparr.add_water_constraints(ff_handle)

Add an ffio_constraints block to the ff_handle for a water ct by reading the ffio_c1 values from the angles and bonds, and append ‘_constrained’ to the functional forms of the angles and bonds.

Parameters:ff_handle (destro.Destro) – the handle of the ffio_block

schrodinger.application.desmond.packages.viparr1.viparr.viparr.main(vargs=[])