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24f1737839
* remove all of the "from __future__" imports * remove the first batch of rdkit.six imports/uses * next step of rdkit.six removal * removing xrange, range, and some maps * next round of removals * next round of cleanups * fix inchi test * last bits of "from rdkit.six" are gone * and the last of the six stuff is gone * strange importlib problem
74 lines
2.7 KiB
Python
74 lines
2.7 KiB
Python
#
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# Copyright (c) 2009, Novartis Institutes for BioMedical Research Inc.
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# All rights reserved.
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#
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# Redistribution and use in source and binary forms, with or without
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# modification, are permitted provided that the following conditions are
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# met:
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#
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# * Redistributions of source code must retain the above copyright
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# notice, this list of conditions and the following disclaimer.
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# * Redistributions in binary form must reproduce the above
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# copyright notice, this list of conditions and the following
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# disclaimer in the documentation and/or other materials provided
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# with the distribution.
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# * Neither the name of Novartis Institutes for BioMedical Research Inc.
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# nor the names of its contributors may be used to endorse or promote
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# products derived from this software without specific prior written permission.
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#
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# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
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# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
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# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
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# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
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# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
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# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
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# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
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# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
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# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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#
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# Created by Greg Landrum and Anna Vulpetti, March 2009
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from rdkit.ML.Cluster import Butina
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from rdkit import DataStructs
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import sys, pickle
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# sims is the list of similarity thresholds used to generate clusters
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sims = [.9, .8, .7, .6]
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smis = []
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uniq = []
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uFps = []
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for fileN in sys.argv[1:]:
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inF = file(sys.argv[1], 'r')
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cols = pickle.load(inF)
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fps = pickle.load(inF)
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for row in fps:
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nm, smi, fp = row[:3]
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if smi not in smis:
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try:
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fpIdx = uFps.index(fp)
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except ValueError:
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fpIdx = len(uFps)
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uFps.append(fp)
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uniq.append([fp, nm, smi, 'FP_%d' % fpIdx] + row[3:])
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smis.append(smi)
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def distFunc(a, b):
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return 1. - DataStructs.DiceSimilarity(a[0], b[0])
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for sim in sims:
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clusters = Butina.ClusterData(uniq, len(uniq), 1. - sim, False, distFunc)
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print('Sim: %.2f, nClusters: %d' % (sim, len(clusters)), file=sys.stderr)
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for i, cluster in enumerate(clusters):
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for pt in cluster:
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uniq[pt].append(str(i + 1))
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cols.append('cluster_thresh_%d' % (int(100 * sim)))
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print(' '.join(cols))
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for row in uniq:
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print(' '.join(row[1:]))
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