Package MolKit

source code

Submodules

[hide private]

MolKit.APBSParameters
MolKit.GapFinder
MolKit.MolecularDescriptor
MolKit.PDBdict
MolKit.VisionInterface

MolKit.amberPrmTop
MolKit.bondClassifier: This module implements a classifier which select bonds based on a dictionary of key, bondSelector.
MolKit.bondSelector: This module implements classes which select bonds based on a list of criteria.
MolKit.chargeCalculator: This module implements the ChargeCalculators classes which addCharges of various sorts to AtomSets.
MolKit.chargeMass
MolKit.data

MolKit.distanceSelector: This module implements classes which compare coordinates of two sets of atoms.
MolKit.genPdbParser
MolKit.getsecondarystructure: This module implements the classes GetSecondaryStructure, GetSecondaryStructureFromFile, GetSecondaryStructureWeb, These classes are expected to be specialized in getting the informations on the secondary Structure of a protein and create a secondarystructureset for a chain
MolKit.groParser: Module Gromacs Parser.
MolKit.hydrogenBondBuilder: This module implements the HydrogenBondBuilder class which builds hydrogen bonds between appropriate atoms.
MolKit.hydrogenBuilder: This module implements the HydrogenBuilder classes which add hydrogens to AtomSets.
MolKit.interactionDescriptor: This module implements the InteractionDescriptor class which builds sets of atoms in close contact and hydrogen bonds for two Molecules
MolKit.introduction: This package contains a number of class to describe molecular entities such as Molecules, Molecular surface
MolKit.listSet: This module implements a Set class that uses a List to store the objects in the set.
MolKit.mmcifParser: Module mmCIF_Parser.
MolKit.mmcifWriter
MolKit.mol2Parser
MolKit.molecule: This module implements the classes Atom, AtomSet, Bond, BondSet and Molecule.
MolKit.moleculeParser
MolKit.moleculeWriter
MolKit.oxtBuilder: This module implements the OxtBuilder class which adds an oxygen atom to a specific carbon atom, presumably in the c-terminus residue.
MolKit.parm94_dat
MolKit.pdb2pqr

MolKit.pdb2pqr.extensions
MolKit.pdb2pqr.pdb2pka

MolKit.pdb2pqr.pdb2pqr: Driver for PDB2PQR
MolKit.pdb2pqr.propka
MolKit.pdb2pqr.src

MolKit.pdb2pqr.src.aa: Amino Acid Structures for PDB2PQR
MolKit.pdb2pqr.src.definitions: Definitions for PDB2PQR
MolKit.pdb2pqr.src.forcefield: Forcefield.py
MolKit.pdb2pqr.src.hydrogens
MolKit.pdb2pqr.src.inputgen: inputgen class Create an APBS input file using psize data Written by Todd Dolinsky based on original sed script by Nathan Baker ---------------------------- PDB2PQR -- An automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations Nathan A.
MolKit.pdb2pqr.src.na: Nucleic Acid Structures for PDB2PQR
MolKit.pdb2pqr.src.pdb: PDB parsing class
MolKit.pdb2pqr.src.protein: Routines for PDB2PQR
MolKit.pdb2pqr.src.psize: psize class Get dimensions and other information from a PQR file.
MolKit.pdb2pqr.src.quatfit: Quatfit routines for PDB2PQR
MolKit.pdb2pqr.src.routines: Routines for PDB2PQR
MolKit.pdb2pqr.src.server: CGI Server for PDB2PQR
MolKit.pdb2pqr.src.structures: Structures for PDB2PQR
MolKit.pdb2pqr.src.utilities: Utilities for PDB2PQR Suite

MolKit.pdbParser: Module pdbParser.
MolKit.pdbWriter
MolKit.pqrWriter
MolKit.protein: This Module implements the classes Residue, Chain and Protein.
MolKit.radii_patterns
MolKit.sets
MolKit.stringSelector
MolKit.torTree
MolKit.trajParser
MolKit.tree: This module implements the classes TreeNode and TreeNodeSet.

Functions

[hide private]

Read(filename)

WritePDB(filename, node)

Variables

[hide private]

CRITICAL_DEPENDENCIES = ['mglutil', 'Numeric']

NONCRITICAL_DEPENDENCIES = ['sff', 'PyBabel', 'stride', 'bhtree', 'NetworkEdito...

Function Details

[hide private]

Read(filename)

source code

None

WritePDB(filename, node)

source code

None

Variables Details

[hide private]

CRITICAL_DEPENDENCIES

None

Value:

['mglutil', 'Numeric']

NONCRITICAL_DEPENDENCIES

None

Value:

['sff',
 'PyBabel',
 'stride',
 'bhtree',
 'NetworkEditor',
 'DejaVu',
 'mslib',
 'Vision',
...