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- Forcefield
- ForcefieldAtom
- ForcefieldResidue
- xml.sax.handler.ContentHandler
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- ForcefieldHandler
class Forcefield |
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Forcefield class
The forcefield class contains definitions for a given forcefield.
Each forcefield object contains a dictionary of residues, with each
residue containing a dictionary of atoms. Dictionaries are used
instead of lists as the ordering is not important. The forcefield
definition files are unedited, directly from the forcefield - all
transformations are done within.
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Methods defined here:
- __init__(self, ff, definition, userff)
- Initialize the class by parsing the definition file
Parameters
ff: The name of the forcefield (string)
definition: The definition objects
userff: A link to the file for CGI based user-defined
forcefields
- getGroup(self, resname, atomname)
- Get the group/type associated with the input
fields. If not found, return a null string.
Parameters:
resname: The residue name (string)
atomname: The atom name (string)
- getNames(self, resname, atomname)
- Get the actual names associated with the input fields.
The names passed in point to ForcefieldResidue and
ForcefieldAtom objects which may have different names;
grab these names and return.
Parameters
resname: The residue name (string)
atomname: The atom name (string)
Returns
rname: The forcefield's name for this residue (string)
aname: The forcefield's name for this atom (string)
- getParams(self, resname, atomname)
- Get the parameters associated with the input fields.
The residue itself is needed instead of simply its name
because the forcefield may use a different residue name
than the standard amino acid name.
Parameters
resname: The residue name (string)
atomname: The atom name (string)
Returns
charge: The charge on the atom (float)
radius: The radius of the atom (float)
- getResidue(self, resname)
- Return the residue object with the given resname
Parameters
resname: The name of the residue (string)
Returns
residue: The residue object (ForcefieldResidue)
- hasResidue(self, resname)
- Check if the residue name is in the map or not.
Parameters
resname: The name to search for (string)
Returns
1 if the resname is in the map, 0 otherwise.
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class ForcefieldAtom |
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ForcefieldAtom class
The ForcefieldAtom object contains fields that are related to the
forcefield at the atom level
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Methods defined here:
- __init__(self, name, charge, radius, resname, group='')
- Initialize the object
Parameters
name: The atom name (string)
charge: The charge on the atom (float)
radius: The radius of the atom (float)
resname: The residue name (string)
group: The group name (string)
- __str__(self)
- String representation of the forcefield atom.
- get(self, name)
- Get a member of the ForcefieldAtom class
Parameters
name: The name of the member (string)
Possible Values
name: The atom name (string)
charge: The charge on the atom (float)
radius: The radius of the atom (float)
epsilon: The epsilon assocaited with the atom (float)
Returns
item: The value of the member
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class ForcefieldHandler(xml.sax.handler.ContentHandler) |
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Methods defined here:
- __init__(self, map, reference)
- characters(self, text)
- Store the information in the object for future use/
Parameters
text: The text value between the XML tags
- endElement(self, name)
- At the end of the element, act on the stored information.
Parameters
name: The name of the element (string)
- findMatchingNames(self, regname, map)
- Find a list of strings that match the given regular
expression.
Parameters
regname: The regular expression (string)
map: The dictionary to search (dict)
Returns
list: A list of regular expression objects that match
the regular expression.
- startElement(self, name, attributes)
- Override the startElement function to keep track of the current
element.
- updateMap(self, toname, fromname, map)
- Update the given map by adding a pointer from a new
name to an object.
Parameters
toname: The new name for the object (string)
fromname: The old name for the object (string)
map: A dictionary of items (dict)
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 ForcefieldResidue |
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ForcefieldResidue class
The ForceFieldResidue class contains a mapping of all atoms within
the residue for easy searching.
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Methods defined here:
- __init__(self, name)
- Initialize the ForceFieldResidue object
Parameters
name: The name of the residue (string)
- addAtom(self, atom)
- Add an atom to the ForcefieldResidue
Parameters
atom: The atom to be added (atom)
- getAtom(self, atomname)
- Return the atom object with the given atomname
Parameters
resname: The name of the atom (string)
Returns
residue: The atom object (ForcefieldAtom)
- getAtoms(self)
- Return the list of atoms in this residue.
- hasAtom(self, atomname)
- Check to see if the atomname is in the current residue.
Parameters
atomname: The name of the atom to search for
Returns
1 if the atom is present in the residue, 0 otherwise
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