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- analyze(potList)
- perform analysis of DistSymmPot terms and return nicely formatted
summary
- create_DistSymmPot(name, restraints=None, sim=None, sim2=None)
- Create a DistSymmPot term with distances specified in a file or sequence.
The form of the sequence should be:
[[ (atom1, atom2), (atom3, atom4) , ...], ...]
where atomN is a atom selection string which selects a single
atom, and each pair of atoms specifies a distance. The sequence
should contain at least two atom pairs.
sim and sim2, if specified, specify the simulations of the first and
second atoms, respectively.
- genDimerRestraints(resids=None, resids2=None, segids=['A', 'B'], extraSels=None, residDelta=5, atomName='CA')
- Generate a set of restraints for DistSymmPot appropriate for a dimer
with identical subunits in the specified segids, with the sequence
of residues numbers in the resids argument corresponding obeying
the symmetry relationship with the corresponding residue numbers
in resids2. Restraints will be created, one for each specified residue
using the specified atom name. If the resids argument is omitted,
restraints will be generated for all residues in either segids or
extraSels separated by residDelta.
If resids2=None it is assumed that the two
subunits have the same residue numbering but different segids.
If segids=None, no segid is used in the atom selection.
The extraSels argument, if specified, should have two elements to be
used in place of the segids argument in generating pairs of selection
selection strings specifying unique atoms.
If resids2 is specified len(resids2) should be equal to len(resids).
In this case segids are omitted.
- genPolyRestraints(resids, resids2=None, resids3=None, segids=['A', 'B', 'C'], atomName='CA')
- generate a set of restraints for DistSymmPot appropriate for a polymer
with identical subunits in the specified segids, with the sequence
of residues numbers in the resids argument corresponding obeying
the symmetry relationship with the corresponding residue numbers
in resids2. Restraints will be created, one for each specified residue
using the specified atom name.
These restraints will enforce the condition that the rotation+translation
taking subunit 1 to subunit 2 is the same as that taking subunit 2 to
subunit 3. Thus, this function should be called at least once for each
adjacent set of three segids, and, for higher symmetry it may be useful
to also include the i,i+2,i+4 distances.
If resids2=None it is assumed that the two
subunits have the same residue numbering but different segids.
If segids=None, no segid is used in the atom selection.
If resids2 and resids3 are specified len(resids2) and len(resids3) should
be equal to len(resids). In this case segids are omitted.
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