- CalculateTorsionAngleDifference
-
CalculateTorsionAngleDifference(TorsionAngle1, TorsionAngle2)
Calculate torsion angle difference in the range from 0 to 180.
Arguments:
TorsionAngle1 (float): First torsion angle.
TorsionAngle2 (float): Second torsion angle.
Returns:
float: Difference between first and second torsion angle.
- DoesSMARTSContainValidSubClassMappedAtoms
-
DoesSMARTSContainValidSubClassMappedAtoms(SMARTS)
Check for the presence of two central mapped atoms in SMARTS pattern. A valid SMARTS pattern must contain only two mapped atoms corresponding to map atom numbers ':2' and ':3'.
Arguments:
SMARTS (str): SMARTS pattern for sub class in torsion library XML tree.
Returns:
bool: True - A valid pattern; Otherwise, false.
- DoesSMARTSContainValidTorsionRuleMappedAtoms
-
DoesSMARTSContainValidTorsionRuleMappedAtoms(SMARTS)
Check for the presence of four mapped atoms in a SMARTS pattern. A valid SMARTS pattern must contain only four mapped atoms corresponding to map atom numbers ':1', ':2', ':3' and ':4'.
Arguments:
SMARTS (str): SMARTS pattern for torsion rule in torsion library XML
tree.
Returns:
bool: True - A valid pattern; Otherwise, false.
- DoesSMARTSContainsMappedAtoms
-
DoesSMARTSContainsMappedAtoms(SMARTS, MappedAtomNumsList)
Check for the presence of specified mapped atoms in SMARTS pattern. The mapped atom numbers in the list are specified as ':1', ':2', ':3' etc.
Arguments:
SMARTS (str): SMARTS pattern in torsion library XML tree.
MappedAtoms (list): Mapped atom numbers as ":1", ":2" etc.
Returns:
bool: True - All mapped atoms present in pattern; Otherwise, false.
- FilterSubstructureMatchesByAtomMapNumbers
-
FilterSubstructureMatchesByAtomMapNumbers(Mol, PatternMol, AtomIndicesList)
Filter a list of lists containing matched atom indices by map atom numbers present in a pattern molecule. The list of atom indices correspond to a list retrieved by RDKit function GetSubstructureMatches using SMILES/SMARTS pattern. The atom map numbers are mapped to appropriate atom indices during the generation of molecules. For example: [O:1]=[S:2](=[O])[C:3][C:4].
Arguments:
Mol (object): RDKit molecule object.
PatternMol (object): RDKit molecule object for a SMILES/SMARTS pattern.
AtomIndicesList (list): A list of lists containing atom indices.
Returns:
list : A list of lists containing filtered atom indices.
- GetAtomPositions
-
GetAtomPositions(Mol, ConfID = -1)
Retrieve a list of lists containing coordinates of all atoms in a molecule.
Arguments:
Mol (object): RDKit molecule object.
ConfID (int): Conformer number.
Returns:
list : List of lists containing atom positions.
Example(s):
for AtomPosition in TorsionAlertsUtil.GetAtomPositions(Mol):
print("X: %s; Y: %s; Z: %s" % (AtomPosition[0], AtomPosition[1], AtomPosition[2]))
- GetGenericHierarchyClassElementNode
-
GetGenericHierarchyClassElementNode(TorsionLibraryInfo)
Get generic hierarchy class element node.
Arguments:
TorsionLibraryInfo (dict): A dictionary containing information for
matching rotatable bonds.
Returns:
object: Generic hierarchy class element node in torsion library XML
tree.
- GetHeavyAtomNeighbors
-
GetHeavyAtomNeighbors(Atom)
Get a list of heavy atom neighbors.
Arguments:
Atom (object): RDKit atom object.
Returns:
list : List of heavy atom neighbors.
- IdentifyRotatableBondsForTorsionLibraryMatch
-
IdentifyRotatableBondsForTorsionLibraryMatch(TorsionLibraryInfo, Mol, RotBondsPatternMol)
Identify rotatable bonds in a molecule for torsion library match.
Arguments:
TorsionLibraryInfo (dict): A dictionary containing information for
matching rotatable bonds.
Mol (object): RDKit molecule object.
RotBondsPatternMol (object): RDKit molecule object for SMARTS pattern
corresponding to rotatable bonds.
Returns:
bool: True - Rotatable bonds present in molecule; Otherwise, false.
None or dict: None - For no rotatable bonds in molecule; otherwise, a
dictionary containing the following informations for rotatable bonds
matched to RotBondsPatternMol:
RotBondsInfo["IDs"] = []
RotBondsInfo["AtomIndices"] = {}
RotBondsInfo["HierarchyClass"] = {}
- IsSpecificHierarchyClass
-
IsSpecificHierarchyClass(TorsionLibraryInfo, HierarchyClass)
Check whether it's a specific hierarchy class.
Arguments:
TorsionLibraryInfo (dict): A dictionary containing information for
matching rotatable bonds.
HierarchyClass (str): Hierarchy class name.
Returns:
bool: True - A valid hierarchy class name; Otherwise, false.
- ListTorsionLibraryInfo
-
ListTorsionLibraryInfo(TorsionLibElementTree)
List torsion library information using XML tree object. The following information is listed:
Summary:
Total number of HierarchyClass nodes: <Number>
Total number of HierarchyClassSubClass nodes: <Number
Total number of TorsionRule nodes: <Number
Details:
HierarchyClass: <Name>; HierarchySubClass nodes: <Number>;
TorsionRule nodes: <SMARTS>
... ... ...
Arguments:
TorsionLibElementTree (object): XML tree object.
Returns:
Nothing.
- RemoveLastHierarchyClassElementNodeFromTracking
-
RemoveLastHierarchyClassElementNodeFromTracking(TorsionLibraryInfo)
Remove last hierarchy class element node from tracking by removing it from a stack.
Arguments:
TorsionLibraryInfo (dict): A dictionary containing information for
matching rotatable bonds.
Returns:
Nothing. The torsion library info is updated.
- RemoveLastHierarchySubClassElementNodeFromTracking
-
RemoveLastHierarchySubClassElementNodeFromTracking(TorsionLibraryInfo)
Remove last hierarchy sub class element node from tracking by removing it from a stack.
Arguments:
TorsionLibraryInfo (dict): A dictionary containing information for
matching rotatable bonds.
Returns:
Nothing. The torsion library info is updated.
- RetrieveTorsionLibraryInfo
-
RetrieveTorsionLibraryInfo(TorsionLibraryFilePath, Quiet = True)
Retrieve torsion library information.
Arguments:
TorsionLibraryFilePath (str): Torsion library XML file path.
Returns:
object: An object returned by xml.etree.ElementTree.parse function.
The XML file is parsed using xml.etree.ElementTree.parse function and object created by the parse function is simply returned.
- SetupHierarchyClassAndSubClassNamesForRotatableBond
-
SetupHierarchyClassAndSubClassNamesForRotatableBond(TorsionLibraryInfo)
Setup hierarchy class and subclass names for a rotatable bond matched to
a torsion rule element node.
Returns:
TorsionLibraryInfo (dict): A dictionary containing information for
matching rotatable bonds.
str: A back slash delimited string containing hierarchy class names at
the level of torsion rule element node.
str: A back slash delimited string containing hierarchy sub class names
at the level of torsion rule element node.
- SetupHierarchySubClassElementPatternMol
-
SetupHierarchySubClassElementPatternMol(TorsionLibraryInfo, ElementNode)
Setup pattern molecule for SMARTS pattern in hierarchy subclass element.
Arguments:
TorsionLibraryInfo (dict): A dictionary containing information for
matching rotatable bonds.
ElementNode (object): A hierarchy sub class element node being matched
in torsion library XML tree.
Returns:
object: RDKit molecule object corresponding to SMARTS pattern for
hierarchy sub class element node.
- SetupTorsionLibraryInfoForMatchingRotatableBonds
-
SetupTorsionLibraryInfoForMatchingRotatableBonds(TorsionLibraryInfo)
Setup torsion library information for matching rotatable bonds. The following information is initialized and updated in torsion library dictionary for matching rotatable bonds:
TorsionLibraryInfo["GenericClass"] = None
TorsionLibraryInfo["GenericClassElementNode"] = None
TorsionLibraryInfo["SpecificClasses"] = {}
TorsionLibraryInfo["SpecificClasses"]["Names"] = []
TorsionLibraryInfo["SpecificClasses"]["ElementNode"] = {}
TorsionLibraryInfo["HierarchyClassNodes"] = []
TorsionLibraryInfo["HierarchySubClassNodes"] = []
TorsionLibraryInfo["DataCache"] = {}
TorsionLibraryInfo["DataCache"]["SubClassPatternMol"] = {}
TorsionLibraryInfo["DataCache"]["TorsionRulePatternMol"] = {}
TorsionLibraryInfo["DataCache"]["TorsionRuleAnglesInfo"] = {}
Arguments:
TorsionLibraryInfo (dict): A dictionary containing root node for
torsion library element tree.
Returns:
Nonthing. The torsion library information dictionary is updated.
- SetupTorsionRuleAnglesInfo
-
SetupTorsionRuleAnglesInfo(TorsionLibraryInfo, TorsionRuleElementNode)
Setup torsion angles and energy info for matching a torsion rule.
Arguments:
TorsionLibraryInfo (dict): A dictionary containing information for
matching rotatable bonds.
TorsionRuleElementNode (object): A torsion rule element node being
matched in torsion library XML tree.
Returns:
dict: A dictionary containing the following information for torsion rule
being matched to a rotatable bond:
RuleAnglesInfo = {}
RuleAnglesInfo["IDs"] = []
RuleAnglesInfo["Value"] = {}
RuleAnglesInfo["Score"] = {}
RuleAnglesInfo["Tolerance1"] = {}
RuleAnglesInfo["Tolerance2"] = {}
RuleAnglesInfo["ValuesList"] = []
RuleAnglesInfo["ValuesIn360RangeList"] = []
RuleAnglesInfo["Tolerances1List"] = []
RuleAnglesInfo["Tolerances2List"] = []
# Strain energy calculations...
RuleAnglesInfo["EnergyMethod"] = None
RuleAnglesInfo["EnergyMethodExact"] = None
RuleAnglesInfo["EnergyMethodApproximate"] = None
# For approximate strain energy calculation...
RuleAnglesInfo["Beta1"] = {}
RuleAnglesInfo["Beta2"] = {}
RuleAnglesInfo["Theta0"] = {}
# For exact strain energy calculation...
RuleAnglesInfo["HistogramEnergy"] = []
RuleAnglesInfo["HistogramEnergyLowerBound"] = []
RuleAnglesInfo["HistogramEnergyUpperBound"] = []
- SetupTorsionRuleElementPatternMol
-
SetupTorsionRuleElementPatternMol(TorsionLibraryInfo, ElementNode, TorsionRuleNodeID, TorsionSMARTSPattern)
Setup pattern molecule for SMARTS pattern in torsion rule element.
Arguments:
TorsionLibraryInfo (dict): A dictionary containing information for
matching rotatable bonds.
ElementNode (object): A torsion rule element node being matched in
torsion library XML tree.
TorsionRuleNodeID (int): Torsion rule element node ID.
TorsionSMARTSPattern (str): SMARTS pattern for torsion rule element node.
Returns:
object: RDKit molecule object corresponding to SMARTS pattern for
torsion rule element node.
- TrackHierarchyClassElementNode
-
TrackHierarchyClassElementNode(TorsionLibraryInfo, ElementNode)
Track hierarchy class element node using a stack.
Arguments:
TorsionLibraryInfo (dict): A dictionary containing information for
matching rotatable bonds.
ElementNode (object): Hierarchy class element node in torsion library
XML tree.
Returns:
Nothing. The torsion library info is updated.
- TrackHierarchySubClassElementNode
-
TrackHierarchySubClassElementNode(TorsionLibraryInfo, ElementNode)
Track hierarchy sub class element node using a stack.
Arguments:
TorsionLibraryInfo (dict): A dictionary containing information for
matching rotatable bonds.
ElementNode (object): Hierarchy sub class element node in torsion
library XML tree.
Returns:
Nothing. The torsion library info is updated.
