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- Definition
- Patch
- src.structures.Atom(src.pdb.ATOM)
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- DefinitionAtom
- src.structures.Residue
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- DefinitionResidue
- xml.sax.handler.ContentHandler
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- DefinitionHandler
class Definition |
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Definition class
The Definition class contains the structured definitions found
in the files and several mappings for easy access to the information.
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Methods defined here:
- __init__(self)
- Create a new Definition Object
- addPatch(self, patch, refname, newname)
- Add a patch to a definition residue.
Parameters
patch: The patch object to add (Patch)
refname: The name of the object to add the patch to (string)
newname: The name of the new (patched) object (string)
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class DefinitionAtom(src.structures.Atom) |
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A trimmed down version of the Atom class
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- Method resolution order:
- DefinitionAtom
- src.structures.Atom
- src.pdb.ATOM
Methods defined here:
- __init__(self)
- Initialize the class
- __str__(self)
- A basic string representation for debugging
- isBackbone(self)
- Return true if atom name is in backbone, otherwise false
Returns
state: 1 if true, 0 if false
Methods inherited from src.structures.Atom:
- addBond(self, bondedatom)
- Add a bond to the list of bonds
Parameters:
bondedatom: The atom to bond to (Atom)
- get(self, name)
- Get a member of the Atom class
Parameters
name: The name of the member (string)
Possible Values
type: The type of Atom (either ATOM or HETATM)
serial: Atom serial number
name: Atom name
altLoc: Alternate location
resName: Residue name
chainID: Chain identifier
resSeq: Residue sequence number
iCode: Code for insertion of residues
x: Orthogonal coordinates for X in Angstroms.
y: Orthogonal coordinates for Y in Angstroms.
z: Orthogonal coordinates for Z in Angstroms.
occupancy: Occupancy
tempFactor: Temperature Factor
segID: Segment identifier
element: Element symbol
charge: Charge on the atom
bonds: The bonds associated with the atom
interbonds: The intrabonds associated with the atom
extrabonds: The extrabonds assocaited with the atom
residue: The parent residue of the atom
radius: The radius of the atom
ffcharge: The forcefield charge on the atom
hdonor: Whether the atom is a hydrogen donor
hacceptor: Whether the atom is a hydrogen acceptor
Returns
item: The value of the member
- getCoords(self)
- Return the x,y,z coordinates of the atom in list form
Returns
List of the coordinates (list)
- hasReference(self)
- Determine if the atom object has a reference object or not.
All known atoms should have reference objects.
Returns
1 if atom has a reference object, 0 otherwise.
- isHydrogen(self)
- Is this atom a Hydrogen atom?
Returns
value: 1 if Atom is a Hydrogen, 0 otherwise
- set(self, name, value)
- Set a member of the Atom class
Parameters
name: The name of the member (string)
value: The value to set the member to
Possible Values
type: The type of Atom (either ATOM or HETATM)
serial: Atom serial number
name: Atom name
altLoc: Alternate location
resName: Residue name
chainID: Chain identifier
resSeq: Residue sequence number
iCode: Code for insertion of residues
x: Orthogonal coordinates for X in Angstroms.
y: Orthogonal coordinates for Y in Angstroms.
z: Orthogonal coordinates for Z in Angstroms.
occupancy: Occupancy
tempFactor: Temperature Factor
segID: Segment identifier
element: Element symbol
charge: Charge on the atom
residue: The parent residue of the atom
radius: The radius of the atom
ffcharge: The forcefield charge on the atom
hdonor: Whether the atom is a hydrogen donor
hacceptor: Whether the atom is a hydrogen acceptor
Returns
item: The value of the member
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class DefinitionHandler(xml.sax.handler.ContentHandler) |
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Methods defined here:
- __init__(self)
- characters(self, text)
- endElement(self, name)
- startElement(self, name, attributes)
Methods inherited from xml.sax.handler.ContentHandler:
- endDocument(self)
- Receive notification of the end of a document.
The SAX parser will invoke this method only once, and it will
be the last method invoked during the parse. The parser shall
not invoke this method until it has either abandoned parsing
(because of an unrecoverable error) or reached the end of
input.
- endElementNS(self, name, qname)
- Signals the end of an element in namespace mode.
The name parameter contains the name of the element type, just
as with the startElementNS event.
- endPrefixMapping(self, prefix)
- End the scope of a prefix-URI mapping.
See startPrefixMapping for details. This event will always
occur after the corresponding endElement event, but the order
of endPrefixMapping events is not otherwise guaranteed.
- ignorableWhitespace(self, whitespace)
- Receive notification of ignorable whitespace in element content.
Validating Parsers must use this method to report each chunk
of ignorable whitespace (see the W3C XML 1.0 recommendation,
section 2.10): non-validating parsers may also use this method
if they are capable of parsing and using content models.
SAX parsers may return all contiguous whitespace in a single
chunk, or they may split it into several chunks; however, all
of the characters in any single event must come from the same
external entity, so that the Locator provides useful
information.
- processingInstruction(self, target, data)
- Receive notification of a processing instruction.
The Parser will invoke this method once for each processing
instruction found: note that processing instructions may occur
before or after the main document element.
A SAX parser should never report an XML declaration (XML 1.0,
section 2.8) or a text declaration (XML 1.0, section 4.3.1)
using this method.
- setDocumentLocator(self, locator)
- Called by the parser to give the application a locator for
locating the origin of document events.
SAX parsers are strongly encouraged (though not absolutely
required) to supply a locator: if it does so, it must supply
the locator to the application by invoking this method before
invoking any of the other methods in the DocumentHandler
interface.
The locator allows the application to determine the end
position of any document-related event, even if the parser is
not reporting an error. Typically, the application will use
this information for reporting its own errors (such as
character content that does not match an application's
business rules). The information returned by the locator is
probably not sufficient for use with a search engine.
Note that the locator will return correct information only
during the invocation of the events in this interface. The
application should not attempt to use it at any other time.
- skippedEntity(self, name)
- Receive notification of a skipped entity.
The Parser will invoke this method once for each entity
skipped. Non-validating processors may skip entities if they
have not seen the declarations (because, for example, the
entity was declared in an external DTD subset). All processors
may skip external entities, depending on the values of the
http://xml.org/sax/features/external-general-entities and the
http://xml.org/sax/features/external-parameter-entities
properties.
- startDocument(self)
- Receive notification of the beginning of a document.
The SAX parser will invoke this method only once, before any
other methods in this interface or in DTDHandler (except for
setDocumentLocator).
- startElementNS(self, name, qname, attrs)
- Signals the start of an element in namespace mode.
The name parameter contains the name of the element type as a
(uri, localname) tuple, the qname parameter the raw XML 1.0
name used in the source document, and the attrs parameter
holds an instance of the Attributes class containing the
attributes of the element.
The uri part of the name tuple is None for elements which have
no namespace.
- startPrefixMapping(self, prefix, uri)
- Begin the scope of a prefix-URI Namespace mapping.
The information from this event is not necessary for normal
Namespace processing: the SAX XML reader will automatically
replace prefixes for element and attribute names when the
http://xml.org/sax/features/namespaces feature is true (the
default).
There are cases, however, when applications need to use
prefixes in character data or in attribute values, where they
cannot safely be expanded automatically; the
start/endPrefixMapping event supplies the information to the
application to expand prefixes in those contexts itself, if
necessary.
Note that start/endPrefixMapping events are not guaranteed to
be properly nested relative to each-other: all
startPrefixMapping events will occur before the corresponding
startElement event, and all endPrefixMapping events will occur
after the corresponding endElement event, but their order is
not guaranteed.
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class DefinitionResidue(src.structures.Residue) |
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DefinitionResidue class
The DefinitionResidue class extends the Residue class to allow for a
trimmed down initializing function.
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Methods defined here:
- __init__(self)
- Initialize the class using a few parameters
Parameters:
name: The abbreviated amino acid name of the DefinitionResidue
- __str__(self)
- A basic string representation for debugging
- addDihedral(self, atom)
- Add the atom to the list of dihedral bonds
Parameters:
atom: The atom to be added
- getNearestBonds(self, atomname)
- Parameters
number: The number of bonds to get
Returns
bonds: A list of atomnames that are within three bonds of
the atom and present in residue (list)
Methods inherited from src.structures.Residue:
- addAtom(self, atom)
- Add the atom object to the residue.
Parameters
atom: The object to be added (ATOM)
- addMissing(self, value)
- Add the value to the list of missing atoms
Parameters
value: The name of the missing atom (string)
- createAtom(self, name, newcoords, type)
- Add a new atom object to the residue. Uses an atom
currently in the residue to seed the new atom
object, then replaces the coordinates and name accordingly.
Parameters
name: The name of the new atom (string)
newcoords: The x,y,z coordinates of the new atom (list)
type: The type of atom, ATOM or HETATM
- get(self, name)
- Get a member of the Residue class
Parameters
name: The name of the member (string)
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chainID: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
missing: List of missing atoms of the residue
Returns
item: The value of the member
- getAtom(self, name)
- Retrieve an atom from the mapping
Parameters
resname: The name of the residue to retrieve (string)
- getAtoms(self)
- getCharge(self)
- Get the total charge of the residue. In order to get rid
of floating point rounding error, do the string
transformation.
Returns:
charge: The charge of the residue (float)
- hasAtom(self, name)
- numAtoms(self)
- Get the number of atoms for the residue
Returns
count: Number of atoms in the residue (int)
- removeAtom(self, atomname)
- Remove an atom from the residue object.
Parameters
atomname: The name of the atom to be removed (string)
- renameAtom(self, oldname, newname)
- Rename an atom to a new name
Parameters
oldname: The old atom name (string)
newname: The new atom name (string)
- renameResidue(self, name)
- Rename a given residue
Parameters
name: The new name of the residue
- reorder(self)
- Reorder the atoms to start with N, CA, C, O if they exist
- rotateTetrahedral(self, atom1, atom2, angle)
- Rotate about the atom1-atom2 bond by a given angle
All atoms connected to atom2 will rotate.
Parameters:
atom1: The first atom of the bond to rotate about (atom)
atom2: The second atom of the bond to rotate about (atom)
angle: The number of degrees to rotate (float)
- set(self, name, value)
- Set a member of the Residue class to a specific value
Parameters
name: The name of the object to set (string)
value: The object to append
Possible Values
atoms: The atoms in the residue
name: The name of the residue
chain: The chainID associated with the residue
resSeq: The sequence number of the residue
icode: The iCode of the residue
SSbonded: 1 if the residue has a SS bond, 0 otherwise
SSbondpartner: The residue of the bond partner
type: The type associated with this residue
isNterm: # of hydrogens if the residue is the N-Terminus, 0 otherwise
isCterm: 1 if the residue is the C-Terminus, 0 otherwise
isDirty: 1 if the residue is not missing atoms,
0 otherwise
Notes
resSeq points to the residue.setResSeq function
Returns
item: The value of the member
- setChainID(self, value)
- Set the chainID field to a certain value
- setDonorsAndAcceptors(self)
- Set the donors and acceptors within the residue
- setResSeq(self, value)
- Set the atom field resSeq to a certain value and
change the residue's information. The icode field is no longer
useful.
Parameters
value: The new value of resSeq (int)
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