Class TwoGroupFingerprintAnalyzer
Summarize the similarity differences within and between two groups
of fingerprints. All i!=j pair-wise similarity comparisons are
made within a group, and all pair-wise similarity comparsions are
made between the groups. However, the list of similarity values is
compressed into a statistical digest (min, max, median, etc.)
API example:
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fp_gen.setType('Linear')
fp_gen.setAtomBondTyping(fp_gen.getDefaultAtomTypingScheme())
group1 = []
group2 = []
# Title is the compound identifer in this example.
for st in structure.StructureReader('actives.mae'):
item = (st.title, fp_gen.generate(st))
group1.append(item)
for st in structure.StructureReader('decoys.mae'):
item = (st.title, fp_gen.generate(st))
group2.append(item)
fp_sim = canvas_sim.CanvasFingerprintSimilarity(logger=logger)
twogrpfp = test.TwoGroupFingerprintAnalyzer(
group1,
group2,
fp_sim,
)
twogrpfp.analyzeGroups()
print twogrpfp.within_group1_global_max
print twogrpfp.within_group2_global_max
print twogrpfp.between_groups_global_max
Instance variables:
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@ivar within_group1_summary:
List of within-group1 StatisticalSummary instances the same
order and length of the number if items emitted from fp_group1.
i=j pairs are excluded from the analysis.
@ivar within_group2_summary:
List of within-group2 StatisticalSummary instances the same order
and length of the number if items emitted from fp_group2. i=j
pairs are excluded from the analysis.
@ivar between_groups_summary:
List of between-group1-and-group2 StatisticalSummary instances
the same order and length of the number if items emitted from
fp_group1. i=j pair are included in the analysis.
@ivar group1_ids:
Ordered list of group1 identifiers.
@ivar group2_ids:
Ordered list of group1 identifiers.
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__init__(self,
fp_group1,
fp_group2,
fp_sim) |
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analyzeGroups(self)
Analyze within each group, and between groups. |
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analyzeWithinGroups(self) |
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analyzeBetweenGroups(self) |
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__init__(self,
fp_group1,
fp_group2,
fp_sim)
(Constructor)
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- Parameters:
fp_group1 (iterable) - A sequence or iterable of (id, fingerprint) tuples for group 1.
fp_group2 (iterable) - A sequence or iterable of (id, fingerprint) tuples for group 2.
fp_sim (canvas.similarity.CanvasFingerprintSimilarity) - Configured Canvas similarity calculator.
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within_group1_global_max(self)
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Maximum value over all group1 summary members.
- Decorators:
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within_group2_global_max(self)
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Maximum value over all group2 summary members.
- Decorators:
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between_groups_global_max(self)
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Maximum value over all between group1-2 summary members.
- Decorators:
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within_group1_global_min(self)
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Minimum value over all group1 summary members.
- Decorators:
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within_group2_global_min(self)
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Minimum value over all group2 summary members.
- Decorators:
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between_groups_global_min(self)
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Minimum value over all between group1-2 summary members.
- Decorators:
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