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- OptimizationHolder
- Optimize
-
- Alcoholic
- Carboxylic
- Flip
- Water
- PotentialBond
- hydrogenRoutines
- xml.sax.handler.ContentHandler
-
- HydrogenHandler
class Alcoholic(Optimize) |
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The class for alcoholic residues
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Methods defined here:
- __init__(self, residue, optinstance, routines)
- Initialize the alcoholic class by removing
the alcoholic hydrogen if it exists.
- complete(self)
- Complete an alcoholic optimization. Call finalize(), and then
remove all extra LP atoms.
- finalize(self)
- Finalize an alcoholic residue. Try to minimize
conflict with nearby atoms by building away
from them. Called when LPs are still present
so as to account for their bonds.
- tryAcceptor(self, acc, donor)
- The main driver for adding an LP to an optimizeable
residue.
- tryBoth(self, donor, acc, accobj)
- Called when both the donor and acceptor are optimizeable;
If one is fixed, we only need to try one side. Otherwise
first try to satisfy the donor - if that's succesful,
try to satisfy the acceptor. An undo may be necessary
if the donor is satisfied and the acceptor isn't.
- tryDonor(self, donor, acc)
- The main driver for adding a hydrogen to an
optimizeable residue.
Methods inherited from Optimize:
- __str__(self)
- String output for debugging
- debug(self, txt)
- Easy way to turn on/off debugging
- getHbondangle(self, atom1, atom2, atom3)
- Get the angle between three atoms
Parameters
atom1: The first atom (atom)
atom2: The second (vertex) atom (atom)
atom3: The third atom (atom)
Returns
angle: The angle between the atoms (float)
- getPairEnergy(self, donor, acceptor)
- Get the energy between two atoms
Parameters
donor: The first atom in the pair (Atom)
acceptor: The second atom in the pair (Atom)
Returns
energy: The energy of the pair (float)
- getPositionWithThreeBonds(self, atom)
- If there's three bonds in a tetrahedral geometry,
there's only one available position. Find that
position.
- getPositionsWithTwoBonds(self, atom)
- Given a tetrahedral geometry with two
existing bonds, return the two potential
sets of coordinates that are possible for
a new bond.
- isHbond(self, donor, acc)
- Determine whether this donor acceptor pair is a
hydrogen bond
- makeAtomWithNoBonds(self, atom, closeatom, addname)
- Called for water oxygen atoms with no current bonds.
Uses the closeatom to place the new atom directly
colinear with the atom and the closeatom.
Parameters
atom: The oxygen atom of the water
closeatom: The nearby atom (donor/acceptor)
addname: The name of the atom to add
- makeAtomWithOneBondH(self, atom, addname)
- Add a hydrogen to an alcoholic donor with one
existing bond.
- makeAtomWithOneBondLP(self, atom, addname)
- Add a lone pair to an alcoholic donor with one
existing bond.
- makeWaterWithOneBond(self, atom, addname)
- Add an atom to a water residue that already has
one bond. Uses the water reference structure to
align the new atom.
- tryPositionsWithThreeBondsH(self, donor, acc, newname, loc)
- Try making a hydrogen bond with the lone available
position.
- tryPositionsWithThreeBondsLP(self, acc, donor, newname, loc)
- Try making a hydrogen bond using the lone
available hydrogen position.
- tryPositionsWithTwoBondsH(self, donor, acc, newname, loc1, loc2)
- Try adding a new hydrogen two the two potential
locations. If both form hydrogen bonds, place at
whatever returns the best bond as determined by
getPairEnergy.
- tryPositionsWithTwoBondsLP(self, acc, donor, newname, loc1, loc2)
- Try placing an LP on a tetrahedral geometry with
two existing bonds. If this isn't a hydrogen bond
it can return - otherwise ensure that the H(D)-A-LP
angle is minimized.
- trySingleAlcoholicH(self, donor, acc, newatom)
- After a new bond has been added using
makeAtomWithOneBond*, try to find the best orientation
by rotating to form a hydrogen bond. If a bond
cannot be formed, remove the newatom (thereby
returning to a single bond).
- trySingleAlcoholicLP(self, acc, donor, newatom)
- After a new bond has been added using
makeAtomWithOneBond*, ensure that a
hydrogen bond has been made. If so, try to
minimze the H(D)-A-LP angle. If that cannot
be minimized, ignore the bond and remove the
atom.
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class Carboxylic(Optimize) |
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The class for carboxylic residues
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Methods defined here:
- __init__(self, residue, optinstance, routines)
- Initialize a case where the lone hydrogen atom
can have four different orientations. Works similar
to initializeFlip by preadding the necessary atoms.
This also takes into account that the carboxyl group
has different bond lengths for the two C-O bonds -
this is probably due to one bond being assigned
as a C=O. As a result hydrogens are only added to
the C-O (longer) bond.
Parameters
residue: The residue to flip (residue)
dihedral: The angle to flip about
hname: The name of one of the hydrogens to add
Returns
optlist: A list of optimizeable donors and
acceptors in the residue (list)
- complete(self)
- If not already fixed, finalize
- finalize(self)
- Finalize a protontated residue. Try to minimize
conflict with nearby atoms.
- fix(self, donor, acc)
- Fix the carboxylic residue.
- isCarboxylicHbond(self, donor, acc)
- Determine whether this donor acceptor pair is a
hydrogen bond
- rename(self, hydatom)
- Rename the optimized atoms appropriately. This is done
since the forcefields tend to require that the hydrogen is
linked to a specific oxygen, and this atom may have different
parameter values.
Parameters
hydatom: The hydrogen atom that was added. (atom)
- tryAcceptor(self, acc, donor)
- The main driver for adding an LP to an optimizeable
residue.
- tryBoth(self, donor, acc, accobj)
- Called when both the donor and acceptor are optimizeable;
If one is fixed, we only need to try one side. Otherwise
first try to satisfy the donor - if that's succesful,
try to satisfy the acceptor. An undo may be necessary
if the donor is satisfied and the acceptor isn't.
- tryDonor(self, donor, acc)
- The main driver for adding a hydrogen to an
optimizeable residue.
Methods inherited from Optimize:
- __str__(self)
- String output for debugging
- debug(self, txt)
- Easy way to turn on/off debugging
- getHbondangle(self, atom1, atom2, atom3)
- Get the angle between three atoms
Parameters
atom1: The first atom (atom)
atom2: The second (vertex) atom (atom)
atom3: The third atom (atom)
Returns
angle: The angle between the atoms (float)
- getPairEnergy(self, donor, acceptor)
- Get the energy between two atoms
Parameters
donor: The first atom in the pair (Atom)
acceptor: The second atom in the pair (Atom)
Returns
energy: The energy of the pair (float)
- getPositionWithThreeBonds(self, atom)
- If there's three bonds in a tetrahedral geometry,
there's only one available position. Find that
position.
- getPositionsWithTwoBonds(self, atom)
- Given a tetrahedral geometry with two
existing bonds, return the two potential
sets of coordinates that are possible for
a new bond.
- isHbond(self, donor, acc)
- Determine whether this donor acceptor pair is a
hydrogen bond
- makeAtomWithNoBonds(self, atom, closeatom, addname)
- Called for water oxygen atoms with no current bonds.
Uses the closeatom to place the new atom directly
colinear with the atom and the closeatom.
Parameters
atom: The oxygen atom of the water
closeatom: The nearby atom (donor/acceptor)
addname: The name of the atom to add
- makeAtomWithOneBondH(self, atom, addname)
- Add a hydrogen to an alcoholic donor with one
existing bond.
- makeAtomWithOneBondLP(self, atom, addname)
- Add a lone pair to an alcoholic donor with one
existing bond.
- makeWaterWithOneBond(self, atom, addname)
- Add an atom to a water residue that already has
one bond. Uses the water reference structure to
align the new atom.
- tryPositionsWithThreeBondsH(self, donor, acc, newname, loc)
- Try making a hydrogen bond with the lone available
position.
- tryPositionsWithThreeBondsLP(self, acc, donor, newname, loc)
- Try making a hydrogen bond using the lone
available hydrogen position.
- tryPositionsWithTwoBondsH(self, donor, acc, newname, loc1, loc2)
- Try adding a new hydrogen two the two potential
locations. If both form hydrogen bonds, place at
whatever returns the best bond as determined by
getPairEnergy.
- tryPositionsWithTwoBondsLP(self, acc, donor, newname, loc1, loc2)
- Try placing an LP on a tetrahedral geometry with
two existing bonds. If this isn't a hydrogen bond
it can return - otherwise ensure that the H(D)-A-LP
angle is minimized.
- trySingleAlcoholicH(self, donor, acc, newatom)
- After a new bond has been added using
makeAtomWithOneBond*, try to find the best orientation
by rotating to form a hydrogen bond. If a bond
cannot be formed, remove the newatom (thereby
returning to a single bond).
- trySingleAlcoholicLP(self, acc, donor, newatom)
- After a new bond has been added using
makeAtomWithOneBond*, ensure that a
hydrogen bond has been made. If so, try to
minimze the H(D)-A-LP angle. If that cannot
be minimized, ignore the bond and remove the
atom.
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class Flip(Optimize) |
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The holder for optimization of flippable residues.
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Methods defined here:
- __init__(self, residue, optinstance, routines)
- Initialize a potential flip. Rather than flipping
the given residue back and forth, take each atom
that would be flipped and pre-flip it, making a
new *FLIP atom in its place.
Parameters
residue: The residue to flip (residue)
optinstance: The optimization instance containing
information about what to optimize
- complete(self)
- Complete the flippable residue optimization. Call the finalize
function, and then rename all FLIP atoms back to their standard
names.
- finalize(self)
- Finalizes a flippable back to its original state -
since the original atoms are now *FLIP, it deletes
the * atoms and renames the *FLIP atoms back to *.
- fixFlip(self, bondatom)
- Called if a hydrogen bond has been found using
the bondatom. If bondatom is *FLIP, remove all *
atoms, otherwise remove all *FLIP atoms.
- tryAcceptor(self, acc, donor)
- The main driver for adding an LP to an optimizeable
residue.
- tryBoth(self, donor, acc, accobj)
- Called when both the donor and acceptor are optimizeable;
If one is fixed, we only need to try one side. Otherwise
first try to satisfy the donor - if that's succesful,
try to satisfy the acceptor. An undo may be necessary
if the donor is satisfied and the acceptor isn't.
- tryDonor(self, donor, acc)
- The main driver for adding a hydrogen to an
optimizeable residue.
Methods inherited from Optimize:
- __str__(self)
- String output for debugging
- debug(self, txt)
- Easy way to turn on/off debugging
- getHbondangle(self, atom1, atom2, atom3)
- Get the angle between three atoms
Parameters
atom1: The first atom (atom)
atom2: The second (vertex) atom (atom)
atom3: The third atom (atom)
Returns
angle: The angle between the atoms (float)
- getPairEnergy(self, donor, acceptor)
- Get the energy between two atoms
Parameters
donor: The first atom in the pair (Atom)
acceptor: The second atom in the pair (Atom)
Returns
energy: The energy of the pair (float)
- getPositionWithThreeBonds(self, atom)
- If there's three bonds in a tetrahedral geometry,
there's only one available position. Find that
position.
- getPositionsWithTwoBonds(self, atom)
- Given a tetrahedral geometry with two
existing bonds, return the two potential
sets of coordinates that are possible for
a new bond.
- isHbond(self, donor, acc)
- Determine whether this donor acceptor pair is a
hydrogen bond
- makeAtomWithNoBonds(self, atom, closeatom, addname)
- Called for water oxygen atoms with no current bonds.
Uses the closeatom to place the new atom directly
colinear with the atom and the closeatom.
Parameters
atom: The oxygen atom of the water
closeatom: The nearby atom (donor/acceptor)
addname: The name of the atom to add
- makeAtomWithOneBondH(self, atom, addname)
- Add a hydrogen to an alcoholic donor with one
existing bond.
- makeAtomWithOneBondLP(self, atom, addname)
- Add a lone pair to an alcoholic donor with one
existing bond.
- makeWaterWithOneBond(self, atom, addname)
- Add an atom to a water residue that already has
one bond. Uses the water reference structure to
align the new atom.
- tryPositionsWithThreeBondsH(self, donor, acc, newname, loc)
- Try making a hydrogen bond with the lone available
position.
- tryPositionsWithThreeBondsLP(self, acc, donor, newname, loc)
- Try making a hydrogen bond using the lone
available hydrogen position.
- tryPositionsWithTwoBondsH(self, donor, acc, newname, loc1, loc2)
- Try adding a new hydrogen two the two potential
locations. If both form hydrogen bonds, place at
whatever returns the best bond as determined by
getPairEnergy.
- tryPositionsWithTwoBondsLP(self, acc, donor, newname, loc1, loc2)
- Try placing an LP on a tetrahedral geometry with
two existing bonds. If this isn't a hydrogen bond
it can return - otherwise ensure that the H(D)-A-LP
angle is minimized.
- trySingleAlcoholicH(self, donor, acc, newatom)
- After a new bond has been added using
makeAtomWithOneBond*, try to find the best orientation
by rotating to form a hydrogen bond. If a bond
cannot be formed, remove the newatom (thereby
returning to a single bond).
- trySingleAlcoholicLP(self, acc, donor, newatom)
- After a new bond has been added using
makeAtomWithOneBond*, ensure that a
hydrogen bond has been made. If so, try to
minimze the H(D)-A-LP angle. If that cannot
be minimized, ignore the bond and remove the
atom.
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class HydrogenHandler(xml.sax.handler.ContentHandler) |
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Extends the SAX XML Parser to parse the Hydrogens.xml
class
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Methods defined here:
- __init__(self)
- Initalize the class.
- characters(self, text)
- Set a given attribute of the object to the text
- endElement(self, name)
- Complete whatever object is currently passed in
by the name parameter
- startElement(self, name, attributes)
- Create optimization holder objects or atoms
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 Optimize |
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The holder class for the hydrogen optimization
routines. Individual optimization types inherit off of this
class. Any functions used by multiple types appear here.
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Methods defined here:
- __init__(self)
- Initialize the class
- __str__(self)
- String output for debugging
- debug(self, txt)
- Easy way to turn on/off debugging
- getHbondangle(self, atom1, atom2, atom3)
- Get the angle between three atoms
Parameters
atom1: The first atom (atom)
atom2: The second (vertex) atom (atom)
atom3: The third atom (atom)
Returns
angle: The angle between the atoms (float)
- getPairEnergy(self, donor, acceptor)
- Get the energy between two atoms
Parameters
donor: The first atom in the pair (Atom)
acceptor: The second atom in the pair (Atom)
Returns
energy: The energy of the pair (float)
- getPositionWithThreeBonds(self, atom)
- If there's three bonds in a tetrahedral geometry,
there's only one available position. Find that
position.
- getPositionsWithTwoBonds(self, atom)
- Given a tetrahedral geometry with two
existing bonds, return the two potential
sets of coordinates that are possible for
a new bond.
- isHbond(self, donor, acc)
- Determine whether this donor acceptor pair is a
hydrogen bond
- makeAtomWithNoBonds(self, atom, closeatom, addname)
- Called for water oxygen atoms with no current bonds.
Uses the closeatom to place the new atom directly
colinear with the atom and the closeatom.
Parameters
atom: The oxygen atom of the water
closeatom: The nearby atom (donor/acceptor)
addname: The name of the atom to add
- makeAtomWithOneBondH(self, atom, addname)
- Add a hydrogen to an alcoholic donor with one
existing bond.
- makeAtomWithOneBondLP(self, atom, addname)
- Add a lone pair to an alcoholic donor with one
existing bond.
- makeWaterWithOneBond(self, atom, addname)
- Add an atom to a water residue that already has
one bond. Uses the water reference structure to
align the new atom.
- tryPositionsWithThreeBondsH(self, donor, acc, newname, loc)
- Try making a hydrogen bond with the lone available
position.
- tryPositionsWithThreeBondsLP(self, acc, donor, newname, loc)
- Try making a hydrogen bond using the lone
available hydrogen position.
- tryPositionsWithTwoBondsH(self, donor, acc, newname, loc1, loc2)
- Try adding a new hydrogen two the two potential
locations. If both form hydrogen bonds, place at
whatever returns the best bond as determined by
getPairEnergy.
- tryPositionsWithTwoBondsLP(self, acc, donor, newname, loc1, loc2)
- Try placing an LP on a tetrahedral geometry with
two existing bonds. If this isn't a hydrogen bond
it can return - otherwise ensure that the H(D)-A-LP
angle is minimized.
- trySingleAlcoholicH(self, donor, acc, newatom)
- After a new bond has been added using
makeAtomWithOneBond*, try to find the best orientation
by rotating to form a hydrogen bond. If a bond
cannot be formed, remove the newatom (thereby
returning to a single bond).
- trySingleAlcoholicLP(self, acc, donor, newatom)
- After a new bond has been added using
makeAtomWithOneBond*, ensure that a
hydrogen bond has been made. If so, try to
minimze the H(D)-A-LP angle. If that cannot
be minimized, ignore the bond and remove the
atom.
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class PotentialBond |
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A small class containing the hbond structure
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Methods defined here:
- __init__(self, atom1, atom2, dist)
- Initialize the class
Parameters
atom1: The first atom in the potential bond (Atom)
atom2: The second atom in the potential bond (Atom)
dist: The distance between the two atoms (float)
- __str__(self)
- String for debugging
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class Water(Optimize) |
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The class for water residues
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Methods defined here:
- __init__(self, residue, optinstance, routines)
- Initialize the water optimization class
- complete(self)
- Complete the water optimization class
- finalize(self)
- Finalize a water residue. Try to minimize
conflict with nearby atoms by building away
from them. Called when LPs are still present
so as to account for their bonds.
- tryAcceptor(self, acc, donor)
- The main driver for adding an LP to an optimizeable
residue.
- tryBoth(self, donor, acc, accobj)
- Called when both the donor and acceptor are optimizeable;
If one is fixed, we only need to try one side. Otherwise
first try to satisfy the donor - if that's succesful,
try to satisfy the acceptor. An undo may be necessary
if the donor is satisfied and the acceptor isn't.
- tryDonor(self, donor, acc)
- The main driver for adding a hydrogen to an
optimizeable residue.
Methods inherited from Optimize:
- __str__(self)
- String output for debugging
- debug(self, txt)
- Easy way to turn on/off debugging
- getHbondangle(self, atom1, atom2, atom3)
- Get the angle between three atoms
Parameters
atom1: The first atom (atom)
atom2: The second (vertex) atom (atom)
atom3: The third atom (atom)
Returns
angle: The angle between the atoms (float)
- getPairEnergy(self, donor, acceptor)
- Get the energy between two atoms
Parameters
donor: The first atom in the pair (Atom)
acceptor: The second atom in the pair (Atom)
Returns
energy: The energy of the pair (float)
- getPositionWithThreeBonds(self, atom)
- If there's three bonds in a tetrahedral geometry,
there's only one available position. Find that
position.
- getPositionsWithTwoBonds(self, atom)
- Given a tetrahedral geometry with two
existing bonds, return the two potential
sets of coordinates that are possible for
a new bond.
- isHbond(self, donor, acc)
- Determine whether this donor acceptor pair is a
hydrogen bond
- makeAtomWithNoBonds(self, atom, closeatom, addname)
- Called for water oxygen atoms with no current bonds.
Uses the closeatom to place the new atom directly
colinear with the atom and the closeatom.
Parameters
atom: The oxygen atom of the water
closeatom: The nearby atom (donor/acceptor)
addname: The name of the atom to add
- makeAtomWithOneBondH(self, atom, addname)
- Add a hydrogen to an alcoholic donor with one
existing bond.
- makeAtomWithOneBondLP(self, atom, addname)
- Add a lone pair to an alcoholic donor with one
existing bond.
- makeWaterWithOneBond(self, atom, addname)
- Add an atom to a water residue that already has
one bond. Uses the water reference structure to
align the new atom.
- tryPositionsWithThreeBondsH(self, donor, acc, newname, loc)
- Try making a hydrogen bond with the lone available
position.
- tryPositionsWithThreeBondsLP(self, acc, donor, newname, loc)
- Try making a hydrogen bond using the lone
available hydrogen position.
- tryPositionsWithTwoBondsH(self, donor, acc, newname, loc1, loc2)
- Try adding a new hydrogen two the two potential
locations. If both form hydrogen bonds, place at
whatever returns the best bond as determined by
getPairEnergy.
- tryPositionsWithTwoBondsLP(self, acc, donor, newname, loc1, loc2)
- Try placing an LP on a tetrahedral geometry with
two existing bonds. If this isn't a hydrogen bond
it can return - otherwise ensure that the H(D)-A-LP
angle is minimized.
- trySingleAlcoholicH(self, donor, acc, newatom)
- After a new bond has been added using
makeAtomWithOneBond*, try to find the best orientation
by rotating to form a hydrogen bond. If a bond
cannot be formed, remove the newatom (thereby
returning to a single bond).
- trySingleAlcoholicLP(self, acc, donor, newatom)
- After a new bond has been added using
makeAtomWithOneBond*, ensure that a
hydrogen bond has been made. If so, try to
minimze the H(D)-A-LP angle. If that cannot
be minimized, ignore the bond and remove the
atom.
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class hydrogenRoutines |
| |
The main routines for hydrogen optimization. This could
potentially be extended from the routines object...
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| |
Methods defined here:
- __init__(self, routines)
- Parse the XML file and store the data in a map
- cleanup(self)
- If there are any extra carboxlyic *1 atoms, delete them.
This may occur when no optimization is chosen
- debug(self, text)
- Print text to stdout for debugging purposes.
Parameters
text: The text to output (string)
- initializeFullOptimization(self)
- Initialize the full optimization. Detects all
optimizeable donors and acceptors and sets the internal
optlist.
- initializeWaterOptimization(self)
- Initialize optimization for waters only. Detects all
optimizeable donors and acceptors and sets the internal
optlist.
- isOptimizeable(self, residue)
- Check to see if the given residue is optimizeable
There are three ways to identify a residue:
1. By name (i.e. HIS)
2. By reference name - a PDB file HSP has
a HIS reference name
3. By patch - applied by PropKa, terminal selection
Parameters
residue: The residue in question (Residue)
Returns
optinstance: None if not optimizeable, otherwise
the OptimizationHolder instance that
corresponds to the residue.
- optimizeHydrogens(self)
- The main driver for the optimization. Should be
called only after the optlist has been initialized.
- setOptimizeableHydrogens(self)
- Set any hydrogen listed in HYDROGENS.xml that
is optimizeable. Used BEFORE hydrogen optimization
to label atoms so that they won't be debumped - i.e.
if SER HG is too close to another atom, don't debump
but wait for optimization. This function should not
be used if full optimization is not taking place.
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