This class is used to find optimal core alignments and determines
r-groups for input structures. This is a base class that uses 'original'
algorithm that tries to minimize the number of r-groups.
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__init__(self,
input_file,
smarts,
temp_dir=None,
thread=None,
use_mm=1,
use_fp_sim=False,
sa_seed=None,
t_factor=None,
tmax_mult=None)
This function creates an instance of RGroupFinder object. |
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_resetData(self)
This function resets data objects used during calculation to their
initial values. |
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calculate(self)
This function is called to compute optimal molecule alignment and
determine attached r-groups. |
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_findCoreMatches(self)
In this function we loop over all molecule and find all possible core
matches. |
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_checkAndTallyCoreMatches(self,
i,
ct,
core_matches,
bond_matches)
Verify that a valid match was found by checking that core atoms contains
any heavy atoms, that current molecule is not a duplicate etc. |
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_checkCoreMatches(self,
ct,
core_matches,
bond_matches)
Verifies that a valid match was found by checking that core atoms
contains any heavy atoms, that current molecule is not a duplicate etc. |
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_checkCoreHeavyAtoms(self,
ct,
core_matches,
bond_matches)
This function verifies that core match has heavy atoms. |
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_generateMessage(self)
This function checks calculation results and generates appropriate
message. |
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list
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_optimizeAlignment(self)
This function finds best core matches for molecules that have
multiple matches. |
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list, int
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_calculateStatesTally(self)
This function calculates number of 'states' (matches) for each
multiply matched molecule as well as the grand total of all states. |
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list
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_findBestMatches(self)
Find best matching core for each multiply matched molecule. |
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DEE_EnergyMatrix
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_calculateEnergyMatrix(self)
This function computes 'energy' matrix that is used in the
optimization procedure that finds best matching cores for each
molecule. |
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dict
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_calculateRGroupSimilarity(self)
This function calculates Tanimoto fingerprint similarities for every
attachment pair defined using SMILES. |
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dict
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dict
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_calculatePairSimilarity(self,
r_group_bitset,
sim_func)
This function calculates similarities for each pair of unique r-group
attachments. |
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float
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_calculatePairSimilarityFP(self,
key1,
key2,
r_group_bitset)
This function calculates Tanimoto FP similarities for a pair of
unique r-group attachments. |
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float
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_calculatePairSimilarityGeneric(self,
key1,
key2,
r_group_bitset)
This function calculates similarities for a pair of unique r-group
attachments using simple sheme. |
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double
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_calculateSimilarityMatrix(self,
ns,
r_group_sim)
This function computes similarity matrix, which contains pairwise
scores between core states of molecules that have multiple core
matches. |
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_finalizeCalculation(self)
This function is used to add r-group data into Data() object after
best matching core has been found. |
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_saveBestMatchData(self)
This function iterates over input structures and stores core and bond
data for 'best matches' in the Data() structure. |
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_savePropertyAndAttachmentData(self)
Iterate over input structures and save property and attachment groups
data in the main Data() structure. |
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