| | |
- addDisulfideBond(sel1, sel2)
deprecated. Calls psfGen.addDisulfideBond
- addPseudoResName(resname)
Add a residue name to the set which correspond to pseudo atoms.
- cartesianTopology(ivm, sel='known', oTensors=[])
configure the ivm.IVM tolopogy for Cartesian dynamics/minimization -
for the specified selection.
This consists of breaking topological bonds, and specifying that all atoms
are tree ``bases.''
This function should be called after any custom changes are made to the
ivm's topology setup, but before torsionTopology().
oTensors is a list of varTensor.VarTensor objects used for alignment
tensors
- downloadPDB(entry)
download a compressed PDB file from the RCSB database
return the PDB record as a string.
- genExtendedStructure(pdbFilename=0, sel=0, verbose=0, maxFixupIters=500)
This assigns X, Y, and Z coordinates to each atom, and then calls
protocol.fixupCovalentGeom() to correct the covalent geometry, using
maxFixupIters as the maxIters argument to that function.
The Y and Z coordinates are random (but small enough (within a range
of -0.5 to 0.5) to allow bonded atoms to form their bonds) and the X
coordinate is the atom number divided by 10. This will result in
an extended configuration along the X axis.
If pdbFilename is nonnull, the file will be read if it exists, and that
structure wil be used as a starting point (an attempt will be made to fix
the the covalent geom).
Whether it exists or not, it will be written to before returning.
- genTopParFilename(filename, useTopParVar=False)
If the given filename exists, it is returned, else the file is
looked for the in the TOPPAR directory, and a full path is returned
if it is found there.
If useTopParVar=True, the XPLOR TOPPAR variable is used for the
filename (instead of expanding its value). This results in
shorter paths, but the path is only valid within the XPLOR interpreter.
- initCarb13(filenames=[], scale=0.5)
initialize the XPLOR carbon chemical shift potential term.
arguments are:
filenames - either a single filename, or a sequence of filenames of
chemical shift assignment tables.
In addition to these files C13SHIFTS:rcoil_c13.tbl and
C13SHIFTS:expected_edited.tbl are always added.
- initCollapse(sel='all', Rtarget=-1, scale=1)
initialize the XPLOR radius of gyration potential term.
parameters are:
sel - string or atom selection specifying atoms in include in the
Rgyr calculation. If this is omitted, all atoms are included.
Rtarget - target radius. If this is omitted, the target Rgyr is
calculated as
Rgyr = 2.2*numResidues^0.38 -1 [angstrom]
scale - scale factor. If omitted, it defaults to 1. Note that the
per-assignment scale is always 100, so the energy is actually
scaled by 100*scale.
- initCoords(files=[], string='', model=-1, verbose=-1, erase=False, useChainID=True, correctSymmetricSidechains=True, strictResNames=False, maxUnreadEntries=(20, 0.20000000000000001), deleteUnknownAtoms=False, selection='all')
Initialize coordinates from one of more pdb file,
or from a string containing a PDB entry.
if model is specified, the specified PDB MODEL record will be read.
if erase is set to True, then atom positions in selection are cleared
before reading the pdb record.
If useChainID is True (the default), then the the chain ID PDB field is
used as the segment name (if set), If the chain ID field is blank it is
ignored regardless.
If deleteUnknownAtoms is True, then atoms whose coordinates are still
unknown after the PDB file is read will be deleted
If correctSymmetricSidechains is True (the default), then the sidechains
of phe, tyr, asp, and glu residues are checked to ensure that their
symmetric torsion angles (chi3 for glu, chi2 for the rest) are in
the correct (0..180 degree) range. If they are incorrect, then atomic
positions are swapped using selectTools.correctSymmetricSidechains.
If strictResNames is True, then residue names in the PDB must match
those in the PSF, otherwise, the residue names need not match
and backbone atoms for mutants can be read. Note that sidechain atoms (or
base atoms in nucleic acids) may be strangely placed if this option is
False.
PDB ATOM records which do not exactly match the expected input (the
atom name is not exactly the same) are attempted to be matched using the
function matchInexactAtomEntry. If more than maxUnreadEntries[0] or
maxUnreadEntries[1]*(num atoms) unmatchable ATOM records are
encountered, an exception is thrown. This check is disabled (no exception
will be thrown) if maxUnreadEntries is set to None.
This function results an InitCoordsResult structure containing bfactors
and occupancies read from the PDB record.
- initDihedrals(filenames=[], string='', scale=1, useDefaults=1, reload=False, simulation=0)
initialize the XPLOR restraints dihe (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).
- initDynamics(ivm, bathTemp=-1, finalTime=0.20000000000000001, numSteps=0, stepsize=0.001, potList=0, printInterval=50, initVelocities=0, eTol_factor=0.001, eTol_minimum=0)
initialize an IVM object (from the ivm module)
for PC6 (6th order predictor-corrector) dynamics.
The default value of bathTemp is the ivm's current value.
In addition to the function arguments, the following IVM parameters are
initialized:
constraintLengths
maxDeltaE
responseTime
eTolerance
adjustStepsize
scaleVel
resetCMInterval
additionally, if initVelocities!=0, the initial velocities will be
randomized.
eTolerance is set by the following formula:
eTolerance = eTol_factor * bathTemp + eTol_minimum
- initHBDA(filename, scale=500, simulation=0)
initialize the XPLOR hbda potential term
- initHBDB(selection='not pseudo', restraintFile=None, prnfrq=0)
initialize the XPLOR hbdb potential term
database hydrogen-bonding term - h-bonds are determined dynamically.
the selection argument specifies which atoms in included in the
calculation.
prnfrq can be changed from zero to periodically print out HBDB info during
dynamics and minimization.
By default, HBDB runs in ``free'' mode, in which hydrogen bonds are
determined on the fly. If you instead wish to use a fixed list of
h-bonds, specify a filename for the restraintFile argument.
The HBDB term may have issues with hetereo multimers. Please use with
caution.
- initMinimize(ivm, potList=0, printInterval=10, numSteps=500, maxCalls=20000, dEPred=0.001)
initialize an IVM object (from the ivm module)
for Powell minimization.
In addition to the function arguments, the following IVM parameters are
initialized:
constrainLengths
maxDeltaE
eTolerance
gTolerance
- initNBond(cutnb=4.5, rcon=4.0, nbxmod=3, selStr='known', tolerance=0.5, repel=0.80000000000000004, onlyCA=0, simulation=0)
standard initialization of the non-bonded repel potential. The XPLOR
nonbonded potential term is described here
note that cutnb should be greater than rmax + 2*tolerance, where rmax
is the largest vdw radius.
selStr specifies which atoms to use in nonbonded energy calculations.
If onlyCA is True, this string gets set to "name CA" - but this option is
deprecated.
- initParams(files, reset=0, weak_omega=0, simulation=0)
file is a structure type or filename or a list of a combination of
these two.
valid structure types are: protein, nucleic, and water
The default protein, nucleic and water parameter files are specified in
the protocol.parameters dictionary. Default values can be modified from
a script using e.g.
import protocol
protocol.parameters['protein'] = '/path/to/other/file.par'
If the argument is a filename, the current directory is first searched
for the file, and then the TOPPAR directory is searched.
XPLOR parameters are documented here.
If reset is true, all previous parameter settings are discarded
If weak_omega is true, improper force constants associated with the
peptide bond are reduced by 1/2 to allow a small amount of flexibility.
- initRamaDatabase(type='protein', simulation=0)
standard initialization of the rama torsion-angle database potential.
- initRandomSeed(seed=None)
set the initial random seed. If the seed argument is omitted, it is set
to seconds from the epoch mod 10^7
- initStruct(files=0, erase=1, simulation=0)
read XPLOR PSF files.
the file argument is a filename or list of filenames to read.
First the current directory is searched for the file, and then TOPPAR
is searched. Alternatively, a psf entry (starting with PSF...) can be
directly passed as the files argument.
Any pre-existing structure information is erased unless the erase argument
is cleared.
- initTopology(files=[], reset=0, simulation=0)
file is a structure type or filename or a list of a combination of
these two.
valid structure types are: protein, nucleic, and water
The default protein, nucleic and water topology files are specified in
the protocol.topology dictionary. Default values can be modified from
a script using e.g.
import protocol
protocol.topology['protein'] = '/path/to/other/file.top'
First the current directory is searched for the file, and then TOPPAR
is searched.
XPLOR topology is documented here.
If reset is true, all previous topology settings are discarded
- initialRandomSeed()
return the initial random seed value, or that from
simulationWorld.random if initRandomSeed has not been called.
- loadPDB(file='', string='', entry='', model=-1, simulation=None, correctSymmetricSidechains=True, deleteUnknownAtoms=False, maxUnreadEntries=(20, 0.20000000000000001), verbose=-1)
load a PDB entry from file, string, or from the RCSB database.
autogenerate the psf and initialize coordinates.
deleteUnknownAtoms and maxUnreadEntries are passed to initCoords()
A side-effect is that protein or nucleic covalent force field parameters
are loaded by initParams()
- massSetup(atomicMass=100, friction=10)
set uniform mass and friction values for all atoms.
Pseudo atoms may have nonuniform masses.
- matchInexactAtomEntry(entry, pdbTool, selection, strictResNames, verbose=0)
try to match a PDB record to an atom if the name is not exactly the
same. The coordinates will only be overwritten if they are unknown.
The current algorithm for matching is as follows:
match H to HT1
else match if there's only a single undefined atom whose name starts
with the same character.
else
match if atom names start with the same character and the remainder
of the characters are simple tranpositions of each other.
else
match if there's only a single undefined atom whose name starts
with and ends with the same character.
else
match if the first name of the name is a digit present in the correct
atom name and the second character matches the first character of the
correct name.
else
match if the two names have two matching characters.
else
match up O --> OT1
OXT --> OT2
If the match is not unique, it is not made.
The residue number and segment id must match.
Entries with nonnumeric residue numbers are ignored.
For atoms with residue names corresponding to those of pseudo atoms
(e.g. ANI), this function prints a warning on missing atoms, but returns
a True value.
If strictResNames is True, then residue names in the PDB must match
those in the PSF (default), otherwise, the residue names need not match
and backbone atoms for mutants can be read. Note that sidechain atoms (or
base atoms in nucleic acids) may be strangely placed if this option is
False.
- syncArrayBeforeDelete(anArray, selectionToDelete)
Given an array of values indexed by atom number, and a selection of
atoms to be deleted, remove the entries in the array so that they will
match up with the correct atoms after the atoms are actually deleted
- torsionTopology(ivm, fixedOmega=0, oTensors=[])
configure the ivm.IVM topology for standard torsion angle setup:
group rigid sidechains and break proline, ribose rings in the
appropriate places. Disulfide bonds are also broken.
This function sets all groupings and hinge types which are not already
specified, so it must be called last in the setup of an IVM's topology.
If fixedOmega is set, also fix protein omega backbone angles.
oTensors is a list of varTensor.VarTensor objects used for alignment
tensors
- updatePseudoAtoms(sim=0)
Update the set of pseudo atoms selected by the PSEUdo atom selection
keyword.
|