1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
|
.. _Reference:
.. |C_alpha| replace:: C\ :sub:`α`
Module Reference
################
.. Undocumented modules
__pkginfo__
AtomEnvironment
CCPNDataModel
ComplexEnvironment
CrystalEnvironment
Database
GroupEnvironment
Features
ForceFields.Amber.AmberData
ForceFields.BondedInteractions
ForceFields.ForceField
ForceFields.NonBondedInteractions
ForceFields.MMForceField
MoleculeEnvironment
NormalModes.Core
PDBML
ProteinEnvironment
PyMOL
surfm
tess
Skeleton
ThreadManager
Tk
Tk.ProteinVisualization
Utility
MMTK
=====
.. automodule:: MMTK
MMTK.Biopolymers
================
.. automodule:: MMTK.Biopolymers
MMTK.Bonds
==========
.. automodule:: MMTK.Bonds
MMTK.ChargeFit
==============
.. automodule:: MMTK.ChargeFit
MMTK.ChemicalObjects
====================
.. automodule:: MMTK.ChemicalObjects
MMTK.Collections
================
.. automodule:: MMTK.Collections
MMTK.ConfigIO
=============
.. automodule:: MMTK.ConfigIO
MMTK.DCD
========
.. automodule:: MMTK.DCD
:exclude-members: writePDB, writeDCD
MMTK.Deformation
================
.. automodule:: MMTK.Deformation
MMTK.Dynamics
=============
.. automodule:: MMTK.Dynamics
MMTK.Environment
================
.. automodule:: MMTK.Environment
MMTK.Field
==========
.. automodule:: MMTK.Field
MMTK.ForceFields
================
MMTK.ForceFields.AmberForceField
--------------------------------
.. automodule:: MMTK.ForceFields.Amber.AmberForceField
:no-members:
MMTK.ForceFields.Amber94ForceField
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. autoclass:: MMTK.ForceFields.Amber.Amber94ForceField
MMTK.ForceFields.Amber99ForceField
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. autoclass:: MMTK.ForceFields.Amber.Amber99ForceField
MMTK.ForceFields.OPLSForceField
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
.. autoclass:: MMTK.ForceFields.Amber.OPLSForceField
MMTK.ForceFields.AnisotropicNetworkForceField
---------------------------------------------
.. autoclass:: MMTK.ForceFields.ANMFF.AnisotropicNetworkForceField
MMTK.ForceFields.CalphaForceField
--------------------------------------
.. autoclass:: MMTK.ForceFields.CalphaFF.CalphaForceField
MMTK.ForceFields.DeformationForceField
--------------------------------------
.. autoclass:: MMTK.ForceFields.DeformationFF.DeformationForceField
MMTK.ForceFields.HarmonicForceField
-----------------------------------
.. autoclass:: MMTK.ForceFields.BondFF.HarmonicForceField
MMTK.ForceFields.LennardJonesForceField
---------------------------------------
.. autoclass:: MMTK.ForceFields.LennardJonesFF.LennardJonesForceField
MMTK.ForceFields.SPCEForceField
-------------------------------
.. autoclass:: MMTK.ForceFields.SPCEFF.SPCEForceField
MMTK.ForceFields.ForceFieldTest
-------------------------------
.. automodule:: MMTK.ForceFields.ForceFieldTest
MMTK.ForceFields.Restraints
---------------------------
.. automodule:: MMTK.ForceFields.Restraints
MMTK.FourierBasis
=================
.. automodule:: MMTK.FourierBasis
MMTK.Geometry
=============
.. automodule:: MMTK.Geometry
MMTK.InternalCoordinates
========================
.. automodule:: MMTK.InternalCoordinates
:show-inheritance:
MMTK.Minimization
=================
.. automodule:: MMTK.Minimization
MMTK.MolecularSurface
=====================
.. automodule:: MMTK.MolecularSurface
MMTK.MoleculeFactory
====================
.. automodule:: MMTK.MoleculeFactory
MMTK.NormalModes
================
.. automodule:: MMTK.NormalModes
MMTK.NormalModes.BrownianModes
------------------------------
.. automodule:: MMTK.NormalModes.BrownianModes
MMTK.NormalModes.EnergeticModes
-------------------------------
.. automodule:: MMTK.NormalModes.EnergeticModes
MMTK.NormalModes.VibrationalModes
---------------------------------
.. automodule:: MMTK.NormalModes.VibrationalModes
MMTK.NucleicAcids
=================
.. automodule:: MMTK.NucleicAcids
MMTK.PDB
========
.. automodule:: MMTK.PDB
MMTK.PDBMoleculeFactory
-----------------------
.. automodule:: MMTK.PDBMoleculeFactory
MMTK.ParticleProperties
=======================
.. automodule:: MMTK.ParticleProperties
MMTK.ProteinFriction
====================
.. automodule:: MMTK.ProteinFriction
MMTK.Proteins
=============
.. automodule:: MMTK.Proteins
MMTK.Random
===========
.. automodule:: MMTK.Random
MMTK.Solvation
==============
.. automodule:: MMTK.Solvation
MMTK.Subspace
=============
.. automodule:: MMTK.Subspace
MMTK.Trajectory
===============
.. automodule:: MMTK.Trajectory
MMTK.Units
==========
.. automodule:: MMTK.Units
MMTK.Universe
=============
.. automodule:: MMTK.Universe
MMTK.Visualization
==================
.. automodule:: MMTK.Visualization
MMTK.XML
========
.. automodule:: MMTK.XML
|
