text stringlengths 0 1.05M | meta dict |
|---|---|
from rdkit import Chem
from rdkit.Chem import rdPartialCharges
import collections
def _isCallable(thing):
return (hasattr(collections,'Callable') and isinstance(thing,collections.Callable)) or \
hasattr(thing,'__call__')
_descList=[]
def _setupDescriptors(namespace):
global _descList,descList
f... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/Chem/Descriptors.py",
"copies": "2",
"size": "5043",
"license": "bsd-3-clause",
"hash": 2475738674977472000,
"line_mean": 25.6825396825,
"line_max": 102,
"alpha_frac": 0.6859012493,
"autogenerated": false,
"ratio": 2.847543760587239,
"config_tes... |
""" SMARTS definitions for the publically available MACCS keys
and a MACCS fingerprinter
I compared the MACCS fingerprints generated here with those from two
other packages (not MDL, unfortunately). Of course there are
disagreements between the various fingerprints still, but I think
these definitions work pretty well... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "rdkit/Chem/MACCSkeys.py",
"copies": "3",
"size": "11266",
"license": "bsd-3-clause",
"hash": -340494744810183800,
"line_mean": 36.1815181518,
"line_max": 426,
"alpha_frac": 0.4567725901,
"autogenerated": false,
"ratio": 1.9264705882352942,
"conf... |
""" functionality for drawing trees on sping canvases
"""
from rdkit.sping import pid as piddle
import math
class VisOpts(object):
circRad = 10
minCircRad = 4
maxCircRad = 16
circColor = piddle.Color(0.6,0.6,0.9)
terminalEmptyColor = piddle.Color(.8,.8,.2)
terminalOnColor = piddle.Color(0.8,0.8,0.8)
... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/ML/DecTree/TreeVis.py",
"copies": "1",
"size": "6400",
"license": "bsd-3-clause",
"hash": -1397623682040078600,
"line_mean": 27.5714285714,
"line_max": 85,
"alpha_frac": 0.65921875,
"autogenerated": false,
"ratio": 3.063666826232647,
"config_test": f... |
""" functionality for drawing trees on sping canvases
"""
from rdkit.sping import pid as piddle
import math
class VisOpts(object):
circRad = 10
minCircRad = 4
maxCircRad = 16
circColor = piddle.Color(0.6, 0.6, 0.9)
terminalEmptyColor = piddle.Color(.8, .8, .2)
terminalOnColor = piddle.Color(0.8, 0.8, 0.8... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/ML/DecTree/TreeVis.py",
"copies": "1",
"size": "6387",
"license": "bsd-3-clause",
"hash": -8702271723224396000,
"line_mean": 27.0131578947,
"line_max": 100,
"alpha_frac": 0.6605605135,
"autogenerated": false,
"ratio": 3.037089871611983,
"config_test"... |
""" functionality for drawing trees on sping canvases
"""
import math
from rdkit.sping import pid as piddle
class VisOpts(object):
circRad = 10
minCircRad = 4
maxCircRad = 16
circColor = piddle.Color(0.6, 0.6, 0.9)
terminalEmptyColor = piddle.Color(.8, .8, .2)
terminalOnColor = piddle.Color(0.8, 0.8, 0.... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/ML/DecTree/TreeVis.py",
"copies": "11",
"size": "6394",
"license": "bsd-3-clause",
"hash": 5713088176838420000,
"line_mean": 26.9213973799,
"line_max": 100,
"alpha_frac": 0.6598373475,
"autogenerated": false,
"ratio": 3.0375296912114016,
"config_t... |
""" primitive license handler
License file format:
(lines beginning with # are ignored)
Expiration_Date: <expiration date of license>
Verification: <verification code>
Date format: day-month-year
The verification code is used to ensure that the date
has not been tampered with
"""
import sha,base64,t... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/utils/Licensing.py",
"copies": "2",
"size": "3541",
"license": "bsd-3-clause",
"hash": -3565820362353905000,
"line_mean": 25.4253731343,
"line_max": 75,
"alpha_frac": 0.6447331262,
"autogenerated": false,
"ratio": 3.48180924287119,
"config_test":... |
""" Basic EState definitions
"""
from __future__ import print_function
import numpy
from rdkit import Chem
def GetPrincipleQuantumNumber(atNum):
if atNum<=2: return 1
elif atNum <= 10: return 2
elif atNum <= 18: return 3
elif atNum <= 36: return 4
elif atNum <= 54: return 5
elif atNum <= 86: return 6
el... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "rdkit/Chem/EState/EState.py",
"copies": "4",
"size": "2309",
"license": "bsd-3-clause",
"hash": 306969762627453250,
"line_mean": 25.2386363636,
"line_max": 71,
"alpha_frac": 0.6569943699,
"autogenerated": false,
"ratio": 2.7132784958871916,
"con... |
""" Basic EState definitions
"""
from __future__ import print_function
import numpy
from rdkit import Chem
def GetPrincipleQuantumNumber(atNum):
""" Get principal quantum number for atom number """
if atNum <= 2:
return 1
elif atNum <= 10:
return 2
elif atNum <= 18:
return 3
elif atNum <= 36:
... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/EState/EState.py",
"copies": "5",
"size": "2569",
"license": "bsd-3-clause",
"hash": -3868424661285106000,
"line_mean": 21.1465517241,
"line_max": 75,
"alpha_frac": 0.6360451538,
"autogenerated": false,
"ratio": 2.804585152838428,
"config_test":... |
""" Basic EState definitions
"""
import numpy
from rdkit import Chem
def GetPrincipleQuantumNumber(atNum):
if atNum<=2: return 1
elif atNum <= 10: return 2
elif atNum <= 18: return 3
elif atNum <= 36: return 4
elif atNum <= 54: return 5
elif atNum <= 86: return 6
else: return 7
def EStateIndices(mol... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/EState/EState.py",
"copies": "1",
"size": "1801",
"license": "bsd-3-clause",
"hash": -3043713140537822000,
"line_mean": 24.3661971831,
"line_max": 71,
"alpha_frac": 0.6307606885,
"autogenerated": false,
"ratio": 2.7836166924265844,
"config_t... |
""" contains a class to store parameters for and results from
Composite building
"""
from rdkit import RDConfig
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase import DbModule
def SetDefaults(runDetails):
""" initializes a details object with default values
**Arguments**
- details:... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/ML/CompositeRun.py",
"copies": "11",
"size": "6898",
"license": "bsd-3-clause",
"hash": -724083832772147800,
"line_mean": 27.622406639,
"line_max": 93,
"alpha_frac": 0.6171354016,
"autogenerated": false,
"ratio": 3.585239085239085,
"config_test": ... |
""" contains a class to store parameters for and results from
Composite building
"""
from rdkit import RDConfig
from rdkit.Dbase.DbConnection import DbConnect
from rdkit import DataStructs
from rdkit.Dbase import DbModule
##from rdkit.ML.SVM import SVMClassificationModel as SVM
def SetDefaults(runDetails):
""" i... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/ML/CompositeRun.py",
"copies": "1",
"size": "6791",
"license": "bsd-3-clause",
"hash": -8996916720078619000,
"line_mean": 26.4939271255,
"line_max": 93,
"alpha_frac": 0.6440877632,
"autogenerated": false,
"ratio": 3.5041279669762644,
"config_test": f... |
""" contains SMARTS definitions and calculators for EState atom types
defined in: Hall and Kier JCICS _35_ 1039-1045 (1995) Table 1
"""
from rdkit import Chem
_rawD = [
('sLi','[LiD1]-*'),
('ssBe','[BeD2](-*)-*'),
('ssssBe','[BeD4](-*)(-*)(-*)-*'),
('ssBH', '[BD2H](-*)-*'),
('sssB', '[BD3](-*)(-*)-*'),
... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/EState/AtomTypes.py",
"copies": "5",
"size": "4037",
"license": "bsd-3-clause",
"hash": -2913885408653060000,
"line_mean": 24.0745341615,
"line_max": 93,
"alpha_frac": 0.4357195938,
"autogenerated": false,
"ratio": 2.0906266183324704,
"confi... |
""" contains SMARTS definitions and calculators for EState atom types
defined in: Hall and Kier JCICS _35_ 1039-1045 (1995) Table 1
"""
from rdkit import Chem
_rawD = [
('sLi', '[LiD1]-*'),
('ssBe', '[BeD2](-*)-*'),
('ssssBe', '[BeD4](-*)(-*)(-*)-*'),
('ssBH', '[BD2H](-*)-*'),
('sssB', '[BD3](-*)(-*)-*'),... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/EState/AtomTypes.py",
"copies": "12",
"size": "4018",
"license": "bsd-3-clause",
"hash": 4815898734133917000,
"line_mean": 26.9027777778,
"line_max": 96,
"alpha_frac": 0.4385266302,
"autogenerated": false,
"ratio": 2.0970772442588728,
"config... |
"""
unit testing code for the SD file handling stuff
"""
import os
import tempfile
import unittest
from rdkit import Chem
from rdkit import RDConfig
from rdkit.six import next
class TestCase(unittest.TestCase):
def setUp(self):
self.fName = os.path.join(RDConfig.RDDataDir, 'NCI', 'first_200.props.sdf')
wi... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/Suppliers/UnitTestSDMolSupplier.py",
"copies": "4",
"size": "5319",
"license": "bsd-3-clause",
"hash": -8817616385638454000,
"line_mean": 28.55,
"line_max": 80,
"alpha_frac": 0.6036849032,
"autogenerated": false,
"ratio": 3.0290432801822322,
... |
"""unit testing code for the SD file handling stuff
"""
import unittest,sys,os
from rdkit import RDConfig
from rdkit import Chem
import tempfile
from cStringIO import StringIO
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
self.fName = os.path.join(RDConfig.RDD... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Suppliers/UnitTestSDMolSupplier.py",
"copies": "2",
"size": "4271",
"license": "bsd-3-clause",
"hash": -1353290518686127600,
"line_mean": 24.4226190476,
"line_max": 77,
"alpha_frac": 0.6019667525,
"autogenerated": false,
"ratio": 3.14970501474... |
""" tools for interacting with chemdraw
"""
from __future__ import print_function
import string,tempfile,os,time
try:
import pythoncom
from win32com.client import gencache,Dispatch,constants
import win32com.client.gencache
cdxModule = win32com.client.gencache.EnsureModule("{5F646AAB-3B56-48D2-904C-A68D7989C25... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/utils/chemdraw.py",
"copies": "1",
"size": "11711",
"license": "bsd-3-clause",
"hash": 1579553171053144300,
"line_mean": 26.3621495327,
"line_max": 102,
"alpha_frac": 0.6540859021,
"autogenerated": false,
"ratio": 3.278555431131019,
"config_test": fa... |
""" tools for interacting with chemdraw
"""
from __future__ import print_function
import string, tempfile, os, time
try:
import pythoncom
from win32com.client import gencache, Dispatch, constants
import win32com.client.gencache
cdxModule = win32com.client.gencache.EnsureModule("{5F646AAB-3B56-48D2-904C-A68D79... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/utils/chemdraw.py",
"copies": "1",
"size": "11869",
"license": "bsd-3-clause",
"hash": 7721305097626846000,
"line_mean": 25.4933035714,
"line_max": 99,
"alpha_frac": 0.6453787177,
"autogenerated": false,
"ratio": 3.2969444444444442,
"config_test": fa... |
""" tools for interacting with chemdraw
"""
from __future__ import print_function
import tempfile, os, time
try:
import pythoncom
from win32com.client import gencache, Dispatch, constants
import win32com.client.gencache
cdxModule = win32com.client.gencache.EnsureModule("{5F646AAB-3B56-48D2-904C-A68D7989C251}"... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/utils/chemdraw.py",
"copies": "4",
"size": "11837",
"license": "bsd-3-clause",
"hash": 4634962496583773000,
"line_mean": 25.421875,
"line_max": 99,
"alpha_frac": 0.6450958858,
"autogenerated": false,
"ratio": 3.2972144846796656,
"config_test": fal... |
""" tools for interacting with chemdraw
"""
import string,tempfile,os,time
try:
import pythoncom
from win32com.client import gencache,Dispatch,constants
import win32com.client.gencache
cdxModule = win32com.client.gencache.EnsureModule("{5F646AAB-3B56-48D2-904C-A68D7989C251}", 0, 7, 0)
except:
cdxModule = Non... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/utils/chemdraw.py",
"copies": "2",
"size": "11604",
"license": "bsd-3-clause",
"hash": -1931042545943586300,
"line_mean": 26.2394366197,
"line_max": 102,
"alpha_frac": 0.6533092037,
"autogenerated": false,
"ratio": 3.2678118839763446,
"config_tes... |
""" unit testing code for surface calculations
FIX: add tests for LabuteASA
"""
from __future__ import print_function
from rdkit import RDConfig
import unittest, os
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import MolSurf
import os.path
def feq(n1, n2, tol=1e-4):
return abs(n1 - n... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/UnitTestSurf.py",
"copies": "1",
"size": "4259",
"license": "bsd-3-clause",
"hash": -8525855581562437000,
"line_mean": 29.4214285714,
"line_max": 99,
"alpha_frac": 0.5632777647,
"autogenerated": false,
"ratio": 2.990870786516854,
"config_test": ... |
"""unit testing code for the Crippen clogp and MR calculators
"""
from __future__ import print_function
from rdkit import RDConfig
import unittest,sys,os
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Crippen
def feq(n1,n2,tol=1e-5):
return abs(n1-n2)<=tol
class TestCase(unittest... | {
"repo_name": "strets123/rdkit",
"path": "rdkit/Chem/UnitTestArom.py",
"copies": "3",
"size": "3129",
"license": "bsd-3-clause",
"hash": -156726008307118560,
"line_mean": 26.6902654867,
"line_max": 92,
"alpha_frac": 0.5343560243,
"autogenerated": false,
"ratio": 3.245850622406639,
"config_test"... |
"""unit testing code for the Crippen clogp and MR calculators
"""
from __future__ import print_function
from rdkit import RDConfig
import unittest, sys, os
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Crippen
def feq(n1, n2, tol=1e-5):
return abs(n1 - n2) <= tol
class TestCas... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/UnitTestArom.py",
"copies": "1",
"size": "3001",
"license": "bsd-3-clause",
"hash": -2269021845948288800,
"line_mean": 29.01,
"line_max": 94,
"alpha_frac": 0.5384871709,
"autogenerated": false,
"ratio": 3.1589473684210527,
"config_test": true,
... |
"""unit testing code for the database utilities
"""
from rdkit import RDConfig
import unittest, os, tempfile
from rdkit.Dbase import DbUtils
from rdkit.Dbase.DbConnection import DbConnect
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
self.baseDir = os.path.jo... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Dbase/UnitTestDbUtils.py",
"copies": "1",
"size": "4183",
"license": "bsd-3-clause",
"hash": -6682755154841806000,
"line_mean": 30.4511278195,
"line_max": 95,
"alpha_frac": 0.635190055,
"autogenerated": false,
"ratio": 3.2176923076923076,
"config_tes... |
"""unit testing code for the database utilities
"""
import os
import tempfile
import unittest
from six import StringIO
from rdkit import RDConfig
from rdkit.Dbase import DbUtils
from rdkit.Dbase.DbConnection import DbConnect
try:
from contextlib import redirect_stdout
except:
from rdkit.TestRunner import redire... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Dbase/UnitTestDbUtils.py",
"copies": "1",
"size": "7275",
"license": "bsd-3-clause",
"hash": 8602061904287650000,
"line_mean": 31.6233183857,
"line_max": 96,
"alpha_frac": 0.6328522337,
"autogenerated": false,
"ratio": 3.200615926088869,
"config_t... |
"""unit testing code for the EState fingerprinting
validation values are from the paper (JCICS _35_ 1039-1045 (1995))
"""
from __future__ import print_function
import unittest
import numpy
from rdkit import Chem
from rdkit.Chem import EState
from rdkit.Chem.EState import Fingerprinter
class TestCase(unittest.TestCas... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/Chem/EState/UnitTestFingerprints.py",
"copies": "4",
"size": "1628",
"license": "bsd-3-clause",
"hash": -6992751113901026000,
"line_mean": 27.5614035088,
"line_max": 69,
"alpha_frac": 0.6222358722,
"autogenerated": false,
"ratio": 2.75932203389830... |
"""unit testing code for the EState indices
validation values are from the paper (JCICS _31_ 76-81 (1991))
"""
from __future__ import print_function
import unittest
import numpy
from rdkit import Chem
from rdkit.Chem import EState
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDe... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/Chem/EState/UnitTestEState.py",
"copies": "4",
"size": "3044",
"license": "bsd-3-clause",
"hash": -4891856366484477000,
"line_mean": 28.8431372549,
"line_max": 95,
"alpha_frac": 0.5384362681,
"autogenerated": false,
"ratio": 2.1742857142857144,
... |
"""unit testing code for the EState indices
validation values are from the paper (JCICS _31_ 76-81 (1991))
"""
from __future__ import print_function
import unittest
from six import StringIO
import numpy as np
from rdkit import Chem
from rdkit.Chem import EState
class TestCase(unittest.TestCase):
def _compareE... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/EState/UnitTestEState.py",
"copies": "1",
"size": "5001",
"license": "bsd-3-clause",
"hash": 3484069669075651600,
"line_mean": 34.4680851064,
"line_max": 100,
"alpha_frac": 0.5852829434,
"autogenerated": false,
"ratio": 2.468410661401777,
"confi... |
"""unit testing code for the signatures
"""
from __future__ import print_function
import unittest
import os
from rdkit.six import next
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem.Pharm2D import Gobbi_Pharm2D,Generate
class TestCase(unittest.TestCase):
def setUp(self):
self.factory = Gobbi_... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/Pharm2D/UnitTestGobbi.py",
"copies": "3",
"size": "5982",
"license": "bsd-3-clause",
"hash": 5901374106605671000,
"line_mean": 31.6885245902,
"line_max": 89,
"alpha_frac": 0.4622199933,
"autogenerated": false,
"ratio": 3.1401574803149606,
"confi... |
"""unit testing code for the signatures
"""
import unittest
import os
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem.Pharm2D import Gobbi_Pharm2D,Generate
class TestCase(unittest.TestCase):
def setUp(self):
self.factory = Gobbi_Pharm2D.factory
def test1Sigs(self):
probes = [
('OC... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Pharm2D/UnitTestGobbi.py",
"copies": "2",
"size": "5463",
"license": "bsd-3-clause",
"hash": -6044508081593510000,
"line_mean": 31.1352941176,
"line_max": 89,
"alpha_frac": 0.449752883,
"autogenerated": false,
"ratio": 3.2003514938488578,
"c... |
""" utility functionality for the 2D pharmacophores code
See Docs/Chem/Pharm2D.triangles.jpg for an illustration of the way
pharmacophores are broken into triangles and labelled.
See Docs/Chem/Pharm2D.signatures.jpg for an illustration of bit
numbering
"""
import numpy
#
# number of points in a scaffold ->... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Pharm2D/Utils.py",
"copies": "2",
"size": "11067",
"license": "bsd-3-clause",
"hash": 1399642563091505200,
"line_mean": 24.3830275229,
"line_max": 78,
"alpha_frac": 0.5827234119,
"autogenerated": false,
"ratio": 2.905487004463114,
"config_te... |
""" Atom-based calculation of LogP and MR using Crippen's approach
Reference:
S. A. Wildman and G. M. Crippen *JCICS* _39_ 868-873 (1999)
"""
from __future__ import print_function
import os
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
import numpy
_smartsPatte... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/Crippen.py",
"copies": "1",
"size": "6023",
"license": "bsd-3-clause",
"hash": 9088291811387158000,
"line_mean": 27.4103773585,
"line_max": 83,
"alpha_frac": 0.6390503072,
"autogenerated": false,
"ratio": 3.044994944388271,
"config_test": false,... |
""" Atom-based calculation of LogP and MR using Crippen's approach
Reference:
S. A. Wildman and G. M. Crippen *JCICS* _39_ 868-873 (1999)
"""
import os
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import rdMolDescriptors
import numpy
_smartsPatterns = {}
_patternOrder = []
# this is ... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Crippen.py",
"copies": "2",
"size": "6051",
"license": "bsd-3-clause",
"hash": 4060617700235010000,
"line_mean": 27.4084507042,
"line_max": 83,
"alpha_frac": 0.6313006115,
"autogenerated": false,
"ratio": 3.0762582613116423,
"config_test": f... |
""" command line utility to report on the contributions of descriptors to
tree-based composite models
Usage: AnalyzeComposite [optional args] <models>
<models>: file name(s) of pickled composite model(s)
(this is the name of the db table if using a database)
Optional Arguments:
-n number: t... | {
"repo_name": "strets123/rdkit",
"path": "rdkit/ML/AnalyzeComposite.py",
"copies": "3",
"size": "9195",
"license": "bsd-3-clause",
"hash": -7755896508726708000,
"line_mean": 27.2923076923,
"line_max": 172,
"alpha_frac": 0.5973898858,
"autogenerated": false,
"ratio": 3.0835010060362174,
"config_... |
""" generation of 2D pharmacophores
**Notes**
- The terminology for this gets a bit rocky, so here's a glossary of what
terms used here mean:
1) *N-point pharmacophore* a combination of N features along with
distances betwen them.
2) *N-point proto-pharmacophore*: a combination of N featu... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Pharm2D/Generate.py",
"copies": "1",
"size": "5078",
"license": "bsd-3-clause",
"hash": -7669428762973347000,
"line_mean": 29.5903614458,
"line_max": 101,
"alpha_frac": 0.6738873572,
"autogenerated": false,
"ratio": 3.475701574264203,
"config_te... |
"""unit testing code for the Crippen clogp and MR calculators
"""
from __future__ import print_function
import unittest,sys,os
import io
import numpy
from rdkit import RDConfig
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Crippen
def feq(n1,n2,tol=1e-5):
return abs(n1-n2)<=tol... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/UnitTestCrippen.py",
"copies": "1",
"size": "5578",
"license": "bsd-3-clause",
"hash": 1608669888562862300,
"line_mean": 28.8288770053,
"line_max": 105,
"alpha_frac": 0.5790605952,
"autogenerated": false,
"ratio": 2.864920390344119,
"config_test... |
"""unit testing code for the Crippen clogp and MR calculators
"""
from __future__ import print_function
import unittest,sys,os
import numpy
from rdkit import RDConfig
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Crippen
def feq(n1,n2,tol=1e-5):
return abs(n1-n2)<=tol
class Te... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "rdkit/Chem/UnitTestCrippen.py",
"copies": "1",
"size": "5562",
"license": "bsd-3-clause",
"hash": -7561816055630777000,
"line_mean": 28.2736842105,
"line_max": 105,
"alpha_frac": 0.5746134484,
"autogenerated": false,
"ratio": 2.9242902208201893,
... |
"""unit testing code for the Crippen clogp and MR calculators
"""
from rdkit import RDConfig
import unittest,sys,os,cPickle
from rdkit import Chem
from rdkit.Chem import Crippen
import numpy
def feq(n1,n2,tol=1e-5):
return abs(n1-n2)<=tol
class TestCase(unittest.TestCase):
def setUp(self):
self.fName = os.pa... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/UnitTestCrippen.py",
"copies": "1",
"size": "5412",
"license": "bsd-3-clause",
"hash": -7279360445538304000,
"line_mean": 28.4130434783,
"line_max": 101,
"alpha_frac": 0.5731707317,
"autogenerated": false,
"ratio": 2.9096774193548387,
"confi... |
""" Various bits and pieces for calculating Molecular descriptors
"""
from rdkit import RDConfig
from rdkit.ML.Descriptors import Descriptors
from rdkit.Chem import Descriptors as DescriptorsMod
from rdkit.RDLogger import logger
logger = logger()
import re
class MolecularDescriptorCalculator(Descriptors.DescriptorCa... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/ML/Descriptors/MoleculeDescriptors.py",
"copies": "1",
"size": "3288",
"license": "bsd-3-clause",
"hash": -5783084161208523000,
"line_mean": 24.8897637795,
"line_max": 87,
"alpha_frac": 0.6435523114,
"autogenerated": false,
"ratio": 4.054254007398273,
... |
""" Various bits and pieces for calculating Molecular descriptors
"""
import re
from rdkit.Chem import Descriptors as DescriptorsMod
from rdkit.ML.Descriptors import Descriptors
from rdkit.RDLogger import logger
from rdkit.six.moves import cPickle
logger = logger()
class MolecularDescriptorCalculator(Descriptors.... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/ML/Descriptors/MoleculeDescriptors.py",
"copies": "4",
"size": "3269",
"license": "bsd-3-clause",
"hash": -7746755550722521000,
"line_mean": 24.3410852713,
"line_max": 87,
"alpha_frac": 0.6402569593,
"autogenerated": false,
"ratio": 4.01104294478527... |
""" functions to match a bunch of fragment descriptors from a file
No user-servicable parts inside. ;-)
"""
import os
from rdkit import RDConfig
from rdkit import Chem
defaultPatternFileName = os.path.join(RDConfig.RDDataDir, 'FragmentDescriptors.csv')
def _CountMatches(mol, patt, unique=True):
return len(mol.G... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/Fragments.py",
"copies": "12",
"size": "1619",
"license": "bsd-3-clause",
"hash": 4765826143733054000,
"line_mean": 26.9137931034,
"line_max": 108,
"alpha_frac": 0.6145768993,
"autogenerated": false,
"ratio": 3.4156118143459917,
"config_test"... |
""" functions to match a bunch of fragment descriptors from a file
No user-servicable parts inside. ;-)
"""
import os
from rdkit import RDConfig
from rdkit import Chem
defaultPatternFileName = os.path.join(RDConfig.RDDataDir,'FragmentDescriptors.csv')
def _CountMatches(mol,patt,unique=True):
return len(mol.GetS... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Fragments.py",
"copies": "2",
"size": "1676",
"license": "bsd-3-clause",
"hash": 6653921213621684000,
"line_mean": 26.4754098361,
"line_max": 101,
"alpha_frac": 0.6097852029,
"autogenerated": false,
"ratio": 3.3927125506072873,
"config_test"... |
""" This is a rough coverage test of the python wrapper
it's intended to be shallow, but broad
"""
import unittest,os
from rdkit.six.moves import cPickle
from rdkit import RDConfig
from rdkit.RDLogger import logger
logger=logger()
from rdkit import Chem
from rdkit.Chem import FragmentCatalog
from rdkit import DataStr... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "Code/GraphMol/FragCatalog/Wrap/rough_test.py",
"copies": "1",
"size": "7613",
"license": "bsd-3-clause",
"hash": -6086574800378182000,
"line_mean": 39.2804232804,
"line_max": 91,
"alpha_frac": 0.5931958492,
"autogenerated": false,
"ratio": 3.09723... |
""" Calculation of topological/topochemical descriptors.
"""
from __future__ import print_function
from rdkit import Chem
from rdkit.Chem import Graphs
from rdkit.Chem import rdchem
from rdkit.Chem import rdMolDescriptors
# FIX: remove this dependency here and below
from rdkit.Chem import pyPeriodicTable as Periodic... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/GraphDescriptors.py",
"copies": "1",
"size": "20134",
"license": "bsd-3-clause",
"hash": 6451918916735926000,
"line_mean": 27.9697841727,
"line_max": 93,
"alpha_frac": 0.6573954505,
"autogenerated": false,
"ratio": 2.9867972110962766,
"config_te... |
""" Calculation of topological/topochemical descriptors.
"""
from rdkit import Chem
from rdkit.Chem import Graphs
from rdkit.Chem import rdchem
from rdkit.Chem import rdMolDescriptors
# FIX: remove this dependency here and below
from rdkit.Chem import pyPeriodicTable as PeriodicTable
import numpy
import math
from rd... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/GraphDescriptors.py",
"copies": "2",
"size": "19929",
"license": "bsd-3-clause",
"hash": -1105920752131393900,
"line_mean": 28.9684210526,
"line_max": 105,
"alpha_frac": 0.6631541974,
"autogenerated": false,
"ratio": 2.975810064207854,
"conf... |
""" class definitions for similarity screening
See _SimilarityScreener_ for overview of required API
"""
from rdkit import DataStructs
from rdkit.DataStructs import TopNContainer
from rdkit import RDConfig
from rdkit import six
class SimilarityScreener(object):
""" base class
important attributes:
probe... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "rdkit/Chem/Fingerprints/SimilarityScreener.py",
"copies": "4",
"size": "4666",
"license": "bsd-3-clause",
"hash": 909492953805852200,
"line_mean": 25.5113636364,
"line_max": 79,
"alpha_frac": 0.6594513502,
"autogenerated": false,
"ratio": 3.927609... |
""" class definitions for similarity screening
See _SimilarityScreener_ for overview of required API
"""
from rdkit import DataStructs
from rdkit import six
from rdkit.DataStructs import TopNContainer
class SimilarityScreener(object):
""" base class
important attributes:
probe: the probe fingerprint ag... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/Fingerprints/SimilarityScreener.py",
"copies": "4",
"size": "4634",
"license": "bsd-3-clause",
"hash": 5622337894783102000,
"line_mean": 25.0337078652,
"line_max": 83,
"alpha_frac": 0.6590418645,
"autogenerated": false,
"ratio": 3.9271186440677... |
""" #DOC
"""
class BitEnsemble(object):
""" used to store a collection of bits and score
BitVects (or signatures) against them.
"""
def __init__(self, bits=None):
if bits is not None:
self._bits = list(bits)
else:
self._bits = []
def SetBits(self, bits):
self._bits = list(bits)... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/DataStructs/BitEnsemble.py",
"copies": "12",
"size": "1192",
"license": "bsd-3-clause",
"hash": 4692827522043586000,
"line_mean": 18.5409836066,
"line_max": 65,
"alpha_frac": 0.6048657718,
"autogenerated": false,
"ratio": 3.376770538243626,
"config_t... |
from __future__ import print_function
import sys
from rdkit import RDConfig
from rdkit.Dbase import DbModule
from rdkit import six
sqlTextTypes = DbModule.sqlTextTypes
sqlIntTypes = DbModule.sqlIntTypes
sqlFloatTypes = DbModule.sqlFloatTypes
sqlBinTypes = DbModule.sqlBinTypes
def GetDbNames(user='sysdba', password=... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Dbase/DbInfo.py",
"copies": "4",
"size": "5375",
"license": "bsd-3-clause",
"hash": -5955944643313870000,
"line_mean": 24.5952380952,
"line_max": 98,
"alpha_frac": 0.6225116279,
"autogenerated": false,
"ratio": 3.5245901639344264,
"config_test": f... |
from __future__ import print_function
import sys
from rdkit import RDConfig
from rdkit.Dbase import DbModule
sqlTextTypes = DbModule.sqlTextTypes
sqlIntTypes = DbModule.sqlIntTypes
sqlFloatTypes = DbModule.sqlFloatTypes
sqlBinTypes = DbModule.sqlBinTypes
def GetDbNames(user='sysdba',password='masterkey',dirName='.'... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Dbase/DbInfo.py",
"copies": "1",
"size": "5367",
"license": "bsd-3-clause",
"hash": -1086339428606968800,
"line_mean": 24.8028846154,
"line_max": 91,
"alpha_frac": 0.6221352711,
"autogenerated": false,
"ratio": 3.5637450199203187,
"config_test": fals... |
from __future__ import print_function
raise NotImplementedError('not finished yet')
""" lazy generator of 2D pharmacophore signature data
"""
import rdkit.Chem
from rdkit.Chem.Pharm2D import SigFactory, Matcher, Utils
class Generator(object):
"""
Important attributes:
- mol: the molecules whose signature i... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Pharm2D/LazyGenerator.py",
"copies": "1",
"size": "4360",
"license": "bsd-3-clause",
"hash": -3783318194017083400,
"line_mean": 26.0807453416,
"line_max": 89,
"alpha_frac": 0.6311926606,
"autogenerated": false,
"ratio": 3.3929961089494163,
"conf... |
from rdkit import RDConfig
import DbModule
import sys
sqlTextTypes = DbModule.sqlTextTypes
sqlIntTypes = DbModule.sqlIntTypes
sqlFloatTypes = DbModule.sqlFloatTypes
sqlBinTypes = DbModule.sqlBinTypes
def GetDbNames(user='sysdba',password='masterkey',dirName='.',dBase='::template1',cn=None):
""" returns a list of da... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Dbase/DbInfo.py",
"copies": "2",
"size": "5239",
"license": "bsd-3-clause",
"hash": 3682971665919595000,
"line_mean": 24.556097561,
"line_max": 91,
"alpha_frac": 0.6220652796,
"autogenerated": false,
"ratio": 3.5736698499317874,
"config_test": fa... |
""" command line utility for growing composite models
**Usage**
_GrowComposite [optional args] filename_
**Command Line Arguments**
- -n *count*: number of new models to build
- -C *pickle file name*: name of file containing composite upon which to build.
- --inNote *note*: note to be used in loading co... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/ML/GrowComposite.py",
"copies": "2",
"size": "19705",
"license": "bsd-3-clause",
"hash": -7406231364026530000,
"line_mean": 33.8144876325,
"line_max": 128,
"alpha_frac": 0.6660746004,
"autogenerated": false,
"ratio": 3.759778668193093,
"config_te... |
"""
unit testing code for the Smiles file handling stuff
"""
import unittest
from rdkit import Chem
from rdkit.six import next
from rdkit import RDLogger
class TestCase(unittest.TestCase):
def setUp(self):
self.smis = ['CC', 'CCC', 'CCCCC', 'CCCCCC', 'CCCCCCC', 'CC', 'CCCCOC']
self.nMolecules = len(self.s... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/Suppliers/UnitTestSmilesMolSupplier.py",
"copies": "4",
"size": "3573",
"license": "bsd-3-clause",
"hash": -4142047755766020600,
"line_mean": 30.6194690265,
"line_max": 85,
"alpha_frac": 0.6644276518,
"autogenerated": false,
"ratio": 3.21312949... |
raise NotImplementedError,'not finished yet'
""" lazy generator of 2D pharmacophore signature data
"""
import rdkit.Chem
from rdkit.Chem.Pharm2D import SigFactory,Matcher,Utils
class Generator(object):
"""
Important attributes:
- mol: the molecules whose signature is being worked with
- sigFactory : the ... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Pharm2D/LazyGenerator.py",
"copies": "2",
"size": "4289",
"license": "bsd-3-clause",
"hash": 6513829194663768000,
"line_mean": 26.4935897436,
"line_max": 112,
"alpha_frac": 0.6348799254,
"autogenerated": false,
"ratio": 3.4120922832140015,
"... |
""" Supplies a class for working with fingerprints from databases
#DOC
"""
from rdkit import RDConfig
from rdkit.VLib.Node import VLibNode
from rdkit import DataStructs
import cPickle
import sys
def warning(msg,dest=sys.stderr):
dest.write(msg)
class DbFpSupplier(VLibNode):
"""
new fps come back with all a... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Fingerprints/DbFpSupplier.py",
"copies": "2",
"size": "4222",
"license": "bsd-3-clause",
"hash": 1819110671782756900,
"line_mean": 21.9456521739,
"line_max": 110,
"alpha_frac": 0.6307437234,
"autogenerated": false,
"ratio": 3.3217938630999213,... |
""" Supplies a class for working with molecules from databases
#DOC
"""
from rdkit import Chem
from rdkit.Chem.Suppliers.MolSupplier import MolSupplier
import sys
def warning(msg,dest=sys.stderr):
dest.write(msg)
class DbMolSupplier(MolSupplier):
"""
new molecules come back with all additional fields from ... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/Suppliers/DbMolSupplier.py",
"copies": "1",
"size": "4108",
"license": "bsd-3-clause",
"hash": 6291392567617086000,
"line_mean": 24.675,
"line_max": 87,
"alpha_frac": 0.6085686465,
"autogenerated": false,
"ratio": 3.594050743657043,
"config_test... |
""" Supplies a class for working with molecules from databases
#DOC
"""
from rdkit import Chem
from rdkit.Chem.Suppliers.MolSupplier import MolSupplier
import sys
def warning(msg, dest=sys.stderr):
dest.write(msg)
class DbMolSupplier(MolSupplier):
"""
new molecules come back with all additional fields fro... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Suppliers/DbMolSupplier.py",
"copies": "1",
"size": "4118",
"license": "bsd-3-clause",
"hash": -184740302200689800,
"line_mean": 23.6586826347,
"line_max": 99,
"alpha_frac": 0.6070908208,
"autogenerated": false,
"ratio": 3.5902353966870098,
"con... |
""" This functionality gets mixed into the BitEnsemble class
"""
from rdkit.DataStructs.BitEnsemble import BitEnsemble
def _InitScoreTable(self,dbConn,tableName,idInfo='',actInfo=''):
""" inializes a db table to store our scores
idInfo and actInfo should be strings with the definitions of the id and
activi... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/DataStructs/BitEnsembleDb.py",
"copies": "2",
"size": "1558",
"license": "bsd-3-clause",
"hash": 4183451119366675500,
"line_mean": 25.406779661,
"line_max": 82,
"alpha_frac": 0.6874197689,
"autogenerated": false,
"ratio": 3.3869565217391306,
"con... |
""" This functionality gets mixed into the BitEnsemble class
"""
from rdkit.DataStructs.BitEnsemble import BitEnsemble
def _InitScoreTable(self, dbConn, tableName, idInfo='', actInfo=''):
""" inializes a db table to store our scores
idInfo and actInfo should be strings with the definitions of the id and
a... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/DataStructs/BitEnsembleDb.py",
"copies": "11",
"size": "1569",
"license": "bsd-3-clause",
"hash": 8975726138144633000,
"line_mean": 24.7213114754,
"line_max": 83,
"alpha_frac": 0.6826003824,
"autogenerated": false,
"ratio": 3.4332603938730855,
"co... |
""" unit testing code for BitEnsembles
"""
from rdkit import RDConfig
import os
import unittest
from rdkit.DataStructs.BitEnsemble import BitEnsemble
from rdkit.DataStructs import BitEnsembleDb
from rdkit.DataStructs import SparseBitVect
class TestCase(unittest.TestCase):
def test1(self):
ensemble = BitEnsemble... | {
"repo_name": "strets123/rdkit",
"path": "rdkit/DataStructs/UnitTestBitEnsemble.py",
"copies": "5",
"size": "3478",
"license": "bsd-3-clause",
"hash": 8430484689723324000,
"line_mean": 27.5081967213,
"line_max": 90,
"alpha_frac": 0.6043703278,
"autogenerated": false,
"ratio": 2.922689075630252,
... |
""" unit testing code for BitEnsembles
"""
import os
import shutil
import tempfile
import unittest
from rdkit import RDConfig
from rdkit.DataStructs import SparseBitVect
# This import is important to initialize the BitEnsemble module
from rdkit.DataStructs import BitEnsembleDb
from rdkit.DataStructs.BitEnsemble import... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/DataStructs/UnitTestBitEnsemble.py",
"copies": "11",
"size": "4181",
"license": "bsd-3-clause",
"hash": 4761375225358302000,
"line_mean": 28.6524822695,
"line_max": 95,
"alpha_frac": 0.6048792155,
"autogenerated": false,
"ratio": 3.0209537572254335,... |
"""unit testing code for fingerprinting
"""
import unittest
from rdkit import Chem
from rdkit import DataStructs
def feq(v1,v2,tol=1e-4):
return abs(v1-v2)<=tol
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
pass
def test1(self):
# FIX: test HashAtom
... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "rdkit/Chem/Fingerprints/UnitTestFingerprints.py",
"copies": "6",
"size": "2703",
"license": "bsd-3-clause",
"hash": -5907833499856262000,
"line_mean": 28.064516129,
"line_max": 85,
"alpha_frac": 0.6141324454,
"autogenerated": false,
"ratio": 2.792... |
"""unit testing code for fingerprinting
"""
import unittest
from rdkit import Chem
from rdkit import DataStructs
class TestCase(unittest.TestCase):
def test1(self):
# FIX: test HashAtom
pass
def test2(self):
# FIX: test HashBond
pass
def test3(self):
# FIX: test HashPath
pass
def... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/Fingerprints/UnitTestFingerprints.py",
"copies": "1",
"size": "2619",
"license": "bsd-3-clause",
"hash": -4491740053794908000,
"line_mean": 31.7375,
"line_max": 97,
"alpha_frac": 0.6227567774,
"autogenerated": false,
"ratio": 2.825242718446602,... |
"""unit testing code for the DbResultSet object
"""
from rdkit import RDConfig
import unittest,os
from rdkit.Dbase.DbConnection import DbConnect
from rdkit.Dbase.DbResultSet import DbResultSet,RandomAccessDbResultSet
class TestCase(unittest.TestCase):
def setUp(self):
self.dbName = RDConfig.RDTestDatabase
... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Dbase/UnitTestDbResultSet.py",
"copies": "1",
"size": "2115",
"license": "bsd-3-clause",
"hash": 3780850110058156000,
"line_mean": 23.3103448276,
"line_max": 71,
"alpha_frac": 0.6226950355,
"autogenerated": false,
"ratio": 3.3150470219435735,
"config... |
"""unit testing code for the lazy signature generator
"""
import unittest
from rdkit import Chem
from rdkit.Chem.Pharm2D import SigFactory,LazyGenerator
class TestCase(unittest.TestCase):
def setUp(self):
self.factory = SigFactory.SigFactory()
self.factory.SetPatternsFromSmarts(['O','N'])
self.factory.S... | {
"repo_name": "strets123/rdkit",
"path": "rdkit/Chem/Pharm2D/UnitTestLazyGenerator.py",
"copies": "6",
"size": "2115",
"license": "bsd-3-clause",
"hash": -5332116773116400000,
"line_mean": 28.375,
"line_max": 86,
"alpha_frac": 0.6382978723,
"autogenerated": false,
"ratio": 3.2790697674418605,
"... |
"""unit testing code for the Smiles file handling stuff
"""
import unittest,sys,os
from rdkit import RDConfig
from rdkit import Chem
from rdkit.six import next
class TestCase(unittest.TestCase):
def setUp(self):
self.smis = ['CC','CCC','CCCCC','CCCCCC','CCCCCCC','CC','CCCCOC']
def test1LazyReader(self):
... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/Suppliers/UnitTestSmilesMolSupplier.py",
"copies": "1",
"size": "3033",
"license": "bsd-3-clause",
"hash": -3372253286232480300,
"line_mean": 27.6132075472,
"line_max": 74,
"alpha_frac": 0.6274315859,
"autogenerated": false,
"ratio": 3.09805924412... |
"""unit testing code for the Smiles file handling stuff
"""
import unittest, sys, os
from rdkit import RDConfig
from rdkit import Chem
from rdkit.six import next
class TestCase(unittest.TestCase):
def setUp(self):
self.smis = ['CC', 'CCC', 'CCCCC', 'CCCCCC', 'CCCCCCC', 'CC', 'CCCCOC']
def test1LazyReader(s... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Suppliers/UnitTestSmilesMolSupplier.py",
"copies": "1",
"size": "3112",
"license": "bsd-3-clause",
"hash": -1082868226116014700,
"line_mean": 28.6380952381,
"line_max": 78,
"alpha_frac": 0.611503856,
"autogenerated": false,
"ratio": 3.047992164544... |
"""unit testing code for the Smiles file handling stuff
"""
import unittest,sys,os
from rdkit import RDConfig
from rdkit import Chem
class TestCase(unittest.TestCase):
def setUp(self):
self.smis = ['CC','CCC','CCCCC','CCCCCC','CCCCCCC','CC','CCCCOC']
def test1LazyReader(self):
" tests lazy reads """
... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Suppliers/UnitTestSmilesMolSupplier.py",
"copies": "2",
"size": "3020",
"license": "bsd-3-clause",
"hash": 9216281417305652000,
"line_mean": 22.0534351145,
"line_max": 74,
"alpha_frac": 0.5860927152,
"autogenerated": false,
"ratio": 3.04128902... |
"""basic unit testing code for atoms
"""
import unittest
from rdkit import Chem
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
self.m = Chem.MolFromSmiles('CC(=O)CCSC')
def test1Implicit(self):
" testing ImplicitValence "
a = self.m.GetAtoms()[0]
... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Chem/UnitTestChemAtom.py",
"copies": "12",
"size": "1868",
"license": "bsd-3-clause",
"hash": 6462359252787914000,
"line_mean": 24.2432432432,
"line_max": 68,
"alpha_frac": 0.6407922912,
"autogenerated": false,
"ratio": 3.03739837398374,
"config_t... |
from __future__ import print_function
try:
from reportlab import platypus
except ImportError:
import sys
sys.stderr.write('ReportLab module could not be imported. Db->PDF functionality not available')
GetReportlabTable = None
QuickReport = None
else:
from rdkit import Chem
try:
from pyRDkit.utils im... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/Dbase/DbReport.py",
"copies": "4",
"size": "7344",
"license": "bsd-3-clause",
"hash": -4693990109312630000,
"line_mean": 28.8536585366,
"line_max": 98,
"alpha_frac": 0.6107026144,
"autogenerated": false,
"ratio": 3.4625176803394626,
"config_test":... |
from __future__ import print_function
try:
from reportlab import platypus
except ImportError:
import sys
sys.stderr.write('ReportLab module could not be imported. Db->PDF functionality not available')
GetReportlabTable = None
QuickReport = None
else:
from rdkit import Chem
try:
from pyRDkit.utils imp... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Dbase/DbReport.py",
"copies": "1",
"size": "7541",
"license": "bsd-3-clause",
"hash": 9116067528467865000,
"line_mean": 28.8063241107,
"line_max": 98,
"alpha_frac": 0.6133138841,
"autogenerated": false,
"ratio": 3.478321033210332,
"config_test": fals... |
from rdkit import RDConfig
if hasattr(RDConfig,"usePgSQL") and RDConfig.usePgSQL:
from pyPgSQL import PgSQL
# as of this writing (March 2004), this results in a speedup in
# getting results back from the wrapper:
PgSQL.fetchReturnsList=1
from pyPgSQL.PgSQL import *
sqlTextTypes = [PG_CHAR,PG_BPCHAR,PG_TEX... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Dbase/DbModule.py",
"copies": "2",
"size": "2081",
"license": "bsd-3-clause",
"hash": 1634136791542979800,
"line_mean": 33.1147540984,
"line_max": 92,
"alpha_frac": 0.7025468525,
"autogenerated": false,
"ratio": 3.2566510172143976,
"config_test":... |
from rdkit import six
from rdkit import RDConfig
if hasattr(RDConfig,"usePgSQL") and RDConfig.usePgSQL:
from pyPgSQL import PgSQL
# as of this writing (March 2004), this results in a speedup in
# getting results back from the wrapper:
PgSQL.fetchReturnsList=1
from pyPgSQL.PgSQL import *
sqlTextTypes = [PG... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/Dbase/DbModule.py",
"copies": "4",
"size": "2131",
"license": "bsd-3-clause",
"hash": -681594176932317000,
"line_mean": 33.3709677419,
"line_max": 92,
"alpha_frac": 0.7048334115,
"autogenerated": false,
"ratio": 3.26840490797546,
"config_test": ... |
from xml.etree import ElementTree
# check the version of ElementTree. We need at least version 1.2
# in order for the XPath-style parsing stuff to work
import re
vers = re.split("[a-zA-Z]",ElementTree.VERSION)[0]
if vers < '1.2':
raise ImportError,'The PubMed record interface requires a version of ElementTree >= 1.2... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Dbase/Pubmed/Records.py",
"copies": "2",
"size": "4495",
"license": "bsd-3-clause",
"hash": 3040483159045184500,
"line_mean": 32.5447761194,
"line_max": 90,
"alpha_frac": 0.6418242492,
"autogenerated": false,
"ratio": 3.598879103282626,
"config_t... |
""" functionality for drawing hierarchical catalogs on sping
canvases
"""
from sping import pid as piddle
class VisOpts(object):
circRad = 10
minCircRad = 4
maxCircRad = 16
circColor = piddle.Color(0.6, 0.6, 0.9)
terminalEmptyColor = piddle.Color(.8, .8, .2)
terminalOnColor = piddle.Color(0.8, 0.8, 0... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/DataStructs/HierarchyVis.py",
"copies": "5",
"size": "3875",
"license": "bsd-3-clause",
"hash": 1510835844414436600,
"line_mean": 30.25,
"line_max": 99,
"alpha_frac": 0.6459354839,
"autogenerated": false,
"ratio": 3.1555374592833876,
"config_test"... |
import bisect
class TopNContainer(object):
""" maintains a sorted list of a particular number of data elements.
"""
def __init__(self,size,mostNeg=-1e99):
self._size = size
self.best = [mostNeg]*self._size
self.extras = [None]*self._size
def Insert(self,val,extra=None):
""" only does the insert... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/DataStructs/TopNContainer.py",
"copies": "1",
"size": "1553",
"license": "bsd-3-clause",
"hash": -8394464511504048000,
"line_mean": 24.8833333333,
"line_max": 70,
"alpha_frac": 0.6258853831,
"autogenerated": false,
"ratio": 3.368763557483731,
"co... |
import copy
urlBase="http://eutils.ncbi.nlm.nih.gov/entrez/eutils"
searchBase=urlBase+"/esearch.fcgi"
summaryBase=urlBase+"/esummary.fcgi"
fetchBase=urlBase+"/efetch.fcgi"
linkBase=urlBase+"/elink.fcgi"
# for links to pubmed web pages:
queryBase="http://www.ncbi.nlm.nih.gov/entrez/query.fcgi"
_details = {
'db':'pub... | {
"repo_name": "AlexanderSavelyev/rdkit",
"path": "rdkit/Dbase/Pubmed/QueryParams.py",
"copies": "3",
"size": "1462",
"license": "bsd-3-clause",
"hash": -1093318081724212900,
"line_mean": 25.5818181818,
"line_max": 100,
"alpha_frac": 0.6751025992,
"autogenerated": false,
"ratio": 3.058577405857740... |
import os
import io
import unittest
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import FragmentCatalog, BuildFragmentCatalog
from rdkit.six.moves import cPickle
def feq(n1,n2,tol=1e-4):
return abs(n1-n2)<tol
class TestCase(unittest.TestCase):
def setUp(self) :
self.smiList = ["S(SC1=NC2=... | {
"repo_name": "strets123/rdkit",
"path": "rdkit/Chem/UnitTestCatalog.py",
"copies": "3",
"size": "9124",
"license": "bsd-3-clause",
"hash": -5355344922590387000,
"line_mean": 35.7903225806,
"line_max": 92,
"alpha_frac": 0.5577597545,
"autogenerated": false,
"ratio": 2.8414824042354407,
"config_... |
import os
import io
import unittest
from rdkit import RDConfig
from rdkit import Chem
from rdkit.Chem import FragmentCatalog, BuildFragmentCatalog
from rdkit.six.moves import cPickle
def feq(n1, n2, tol=1e-4):
return abs(n1 - n2) < tol
class TestCase(unittest.TestCase):
def setUp(self):
self.smiList = ["S(... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/UnitTestCatalog.py",
"copies": "1",
"size": "9354",
"license": "bsd-3-clause",
"hash": -8283884744181282000,
"line_mean": 36.5662650602,
"line_max": 99,
"alpha_frac": 0.5440453282,
"autogenerated": false,
"ratio": 2.8285455095252496,
"config_tes... |
import random
import unittest
from rdkit.six import StringIO
from rdkit.DataStructs.TopNContainer import TopNContainer, _exampleCode
from rdkit.TestRunner import redirect_stdout
class TestCase(unittest.TestCase):
def test1(self):
# simple test with a known answer
cont = TopNContainer(4)
for foo in ra... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/DataStructs/UnitTestTopNContainer.py",
"copies": "4",
"size": "2548",
"license": "bsd-3-clause",
"hash": -4922052235652594000,
"line_mean": 24.7373737374,
"line_max": 71,
"alpha_frac": 0.6087127159,
"autogenerated": false,
"ratio": 3.225316455696202... |
import unittest
import random
from rdkit.DataStructs.TopNContainer import TopNContainer
class TestCase(unittest.TestCase):
def test1(self):
""" simple test with a known answer """
cont = TopNContainer(4)
for foo in range(10):
cont.Insert(foo,str(foo))
assert cont.GetPts()==range(6,10)
asser... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/DataStructs/UnitTestTopNContainer.py",
"copies": "5",
"size": "1888",
"license": "bsd-3-clause",
"hash": -8907564040054778000,
"line_mean": 25.5915492958,
"line_max": 63,
"alpha_frac": 0.6054025424,
"autogenerated": false,
"ratio": 3.1362126245847... |
"""basic unit testing code for the Bond wrapper
"""
import unittest
from rdkit import Chem
class TestCase(unittest.TestCase):
def setUp(self):
#print '\n%s: '%self.shortDescription(),
self.m = Chem.MolFromSmiles('CCCC1=CC=C1')
def test1Get(self):
" testing GetBond "
ok = 1
try:
b = se... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/UnitTestChemBond.py",
"copies": "1",
"size": "1727",
"license": "bsd-3-clause",
"hash": 3068124647451514000,
"line_mean": 25.984375,
"line_max": 80,
"alpha_frac": 0.6763173133,
"autogenerated": false,
"ratio": 2.84983498349835,
"config_test": tr... |
""" Tools for doing PubMed searches and processing the results
NOTE: much of the example code in the documentation here uses XML
files from the test_data directory in order to avoid having to call
out to PubMed itself. Actual calls to the functions would not include
the _conn_ argument.
"""
from rdkit import RDConfi... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Dbase/Pubmed/Searches.py",
"copies": "2",
"size": "7576",
"license": "bsd-3-clause",
"hash": -8097189635520018000,
"line_mean": 24.3377926421,
"line_max": 95,
"alpha_frac": 0.6446673706,
"autogenerated": false,
"ratio": 3.1765199161425577,
"confi... |
try:
from reportlab import platypus
except ImportError:
import sys
sys.stderr.write('ReportLab module could not be imported. Db->PDF functionality not available')
GetReportlabTable = None
QuickReport = None
else:
from rdkit import Chem
try:
from pyRDkit.utils import chemdraw
except ImportError:
... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Dbase/DbReport.py",
"copies": "1",
"size": "7416",
"license": "bsd-3-clause",
"hash": 6540975674846323000,
"line_mean": 29.024291498,
"line_max": 98,
"alpha_frac": 0.6115156419,
"autogenerated": false,
"ratio": 3.4719101123595504,
"config_test": ... |
""" Unit Test code for Fragment Descriptors
"""
import unittest
from rdkit import Chem
from rdkit.Chem import Fragments
class TestCase(unittest.TestCase):
def setUp(self) :
pass
def _runTest(self,data,fn):
for smi,tgtVal in data:
mol = Chem.MolFromSmiles(smi)
assert mol,"Smiles parsing failed... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/UnitTestFragmentDescriptors.py",
"copies": "1",
"size": "8371",
"license": "bsd-3-clause",
"hash": 1416664396338389800,
"line_mean": 35.2380952381,
"line_max": 159,
"alpha_frac": 0.482499104,
"autogenerated": false,
"ratio": 2.095893840761142,
"... |
"""unit testing code for graph-theoretical descriptors
"""
from __future__ import print_function
from rdkit import RDConfig
import unittest,os.path
from rdkit import Chem
from rdkit.Chem import GraphDescriptors,MolSurf,Lipinski,Crippen
def feq(n1,n2,tol=1e-4):
return abs(n1-n2)<=tol
class TestCase(unittest.TestCas... | {
"repo_name": "soerendip42/rdkit",
"path": "rdkit/Chem/UnitTestGraphDescriptors.2.py",
"copies": "3",
"size": "24674",
"license": "bsd-3-clause",
"hash": -6053846350987624000,
"line_mean": 30.6333333333,
"line_max": 302,
"alpha_frac": 0.5775310043,
"autogenerated": false,
"ratio": 2.5072655217965... |
""" unit testing code for Lipinski parameter calculation
This provides a workout for the SMARTS matcher
"""
from __future__ import print_function
from rdkit import RDConfig
import unittest,os
from rdkit.six.moves import cPickle
from rdkit import Chem
from rdkit.Chem import Lipinski, rdMolDescriptors
NonStrict = "N... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/UnitTestLipinski.py",
"copies": "1",
"size": "4077",
"license": "bsd-3-clause",
"hash": 8906459942523702000,
"line_mean": 41.0309278351,
"line_max": 109,
"alpha_frac": 0.6661761099,
"autogenerated": false,
"ratio": 2.794379712131597,
"config_tes... |
""" unit testing code for molecule suppliers
"""
from rdkit import RDConfig
import unittest,cPickle,os
from rdkit import Chem
class TestCase(unittest.TestCase):
def setUp(self):
self._files=[]
def tearDown(self):
for fileN in self._files:
try:
os.unlink(fileN)
except OSError:
... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/UnitTestSuppliers.py",
"copies": "2",
"size": "2680",
"license": "bsd-3-clause",
"hash": -6046542816694804000,
"line_mean": 22.9285714286,
"line_max": 91,
"alpha_frac": 0.5873134328,
"autogenerated": false,
"ratio": 3.055872291904219,
"confi... |
""" utility functionality for clustering molecules using fingerprints
includes a command line app for clustering
Sample Usage:
python ClusterMols.py -d data.gdb -t daylight_sig \
--idName="CAS_TF" -o clust1.pkl \
--actTable="dop_test" --actName="moa_quant"
"""
from rdkit.Dbase.DbConnection import DbConne... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Fingerprints/ClusterMols.py",
"copies": "2",
"size": "6021",
"license": "bsd-3-clause",
"hash": 8993781663323533000,
"line_mean": 30.1968911917,
"line_max": 96,
"alpha_frac": 0.6799534961,
"autogenerated": false,
"ratio": 3.5564087418783226,
... |
""" utility functionality for fingerprinting sets of molecules
includes a command line app for working with fingerprints
and databases
Sample Usage:
python FingerprintMols.py -d data.gdb \
-t 'raw_dop_data' --smilesName="Structure" --idName="Mol_ID" \
--outTable="daylight_sig"
"""
from __futu... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Fingerprints/FingerprintMols.py",
"copies": "1",
"size": "17861",
"license": "bsd-3-clause",
"hash": -1879890710035294000,
"line_mean": 29.6890034364,
"line_max": 92,
"alpha_frac": 0.5855775153,
"autogenerated": false,
"ratio": 3.762586896987571,
... |
""" utility functionality for molecular similarity
includes a command line app for screening databases
Sample Usage:
python MolSimilarity.py -d data.gdb -t daylight_sig --idName="Mol_ID" \
--topN=100 --smiles='c1(C=O)ccc(Oc2ccccc2)cc1' --smilesTable=raw_dop_data \
--smilesName="structure" -o results.... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Fingerprints/MolSimilarity.py",
"copies": "1",
"size": "10616",
"license": "bsd-3-clause",
"hash": -5818794250270112000,
"line_mean": 30.9759036145,
"line_max": 99,
"alpha_frac": 0.6589110776,
"autogenerated": false,
"ratio": 3.641852487135506,
... |
"""
"""
from __future__ import print_function
import copy
import random
import numpy
from rdkit.DataStructs.VectCollection import VectCollection
from rdkit.ML import InfoTheory
from rdkit.ML.DecTree import SigTree
try:
from rdkit.ML.FeatureSelect import CMIM
except ImportError:
CMIM = None
def _GenerateRando... | {
"repo_name": "rvianello/rdkit",
"path": "rdkit/ML/DecTree/BuildSigTree.py",
"copies": "4",
"size": "7570",
"license": "bsd-3-clause",
"hash": 7574152487346788000,
"line_mean": 31.6293103448,
"line_max": 100,
"alpha_frac": 0.6389696169,
"autogenerated": false,
"ratio": 3.680116674769081,
"confi... |
""" command line utility for working with FragmentCatalogs (CASE-type analysis)
**Usage**
BuildFragmentCatalog [optional args] <filename>
filename, the name of a delimited text file containing InData, is required
for some modes of operation (see below)
**Command Line Arguments**
- -n *maxNumMols*: specify t... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/BuildFragmentCatalog.py",
"copies": "1",
"size": "19243",
"license": "bsd-3-clause",
"hash": -1612010710715912700,
"line_mean": 27.8068862275,
"line_max": 95,
"alpha_frac": 0.6305669594,
"autogenerated": false,
"ratio": 3.328662861096696,
"confi... |
""" contains factory class for producing signatures
"""
from __future__ import print_function, division
from rdkit.DataStructs import SparseBitVect,IntSparseIntVect,LongSparseIntVect
from rdkit.Chem.Pharm2D import Utils
import copy
import numpy
_verbose = False
class SigFactory(object):
"""
SigFactory's are... | {
"repo_name": "adalke/rdkit",
"path": "rdkit/Chem/Pharm2D/SigFactory.py",
"copies": "4",
"size": "10111",
"license": "bsd-3-clause",
"hash": -5578234675312812000,
"line_mean": 28.3924418605,
"line_max": 133,
"alpha_frac": 0.6512708931,
"autogenerated": false,
"ratio": 3.551457674745346,
"config... |
""" contains factory class for producing signatures
"""
from __future__ import print_function, division
from rdkit.DataStructs import SparseBitVect, IntSparseIntVect, LongSparseIntVect
from rdkit.Chem.Pharm2D import Utils
import copy
import numpy
_verbose = False
class SigFactory(object):
"""
SigFactory's a... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Pharm2D/SigFactory.py",
"copies": "1",
"size": "10272",
"license": "bsd-3-clause",
"hash": 7061588894478114000,
"line_mean": 28.4326647564,
"line_max": 99,
"alpha_frac": 0.6410630841,
"autogenerated": false,
"ratio": 3.584089323098395,
"config_t... |
""" contains factory class for producing signatures
"""
from rdkit.DataStructs import SparseBitVect,IntSparseIntVect,LongSparseIntVect
from rdkit.Chem.Pharm2D import Utils
import copy
import numpy
_verbose = False
class SigFactory(object):
"""
SigFactory's are used by creating one, setting the relevant
... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Pharm2D/SigFactory.py",
"copies": "2",
"size": "10043",
"license": "bsd-3-clause",
"hash": 6364832570176836000,
"line_mean": 28.2798833819,
"line_max": 132,
"alpha_frac": 0.6519964154,
"autogenerated": false,
"ratio": 3.543754410726888,
"con... |
""" Definitions for 2D Pharmacophores from:
Gobbi and Poppinger, Biotech. Bioeng. _61_ 47-54 (1998)
"""
from rdkit import Chem
from rdkit.Chem.Pharm2D.SigFactory import SigFactory
from rdkit.Chem import ChemicalFeatures
fdef = """
DefineFeature Hydrophobic [$([C;H2,H1](!=*)[C;H2,H1][C;H2,H1][$([C;H1,H2,H3]);!$(C=*)... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/Pharm2D/Gobbi_Pharm2D.py",
"copies": "1",
"size": "1931",
"license": "bsd-3-clause",
"hash": -49881716686581150,
"line_mean": 29.171875,
"line_max": 197,
"alpha_frac": 0.6105644744,
"autogenerated": false,
"ratio": 2.1819209039548024,
"config_te... |
from rdkit import Chem
from rdfragcatalog import *
import sys
def message(msg,dest=sys.stdout):
dest.write(msg)
class BitGainsInfo(object):
id=-1
description=''
gain=0.0
nPerClass=None
def ProcessGainsFile(fileName,nToDo=-1,delim=',',haveDescriptions=1):
inFile = open(fileName,'r')
nRead = 0
res ... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/FragmentCatalog.py",
"copies": "2",
"size": "2388",
"license": "bsd-3-clause",
"hash": -2844270085012729000,
"line_mean": 24.4042553191,
"line_max": 69,
"alpha_frac": 0.6264656616,
"autogenerated": false,
"ratio": 3.175531914893617,
"config_... |
""" functionality for finding pharmacophore matches in molecules
See Docs/Chem/Pharm2D.triangles.jpg for an illustration of the way
pharmacophores are broken into triangles and labelled.
See Docs/Chem/Pharm2D.signatures.jpg for an illustration of bit
numbering
"""
from rdkit import Chem
from rdkit.Chem.Phar... | {
"repo_name": "rdkit/rdkit-orig",
"path": "rdkit/Chem/Pharm2D/Matcher.py",
"copies": "2",
"size": "4099",
"license": "bsd-3-clause",
"hash": -6898277712822001000,
"line_mean": 26.6959459459,
"line_max": 88,
"alpha_frac": 0.6728470359,
"autogenerated": false,
"ratio": 3.404485049833887,
"config_... |
import sys
from rdkit import Chem
from rdkit.Chem.rdfragcatalog import *
def message(msg, dest=sys.stdout):
dest.write(msg)
class BitGainsInfo(object):
id = -1
description = ''
gain = 0.0
nPerClass = None
def ProcessGainsFile(fileName, nToDo=-1, delim=',', haveDescriptions=1):
inFile = open(fileName,... | {
"repo_name": "jandom/rdkit",
"path": "rdkit/Chem/FragmentCatalog.py",
"copies": "12",
"size": "2420",
"license": "bsd-3-clause",
"hash": 8292472122260891000,
"line_mean": 23.9484536082,
"line_max": 72,
"alpha_frac": 0.6219008264,
"autogenerated": false,
"ratio": 3.1758530183727034,
"config_tes... |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.