parmed.tinker.topologyobjects module

Contains all of the class objects for the Tinker topology

class parmed.tinker.topologyobjects.AngleBend(atom1, atom2, atom3, k, theteq, fold, type_)

Bases: object

An angle-bending term

class parmed.tinker.topologyobjects.AngleList

Bases: parmed.tinker.topologyobjects._ParamTypeList

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of AngleBend

add

typeclass

alias of AngleBend

class parmed.tinker.topologyobjects.Atom(symbol, type_, class_, atomic_number, mass, valence, desc)

Bases: object

An atom in the system

Methods

add_vdw(radius, epsilon, radius14, …)

Adds van der Waals terms to the atom

add_vdw(radius, epsilon, radius14, epsilon14, reduction)

Adds van der Waals terms to the atom

class parmed.tinker.topologyobjects.AtomList

Bases: parmed.tinker.topologyobjects._ParamTypeList

List for Atom instances

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of Atom

add

typeclass

alias of Atom

class parmed.tinker.topologyobjects.AtomicMultipole(atom, frame, definition, moments)

Bases: object

Atomic multipole parameter

class parmed.tinker.topologyobjects.AtomicMultipoleList

Bases: parmed.tinker.topologyobjects._ParamTypeList

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of AtomicMultipole

add

typeclass

alias of AtomicMultipole

class parmed.tinker.topologyobjects.BondList

Bases: parmed.tinker.topologyobjects._ParamTypeList

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of BondStretch

add

typeclass

alias of BondStretch

class parmed.tinker.topologyobjects.BondStretch(atom1, atom2, k, req)

Bases: object

A bond-stretching term

class parmed.tinker.topologyobjects.DipolePolarizability(atom, alpha, group)

Bases: object

A dipole polarizability parameter

class parmed.tinker.topologyobjects.DipolePolarizabilityList

Bases: parmed.tinker.topologyobjects._ParamTypeList

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of DipolePolarizability

add

typeclass

alias of DipolePolarizability

class parmed.tinker.topologyobjects.OutOfPlaneBend(atom1, atom2, atom3, atom4, k)

Bases: object

An out-of-plane bending term

class parmed.tinker.topologyobjects.OutOfPlaneBendList

Bases: parmed.tinker.topologyobjects._ParamTypeList

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of OutOfPlaneBend

add

typeclass

alias of OutOfPlaneBend

class parmed.tinker.topologyobjects.OutOfPlaneDist(atom1, atom2, atom3, atom4, k)

Bases: parmed.tinker.topologyobjects.OutOfPlaneBend

An out-of-plane distance (functionally equivalent to OOP Bend

class parmed.tinker.topologyobjects.OutOfPlaneDistList

Bases: parmed.tinker.topologyobjects._ParamTypeList

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of OutOfPlaneDist

add

typeclass

alias of OutOfPlaneDist

class parmed.tinker.topologyobjects.PiTorsion(atom1, atom2, amplitude)

Bases: object

A Pi-Orbital Torsion parameter

class parmed.tinker.topologyobjects.PiTorsionList

Bases: parmed.tinker.topologyobjects._ParamTypeList

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of PiTorsion

add

typeclass

alias of PiTorsion

class parmed.tinker.topologyobjects.StretchBend(atom1, atom2, atom3, k, theteq, r1eq, r2eq)

Bases: object

A stretch-bending term

class parmed.tinker.topologyobjects.StretchBendList

Bases: parmed.tinker.topologyobjects._ParamTypeList

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of StretchBend

add

typeclass

alias of StretchBend

class parmed.tinker.topologyobjects.TorsionAngle(atom1, atom2, atom3, atom4, args)

Bases: object

Torsional Angle parameter

class parmed.tinker.topologyobjects.TorsionAngleList

Bases: parmed.tinker.topologyobjects._ParamTypeList

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of TorsionAngle

add

typeclass

alias of TorsionAngle

class parmed.tinker.topologyobjects.TorsionTorsion(atom1, atom2, atom3, atom4, atom5, spline1, spline2)

Bases: object

A coupled-torsion parameter (like CMAP)

class parmed.tinker.topologyobjects.TorsionTorsionGrid

Bases: collections.OrderedDict

The interpolation grid of a coupled-torsion correction map. Every unique grid is cached and if a duplicate grid is instantiated, a reference to the original grid is returned. As a result, all unique TorsionTorsionGrid instances are singletons and should be compared for equality with “is”

Methods

clear()
copy()
fromkeys(/, iterable[, value])	Create a new ordered dictionary with keys from iterable and values set to value.
get(key[, default])	Return the value for key if key is in the dictionary, else default.
items()
keys()
move_to_end(/, key[, last])	Move an existing element to the end (or beginning if last is false).
pop(k[,d])	value.
popitem(/[, last])	Remove and return a (key, value) pair from the dictionary.
setdefault(/, key[, default])	Insert key with a value of default if key is not in the dictionary.
update([E, ]**F)	If E is present and has a .keys() method, then does: for k in E: D[k] = E[k] If E is present and lacks a .keys() method, then does: for k, v in E: D[k] = v In either case, this is followed by: for k in F: D[k] = F[k]
values()

new

classmethod new(data)

class parmed.tinker.topologyobjects.TorsionTorsionList

Bases: parmed.tinker.topologyobjects._ParamTypeList

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of TorsionTorsion

add

typeclass

alias of TorsionTorsion

class parmed.tinker.topologyobjects.UreyBradley(atom1, atom2, k, req)

Bases: parmed.tinker.topologyobjects.BondStretch

A urey-bradley term – functionally identical to a bond-stretch

class parmed.tinker.topologyobjects.UreyBradleyList

Bases: parmed.tinker.topologyobjects._ParamTypeList

Methods

append(thing)	Append object to the end of the list.
clear(/)	Remove all items from list.
copy(/)	Return a shallow copy of the list.
count(value, /)	Return number of occurrences of value.
extend(things)	Extend list by appending elements from the iterable.
index(value[, start, stop])	Return first index of value.
insert(index, object, /)	Insert object before index.
pop([index])	Remove and return item at index (default last).
remove(value, /)	Remove first occurrence of value.
reverse(/)	Reverse IN PLACE.
sort(*[, key, reverse])	Stable sort IN PLACE.
typeclass	alias of UreyBradley

add

typeclass

alias of UreyBradley