Package schrodinger :: Package analysis :: Module enrichment :: Class TwoGroupFingerprintAnalyzer
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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:
------------
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:
-------------------
@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.

Instance Methods [hide private]
 
__init__(self, fp_group1, fp_group2, fp_sim)
 
analyzeGroups(self)
Analyze within each group, and between groups.
 
analyzeWithinGroups(self)
 
analyzeBetweenGroups(self)
Properties [hide private]
  within_group1_global_max
Maximum value over all group1 summary members.
  within_group2_global_max
Maximum value over all group2 summary members.
  between_groups_global_max
Maximum value over all between group1-2 summary members.
  within_group1_global_min
Minimum value over all group1 summary members.
  within_group2_global_min
Minimum value over all group2 summary members.
  between_groups_global_min
Minimum value over all between group1-2 summary members.
Method Details [hide private]

__init__(self, fp_group1, fp_group2, fp_sim)
(Constructor)

 
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.

Property Details [hide private]

within_group1_global_max

Maximum value over all group1 summary members.

Get Method:
unreachable.within_group1_global_max(self) - Maximum value over all group1 summary members.

within_group2_global_max

Maximum value over all group2 summary members.

Get Method:
unreachable.within_group2_global_max(self) - Maximum value over all group2 summary members.

between_groups_global_max

Maximum value over all between group1-2 summary members.

Get Method:
unreachable.between_groups_global_max(self) - Maximum value over all between group1-2 summary members.

within_group1_global_min

Minimum value over all group1 summary members.

Get Method:
unreachable.within_group1_global_min(self) - Minimum value over all group1 summary members.

within_group2_global_min

Minimum value over all group2 summary members.

Get Method:
unreachable.within_group2_global_min(self) - Minimum value over all group2 summary members.

between_groups_global_min

Minimum value over all between group1-2 summary members.

Get Method:
unreachable.between_groups_global_min(self) - Minimum value over all between group1-2 summary members.