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mmLib
AtomMath: Mathmatical operations performed on mmLib.Strcuture.Atom objects.
Colors: Library of colors matching PyMol color names.
ConsoleOutput: Console output.
FileIO: Load and save mmLib.Structure objects from/to mmLib supported
formats.
Gaussian: Library of tables and classes for analsis of Gaussian probability
distributions.
GeometryDict: Geometry hasing/fast lookup classes.
Library: Monomer and element library data classes.
mmCIF: mmCIF file and mmCIF dictionary parser.
mmCIFBuilder: Convert a Structure object into its mmCIFFile description.
mmCIFDB: Structural database based on mmCIF.
OpenGLDriver: OpenGL rendering classes.
PDB: Brookhaven PDB v2.2 file parser.
PDBBuilder: Convert a Structure object to its PDBFile description.
R3DDriver: Viewer.py graphics driver for producing a output file for the Raster3D
ray tracer.
SpaceGroups: Symmetry operations as functions on vectors or arrays.
Structure: Classes for representing biological macromolecules.
StructureBuilder: Classes for building a mmLib.Structure representation of biological
macromolecules.
Superposition: Class for least-squares structural superposition.
TLS: Utility classes for loading, manipulating, and analyzing TLS
parameters.
UnitCell: Classes for handling unit cell transformation.
Viewer: Visualization system for Structure objects.
Constants
NumericCompat
Sequence
__builtin__.object:
The most base type
mmLib.Structure.AlphaHelix:
Class containing information on a protein alpha helix.
mmLib.Structure.Atom:
Class representing a single atom.
mmLib.Structure.BetaSheet:
Class containing information on a protein beta sheet.
mmLib.Structure.Bond:
Indicates two atoms are bonded together.
mmLib.ConsoleOutput.ConesoleOutput
__builtin__.dict:
dict() -> new empty dictionary.
mmLib.Structure.Altloc:
Container holding the same atom, but for different conformations and
occupancies.
mmLib.Viewer.GLPropertyDict:
Property cache/routing dictionary
mmLib.mmCIF.mmCIFRow:
Contains one row of data.
mmLib.PDB.PDBRecord:
Base class for all PDB file records.
mmLib.PDB.ANISOU:
The ANISOU records present the anisotropic temperature factors.
mmLib.PDB.ATOM:
The ATOM records present the atomic coordinates for standard
residues.
mmLib.PDB.HETATM:
The HETATM records present the atomic coordinate records for atoms
within "non-standard" groups.
mmLib.PDB.AUTHOR:
The AUTHOR record contains the names of the people responsible for the
contents of the entry.
mmLib.PDB.CAVEAT:
CAVEAT warns of severe errors in an entry.
mmLib.PDB.CISPEP:
CISPEP records specify the prolines and other peptides found to be in
the cis conformation.
mmLib.PDB.COMPND:
The COMPND record describes the macromolecular contents of an
entry.
mmLib.PDB.CONECT:
The CONECT records specify connectivity between atoms for which
coordinates are supplied.
mmLib.PDB.CRYSTn:
The CRYSTn (n=1,2,3) record presents the unit cell parameters, space
group, and Z value.
mmLib.PDB.DBREF:
The DBREF record provides cross-reference links between PDB sequences
and the corresponding database entry or entries.
mmLib.PDB.END:
The END record marks the end of the PDB file.
mmLib.PDB.ENDMDL:
The ENDMDL records are paired with MODEL records to group individual
structures found in a coordinate entry.
mmLib.PDB.EXPDTA:
The EXPDTA record presents information about the experiment.
mmLib.PDB.FORMUL:
The FORMUL record presents the chemical formula and charge of a
non-standard group.
mmLib.PDB.HEADER:
This section contains records used to describe the experiment and the
biological macromolecules present in the entry: HEADER, OBSLTE, TITLE,
CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, AUTHOR, REVDAT, SPRSDE, JRNL, and
REMARK records.
mmLib.PDB.HELIX:
HELIX records are used to identify the position of helices in the
molecule.
mmLib.PDB.HET:
The HET records are used to describe non-standard residues, such as
prosthetic groups, inhibitors, solvent molecules, and ions for
which coordinates are supplied.
mmLib.PDB.HETNAM:
This record gives the chemical name of the compound with the given
hetID.
mmLib.PDB.HETSYN:
This record provides synonyms, if any, for the compound in the
corresponding (i.e., same hetID) HETNAM record.
mmLib.PDB.HYDBND:
The HYDBND records specify hydrogen bonds in the entry.
mmLib.PDB.JRNL:
The JRNL record contains the primary literature citation that
describes the experiment which resulted in the deposited coordinate
set.
mmLib.PDB.KEYWDS:
The KEYWDS record contains a set of terms relevant to the entry.
mmLib.PDB.LINK:
The LINK records specify connectivity between residues that is not
implied by the primary structure.
mmLib.PDB.MASTER:
The MASTER record is a control record for bookkeeping.
mmLib.PDB.MODEL:
The MODEL record specifies the model serial number when multiple
structures are presented in a single coordinate entry, as is often the
case with structures determined by NMR.
mmLib.PDB.MODRES:
The MODRES record provides descriptions of modifications (e.g.,
chemical or post-translational) to protein and nucleic acid residues.
mmLib.PDB.MTRIXn:
The MTRIXn (n = 1, 2, or 3) records present transformations expressing
non-crystallographic symmetry.
mmLib.PDB.OBSLTE:
OBSLTE appears in entries which have been withdrawn from
distribution.
mmLib.PDB.ORIGXn:
The ORIGXn (n = 1, 2, or 3) records present the transformation from
the orthogonal coordinates contained in the entry to the submitted
coordinates.
mmLib.PDB.REMARK:
REMARK records present experimental details, annotations, comments,
and information not included in other records.
mmLib.PDB.REVDAT:
REVDAT records contain a history of the modifications made to an entry
since its release.
mmLib.PDB.SCALEn:
The SCALEn (n = 1, 2, or 3) records present the transformation from
the orthogonal coordinates as contained in the entry to fractional
crystallographic coordinates.
mmLib.PDB.SEQADV:
The SEQADV record identifies conflicts between sequence information in
the ATOM records of the PDB entry and the sequence database entry given
on DBREF.
mmLib.PDB.SEQRES:
The SEQRES records contain the amino acid or nucleic acid sequence of
residues in each chain of the macromolecule that was studied.
mmLib.PDB.SHEET:
SHEET records are used to identify the position of sheets in the
molecule.
mmLib.PDB.SIGATM:
The SIGATM records present the standard deviation of atomic parameters
as they appear in ATOM and HETATM records.
mmLib.PDB.SIGUIJ:
The SIGUIJ records present the standard deviations of anisotropic
temperature factors scaled by a factor of 10**4 (Angstroms**2).
mmLib.PDB.SITE:
The SITE records supply the identification of groups comprising
important sites in the macromolecule.
mmLib.PDB.SLTBRG:
The SLTBRG records specify salt bridges in the entry.
mmLib.PDB.SOURCE:
The SOURCE record specifies the biological and/or chemical source of
each biological molecule in the entry.
mmLib.PDB.SPRSDE:
The SPRSDE records contain a list of the ID codes of entries that were
made obsolete by the given coordinate entry and withdrawn from the PDB
release set.
mmLib.PDB.SSBOND:
The SSBOND record identifies each disulfide bond in protein and
polypeptide structures by identifying the two residues involved in the
bond.
mmLib.PDB.TER:
The TER record indicates the end of a list of ATOM/HETATM records for
a chain.
mmLib.PDB.TITLE:
The TITLE record contains a title for the experiment or analysis that
is represented in the entry.
mmLib.PDB.TURN:
The TURN records identify turns and other short loop turns which
normally connect other secondary structure segments.
mmLib.PDB.TVECT:
The TVECT records present the translation vector for infinite
covalently connected structures.
mmLib.Library.ElementDesc:
Element description class returned by library_get_element_desc().
mmLib.Structure.Fragment:
Fragment objects are a basic unit for organizing small groups of
Atoms.
mmLib.Structure.Residue:
A subclass of Fragment representing one residue in a polymer
chain.
mmLib.Structure.AminoAcidResidue:
A subclass of Residue representing one amino acid residue in a
polypeptide chain.
mmLib.Structure.NucleicAcidResidue:
A subclass of Residue representing one nuclic acid in a strand of DNA
or RNA.
mmLib.Structure.FragmentID:
Stores a fragment_id as integer residue sequence number and a
single-charactor insertion code.
mmLib.Viewer.GLObject:
Base class for all OpenGL rendering objects.
mmLib.Viewer.GLDrawList:
Fundamental OpenGL rigid entity.
mmLib.Viewer.GLAtomList:
OpenGL renderer for a list of atoms.
mmLib.Viewer.GLChain:
Visualization object for mmLib.Structure.Chain.
mmLib.TLS.GLTLSAtomList:
OpenGL visualizations of TLS group atoms.
mmLib.Viewer.GLAxes:
Draw orthogonal axes in red = x, green = y, blue = z.
mmLib.Viewer.GLStructure:
Visualization object for a mmLib.Structure.Structure.
mmLib.TLS.GLTLSChain:
Collects a list of GLTLSGroup instances which are all in the same
chain.
mmLib.TLS.GLTLSGroup:
Top level visualization object for a TLS group.
mmLib.Viewer.GLUnitCell:
Draw unit cell.
mmLib.Viewer.GLViewer:
This class renders a list of GLDrawList (or subclasses of) onto the
given glcontext and gldrawable objects.
mmLib.Viewer.GLPropertyDefault:
This value means a property should use its default value.
__builtin__.list:
list() -> new list list(sequence) -> new list initialized from
sequence's items
mmLib.Structure.AtomList:
Provides the functionallity of a Python list class for containing Atom
instances.
mmLib.TLS.TLSGroup:
A subclass of AtomList implementing methods for performing TLS
calculations on the contained Atom instances.
mmLib.mmCIF.mmCIFData:
Contains all information found under a data_ block in a mmCIF
file.
mmLib.mmCIFDB.mmCIFDB:
Database class for the storage and access of structural data.
mmLib.mmCIF.mmCIFSave:
Class to store data from mmCIF dictionary save_ blocks.
mmLib.mmCIF.mmCIFFile:
Class representing a mmCIF files.
mmLib.mmCIF.mmCIFDictionary:
Class representing a mmCIF dictionary.
mmLib.mmCIF.mmCIFTable:
Contains columns and rows of data for a mmCIF section.
mmLib.PDB.PDBFile:
Class for managing a PDB file.
mmLib.mmCIFBuilder.mmCIFFileBuilder:
Builds a mmCIF file from a Structure object.
mmLib.mmCIF.mmCIFFileParser:
Stateful parser which uses the mmCIFElementFile tokenizer to read a
mmCIF file and convert it into the mmCIFData/mmCIFTable/mmCIFRow data
hierarchy.
mmLib.mmCIF.mmCIFFileWriter:
Writes out a mmCIF file using the data in the mmCIFData list.
mmLib.Structure.Model:
Multiple models support.
mmLib.Library.MonomerDesc:
Monomer description class returned by library_get_monomer_desc().
mmLib.OpenGLDriver.OpenGLDriver:
OpenGL render driver for Viewer.py
mmLib.PDBBuilder.PDBFileBuilder:
Builds a PDBFile object from a Structure object.
mmLib.R3DDriver.Raster3DDriver:
Viewer.py graphics driver for producing a output file for the Raster3D
ray tracer.
mmLib.PDB.RecordProcessor
mmLib.PDBBuilder.PDBStructureBuilder:
Builds a new Structure object by loading a PDB file.
mmLib.TLS.TLSFileFormatPDB:
Reads TLS descriptions from the REMARK records in PDB files.
mmLib.Structure.Segment:
Segment objects are a container for Fragment objects, but are
disaccociated with the Structure object hierarch.
mmLib.Structure.Chain:
Chain objects conatain a ordered list of Fragment objects.
mmLib.Structure.Site:
List of Fragments within a structure involved in a SITE
description.
mmLib.Structure.Strand:
One strand of a BetaSheet.
mmLib.Structure.Structure:
The Structure object is the parent container object for the entire
macromolecular data structure.
mmLib.StructureBuilder.StructureBuilder:
Builder class for the mmLib.Structure object hierarchy.
mmLib.mmCIFBuilder.mmCIFStructureBuilder:
Builds a new Structure object by loading a mmCIF file.
mmLib.PDBBuilder.PDBStructureBuilder:
Builds a new Structure object by loading a PDB file.
mmLib.Superposition.SuperpositionResults:
Returns the results of a superposition.
mmLib.R3DDriver.TeeWrite
mmLib.TLS.TLSFile:
Read/Write a TLS files containing one or more TLSGroupDesc
objects.
mmLib.TLS.TLSFileFormat:
Base class for TLS file types.
mmLib.TLS.TLSFileFormatPDB:
Reads TLS descriptions from the REMARK records in PDB files.
mmLib.TLS.TLSFileFormatTLSOUT:
Read/Write REFMAC5 TLSIN/TLSOUT files.
mmLib.TLS.TLSGroupDesc:
Description of one TLS Group.
mmLib.TLS.TLSStructureAnalysis:
Algorithm object for rigid body searches on Structure objects.
__builtin__.type:
type(object) -> the object's type type(name, bases, dict) -> a
new type
mmLib.UnitCell.UnitCell:
Class for storing and performing calculations on unit cell
parameters.
mmLib.GeometryDict.XYZDict:
Hash all objects according to their position, allowing spacial
location of objects quickly.
mmLib.FileIO.ZCat
mmLib.Sequence.Sequence:
Sequence information for a biopolymer chain.
exceptions.Exception:
Common base class for all exceptions.
mmLib.FileIO.FileIOUnsupportedFormat
mmLib.R3DDriver.FinishMe
mmLib.mmCIF.mmCIFError:
Base class of errors raised by Structure objects.
mmLib.mmCIF.mmCIFSyntaxError:
Base class of errors raised by Structure objects.
mmLib.PDB.PDBError
mmLib.StructureBuilder.StructureBuilderError:
Base class of errors raised by Structure objects.
mmLib.Structure.StructureError:
Base class of errors raised by Structure objects.
mmLib.Structure.AtomOverwrite:
Raised by Structure.add_atom() or Fragment.add_atom() when a Atom
added to a Structure or Fragment has the same chain_id, fragment_id,
name, and alt_loc as a Atom already in the Structure or Fragment.
mmLib.Structure.ChainOverwrite:
Raised by Structure.add_chain() or by Model.add_chain() when a Chain
added to a Structure has the same chain_id of a Chain already in the
Structure.
mmLib.Structure.FragmentOverwrite:
Raised by Chain.add_fragment() when a Fragment added to a Chain has
the same fragment_id as a Fragment already in the Chain.
mmLib.Structure.ModelOverwrite:
Raised by Structure.add_model() when a Model added to a Structure has
the same model_id of a Model already in the Structure.
mmLib.TLS.TLSError:
Base exception class for TLS module exceptions.
mmLib.TLS.TLSFileFormatError:
Raised when a file format error is encountered while loading a TLS
group description file.
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