Pydoc: module xplorPotTools
Tools to help manipulate and analyze XPLOR energy terms
Classes |
| | |
- builtins.object
-
- PY_Restraint
- PotData
class PY_Restraint(builtins.object) |
| |
PY_Restraint(pot, name, diff)
|
| |
Methods defined here:
- __init__(s, pot, name, diff)
- Initialize self. See help(type(self)) for accurate signature.
- diff(s)
- name(s)
- violated(s)
Data descriptors defined here:
- __dict__
dictionary for instance variables (if defined)
- __weakref__
list of weak references to the object (if defined)
|
class PotData(builtins.object) |
| |
PotData(pot)
|
| |
Methods defined here:
- __init__(s, pot)
- Initialize self. See help(type(self)) for accurate signature.
Data descriptors defined here:
- __dict__
dictionary for instance variables (if defined)
- __weakref__
list of weak references to the object (if defined)
| |
Functions |
| | |
- addRestraintsMethod(term)
- add a restraints() method
- analyze(potList)
- perform analysis of XplorPot terms and return nicely formatted summary.
Note on VDW (nonbonded) violations:
The analysis here does not heed any XPLOR constraints interaction
statements: all nonbonded violations are always reported.
- calcPotData(term)
- return PotData values for the given XPLOR term
- getHBDBbonds()
- Return info from the XPLOR HBDB energy term on each backbone H-bond in a
list of named tuples. The tuples have entries:
resid_CO, resid_HN, dir_type, lin_type, dist_OH, ang_COH, ang_CaCO, ang_OHN
Edir, Elin
- initDihedrals(filenames=[], string='', scale=1, useDefaults=True, reload=False, simulation=0)
- Initialize the XPLOR dihedral restraints (CDIH) potential term.
Parameters are:
filenames - either a single filename, or a sequence of filenames of
dihedral restraint assignment tables.
string - assignment table as a plain string.
scale - scale factor (defaults to 1).
useDefaults - use the default sidechain restraints (default: True)
these force chi2 angles of PHE, TYR, ASP, and chi3 of GLU
to obey IUPAC naming conventions.
reload - if True, reload the previously-loaded dihedral restraints.
This is useful if the restraints are lost do to the
number of atoms changing (SCRATCHing).
- restraints_meth(pot)
|
Data |
| | |
defaultThresholds = {'ANGL': 2, 'BOND': 0.05, 'CARB': 1.0, 'CDIH': 5, 'COUP': 1.0, 'DIHE': 10, 'HBDA': 0.0, 'IMPR': 2, 'NOE': 0.5, 'VDW': 0.2, ...} |
