| | |
- analyze(potList)
- perform analysis of RepelPot terms and return nicely formatted summary.
- checkGetRepel(repel=None, suppressException=False)
- Given a repel value, check that it is consistent with the loaded Xplor-NIH
parameter set, and throw an exception if it is inconsistent, unless the
suppressException argument is set to True. A check is also made that
the parameter sets for proteins and nucleic acids take the same repel
value.
If the default Xplor-NIH parameter set is not loaded, do not modify repel.
- create_RepelPot(name, selection='not PSEUDO', moveTol=0.5, repel=None, use14=False, selPairs=[], extraRadii=[], suppressException=False, paramSet='toppar', verbose=False)
- Return an instance of repelPot.RepelPot.
The selection argument specifies which atoms are included in the
nonbonded calculation. moveTol specifies the maximum atom
displacement before the nonbonded list is recalculated. repel is
a scale factor for the atomic radii which is set by the function
initRepel. The selPairs argument is an optional sequence of pairs
of atom selection strings which specify particular pairs of atoms
to compute interactions between. The actual selections used will
be the intersections of the selection argument and each selection
pair entry. The use14 argument controls whether or not 1-4
interactions are enabled. Setting use14=False is equivalent to
nbxmod=4 in the older
XPLOR VDW term. The default setting of use14=False is
appropriate when using TorsionDBPot created by
torsionDBPotTools.create_TorsionDBPot. The suppressException argument
should be set to True only if a nonstandard repel value is specified, and
should only be used for testing purposes.
The extraRadii argument contains a list of pairs (chemType,radius) which
can be used to specify atomic radii for chemical types not present in
the XPLOR PSF.
The paramSet argument sepcifies the source of the parameters to be used
by the returned RepelPot. The default value "toppar" implements the setup
behavior implemented up to this point, where nonboned parameters and
exclusions are read from XPLOR's parameters, and PSF. If set to a
different value, parameters are read from the string, or from a file with
the given name, either in the current directory, or in the directory given
by the environment variable REPELDB. The syntax of this file is specified
below in readParams.
- initRepel(term, scale=1, use14=None, moveTol=0.5, repel=None, interactingAtoms=None, suppressException=False)
- A helper routine for resetting a RepelPot terms to default values.
FIX: rationalize default values vs. None
Additionally, a simple selection pair can be specified by specifying a
single atom selection string as the interactingAtoms argument. If the
interactingAtoms argument is omitted, the selection pairs will be reset to
those specified in create_RepelPot.
The default value of repel is 0.8 for pre-3.1 version Xplor-NIH protein
and nucleic acid parameters, and 0.9 for later versions. If a repel value
less than 0.9 is specified to be used with post-3.0 parameter sets, an
exception will be raised, unless suppressExceptions is set to True.
- readParams(filenameOrContents, verbose=False)
- Read in repelPot parameter file
this file will have the following statements:
nonbond <chemType> <epsilon> <sigma> <epsilon14> <sigma14>
nonbond (<selection>) <epsilon> <sigma> <epsilon14> <sigma14>
nbfix <chemType1> <chemType2> <A> <B> <A14> <B14>
nbfix (<selection1>) (<selection2>) <A> <B> <A14> <B14>
exclusion (<selection1>) (<selection2>)
resExclusion <residue name> (<atoms1>) (<atoms2>)
The exclusion statement is applied in the following manner: if one
of the selections contains the literal string "_RESID" then that statement
is applied to every residue in the selection argument of create_RepelPot
with _RESID replaced with the residue number of each residue.
_RESID+<N>. or_RESID-<N>, where <N> is an integer (spaces are allowed
before and after the arithmatic symbol), thus allowing specification of
inter-residue exclusions.
The resExclusion statement specifies exclusions to be applied within
all residues with the given residue type name. The atom names listed in
parentheses are separated by the space character, and may contain
wildcards as specified in atomSelLang.
Two syntax notes:
-the '!', '{', and '}' characters are ignored.
-the '#' character preceeded by one or more spaces, or at the start
of a line introduces an ignored comment.
This function returns a tuple containing (nonbonds,nbfixes,excludes,
resExcludes).
- readToken(string)
- Read a token from the leading portion of string.
Return a tuple of the token and the string with the number removed.
The token can be a single space-delimited work, or a collection of words
quoted with (possibly nested) parentheses or single (') or double (")
quotes. All quote characters are returned.
|
