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"""unit testing code for the BuildComposite functionality
"""
from rdkit import RDConfig
import unittest,os
from rdkit.ML import BuildComposite
from rdkit.ML import ScreenComposite
from rdkit.Dbase.DbConnection import DbConnect
import cPickle as pickle
def feq(a,b,tol=1e-4):
if abs(a-b)>tol: return 0
else: return... | {
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"""unit testing code for the BuildComposite functionality
"""
import io
import os
import unittest
from rdkit import RDConfig
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.ML import BuildComposite
from rdkit.six.moves import cPickle as pickle
class TestCase(unittest.TestCase):
def setUp(self):
sel... | {
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"path": "rdkit/ML/UnitTestBuildComposite.py",
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"""unit testing code for the BuildComposite functionality
"""
import unittest,os
from rdkit.six.moves import cPickle as pickle
from rdkit.six import cmp
from rdkit import RDConfig
from rdkit.ML import BuildComposite
from rdkit.ML import ScreenComposite
from rdkit.Dbase.DbConnection import DbConnect
class TestCase(uni... | {
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"path": "rdkit/ML/UnitTestBuildComposite.py",
"copies": "1",
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"hash": -6177026492547434000,
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"autogenerated": false,
"ratio": 3.074727555786196,
... |
"""unit testing code for the ScreenComposite functionality
"""
from rdkit import RDConfig
import unittest,os
from rdkit.ML import BuildComposite
from rdkit.ML import ScreenComposite
from rdkit.six.moves import cPickle as pickle
def feq(a,b,tol=1e-4):
if abs(a-b)>tol: return 0
else: return 1
class TestCase(unit... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "rdkit/ML/UnitTestScreenComposite.py",
"copies": "1",
"size": "10507",
"license": "bsd-3-clause",
"hash": 6088741859960249000,
"line_mean": 34.2583892617,
"line_max": 111,
"alpha_frac": 0.6851622728,
"autogenerated": false,
"ratio": 3.0393404686144... |
"""unit testing code for the ScreenComposite functionality
"""
from rdkit import RDConfig
import unittest,os
from rdkit.ML import BuildComposite
from rdkit.ML import ScreenComposite
import cPickle as pickle
def feq(a,b,tol=1e-4):
if abs(a-b)>tol: return 0
else: return 1
class TestCase(unittest.TestCase):
def... | {
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"path": "rdkit/ML/UnitTestScreenComposite.py",
"copies": "2",
"size": "9996",
"license": "bsd-3-clause",
"hash": -4490366876140209700,
"line_mean": 33.2328767123,
"line_max": 111,
"alpha_frac": 0.6396558623,
"autogenerated": false,
"ratio": 3.103384042222912,
"... |
from __future__ import print_function
from rdkit import RDConfig
import os, sys, time
try:
import subprocess
except ImportError:
subprocess = None
TEST_FAILED = -1
TEST_PASSED = 0
def RunTest(exeName, args, extras):
if exeName == "python":
exeName = RDConfig.pythonExe
args = args.split(' ')
startDir =... | {
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"path": "rdkit/TestRunner.py",
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"size": "9112",
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"hash": -8739317964714115000,
"line_mean": 29.8881355932,
"line_max": 99,
"alpha_frac": 0.6187445127,
"autogenerated": false,
"ratio": 3.4423876086135246,
"config_test": tru... |
""" Hybrid EState-VSA descriptors (like the MOE VSA descriptors)
"""
import numpy
from rdkit.Chem.EState.EState import EStateIndices as EStateIndices_
from rdkit.Chem.MolSurf import _LabuteHelper as VSAContribs_
import bisect
"""
These default VSA bins were chosen using the PP3K solubility data
set. An arbitrary nu... | {
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"path": "rdkit/Chem/EState/EState_VSA.py",
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"size": "3368",
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"hash": -6254493243906284000,
"line_mean": 29.8990825688,
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"alpha_frac": 0.6591448931,
"autogenerated": false,
"ratio": 2.6108527131782946,
"co... |
""" Hybrid EState-VSA descriptors (like the MOE VSA descriptors)
"""
import bisect
import numpy
from rdkit.Chem.EState.EState import EStateIndices as EStateIndices_
from rdkit.Chem.MolSurf import _LabuteHelper as VSAContribs_
"""
These default VSA bins were chosen using the PP3K solubility data
set. An arbitrary ... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/EState/EState_VSA.py",
"copies": "6",
"size": "3552",
"license": "bsd-3-clause",
"hash": 8627994845224181000,
"line_mean": 25.7067669173,
"line_max": 80,
"alpha_frac": 0.6675112613,
"autogenerated": false,
"ratio": 2.8190476190476192,
"config_te... |
from __future__ import print_function
import bisect
class TopNContainer(object):
""" maintains a sorted list of a particular number of data elements.
"""
def __init__(self,size,mostNeg=-1e99):
"""
if size is negative, all entries will be kept in sorted order
"""
self._size = size
if(size>=0):... | {
"repo_name": "strets123/rdkit",
"path": "rdkit/DataStructs/TopNContainer.py",
"copies": "4",
"size": "1915",
"license": "bsd-3-clause",
"hash": -4584533402615983000,
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from __future__ import print_function
import bisect
class TopNContainer(object):
""" maintains a sorted list of a particular number of data elements.
"""
def __init__(self, size, mostNeg=-1e99):
"""
if size is negative, all entries will be kept in sorted order
"""
self._size = size
if (siz... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/DataStructs/TopNContainer.py",
"copies": "5",
"size": "2074",
"license": "bsd-3-clause",
"hash": 3134968020779097000,
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"alpha_frac": 0.599807136,
"autogenerated": false,
"ratio": 3.428099173553719,
"config_t... |
""" functionality to allow adjusting composite model contents
"""
from __future__ import print_function
import numpy
import copy
def BalanceComposite(model, set1, set2, weight, targetSize, names1=None, names2=None):
""" adjusts the contents of the composite model so as to maximize
the weighted classification a... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/ML/Composite/AdjustComposite.py",
"copies": "1",
"size": "2617",
"license": "bsd-3-clause",
"hash": -4321554604370946600,
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"alpha_frac": 0.6679403898,
"autogenerated": false,
"ratio": 3.3042929292929295,
"co... |
""" functionality to allow adjusting composite model contents
"""
from __future__ import print_function
import copy
import numpy
def BalanceComposite(model, set1, set2, weight, targetSize, names1=None, names2=None):
""" adjusts the contents of the composite model so as to maximize
the weighted classification... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/ML/Composite/AdjustComposite.py",
"copies": "4",
"size": "2628",
"license": "bsd-3-clause",
"hash": -604106757098932400,
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"line_max": 86,
"alpha_frac": 0.6651445967,
"autogenerated": false,
"ratio": 3.3056603773584907,
"config_te... |
""" functionality to allow adjusting composite model contents
"""
import numpy
import copy
def BalanceComposite(model,set1,set2,weight,targetSize,names1=None,names2=None):
""" adjusts the contents of the composite model so as to maximize
the weighted classification accuracty across the two data sets.
The r... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/ML/Composite/AdjustComposite.py",
"copies": "2",
"size": "2529",
"license": "bsd-3-clause",
"hash": 7237315060509842000,
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"autogenerated": false,
"ratio": 3.2674418604651163,
... |
""" Define the class _KNNClassificationModel_, used to represent a k-nearest neighbhors
classification model
Inherits from _KNNModel_
"""
from rdkit.ML.KNN import KNNModel
class KNNClassificationModel(KNNModel.KNNModel):
""" This is used to represent a k-nearest neighbor classifier
"""
def __init__(... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/ML/KNN/KNNClassificationModel.py",
"copies": "11",
"size": "1992",
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"autogenerated": false,
"ratio": 3.808795411089866,
"config_te... |
""" Define the class _KNNRegressionModel_, used to represent a k-nearest neighbhors
regression model
Inherits from _KNNModel_
"""
from rdkit.ML.KNN import KNNModel
class KNNRegressionModel(KNNModel.KNNModel):
""" This is used to represent a k-nearest neighbor classifier
"""
def __init__(self, k, attrs, ... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/ML/KNN/KNNRegressionModel.py",
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"conf... |
from __future__ import print_function
from rdkit import RDConfig
from rdkit import Chem
import os.path
from rdkit.VLib.NodeLib import *
from rdkit.VLib import Supply,Filter
# this would be a real input, from an sd file:
#fName = os.path.join(RDConfig.RDCodeDir,'VLib','NodeLib','test_data','NCI_aids.10.dupes.sdf')
#su... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/VLib/NodeLib/demo.py",
"copies": "4",
"size": "2022",
"license": "bsd-3-clause",
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"alpha_frac": 0.696834817,
"autogenerated": false,
"ratio": 2.6328125,
"config_test": fals... |
from qt import *
import sys
if sys.platform == 'win32':
from rdkit.qtGui.qtActiveX import MakeActiveXClass
import win32com.client.gencache
import win32clipboard
try:
cdxModule = win32com.client.gencache.EnsureModule("{AF2D2DBA-75E4-4123-BC0B-A57BD5C5C5D2}", 0, 7, 0)
except Exception:
raise ImportError... | {
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"path": "rdkit/utils/chemdraw_qax.py",
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"autogenerated": false,
"ratio": 3.2142857142857144,
"config_test... |
from rdkit import Chem
from rdkit.VLib.Filter import FilterNode
class DupeFilter(FilterNode):
""" canonical-smiles based duplicate filter
Assumptions:
- inputs are molecules
Sample Usage:
>>> import os
>>> from rdkit import RDConfig
>>> from rdkit.VLib.NodeLib.SDSupply import SDSupplyNode
... | {
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from rdkit import Chem
from rdkit.VLib.Filter import FilterNode
class SmartsFilter(FilterNode):
""" filter out molecules matching one or more SMARTS patterns
There is a count associated with each pattern. Molecules are
allowed to match the pattern up to this number of times.
Assumptions:
- inputs are m... | {
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"path": "rdkit/VLib/NodeLib/SmartsMolFilter.py",
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"... |
from rdkit import RDConfig
from rdkit import Chem
import os.path
from rdkit.VLib.NodeLib import *
from rdkit.VLib import Supply,Filter
# this would be a real input, from an sd file:
#fName = os.path.join(RDConfig.RDCodeDir,'VLib','NodeLib','test_data','NCI_aids.10.dupes.sdf')
#supplier = SDSupply.SDSupplyNode(fName)
... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/VLib/NodeLib/demo.py",
"copies": "2",
"size": "1977",
"license": "bsd-3-clause",
"hash": 4897881568559909000,
"line_mean": 33.6842105263,
"line_max": 176,
"alpha_frac": 0.6980273141,
"autogenerated": false,
"ratio": 2.608179419525066,
"config_tes... |
from rdkit import RDConfig
import sys,os,types
from rdkit import Chem
from rdkit.VLib.Filter import FilterNode
class SmartsFilter(FilterNode):
""" filter out molecules matching one or more SMARTS patterns
There is a count associated with each pattern. Molecules are
allowed to match the pattern up to this number... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/VLib/NodeLib/SmartsMolFilter.py",
"copies": "2",
"size": "2725",
"license": "bsd-3-clause",
"hash": 1067319250771499500,
"line_mean": 24.4672897196,
"line_max": 83,
"alpha_frac": 0.5941284404,
"autogenerated": false,
"ratio": 3.2517899761336517,
... |
from rdkit import RDConfig
import sys,os,types
from rdkit import Chem
from rdkit.VLib.Transform import TransformNode
class SmartsRemover(TransformNode):
""" transforms molecules by removing atoms matching smarts patterns
Assumptions:
- inputs are molecules
Sample Usage:
>>> smis = ['C1CCC1.C=O','C1CC... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/VLib/NodeLib/SmartsRemover.py",
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"c... |
from rdkit import six
from rdkit.VLib.Node import VLibNode
class SupplyNode(VLibNode):
""" base class for nodes which supply things
Assumptions:
1) no parents
Usage Example:
>>> supplier = SupplyNode(contents=[1,2,3])
>>> supplier.next()
1
>>> supplier.next()
2
>>> supplier.next()
... | {
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"config_test": true... |
import sys
from rdkit import six
from rdkit.VLib.Node import VLibNode
class TransformNode(VLibNode):
""" base class for nodes which filter their input
Assumptions:
- transform function takes a number of arguments equal to the
number of inputs we have. We return whatever it returns
- inputs (pare... | {
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import sys, os.path
from rdkit import six
from rdkit import RDConfig
from rdkit.VLib.Supply import SupplyNode
from rdkit import Chem
class SDSupplyNode(SupplyNode):
""" SD supplier
Sample Usage:
>>> fileN = os.path.join(RDConfig.RDCodeDir,'VLib','NodeLib',\
'test_data','NCI_aids.... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/VLib/NodeLib/SDSupply.py",
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import sys, types
from rdkit import Chem
from rdkit import six
from rdkit.VLib.Output import OutputNode as BaseOutputNode
class OutputNode(BaseOutputNode):
""" dumps smiles output
Assumptions:
- destination supports a write() method
- inputs (parents) can be stepped through in lockstep
Usage Examp... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/VLib/NodeLib/SmilesOutput.py",
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"size": "1925",
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"hash": -6269298467054758000,
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"ratio": 3.1505728314238954,
"confi... |
import sys,types
from rdkit import Chem
from rdkit.VLib.Output import OutputNode as BaseOutputNode
class OutputNode(BaseOutputNode):
""" dumps smiles output
Assumptions:
- destination supports a write() method
- inputs (parents) can be stepped through in lockstep
Usage Example:
>>> smis = ['C1C... | {
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""" Define the class _KNNClassificationModel_, used to represent a k-nearest neighbhors classification model
Inherits from _KNNModel_
"""
from rdkit.ML.KNN import KNNModel
class KNNClassificationModel(KNNModel.KNNModel) :
""" This is used to represent a k-nearest neighbor classifier
"""
def __init__(sel... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/ML/KNN/KNNClassificationModel.py",
"copies": "2",
"size": "2016",
"license": "bsd-3-clause",
"hash": -211442763568115620,
"line_mean": 24.5189873418,
"line_max": 108,
"alpha_frac": 0.6607142857,
"autogenerated": false,
"ratio": 3.7611940298507465,
... |
""" Define the class _KNNModel_, used to represent a k-nearest neighbhors model
"""
from rdkit.DataStructs.TopNContainer import TopNContainer
class KNNModel(object):
""" This is a base class used by KNNClassificationModel
and KNNRegressionModel to represent a k-nearest neighbor predictor. In general
one of this... | {
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""" Define the class _KNNRegressionModel_, used to represent a k-nearest neighbhors
regression model
Inherits from _KNNModel_
"""
from rdkit.ML.KNN import KNNModel
class KNNRegressionModel(KNNModel.KNNModel) :
""" This is used to represent a k-nearest neighbor classifier
"""
def __init__(self, k, attrs... | {
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"path": "rdkit/ML/KNN/KNNRegressionModel.py",
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"alpha_frac": 0.6497232008,
"autogenerated": false,
"ratio": 3.8657587548638133,
"c... |
import math
def EuclideanDist(ex1, ex2, attrs):
"""
>>> v1 = [0,1,0,1]
>>> v2 = [1,0,1,0]
>>> EuclideanDist(v1,v2,range(4))
2.0
>>> EuclideanDist(v1,v1,range(4))
0.0
>>> v2 = [0,0,0,1]
>>> EuclideanDist(v1,v2,range(4))
1.0
>>> v2 = [0,.5,0,.5]
>>> abs(EuclideanDist(v1,v2... | {
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""" handles doing cross validation with naive bayes models
and evaluation of individual models
"""
from __future__ import print_function
from rdkit.ML.Data import SplitData
from rdkit.ML.NaiveBayes.ClassificationModel import NaiveBayesClassifier
try:
from rdkit.ML.FeatureSelect import CMIM
except ImportError:
CM... | {
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import Chem
from Chem.Draw.MolDrawing import MolDrawing
from Chem import TemplateAlign
from sping.SVG.pidSVG import SVGCanvas as Canvas
from mod_python import apache
from utils import cactvs
import sys,os,tempfile
def gif(req,smiles,width=100,height=100,highlight='[]',frame=0,
dblSize=0,**kwargs):
req.conte... | {
"repo_name": "adalke/rdkit",
"path": "Web/RDExtras/MolImage.py",
"copies": "1",
"size": "1865",
"license": "bsd-3-clause",
"hash": -740125204472663900,
"line_mean": 23.8666666667,
"line_max": 79,
"alpha_frac": 0.6691689008,
"autogenerated": false,
"ratio": 3.134453781512605,
"config_test": fal... |
import os
import unittest
from rdkit import RDConfig
from rdkit.DataStructs import ExplicitBitVect
from rdkit.ML.Data import DataUtils
from rdkit.ML.NaiveBayes import CrossValidate
from rdkit.ML.NaiveBayes.ClassificationModel import NaiveBayesClassifier
class TestCase(unittest.TestCase):
def setUp(self):
Data... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/ML/NaiveBayes/UnitTestNB.py",
"copies": "11",
"size": "7351",
"license": "bsd-3-clause",
"hash": 3094732866560428000,
"line_mean": 32.7201834862,
"line_max": 97,
"alpha_frac": 0.597469732,
"autogenerated": false,
"ratio": 2.9869971556277934,
"conf... |
from rdkit import RDConfig
import unittest,sys,os
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures,AllChem
import EmbedLib
import gzip
from rdkit import DistanceGeometry as DG
from rdkit import Geometry
import Pharmacophore
def feq(n1,n2,tol=1e-5):
return abs(n1-n2)... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/Chem/Pharm3D/UnitTestPharmacophore.py",
"copies": "3",
"size": "5219",
"license": "bsd-3-clause",
"hash": -6000396559295810000,
"line_mean": 37.375,
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"autogenerated": false,
"ratio": 2.8834254143646407,
... |
"""unit testing code for the AnalyzeComposite functionality
"""
from rdkit import RDConfig
import unittest,os
from rdkit.ML import AnalyzeComposite
from rdkit.six.moves import cPickle as pickle
def feq(a,b,tol=1e-4):
if abs(a-b)>tol: return 0
else: return 1
class TestCase(unittest.TestCase):
def setUp(self):
... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/ML/UnitTestAnalyzeComposite.py",
"copies": "1",
"size": "1598",
"license": "bsd-3-clause",
"hash": 9045071593346077000,
"line_mean": 25.1967213115,
"line_max": 68,
"alpha_frac": 0.6495619524,
"autogenerated": false,
"ratio": 3.1089494163424125,
"conf... |
from __future__ import print_function
from rdkit import RDConfig
import os,sys,copy
import unittest
import math
from rdkit import Chem
from rdkit.Chem import rdMolAlign,rdMolTransforms,rdMolDescriptors,rdDistGeom,ChemicalForceFields
def lstFeq(l1, l2, tol=1.e-4):
if (len(list(l1)) != len(list(l2))):
return 0
f... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "Code/GraphMol/MolAlign/Wrap/testMolAlign.py",
"copies": "1",
"size": "16282",
"license": "bsd-3-clause",
"hash": -2526764635969939000,
"line_mean": 38.5194174757,
"line_max": 121,
"alpha_frac": 0.6134381526,
"autogenerated": false,
"ratio": 2.9023... |
from rdkit import RDConfig
import os,sys
import unittest
from rdkit import Chem
from rdkit.Chem import rdMolAlign,rdDistGeom,ChemicalForceFields
def lstFeq(l1, l2, tol=1.e-4):
if (len(list(l1)) != len(list(l2))):
return 0
for i in range(len(list(l1))):
if not feq(l1[i], l2[i], tol):
return 0
return... | {
"repo_name": "rdkit/rdkit-orig",
"path": "Code/GraphMol/MolAlign/Wrap/testMolAlign.py",
"copies": "1",
"size": "3881",
"license": "bsd-3-clause",
"hash": 4433754164010141700,
"line_mean": 33.6517857143,
"line_max": 87,
"alpha_frac": 0.5766555012,
"autogenerated": false,
"ratio": 2.96485867074102... |
""" Contains an implementation of Topological-torsion fingerprints, as
described in:
R. Nilakantan, N. Bauman, J. S. Dixon, R. Venkataraghavan;
"Topological Torsion: A New Molecular Descriptor for SAR Applications.
Comparison with Other Descriptors" JCICS 27, 82-85 (1987).
"""
from rdkit import Chem
from rdkit.Chem i... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/AtomPairs/Torsions.py",
"copies": "2",
"size": "4994",
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"hash": 586635135906475300,
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"line_max": 188,
"alpha_frac": 0.6177412895,
"autogenerated": false,
"ratio": 2.6763129689174705,
"conf... |
from __future__ import division
from rdkit import rdBase
from rdkit.DataStructs import cDataStructs
__doc__ = cDataStructs.__doc__
from rdkit.DataStructs.cDataStructs import *
similarityFunctions = [
('Tanimoto', TanimotoSimilarity, ''),
("Dice", DiceSimilarity, ''),
("Cosine", CosineSimilarity, ''),
("Sokal",... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/DataStructs/__init__.py",
"copies": "1",
"size": "1624",
"license": "bsd-3-clause",
"hash": 5260115597227195000,
"line_mean": 29.0740740741,
"line_max": 75,
"alpha_frac": 0.7013546798,
"autogenerated": false,
"ratio": 3.012987012987013,
"config_test"... |
from __future__ import division
from rdkit import rdBase
from rdkit.DataStructs import cDataStructs
from rdkit.DataStructs.cDataStructs import *
__doc__ = cDataStructs.__doc__
similarityFunctions = [
('Tanimoto', TanimotoSimilarity, ''),
("Dice", DiceSimilarity, ''),
("Cosine", CosineSimilarity, ''),
("Sokal"... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/DataStructs/__init__.py",
"copies": "4",
"size": "1625",
"license": "bsd-3-clause",
"hash": -4876271652371967000,
"line_mean": 28.5454545455,
"line_max": 75,
"alpha_frac": 0.7009230769,
"autogenerated": false,
"ratio": 3.009259259259259,
"config_t... |
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
import math
def ExplainAtomCode(code, branchSubtract=0):
"""
**Arguments**:
- the code to be considered
- branchSubtract: (optional) the constant that was subtracted off
the number of neighbors be... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/AtomPairs/Utils.py",
"copies": "2",
"size": "7283",
"license": "bsd-3-clause",
"hash": 1631624067527401500,
"line_mean": 21.4783950617,
"line_max": 76,
"alpha_frac": 0.6088150487,
"autogenerated": false,
"ratio": 2.7451941198643044,
"config_test... |
from rdkit import rdBase
import cDataStructs
__doc__=cDataStructs.__doc__
from cDataStructs import *
similarityFunctions=[
('Tanimoto',TanimotoSimilarity,''),
("Dice",DiceSimilarity,''),
("Cosine",CosineSimilarity,''),
("Sokal",SokalSimilarity,''),
("Russel",RusselSimilarity,''),
("RogotGoldberg",RogotGol... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/DataStructs/__init__.py",
"copies": "2",
"size": "1506",
"license": "bsd-3-clause",
"hash": 972658805899757000,
"line_mean": 27.9615384615,
"line_max": 73,
"alpha_frac": 0.7197875166,
"autogenerated": false,
"ratio": 2.9129593810444874,
"config_t... |
""" unit testing code for MOE-type descriptors with EStates
"""
from __future__ import print_function
from rdkit import RDConfig
import unittest,os
from rdkit import Chem
from rdkit.Chem.EState import EState_VSA
import os.path
def feq(n1,n2,tol=1e-4):
return abs(n1-n2)<=tol
class TestCase(unittest.TestCase):
def... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/EState/UnitTestVSA.py",
"copies": "4",
"size": "1739",
"license": "bsd-3-clause",
"hash": -1630963691464598500,
"line_mean": 27.5081967213,
"line_max": 73,
"alpha_frac": 0.6198964922,
"autogenerated": false,
"ratio": 3.0138648180242633,
"config_... |
""" Contains an implementation of Atom-pair fingerprints, as
described in:
R.E. Carhart, D.H. Smith, R. Venkataraghavan;
"Atom Pairs as Molecular Features in Structure-Activity Studies:
Definition and Applications" JCICS 25, 64-73 (1985).
"""
from rdkit.DataStructs import IntSparseIntVect
from rdkit import Chem
from ... | {
"repo_name": "strets123/rdkit",
"path": "rdkit/Chem/AtomPairs/Pairs.py",
"copies": "4",
"size": "4247",
"license": "bsd-3-clause",
"hash": -7505089715439233000,
"line_mean": 30.4592592593,
"line_max": 111,
"alpha_frac": 0.700023546,
"autogenerated": false,
"ratio": 2.871534820824882,
"config_t... |
""" Defines Naive Baysean classification model
Based on development in: Chapter 6 of "Machine Learning" by Tom Mitchell
"""
import numpy
from rdkit.ML.Data import Quantize
from rdkit.six import iteritems
def _getBinId(val, qBounds):
bid = 0
for bnd in qBounds:
if (val > bnd):
bid += 1
return bid
... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/ML/NaiveBayes/ClassificationModel.py",
"copies": "1",
"size": "8719",
"license": "bsd-3-clause",
"hash": -2859280128291355600,
"line_mean": 30.3633093525,
"line_max": 100,
"alpha_frac": 0.6105057919,
"autogenerated": false,
"ratio": 3.5675122749590833,... |
from __future__ import print_function
from rdkit import RDConfig
import unittest,sys,os
from rdkit.six import PY3
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures,rdDistGeom
import EmbedLib
import gzip
from rdkit import DistanceGeometry as DG
from rdkit import Geometry
... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "rdkit/Chem/Pharm3D/UnitTestEmbed.py",
"copies": "1",
"size": "10065",
"license": "bsd-3-clause",
"hash": 8775973549836883000,
"line_mean": 36.6966292135,
"line_max": 85,
"alpha_frac": 0.5786388475,
"autogenerated": false,
"ratio": 3.18411894969946... |
from __future__ import print_function
from rdkit import RDConfig
import sys,time,math
from rdkit.ML.Data import Stats
import rdkit.DistanceGeometry as DG
from rdkit import Chem
import numpy
from rdkit.Chem import rdDistGeom as MolDG
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem import ChemicalForceFields
imp... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/Pharm3D/EmbedLib.py",
"copies": "1",
"size": "38756",
"license": "bsd-3-clause",
"hash": -8048911424920958000,
"line_mean": 30.4833468725,
"line_max": 130,
"alpha_frac": 0.6207554959,
"autogenerated": false,
"ratio": 3.03611437524481,
"config_te... |
from __future__ import print_function
from rdkit import RDConfig
import sys, time, math
from rdkit.ML.Data import Stats
import rdkit.DistanceGeometry as DG
from rdkit import Chem
import numpy
from rdkit.Chem import rdDistGeom as MolDG
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem import ChemicalForceFields
i... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Pharm3D/EmbedLib.py",
"copies": "1",
"size": "38924",
"license": "bsd-3-clause",
"hash": 4507648311856197600,
"line_mean": 30.4410339257,
"line_max": 119,
"alpha_frac": 0.6180762512,
"autogenerated": false,
"ratio": 3.0383264382171573,
"config_t... |
from rdkit import Geometry
from rdkit import Chem
import numpy
import math
# BIG NOTE: we are going assume atom IDs starting from 0 instead of 1
# for all the functions in this file. This is so that they
# are reasonably indepedent of the combicode. However when using
# with combicode the caller needs to make sure the... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Features/FeatDirUtilsRD.py",
"copies": "2",
"size": "12281",
"license": "bsd-3-clause",
"hash": -2614181898708243000,
"line_mean": 27.5604651163,
"line_max": 104,
"alpha_frac": 0.64929566,
"autogenerated": false,
"ratio": 3.1257317383558156,
"co... |
from rdkit import Geometry
import numpy
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures
from rdkit.RDLogger import logger
logger = logger()
class Pharmacophore:
def __init__(self, feats, initMats=True):
self._initializeFeats(feats)
nf = len(feats)
self._boundsMat = numpy.zeros((nf, nf), ... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Pharm3D/Pharmacophore.py",
"copies": "1",
"size": "6085",
"license": "bsd-3-clause",
"hash": 8974841837638450000,
"line_mean": 26.9128440367,
"line_max": 96,
"alpha_frac": 0.5753492194,
"autogenerated": false,
"ratio": 3.174230568596766,
"config... |
from rdkit import RDConfig
import unittest,sys,os,cPickle
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures,rdDistGeom
import EmbedLib
import gzip
from rdkit import DistanceGeometry as DG
from rdkit import Geometry
import Pharmacophore
import cPickle
import numpy
def feq(n1,n2,tol=1e-5):
return abs(n1-n... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Pharm3D/UnitTestEmbed.py",
"copies": "1",
"size": "9675",
"license": "bsd-3-clause",
"hash": 5872861235074889000,
"line_mean": 36.79296875,
"line_max": 85,
"alpha_frac": 0.5804651163,
"autogenerated": false,
"ratio": 3.210019907100199,
"conf... |
from rdkit import RDConfig
import sys,time,math
from rdkit.ML.Data import Stats
import rdkit.DistanceGeometry as DG
from rdkit import Chem
import numpy
from rdkit.Chem import rdDistGeom as MolDG
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem import ChemicalForceFields
import Pharmacophore,ExcludedVolume
from ... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Pharm3D/EmbedLib.py",
"copies": "1",
"size": "38529",
"license": "bsd-3-clause",
"hash": -8608010837664877000,
"line_mean": 30.3754071661,
"line_max": 130,
"alpha_frac": 0.621194425,
"autogenerated": false,
"ratio": 3.030438886267107,
"confi... |
""" uses pymol to interact with molecules
"""
from rdkit import Chem
import os, tempfile
# Python3 compatibility
try:
from xmlrpclib import Server
except ImportError:
from xmlrpc.client import Server
_server=None
class MolViewer(object):
def __init__(self,host=None,port=9123,force=0,**kwargs):
global _ser... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/Chem/PyMol.py",
"copies": "2",
"size": "7796",
"license": "bsd-3-clause",
"hash": -5112879296776743000,
"line_mean": 29.5725490196,
"line_max": 102,
"alpha_frac": 0.6222421755,
"autogenerated": false,
"ratio": 3.3487972508591066,
"config_test": ... |
""" uses pymol to interact with molecules
"""
from rdkit import Chem
import os, tempfile, sys
# Python3 compatibility
try:
from xmlrpclib import Server
except ImportError:
from xmlrpc.client import Server
_server=None
class MolViewer(object):
def __init__(self,host=None,port=9123,force=0,**kwargs):
global... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/PyMol.py",
"copies": "1",
"size": "8287",
"license": "bsd-3-clause",
"hash": -2759578170375097300,
"line_mean": 29.921641791,
"line_max": 102,
"alpha_frac": 0.6250754193,
"autogenerated": false,
"ratio": 3.3921408104789195,
"config_test": false,... |
""" uses pymol to interact with molecules
"""
from rdkit import Chem
import xmlrpclib,os,tempfile
_server=None
class MolViewer(object):
def __init__(self,host=None,port=9123,force=0,**kwargs):
global _server
if not force and _server is not None:
self.server=_server
else:
if not host:
... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "rdkit/Chem/PyMol.py",
"copies": "1",
"size": "7617",
"license": "bsd-3-clause",
"hash": -6033795344289171000,
"line_mean": 29.8380566802,
"line_max": 102,
"alpha_frac": 0.616253118,
"autogenerated": false,
"ratio": 3.342255375164546,
"config_tes... |
from __future__ import print_function
from rdkit import RDConfig
import sys, os.path
from rdkit.VLib.Supply import SupplyNode
from rdkit.six.moves import cPickle
if RDConfig.usePgSQL:
from pyPgSQL import PgSQL as sql
class _lazyDataSeq:
"""
These classes are used to speed up (a lot) the process of
pul... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/VLib/NodeLib/DbPickleSupplier.py",
"copies": "5",
"size": "5791",
"license": "bsd-3-clause",
"hash": -1577467328491821800,
"line_mean": 26.7081339713,
"line_max": 88,
"alpha_frac": 0.5862545329,
"autogenerated": false,
"ratio": 3.6932397959183674,
... |
from rdkit import RDConfig
import os,sys
import unittest
from rdkit import Chem
from rdkit.Geometry import Point3D
def feq(v1,v2,tol2=1e-4):
return abs(v1-v2)<=tol2
def ptEq(pt1, pt2, tol=1e-4):
return feq(pt1.x,pt2.x,tol) and feq(pt1.y,pt2.y,tol) and feq(pt1.z,pt2.z,tol)
def addConf(mol):
conf = Chem.Conforme... | {
"repo_name": "rdkit/rdkit-orig",
"path": "Code/GraphMol/Wrap/testConformer.py",
"copies": "2",
"size": "3548",
"license": "bsd-3-clause",
"hash": 7824153832633648000,
"line_mean": 26.937007874,
"line_max": 79,
"alpha_frac": 0.6087936866,
"autogenerated": false,
"ratio": 2.6300963676797626,
"co... |
from rdkit import RDConfig
import os, sys
import unittest
from rdkit import Chem
from rdkit import Geometry
from rdkit.Geometry import Point3D
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
def ptEq(pt1, pt2, tol=1e-4):
return feq(pt1.x, pt2.x, tol) and feq(pt1.y, pt2.y, tol) and feq(pt1.z, pt2.z, tol)... | {
"repo_name": "rvianello/rdkit",
"path": "Code/GraphMol/Wrap/testConformer.py",
"copies": "6",
"size": "3871",
"license": "bsd-3-clause",
"hash": 5609444473556453000,
"line_mean": 25.8819444444,
"line_max": 100,
"alpha_frac": 0.6274864376,
"autogenerated": false,
"ratio": 2.6208530805687205,
"c... |
def ConstructEnsembleBV(bv,bitsToKeep):
"""
>>> from rdkit import DataStructs
>>> bv = DataStructs.ExplicitBitVect(128)
>>> bv.SetBitsFromList((1,5,47,99,120))
>>> r = ConstructEnsembleBV(bv,(0,1,2,3,45,46,47,48,49))
>>> r.GetNumBits()
9
>>> r.GetBit(0)
0
>>> r.GetBit(1)
1
>>> r.GetBit(5)
0
... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "rdkit/DataStructs/BitUtils.py",
"copies": "6",
"size": "1061",
"license": "bsd-3-clause",
"hash": 6826026387626297000,
"line_mean": 19.0188679245,
"line_max": 67,
"alpha_frac": 0.6041470311,
"autogenerated": false,
"ratio": 2.891008174386921,
"c... |
from __future__ import print_function
import copy
import struct
from rdkit.six import iterkeys
from rdkit import six
from rdkit import DataStructs
class VectCollection(object):
"""
>>> vc = VectCollection()
>>> bv1 = DataStructs.ExplicitBitVect(10)
>>> bv1.SetBitsFromList((1,3,5))
>>> vc.AddVect(1,bv1)
>... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/DataStructs/VectCollection.py",
"copies": "1",
"size": "6326",
"license": "bsd-3-clause",
"hash": 939121153869144400,
"line_mean": 21.5928571429,
"line_max": 92,
"alpha_frac": 0.5722415428,
"autogenerated": false,
"ratio": 2.8912248628884827,
"config... |
from __future__ import print_function
import copy,struct,sys
from rdkit.six.moves import cPickle
from rdkit.six import iterkeys
from rdkit import six
from rdkit import DataStructs
class VectCollection(object):
"""
>>> vc = VectCollection()
>>> bv1 = DataStructs.ExplicitBitVect(10)
>>> bv1.SetBitsFromList((1,3... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/DataStructs/VectCollection.py",
"copies": "1",
"size": "6312",
"license": "bsd-3-clause",
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"line_mean": 21.3038869258,
"line_max": 87,
"alpha_frac": 0.5739860583,
"autogenerated": false,
"ratio": 2.87693710118505,
"config... |
from rdkit.rdBase import EnableLog, DisableLog, AttachFileToLog, LogMessage
import sys, traceback
_levels = ['rdApp.debug', 'rdApp.info', 'rdApp.warning', 'rdApp.error']
DEBUG = 0
INFO = 1
WARNING = 2
ERROR = 3
CRITICAL = 4
class logger(object):
def logIt(self, dest, msg, *args, **kwargs):
if (args):
m... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/RDLogger.py",
"copies": "12",
"size": "1622",
"license": "bsd-3-clause",
"hash": 3278426643006919000,
"line_mean": 27.9642857143,
"line_max": 76,
"alpha_frac": 0.6251541307,
"autogenerated": false,
"ratio": 3.0317757009345794,
"config_test": false,
... |
from __future__ import print_function
from rdkit import Chem
import sys
from rdkit.Chem import Randomize
def TestMolecule(mol):
try:
Chem.SanitizeMol(mol)
mol = Chem.RemoveHs(mol)
except ValueError as msg:
return -1
except Exception:
import traceback
traceback.print_exc()
return -2
if ... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/ChemUtils/BulkTester.py",
"copies": "1",
"size": "2012",
"license": "bsd-3-clause",
"hash": -5640717515552599000,
"line_mean": 23.5365853659,
"line_max": 75,
"alpha_frac": 0.6197813121,
"autogenerated": false,
"ratio": 3.4275979557069847,
"confi... |
from __future__ import print_function
from rdkit import Chem
import sys
from rdkit.Chem import Randomize
def TestMolecule(mol):
try:
Chem.SanitizeMol(mol)
mol = Chem.RemoveHs(mol)
except ValueError as msg:
return -1
except Exception:
import traceback
traceback.print_exc()
return -2
if... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/ChemUtils/BulkTester.py",
"copies": "5",
"size": "2011",
"license": "bsd-3-clause",
"hash": 8403946734130894000,
"line_mean": 23.2289156627,
"line_max": 97,
"alpha_frac": 0.6200895077,
"autogenerated": false,
"ratio": 3.3912310286677907,
"con... |
from __future__ import print_function
_version = "$Rev$"
_splashMessage = """
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
FeatFinderCLI version %s
Copyright (C) 2005 Rational Discovery LLC
This software is copyrighted. The software may not be copied,
reproduced, translated or reduced to... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/FeatFinderCLI.py",
"copies": "1",
"size": "3262",
"license": "bsd-3-clause",
"hash": -8944519266990291000,
"line_mean": 27.3652173913,
"line_max": 82,
"alpha_frac": 0.6085223789,
"autogenerated": false,
"ratio": 3.191780821917808,
"config_test":... |
from rdkit import Chem
from rdkit.Chem import rdDepictor
from rdkit import Geometry
def AlignMolToTemplate2D(mol,template,match=None,clearConfs=False,
templateConfId=-1,):
"""
Arguments:
- mol: the molecule to be aligned
- template: the template to align to
- match: ... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/TemplateAlign.py",
"copies": "2",
"size": "3130",
"license": "bsd-3-clause",
"hash": 3981429026796701700,
"line_mean": 30.3,
"line_max": 102,
"alpha_frac": 0.6428115016,
"autogenerated": false,
"ratio": 3.1776649746192893,
"config_test": tru... |
from rdkit import Chem
from rdkit.Chem import rdDepictor
from rdkit import Geometry
def AlignMolToTemplate2D(mol,
template,
match=None,
clearConfs=False,
templateConfId=-1, ):
"""
Arguments:
- mol: the ... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/TemplateAlign.py",
"copies": "2",
"size": "3215",
"license": "bsd-3-clause",
"hash": -6950193799603544000,
"line_mean": 29.9134615385,
"line_max": 102,
"alpha_frac": 0.6258164852,
"autogenerated": false,
"ratio": 3.2540485829959516,
"config_t... |
from rdkit import Chem
import sys
from rdkit.Chem import Randomize
def TestMolecule(mol):
try:
Chem.SanitizeMol(mol)
mol = Chem.RemoveHs(mol)
except ValueError,msg:
return -1
except:
import traceback
traceback.print_exc()
return -2
if mol.GetNumAtoms():
try:
Randomize.CheckCan... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/ChemUtils/BulkTester.py",
"copies": "2",
"size": "1898",
"license": "bsd-3-clause",
"hash": -884859499107085300,
"line_mean": 22.725,
"line_max": 75,
"alpha_frac": 0.6111696523,
"autogenerated": false,
"ratio": 3.401433691756272,
"config_tes... |
import random
from rdkit import Chem
def RandomizeMolBlock(molB):
splitB = molB.split('\n')
res = []
res.extend(splitB[0:3])
idx = 3
inL = splitB[idx]
res.append(inL)
nAts = int(inL[0:3])
nBonds = int(inL[3:6])
idx+=1
atLines = splitB[idx:idx+nAts]
order = range(nAts)
random.shuffle(order)
... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Randomize.py",
"copies": "2",
"size": "1626",
"license": "bsd-3-clause",
"hash": 7852179043251908000,
"line_mean": 22.2285714286,
"line_max": 63,
"alpha_frac": 0.6402214022,
"autogenerated": false,
"ratio": 2.585055643879173,
"config_test": ... |
import random
from rdkit.six.moves import range
from rdkit import Chem
def RandomizeMolBlock(molB):
splitB = molB.split('\n')
res = []
res.extend(splitB[0:3])
idx = 3
inL = splitB[idx]
res.append(inL)
nAts = int(inL[0:3])
nBonds = int(inL[3:6])
idx+=1
atLines = splitB[idx:idx+nAts]
order = list... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/Chem/Randomize.py",
"copies": "4",
"size": "1688",
"license": "bsd-3-clause",
"hash": -4444090380005678600,
"line_mean": 22.7746478873,
"line_max": 63,
"alpha_frac": 0.6463270142,
"autogenerated": false,
"ratio": 2.613003095975232,
"config_test"... |
import random
from rdkit.six.moves import range
from rdkit import Chem
def RandomizeMolBlock(molB):
splitB = molB.split('\n')
res = []
res.extend(splitB[0:3])
idx = 3
inL = splitB[idx]
res.append(inL)
nAts = int(inL[0:3])
nBonds = int(inL[3:6])
idx += 1
atLines = splitB[idx:idx + nAts]
order =... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Randomize.py",
"copies": "5",
"size": "1704",
"license": "bsd-3-clause",
"hash": -4938258008736394000,
"line_mean": 22.6666666667,
"line_max": 63,
"alpha_frac": 0.640258216,
"autogenerated": false,
"ratio": 2.6175115207373274,
"config_test": fal... |
""" uses DSViewer to interact with molecules
"""
from rdkit import Chem
from win32com.client import Dispatch
import tempfile,os
_nextDisplayId=1
class Displayable(object):
def __init__(self,doc,id=-1):
global _nextDisplayId
if id<0:
id = _nextDisplayId
_nextDisplayId += 1
self.doc = doc
... | {
"repo_name": "strets123/rdkit",
"path": "rdkit/Chem/DSViewer.py",
"copies": "5",
"size": "12172",
"license": "bsd-3-clause",
"hash": 3953421219471895600,
"line_mean": 31.7204301075,
"line_max": 114,
"alpha_frac": 0.6196187972,
"autogenerated": false,
"ratio": 3.4123913652929634,
"config_test":... |
""" uses DSViewer to interact with molecules
"""
from rdkit import Chem
from win32com.client import Dispatch
import tempfile, os
_nextDisplayId = 1
class Displayable(object):
def __init__(self, doc, id=-1):
global _nextDisplayId
if id < 0:
id = _nextDisplayId
_nextDisplayId += 1
self.doc... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/DSViewer.py",
"copies": "5",
"size": "12113",
"license": "bsd-3-clause",
"hash": -6413528897471017000,
"line_mean": 31.6495956873,
"line_max": 100,
"alpha_frac": 0.6223891687,
"autogenerated": false,
"ratio": 3.370339454646633,
"config_test":... |
_version = "$Rev$"
_splashMessage="""
-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*-*
FeatFinderCLI version %s
Copyright (C) 2005 Rational Discovery LLC
This software is copyrighted. The software may not be copied,
reproduced, translated or reduced to any electronic medium or
machine-reada... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/FeatFinderCLI.py",
"copies": "2",
"size": "3166",
"license": "bsd-3-clause",
"hash": 6317289670174538000,
"line_mean": 25.8305084746,
"line_max": 79,
"alpha_frac": 0.6099178774,
"autogenerated": false,
"ratio": 3.1851106639839033,
"config_te... |
from rdkit import RDConfig
import unittest,os,sys
from rdkit.ML.DecTree.SigTree import SigTreeNode
from rdkit.ML import InfoTheory
from rdkit.DataStructs import ExplicitBitVect
from rdkit.DataStructs.VectCollection import VectCollection
class TestCase(unittest.TestCase):
def setUp(self):
t1 = SigTreeNode(None,'r... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/ML/DecTree/UnitTestSigTree.py",
"copies": "4",
"size": "3894",
"license": "bsd-3-clause",
"hash": -8748136318955324000,
"line_mean": 23.8025477707,
"line_max": 78,
"alpha_frac": 0.6325115562,
"autogenerated": false,
"ratio": 2.8014388489208635,
"conf... |
import gzip
import os
import unittest
from rdkit import RDConfig
from rdkit.DataStructs import ExplicitBitVect
from rdkit.DataStructs.VectCollection import VectCollection
from rdkit.ML import InfoTheory
from rdkit.ML.DecTree.BuildSigTree import BuildSigTree, _GenerateRandomEnsemble
from rdkit.ML.DecTree.SigTree import... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/ML/DecTree/UnitTestSigTree.py",
"copies": "4",
"size": "4513",
"license": "bsd-3-clause",
"hash": -7371638601603785000,
"line_mean": 24.9367816092,
"line_max": 97,
"alpha_frac": 0.6456902282,
"autogenerated": false,
"ratio": 2.863578680203046,
"co... |
__doc__ = """hashlib module - A common interface to many hash functions.
new(name, string='') - returns a new hash object implementing the
given hash function; initializing the hash
using the given string data.
Named constructor functions are also available, these are mu... | {
"repo_name": "johnkeepmoving/oss-ftp",
"path": "python27/win32/Lib/hashlib.py",
"copies": "51",
"size": "7842",
"license": "mit",
"hash": 1618744083514250200,
"line_mean": 34.4841628959,
"line_max": 84,
"alpha_frac": 0.6169344555,
"autogenerated": false,
"ratio": 3.9466532460996477,
"config_te... |
""" for the moment this is using Francois Fleuret's cmim library
to do the feature selection
Reference: F. Fleuret "Fast Binary Feature Selection with Conditional
Mutual Information", J. Machine Learn. Res. 5, 1531-1535
(2004)
"""
from rdkit import RDConfig
from rdkit import DataStructs
im... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/ML/FeatureSelect/CMIM.py",
"copies": "2",
"size": "1551",
"license": "bsd-3-clause",
"hash": 7530698759182581000,
"line_mean": 24.0161290323,
"line_max": 75,
"alpha_frac": 0.6718246293,
"autogenerated": false,
"ratio": 2.9154135338345863,
"config... |
class LazySig:
def __init__(self,computeFunc,sigSize):
"""
computeFunc should take a single argument, the integer bit id
to compute
"""
if sigSize<=0:
raise ValueError('zero size')
self.computeFunc=computeFunc
self.size=sigSize
self._cache={}
def __len__(self):
"""
... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/DataStructs/LazySignature.py",
"copies": "1",
"size": "1391",
"license": "bsd-3-clause",
"hash": 843844296093386600,
"line_mean": 15.9634146341,
"line_max": 65,
"alpha_frac": 0.4996405464,
"autogenerated": false,
"ratio": 3.5850515463917527,
"config_... |
class LazySig:
def __init__(self, computeFunc, sigSize):
"""
computeFunc should take a single argument, the integer bit id
to compute
"""
if sigSize <= 0:
raise ValueError('zero size')
self.computeFunc = computeFunc
self.size = sigSize
self._cache = {}
def __len__(self):
... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/DataStructs/LazySignature.py",
"copies": "12",
"size": "1472",
"license": "bsd-3-clause",
"hash": -49117080255145340,
"line_mean": 16.734939759,
"line_max": 76,
"alpha_frac": 0.5149456522,
"autogenerated": false,
"ratio": 3.607843137254902,
"confi... |
from __future__ import print_function
import os, sys
import io
import unittest
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures
from rdkit.Geometry import rdGeometry as geom
def feq(v1, v2, tol2=1e-4):
return abs(v1 - v2) <= tol2
def lst... | {
"repo_name": "rvianello/rdkit",
"path": "Code/ChemicalFeatures/Wrap/testFeatures.py",
"copies": "5",
"size": "4279",
"license": "bsd-3-clause",
"hash": 3779023811508788000,
"line_mean": 35.2627118644,
"line_max": 119,
"alpha_frac": 0.6375321337,
"autogenerated": false,
"ratio": 2.986043265875785... |
from __future__ import print_function
import os,sys
import unittest
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import ChemicalFeatures
from rdkit.Geometry import rdGeometry as geom
def feq(v1,v2,tol2=1e-4):
return abs(v1-v2)<=tol2
def lstFeq(l1, l2, tol=1.e... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "Code/ChemicalFeatures/Wrap/testFeatures.py",
"copies": "1",
"size": "4027",
"license": "bsd-3-clause",
"hash": 608325846380943700,
"line_mean": 37.7211538462,
"line_max": 134,
"alpha_frac": 0.6481251552,
"autogenerated": false,
"ratio": 2.96539027... |
""" Import all RDKit chemistry modules
"""
from rdkit import rdBase
from rdkit import RDConfig
from rdkit import DataStructs
from rdkit.Geometry import rdGeometry
from rdkit.Chem import *
from rdkit.Chem.rdPartialCharges import *
from rdkit.Chem.rdDepictor import *
from rdkit.Chem.rdForceFieldHelpers import *
from rdk... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/Chem/AllChem.py",
"copies": "1",
"size": "19475",
"license": "bsd-3-clause",
"hash": 264373935059233470,
"line_mean": 36.2370936902,
"line_max": 145,
"alpha_frac": 0.6744544288,
"autogenerated": false,
"ratio": 3.3393347050754456,
"config_test":... |
import os
from rdkit.six import iteritems
from rdkit.Chem.Draw.MolDrawing import MolDrawing,DrawingOptions
from rdkit.Chem.Draw.rdMolDraw2D import *
def _getCanvas():
useAGG=False
useCairo=False
useSping=False
Canvas=None
if not os.environ.get('RDKIT_CANVAS',''):
try:
from rdkit.Chem.Draw.cairoCanv... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/Chem/Draw/__init__.py",
"copies": "2",
"size": "11955",
"license": "bsd-3-clause",
"hash": -6749942334766245000,
"line_mean": 29.9715025907,
"line_max": 108,
"alpha_frac": 0.6625679632,
"autogenerated": false,
"ratio": 3.114092211513415,
"config... |
import os
def _getCanvas():
useAGG=False
useCairo=False
Canvas=None
if not os.environ.get('RDKIT_CANVAS',''):
try:
from cairoCanvas import Canvas
useCairo=True
except ImportError:
try:
from aggCanvas import Canvas
useAGG=True
except ImportError:
from spin... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Draw/__init__.py",
"copies": "1",
"size": "8895",
"license": "bsd-3-clause",
"hash": -2760273108516460000,
"line_mean": 29.4623287671,
"line_max": 106,
"alpha_frac": 0.671950534,
"autogenerated": false,
"ratio": 2.9473161033797215,
"config_t... |
from rdkit.Chem.FeatMaps.FeatMapPoint import FeatMapPoint
import math
class FeatMapScoreMode(object):
All = 0
""" score each feature in the probe against every matching
feature in the FeatMap.
"""
Closest = 1
""" score each feature in the probe against the closest
matching feature in the FeatMa... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/FeatMaps/FeatMaps.py",
"copies": "12",
"size": "7458",
"license": "bsd-3-clause",
"hash": -6629856976347529000,
"line_mean": 29.3170731707,
"line_max": 97,
"alpha_frac": 0.6427996782,
"autogenerated": false,
"ratio": 3.435283279594657,
"config_t... |
from rdkit import Geometry
from rdkit.Chem.FeatMaps import FeatMaps, FeatMapPoint
import re
"""
ScoreMode=All
DirScoreMode=Ignore
BeginParams
family=Aromatic radius=2.5 width=1.0 profile=Gaussian
family=Acceptor radius=1.5
EndParams
# optional
BeginPoints
family=Acceptor pos=(1.0, 0.0, 5.0) weight=1.25 dir=(1,... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/FeatMaps/FeatMapParser.py",
"copies": "12",
"size": "5307",
"license": "bsd-3-clause",
"hash": 5239492474791536000,
"line_mean": 26.7853403141,
"line_max": 100,
"alpha_frac": 0.5577539099,
"autogenerated": false,
"ratio": 3.5498327759197323,
"co... |
from rdkit import Geometry
from rdkit.Chem import ChemicalFeatures
from rdkit.Chem.FeatMaps import FeatMaps,FeatMapPoint
import re
"""
ScoreMode=All
DirScoreMode=Ignore
BeginParams
family=Aromatic radius=2.5 width=1.0 profile=Gaussian
family=Acceptor radius=1.5
EndParams
# optional
BeginPoints
family=Acceptor... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/FeatMaps/FeatMapParser.py",
"copies": "2",
"size": "5354",
"license": "bsd-3-clause",
"hash": 1657975308928289800,
"line_mean": 25.9045226131,
"line_max": 105,
"alpha_frac": 0.5821815465,
"autogenerated": false,
"ratio": 3.481144343302991,
"... |
import copy
from rdkit.Chem.FeatMaps import FeatMaps
class MergeMethod(object):
# Put the new point at the weighted average position of the two fused points
WeightedAverage = 0
# Put the new point at the un-weighted average position of the two fused points
Average = 1
# Put the new point at the position of ... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/FeatMaps/FeatMapUtils.py",
"copies": "12",
"size": "7261",
"license": "bsd-3-clause",
"hash": 8989646949305047000,
"line_mean": 29.5084033613,
"line_max": 95,
"alpha_frac": 0.6412339898,
"autogenerated": false,
"ratio": 3.5733267716535435,
"c... |
import unittest,os,sys
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit import Chem
from rdkit import DataStructs
from rdkit.Chem import MolCatalog
class TestCase(unittest.TestCase):
def test1(self):
cat = MolCatalog.CreateMolCatalog()
es = []
for smi in ('C1CCC1OC','C1CCC1','C')... | {
"repo_name": "strets123/rdkit",
"path": "Code/GraphMol/MolCatalog/Wrap/rough_test.py",
"copies": "4",
"size": "1285",
"license": "bsd-3-clause",
"hash": 2677997044440974300,
"line_mean": 21.1551724138,
"line_max": 50,
"alpha_frac": 0.6435797665,
"autogenerated": false,
"ratio": 2.920454545454545... |
import unittest, os, sys
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit import Chem
from rdkit import DataStructs
from rdkit.Chem import MolCatalog
class TestCase(unittest.TestCase):
def test1(self):
cat = MolCatalog.CreateMolCatalog()
es = []
for smi in ('C1CCC1OC', 'C1CCC1'... | {
"repo_name": "rvianello/rdkit",
"path": "Code/GraphMol/MolCatalog/Wrap/rough_test.py",
"copies": "5",
"size": "1303",
"license": "bsd-3-clause",
"hash": -4307203768100849000,
"line_mean": 22.2678571429,
"line_max": 52,
"alpha_frac": 0.6346891788,
"autogenerated": false,
"ratio": 2.96810933940774... |
from __future__ import print_function
from rdkit import RDLogger
logger = RDLogger.logger()
from rdkit import Chem, Geometry
import numpy
from rdkit.Numerics import Alignment
from rdkit.Chem.Subshape import SubshapeObjects
class SubshapeAlignment(object):
transform = None
triangleSSD = None
targetTri = None
... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Subshape/SubshapeAligner.py",
"copies": "1",
"size": "13420",
"license": "bsd-3-clause",
"hash": -5043293890927798000,
"line_mean": 36.8028169014,
"line_max": 99,
"alpha_frac": 0.6524590164,
"autogenerated": false,
"ratio": 3.286798922361009,
"c... |
from rdkit import RDLogger
logger = RDLogger.logger()
from rdkit import Chem,Geometry
import numpy
from rdkit.Numerics import Alignment
from rdkit.Chem.Subshape import SubshapeObjects
class SubshapeAlignment(object):
transform=None
triangleSSD=None
targetTri=None
queryTri=None
alignedConfId=-1
dirMatch=0.0... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Subshape/SubshapeAligner.py",
"copies": "2",
"size": "13196",
"license": "bsd-3-clause",
"hash": 552674047822483100,
"line_mean": 36.4886363636,
"line_max": 108,
"alpha_frac": 0.6615641103,
"autogenerated": false,
"ratio": 3.2842210054753607,
... |
""" Implementation of the clustering algorithm published in:
Butina JCICS 39 747-750 (1999)
"""
import numpy
from rdkit import RDLogger
logger=RDLogger.logger()
def EuclideanDist(pi,pj):
dv = numpy.array(pi)- numpy.array(pj)
return numpy.sqrt(dv*dv)
def ClusterData(data,nPts,distThresh,isDistData=False,di... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/ML/Cluster/Butina.py",
"copies": "2",
"size": "2393",
"license": "bsd-3-clause",
"hash": -7361614801745215000,
"line_mean": 25.8876404494,
"line_max": 78,
"alpha_frac": 0.6130380276,
"autogenerated": false,
"ratio": 3.5663189269746645,
"config_te... |
""" Implementation of the clustering algorithm published in:
Butina JCICS 39 747-750 (1999)
"""
import numpy
from rdkit import RDLogger
logger = RDLogger.logger()
def EuclideanDist(pi, pj):
dv = numpy.array(pi) - numpy.array(pj)
return numpy.sqrt(dv * dv)
def ClusterData(data, nPts, distThresh, isDistData=Fa... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/ML/Cluster/Butina.py",
"copies": "1",
"size": "3551",
"license": "bsd-3-clause",
"hash": -6320237006247684000,
"line_mean": 30.149122807,
"line_max": 100,
"alpha_frac": 0.6212334554,
"autogenerated": false,
"ratio": 3.683609958506224,
"config_test": ... |
import unittest
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit.ML.Cluster import Butina
class TestCase(unittest.TestCase):
def test1(self):
dists = [1, 2, 1, 4, 3, 2, 6, 5, 4, 2, 7, 6, 5, 3, 1]
nPts = 6
cs = Butina.ClusterData(dists, nPts, 1.1, isDistData=1)
self.assertT... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/ML/Cluster/UnitTestButina.py",
"copies": "1",
"size": "4057",
"license": "bsd-3-clause",
"hash": 8340812294716463000,
"line_mean": 21.6648044693,
"line_max": 76,
"alpha_frac": 0.4269164407,
"autogenerated": false,
"ratio": 3.0230998509687033,
"config... |
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Lipinski,Descriptors,Crippen
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbModule
import re
#set up the logger:
import rdkit.RDLogger as logging
logger = logging.logger()
logger.setLevel(logging.INFO)
def ProcessMo... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/MolDb/Loader_orig.py",
"copies": "1",
"size": "6608",
"license": "bsd-3-clause",
"hash": -8750633315164838000,
"line_mean": 30.317535545,
"line_max": 92,
"alpha_frac": 0.6372578692,
"autogenerated": false,
"ratio": 3.209324915007285,
"config_tes... |
from rdkit import Chem
from rdkit.Chem import AllChem
from rdkit.Chem import Lipinski, Descriptors, Crippen
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbModule
import re
#set up the logger:
import rdkit.RDLogger as logging
logger = logging.logger()
logger.setLevel(logging.INFO)
def Proces... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/MolDb/Loader_orig.py",
"copies": "12",
"size": "6741",
"license": "bsd-3-clause",
"hash": 645975154123385900,
"line_mean": 30.9478672986,
"line_max": 99,
"alpha_frac": 0.6246847649,
"autogenerated": false,
"ratio": 3.220735785953177,
"config_... |
import os
import io
import sys
import unittest
from rdkit import RDConfig
#import pickle
from rdkit.six.moves import cPickle as pickle
from rdkit import DataStructs as ds
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def test1Discrete(self):
v1 = ds.DiscreteValueVect(ds.DiscreteValueType.ONEB... | {
"repo_name": "soerendip42/rdkit",
"path": "Code/DataStructs/Wrap/testDiscreteValueVect.py",
"copies": "3",
"size": "7784",
"license": "bsd-3-clause",
"hash": -1170882445160915700,
"line_mean": 28.7099236641,
"line_max": 96,
"alpha_frac": 0.6202466598,
"autogenerated": false,
"ratio": 2.654843110... |
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