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- Cells
- Routines
class Cells |
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The cells object provides a better way to search for nearby atoms. A
pure all versus all search is O(n^2) - for every atom, every other atom
must be searched. This is rather inefficient, especially for large
proteins where cells may be tens of angstroms apart. The cell class
breaks down the xyz protein space into several 3-D cells of desired
size - then by simply examining atoms that fall into the adjacent
cells one can quickly find nearby cells.
NOTE: Ideally this should be somehow separated from the routines
object...
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Methods defined here:
- __init__(self, cellsize)
- Initialize the cells.
Parameters
cellsize: The size of each cell (int)
- addCell(self, atom)
- Add an atom to the cell
Parameters
atom: The atom to add (atom)
- assignCells(self, protein)
- Place each atom in a virtual cell for easy neighbor comparison
- getNearCells(self, atom)
- Find all atoms in bordering cells to an atom
Parameters
atom: The atom to use (atom)
Returns
closeatoms: A list of nearby atoms (list)
- removeCell(self, atom)
- Remove the atom from a cell
Parameters
atom: The atom to add (atom)
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class Routines |
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Methods defined here:
- __init__(self, protein, verbose)
- Initialize the Routines class. The class contains most
of the main routines that run PDB2PQR
Parameters
protein: The protein to run PDB2PQR on (Protein)
verbose: A flag to determine whether to write to
stdout
- addHydrogens(self)
- Add the hydrogens to the protein. This requires either
the rebuildTetrahedral function for tetrahedral geometries
or the standard quatfit methods. These methods use three
nearby bonds to rebuild the atom; the closer the bonds, the
more accurate the results. As such the peptide bonds are
used when available.
- applyForcefield(self, forcefield)
- Apply the forcefield to the atoms within the protein
Parameters
forcefield: The forcefield object (forcefield)
Returns
hitlist: A list of atoms that were found in
the forcefield (list)
misslist: A list of atoms that were not found in
the forcefield (list)
- applyNameScheme(self, forcefield)
- Apply the naming scheme of the give forcefield to the atoms
within the protein
Parameters
forcefield: The forcefield object (forcefield)
- applyPatch(self, patchname, residue)
- Apply a patch to the given residue. This is one of the key
functions in PDB2PQR. A similar function appears in
definitions.py - that version is needed for residue level
subtitutions so certain protonation states (i.e. CYM, HSE)
are detectatble on input.
This version looks up the particular patch name in the
patchmap stored in the protein, and then applies the
various commands to the reference and actual residue
structures.
See the inline comments for a more detailed explanation.
Parameters
patchname: The name of the patch (string)
residue: The residue to apply the patch to (residue)
- assignTermini(self, chain)
- Assign the termini for the given chain by looking at
the start and end residues.
- calculateDihedralAngles(self)
- Calculate the dihedral angle for every residue within the protein
- debumpProtein(self)
- Make sure that none of the added atoms were rebuilt
on top of existing atoms. See each called function
for more information.
- debumpResidue(self, residue, conflictnames)
- Debump a specific residue. Only should be called
if the residue has been detected to have a conflict.
If called, try to rotate about dihedral angles to
resolve the conflict.
Parameters
residue: The residue in question
conflictnames: A list of atomnames that were
rebuilt too close to other atoms
Returns
1 if successful, 0 otherwise
- findMissingHeavy(self)
- Repair residues that contain missing heavy (non-Hydrogen) atoms
- findNearbyAtoms(self, atom)
- Find nearby atoms for conflict-checking. Uses
neighboring cells to compare atoms rather than an all
versus all O(n^2) algorithm, which saves a great deal
of time. There are several instances where we ignore
potential conflicts; these include donor/acceptor pairs,
atoms in the same residue, and bonded CYS bridges.
Parameters
atom: Find nearby atoms to this atom (Atom)
Returns
nearatoms: A list of atoms close to the atom.
- getClosestAtom(self, atom)
- Get the closest atom that does not form a donor/acceptor pair.
Used to detect potential conflicts.
NOTE: Cells must be set before using this function.
Parameters
atom: The atom in question (Atom)
Returns
bestatom: The closest atom to the input atom that does not
satisfy a donor/acceptor pair.
- getMoveableNames(self, residue, pivot)
- Return all atomnames that are further away than the
pivot atom.
Parameters
residue: The residue to use
pivot: The pivot atomname
- getWarnings(self)
- Get all warnings generated from routines
- pickDihedralAngle(self, residue, conflictnames, oldnum=None)
- Choose an angle number to use in debumping
Algorithm
Instead of simply picking a random chiangle, this function
uses a more intelligent method to improve efficiency.
The algorithm uses the names of the conflicting atoms
within the residue to determine which angle number
has the best chance of fixing the problem(s). The method
also insures that the same chiangle will not be run twice
in a row.
Parameters
residue: The residue that is being debumped (Residue)
conflictnames: A list of atom names that are currently
conflicts (list)
oldnum : The old dihedral angle number (int)
Returns
bestnum : The new dihedral angle number (int)
- rebuildTetrahedral(self, residue, atomname)
- Rebuild a tetrahedral hydrogen group. This is necessary
due to the shortcomings of the quatfit routine - given a
tetrahedral geometry and two existing hydrogens, the
quatfit routines have two potential solutions. This function
uses basic tetrahedral geometry to fix this issue.
Parameters
residue: The residue in question (residue)
atomname: The atomname to add (string)
Returns
1 if successful, 0 otherwise
- repairHeavy(self)
- Repair all heavy atoms. Unfortunately the first time we
get to an atom we might not be able to rebuild it - it
might depend on other atoms to be rebuild first (think side
chains). As such a 'seenmap' is used to keep track of what
we've already seen and subsequent attempts to rebuild the
atom.
- runPROPKA(self, ph, ff, outname)
- Run PROPKA on the current protein, setting protonation states to
the correct values
Parameters
ph: The desired pH of the system
ff: The forcefield name to be used
outname: The name of the PQR outfile
- setDihedralAngle(self, residue, anglenum, angle)
- Rotate a residue about a given angle. Uses the quatfit
methods to perform the matrix mathematics.
Parameters
residue: The residue to rotate
anglenum: The number of the angle to rotate as
listed in residue.dihedrals
angle: The desired angle.
- setDonorsAndAcceptors(self)
- Set the donors and acceptors within the protein
- setReferenceDistance(self)
- Set the distance to the CA atom in the residue.
This is necessary for determining which atoms are
allowed to move during rotations. Uses the
shortestPath algorithm found in utilities.py.
- setStates(self)
- Set the state of each residue. This is the last step
before assigning the forcefield, but is necessary so
as to distinguish between various protonation states.
See aa.py for residue-specific functions.
- setTermini(self)
- Set the termini for the protein. First set all known
termini by looking at the ends of the chain. Then
examine each residue, looking for internal chain breaks.
- updateBonds(self)
- Update the bonding network of the protein. This happens
in 3 steps:
1. Applying the PEPTIDE patch to all Amino residues
so as to add reference for the N(i+1) and C(i-1)
atoms
2. UpdateInternalBonds for inter-residue linking
3. Set the links to the N(i+1) and C(i-1) atoms
- updateInternalBonds(self)
- Update the internal bonding network using the reference
objects in each atom.
- updateSSbridges(self)
- Check for SS-bridge partners, and if present, set appropriate
partners
- write(self, message, indent=0)
- Write a message to stderr for debugging if verbose
Parameters
message: The message to write (string)
indent : The indent level (int, default=0)
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