mirror of
https://github.com/rdkit/rdkit.git
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Vdv radii from blue obelisk (#2154)
* updated atomic radii to follow the Blue Obelisk Data Repository Ubuntu package bodr version 10-1; radii are from file /usr/share/bodr/elements.xml * typo * use 2.0 as default VDW radius instead of 1.7 for elements missing from the Blue Obelisk Data Repository * Document the atomic_data * update expected test results * update java tests * allow a bit more slop when comparing confs For cross-platform stability
This commit is contained in:
Francois Berenger
committed by
Greg Landrum
Greg Landrum
parent
874641cd43
commit
7ec8ec0bb9
@@ -1,6 +1,7 @@
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import unittest
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import os, copy
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import os
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import copy
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import math
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import numpy
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@@ -16,517 +17,523 @@ logger = logger()
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def feq(v1, v2, tol=1.e-4):
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return abs(v1 - v2) < tol
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return abs(v1 - v2) < tol
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def lstEq(l1, l2, tol=1.0e-4):
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ln = len(l1)
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if (ln != len(l2)):
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return 0
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ln = len(l1)
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if (ln != len(l2)):
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return 0
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for i in range(ln):
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if abs(l1[i] - l2[i]) > tol:
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return 0
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return 1
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for i in range(ln):
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if abs(l1[i] - l2[i]) > tol:
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return 0
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return 1
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def compareWithOld(smilesFile, sdFile):
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smiSup = Chem.SmilesMolSupplier(smilesFile, ",", 0, -1)
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sdsup = Chem.SDMolSupplier(sdFile)
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im = 0
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for mol in smiSup:
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cid = rdDistGeom.EmbedMolecule(mol, 10, 1)
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omol = sdsup[im]
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assert cid == 0
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conf = mol.GetConformer(0)
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oconf = omol.GetConformer()
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nat = mol.GetNumAtoms()
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for i in range(nat):
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#atm = mol.GetAtomWithIdx(i)
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#oatm = omol.GetAtomWithIdx(i)
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pos = conf.GetAtomPosition(i)
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opos = oconf.GetAtomPosition(i)
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if not lstEq(pos, opos):
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return 0
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im += 1
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return 1
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smiSup = Chem.SmilesMolSupplier(smilesFile, ",", 0, -1)
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sdsup = Chem.SDMolSupplier(sdFile)
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im = 0
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for mol in smiSup:
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cid = rdDistGeom.EmbedMolecule(mol, 10, 1)
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omol = sdsup[im]
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assert cid == 0
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conf = mol.GetConformer(0)
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oconf = omol.GetConformer()
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nat = mol.GetNumAtoms()
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for i in range(nat):
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#atm = mol.GetAtomWithIdx(i)
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#oatm = omol.GetAtomWithIdx(i)
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pos = conf.GetAtomPosition(i)
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opos = oconf.GetAtomPosition(i)
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if not lstEq(pos, opos):
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return 0
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im += 1
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return 1
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def compareMatrices(bm1, bm2, map, tol=1.0e-5):
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N = numpy.shape(bm1)[0]
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for i in range(1, N):
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for j in range(i):
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l, m = map[i], map[j]
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if (l < m):
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l, m = m, l
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if (abs(bm1[l, m] - bm2[i, j]) > tol):
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return 0
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N = numpy.shape(bm1)[0]
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for i in range(1, N):
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for j in range(i):
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l, m = map[i], map[j]
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if (l < m):
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l, m = m, l
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if (abs(bm1[l, m] - bm2[i, j]) > tol):
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return 0
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if (abs(bm1[m, l] - bm2[j, i]) > tol):
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return 0
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if (abs(bm1[m, l] - bm2[j, i]) > tol):
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return 0
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return 1
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return 1
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def compareOrder(smi1, smi2, tol=1.0e-5):
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m1 = Chem.MolFromSmiles(smi1)
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m2 = Chem.MolFromSmiles(smi2)
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bm1 = rdDistGeom.GetMoleculeBoundsMatrix(m1)
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bm2 = rdDistGeom.GetMoleculeBoundsMatrix(m2)
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map = m1.GetSubstructMatch(m2)
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return compareMatrices(bm1, bm2, map, tol)
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m1 = Chem.MolFromSmiles(smi1)
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m2 = Chem.MolFromSmiles(smi2)
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bm1 = rdDistGeom.GetMoleculeBoundsMatrix(m1)
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bm2 = rdDistGeom.GetMoleculeBoundsMatrix(m2)
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map = m1.GetSubstructMatch(m2)
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return compareMatrices(bm1, bm2, map, tol)
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def computeDist(lst1, lst2):
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res = 0.0
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for i, val in enumerate(lst1):
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res += (val - lst2[i]) * (val - lst2[i])
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res = math.sqrt(res)
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return res
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res = 0.0
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for i, val in enumerate(lst1):
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res += (val - lst2[i]) * (val - lst2[i])
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res = math.sqrt(res)
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return res
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def computeChiralVol(pt1, pt2, pt3, pt4):
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v1 = pt1 - pt4
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v2 = pt2 - pt4
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v3 = pt3 - pt4
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cp = v2.CrossProduct(v3)
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vol = v1.DotProduct(cp)
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return vol
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v1 = pt1 - pt4
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v2 = pt2 - pt4
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v3 = pt3 - pt4
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cp = v2.CrossProduct(v3)
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vol = v1.DotProduct(cp)
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return vol
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class TestCase(unittest.TestCase):
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def setUp(self):
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pass
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def setUp(self):
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pass
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def _test0Cdk2(self):
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fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
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'cis_trans_cases.csv')
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def _test0Cdk2(self):
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fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
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'cis_trans_cases.csv')
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ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
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'embedDistOpti.sdf')
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self.assertTrue(compareWithOld(fileN, ofile))
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ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
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'embedDistOpti.sdf')
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self.assertTrue(compareWithOld(fileN, ofile))
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def test1Small(self):
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#writer = Chem.SDWriter("test.sdf")
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# single double and tripple atoms cases should not fail
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mol = Chem.MolFromSmiles('O')
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rdDistGeom.EmbedMolecule(mol, 10, 1)
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conf = mol.GetConformer()
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self.assertTrue(lstEq(conf.GetAtomPosition(0), [0.0, 0.0, 0.0]))
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#writer.write(mol)
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def test1Small(self):
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#writer = Chem.SDWriter("test.sdf")
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# single double and tripple atoms cases should not fail
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mol = Chem.MolFromSmiles('O')
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rdDistGeom.EmbedMolecule(mol, 10, 1)
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conf = mol.GetConformer()
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self.assertTrue(lstEq(conf.GetAtomPosition(0), [0.0, 0.0, 0.0]))
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# writer.write(mol)
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mol = Chem.MolFromSmiles('CO')
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rdDistGeom.EmbedMolecule(mol, 10, 1)
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conf = mol.GetConformer()
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self.assertTrue(lstEq(conf.GetAtomPosition(0), [0.69192, 0.0, 0.0]))
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self.assertTrue(lstEq(conf.GetAtomPosition(1), [-0.69192, 0.0, 0.0]))
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#writer.write(mol)
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mol = Chem.MolFromSmiles('CO')
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rdDistGeom.EmbedMolecule(mol, 10, 1)
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conf = mol.GetConformer()
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self.assertTrue(lstEq(conf.GetAtomPosition(0), [0.69192, 0.0, 0.0]))
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self.assertTrue(lstEq(conf.GetAtomPosition(1), [-0.69192, 0.0, 0.0]))
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# writer.write(mol)
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mol = Chem.MolFromSmiles('CCC')
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rdDistGeom.EmbedMolecule(mol, 10, 1)
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conf = mol.GetConformer()
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self.assertTrue(lstEq(conf.GetAtomPosition(0), [-1.21676, -0.2989, 0.0]))
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self.assertTrue(lstEq(conf.GetAtomPosition(1), [-0.00604, 0.59337, 0.0]))
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self.assertTrue(lstEq(conf.GetAtomPosition(2), [1.22281, -0.29446, 0.0]))
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#writer.write(mol)
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mol = Chem.MolFromSmiles('CCC')
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rdDistGeom.EmbedMolecule(mol, 10, 1)
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conf = mol.GetConformer()
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self.assertTrue(lstEq(conf.GetAtomPosition(0), [-1.21676, -0.2989, 0.0]))
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self.assertTrue(lstEq(conf.GetAtomPosition(1), [-0.00604, 0.59337, 0.0]))
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self.assertTrue(lstEq(conf.GetAtomPosition(2), [1.22281, -0.29446, 0.0]))
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# writer.write(mol)
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mol = Chem.MolFromSmiles('O=C=O')
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rdDistGeom.EmbedMolecule(mol, 10, 1)
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conf = mol.GetConformer()
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mol = Chem.MolFromSmiles('O=C=O')
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rdDistGeom.EmbedMolecule(mol, 10, 1)
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conf = mol.GetConformer()
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#writer.write(mol)
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self.assertTrue(lstEq(conf.GetAtomPosition(0), [-1.2180, -0.06088, 0.0]))
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self.assertTrue(lstEq(conf.GetAtomPosition(1), [-0.00408, 0.12116, 0.0]))
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self.assertTrue(lstEq(conf.GetAtomPosition(2), [1.22207, -0.060276, 0.0]))
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# writer.write(mol)
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self.assertTrue(lstEq(conf.GetAtomPosition(0), [-1.2180, -0.06088, 0.0]))
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self.assertTrue(lstEq(conf.GetAtomPosition(1), [-0.00408, 0.12116, 0.0]))
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self.assertTrue(lstEq(conf.GetAtomPosition(2), [1.22207, -0.060276, 0.0]))
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mol = Chem.MolFromSmiles('C=C=C=C')
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rdDistGeom.EmbedMolecule(mol, 10, 1, useExpTorsionAnglePrefs=False,
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useBasicKnowledge=False)
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conf = mol.GetConformer()
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mol = Chem.MolFromSmiles('C=C=C=C')
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rdDistGeom.EmbedMolecule(mol, 10, 1, useExpTorsionAnglePrefs=False,
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useBasicKnowledge=False)
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conf = mol.GetConformer()
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#writer.write(mol)
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# writer.write(mol)
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d1 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(1))
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self.assertTrue(feq(d1, 1.31, 0.01))
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d2 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(2))
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self.assertTrue(feq(d2, 2.59, 0.05))
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d3 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(3))
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self.assertTrue(feq(d3, 3.84, 0.1))
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d4 = computeDist(conf.GetAtomPosition(1), conf.GetAtomPosition(2))
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self.assertTrue(feq(d4, 1.29, 0.01))
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d5 = computeDist(conf.GetAtomPosition(1), conf.GetAtomPosition(3))
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self.assertTrue(feq(d5, 2.54, 0.1))
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d6 = computeDist(conf.GetAtomPosition(2), conf.GetAtomPosition(3))
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self.assertTrue(feq(d6, 1.31, 0.01))
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d1 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(1))
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self.assertTrue(feq(d1, 1.31, 0.01))
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d2 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(2))
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self.assertTrue(feq(d2, 2.59, 0.05))
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d3 = computeDist(conf.GetAtomPosition(0), conf.GetAtomPosition(3))
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self.assertTrue(feq(d3, 3.84, 0.1))
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d4 = computeDist(conf.GetAtomPosition(1), conf.GetAtomPosition(2))
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self.assertTrue(feq(d4, 1.29, 0.01))
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d5 = computeDist(conf.GetAtomPosition(1), conf.GetAtomPosition(3))
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self.assertTrue(feq(d5, 2.54, 0.1))
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d6 = computeDist(conf.GetAtomPosition(2), conf.GetAtomPosition(3))
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self.assertTrue(feq(d6, 1.31, 0.01))
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def test2Utils(self):
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mol = Chem.MolFromSmiles('CC')
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bm = rdDistGeom.GetMoleculeBoundsMatrix(mol)
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self.assertTrue(bm[1, 0] > 0)
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self.assertTrue(bm[0, 1] > 0)
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self.assertTrue(bm[0, 1] >= bm[1, 0])
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self.assertTrue(bm[1, 0] < 1.510)
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self.assertTrue(bm[0, 1] > 1.510)
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def test2Utils(self):
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mol = Chem.MolFromSmiles('CC')
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bm = rdDistGeom.GetMoleculeBoundsMatrix(mol)
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self.assertTrue(bm[1, 0] > 0)
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self.assertTrue(bm[0, 1] > 0)
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self.assertTrue(bm[0, 1] >= bm[1, 0])
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self.assertTrue(bm[1, 0] < 1.510)
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self.assertTrue(bm[0, 1] > 1.510)
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def test3MultiConf(self):
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mol = Chem.MolFromSmiles("CC(C)(C)c(cc12)n[n]2C(=O)/C=C(N1)/COC")
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cids = rdDistGeom.EmbedMultipleConfs(mol, 10, maxAttempts=30, randomSeed=100,
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useExpTorsionAnglePrefs=False,
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useBasicKnowledge=False)
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energies = [112.98, 103.57, 110.78, 100.40, 95.37, 101.64, 114.72, 112.65, 124.53, 107.50]
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nenergies = []
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for cid in cids:
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ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, cid)
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ee = ff.CalcEnergy()
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nenergies.append(ee)
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#print(['%.2f'%x for x in nenergies])
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#print(nenergies)
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self.assertTrue(lstEq(energies, nenergies, tol=1e-2))
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def test3MultiConf(self):
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mol = Chem.MolFromSmiles("CC(C)(C)c(cc12)n[n]2C(=O)/C=C(N1)/COC")
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cids = rdDistGeom.EmbedMultipleConfs(mol, 10, maxAttempts=30, randomSeed=100,
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useExpTorsionAnglePrefs=False,
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useBasicKnowledge=False)
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energies = [115.460, 105.891, 109.868, 104.415,
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92.944, 140.917, 139.468, 95.081, 123.528, 107.885]
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nenergies = []
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for cid in cids:
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ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, cid)
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ee = ff.CalcEnergy()
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nenergies.append(ee)
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#print(['%.2f' % x for x in nenergies])
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# print(nenergies)
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self.assertTrue(lstEq(energies, nenergies, tol=1e-2))
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def test4OrderDependence(self):
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self.assertTrue(
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compareOrder("CC(C)(C)C(=O)NC(C1)CC(N2C)CCC12", "CN1C2CCC1CC(NC(=O)C(C)(C)C)C2"))
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#issue 230
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self.assertTrue(compareOrder("C#CC(C)(C)N(CN1)C\\N=C/1SC", "CSC1=NCN(C(C)(C)C#C)CN1"))
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#issue 232
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self.assertTrue(
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compareOrder("CC(C)(C)C(=O)NC(C1)CC(N2C)CCC12", "CN1C2CCC1CC(NC(=O)C(C)(C)C)C2"))
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def test4OrderDependence(self):
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self.assertTrue(
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compareOrder("CC(C)(C)C(=O)NC(C1)CC(N2C)CCC12", "CN1C2CCC1CC(NC(=O)C(C)(C)C)C2"))
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# issue 230
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self.assertTrue(compareOrder("C#CC(C)(C)N(CN1)C\\N=C/1SC", "CSC1=NCN(C(C)(C)C#C)CN1"))
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# issue 232
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self.assertTrue(
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compareOrder("CC(C)(C)C(=O)NC(C1)CC(N2C)CCC12", "CN1C2CCC1CC(NC(=O)C(C)(C)C)C2"))
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def test5Issue285(self):
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m = Chem.MolFromSmiles('CNC=O')
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cs = rdDistGeom.EmbedMultipleConfs(m, 10)
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for i, ci in enumerate(cs):
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for j in range(i + 1, len(cs)):
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cj = cs[j]
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self.assertTrue(Chem.MolToMolBlock(m, confId=ci) != Chem.MolToMolBlock(m, confId=cj))
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def test5Issue285(self):
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m = Chem.MolFromSmiles('CNC=O')
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cs = rdDistGeom.EmbedMultipleConfs(m, 10)
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for i, ci in enumerate(cs):
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for j in range(i + 1, len(cs)):
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cj = cs[j]
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self.assertTrue(Chem.MolToMolBlock(m, confId=ci)
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!= Chem.MolToMolBlock(m, confId=cj))
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def test6RmsPruning(self):
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smiles = [
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'CC(C)CC(NC(C1[N+]CCC1)=O)C([O-])=O', 'CC(NC(CO)C(O)c1ccc([N+]([O-])=O)cc1)=O',
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'CC([N+])C(NC(C)C(N1C(C=O)CCC1)=O)=O', 'CC(NC1C(O)C=C(C([O-])=O)OC1C(O)C(O)CO)=O',
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'CCCC=C(NC(C1CC1(C)C)=O)C([O-])=O', 'OCC(O)C(O)C(Cn1c2c(cc(C)c(C)c2)nc-2c(=O)[nH]c(=O)nc12)O'
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]
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def test6RmsPruning(self):
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smiles = [
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'CC(C)CC(NC(C1[N+]CCC1)=O)C([O-])=O', 'CC(NC(CO)C(O)c1ccc([N+]([O-])=O)cc1)=O',
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'CC([N+])C(NC(C)C(N1C(C=O)CCC1)=O)=O', 'CC(NC1C(O)C=C(C([O-])=O)OC1C(O)C(O)CO)=O',
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'CCCC=C(NC(C1CC1(C)C)=O)C([O-])=O', 'OCC(O)C(O)C(Cn1c2c(cc(C)c(C)c2)nc-2c(=O)[nH]c(=O)nc12)O'
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]
|
||||
|
||||
nconfs = []
|
||||
expected = [5, 6, 6, 6, 6, 3]
|
||||
for smi in smiles:
|
||||
mol = Chem.MolFromSmiles(smi)
|
||||
cids = rdDistGeom.EmbedMultipleConfs(mol, 50, maxAttempts=30, randomSeed=100,
|
||||
pruneRmsThresh=1.5)
|
||||
nconfs.append(len(cids))
|
||||
nconfs = []
|
||||
expected = [4, 5, 5, 4, 5, 4]
|
||||
for smi in smiles:
|
||||
mol = Chem.MolFromSmiles(smi)
|
||||
cids = rdDistGeom.EmbedMultipleConfs(mol, 50, maxAttempts=30, randomSeed=100,
|
||||
pruneRmsThresh=1.5)
|
||||
nconfs.append(len(cids))
|
||||
|
||||
d = [abs(x - y) for x, y in zip(expected, nconfs)]
|
||||
d = [abs(x - y) for x, y in zip(expected, nconfs)]
|
||||
# print(nconfs)
|
||||
self.assertTrue(max(d) <= 1)
|
||||
|
||||
self.assertTrue(max(d) <= 1)
|
||||
def test6Chirality(self):
|
||||
# turn on chirality and we should get chiral volume that is pretty consistent and
|
||||
# positive
|
||||
tgtVol = 13.0
|
||||
smiles = "Cl[C@](C)(F)Br"
|
||||
mol = Chem.MolFromSmiles(smiles)
|
||||
cids = rdDistGeom.EmbedMultipleConfs(mol, 30, maxAttempts=30, randomSeed=100)
|
||||
self.assertTrue(len(cids) == 30)
|
||||
for cid in cids:
|
||||
conf = mol.GetConformer(cid)
|
||||
vol = computeChiralVol(
|
||||
conf.GetAtomPosition(0),
|
||||
conf.GetAtomPosition(2), conf.GetAtomPosition(3), conf.GetAtomPosition(4))
|
||||
self.assertTrue(abs(vol - tgtVol) < 1)
|
||||
|
||||
def test6Chirality(self):
|
||||
# turn on chirality and we should get chiral volume that is pretty consistent and
|
||||
# positive
|
||||
tgtVol = 13.0
|
||||
smiles = "Cl[C@](C)(F)Br"
|
||||
mol = Chem.MolFromSmiles(smiles)
|
||||
cids = rdDistGeom.EmbedMultipleConfs(mol, 30, maxAttempts=30, randomSeed=100)
|
||||
self.assertTrue(len(cids) == 30)
|
||||
for cid in cids:
|
||||
conf = mol.GetConformer(cid)
|
||||
vol = computeChiralVol(
|
||||
conf.GetAtomPosition(0),
|
||||
conf.GetAtomPosition(2), conf.GetAtomPosition(3), conf.GetAtomPosition(4))
|
||||
self.assertTrue(abs(vol - tgtVol) < 1)
|
||||
# turn of chirality and now we should see both chiral forms
|
||||
smiles = "ClC(C)(F)Br"
|
||||
mol = Chem.MolFromSmiles(smiles)
|
||||
cids = rdDistGeom.EmbedMultipleConfs(mol, 30, maxAttempts=30, randomSeed=120)
|
||||
self.assertTrue(len(cids) == 30)
|
||||
nPos = 0
|
||||
nNeg = 0
|
||||
for cid in cids:
|
||||
conf = mol.GetConformer(cid)
|
||||
vol = computeChiralVol(
|
||||
conf.GetAtomPosition(0),
|
||||
conf.GetAtomPosition(2), conf.GetAtomPosition(3), conf.GetAtomPosition(4))
|
||||
self.assertTrue(abs(vol - tgtVol) < 1 or abs(vol + tgtVol) < 1)
|
||||
if vol < 0:
|
||||
nNeg += 1
|
||||
else:
|
||||
nPos += 1
|
||||
self.assertTrue(nPos > 0)
|
||||
self.assertTrue(nNeg > 0)
|
||||
|
||||
# turn of chirality and now we should see both chiral forms
|
||||
smiles = "ClC(C)(F)Br"
|
||||
mol = Chem.MolFromSmiles(smiles)
|
||||
cids = rdDistGeom.EmbedMultipleConfs(mol, 30, maxAttempts=30, randomSeed=120)
|
||||
self.assertTrue(len(cids) == 30)
|
||||
nPos = 0
|
||||
nNeg = 0
|
||||
for cid in cids:
|
||||
conf = mol.GetConformer(cid)
|
||||
vol = computeChiralVol(
|
||||
conf.GetAtomPosition(0),
|
||||
conf.GetAtomPosition(2), conf.GetAtomPosition(3), conf.GetAtomPosition(4))
|
||||
self.assertTrue(abs(vol - tgtVol) < 1 or abs(vol + tgtVol) < 1)
|
||||
if vol < 0:
|
||||
nNeg += 1
|
||||
else:
|
||||
nPos += 1
|
||||
self.assertTrue(nPos > 0)
|
||||
self.assertTrue(nNeg > 0)
|
||||
tgtVol = 5.0
|
||||
for i in range(10):
|
||||
smiles = "Cl[C@H](F)Br"
|
||||
mol = Chem.MolFromSmiles(smiles)
|
||||
ci = rdDistGeom.EmbedMolecule(mol, 30, (i + 1) * 10)
|
||||
conf = mol.GetConformer(ci)
|
||||
vol = computeChiralVol(
|
||||
conf.GetAtomPosition(0),
|
||||
conf.GetAtomPosition(1), conf.GetAtomPosition(2), conf.GetAtomPosition(3))
|
||||
self.assertTrue(abs(vol - tgtVol) < 1, "%s %s" % (vol, tgtVol))
|
||||
|
||||
tgtVol = 5.0
|
||||
for i in range(10):
|
||||
smiles = "Cl[C@H](F)Br"
|
||||
mol = Chem.MolFromSmiles(smiles)
|
||||
ci = rdDistGeom.EmbedMolecule(mol, 30, (i + 1) * 10)
|
||||
conf = mol.GetConformer(ci)
|
||||
vol = computeChiralVol(
|
||||
conf.GetAtomPosition(0),
|
||||
conf.GetAtomPosition(1), conf.GetAtomPosition(2), conf.GetAtomPosition(3))
|
||||
self.assertTrue(abs(vol - tgtVol) < 1, "%s %s" % (vol, tgtVol))
|
||||
tgtVol = 3.5
|
||||
expected = [-3.62, -3.67, -3.72, 3.91, 3.95, 3.98, 3.90, 3.94, 3.98, 3.91]
|
||||
nPos = 0
|
||||
nNeg = 0
|
||||
for i in range(30):
|
||||
smiles = "ClC(F)Br"
|
||||
mol = Chem.MolFromSmiles(smiles)
|
||||
ci = rdDistGeom.EmbedMolecule(mol, 30, (i + 1) * 10)
|
||||
conf = mol.GetConformer(ci)
|
||||
vol = computeChiralVol(
|
||||
conf.GetAtomPosition(0),
|
||||
conf.GetAtomPosition(1), conf.GetAtomPosition(2), conf.GetAtomPosition(3))
|
||||
self.assertTrue(abs(vol - tgtVol) < 1 or abs(vol + tgtVol) < 1)
|
||||
if vol < 0:
|
||||
nNeg += 1
|
||||
else:
|
||||
nPos += 1
|
||||
|
||||
tgtVol = 3.5
|
||||
expected = [-3.62, -3.67, -3.72, 3.91, 3.95, 3.98, 3.90, 3.94, 3.98, 3.91]
|
||||
nPos = 0
|
||||
nNeg = 0
|
||||
for i in range(30):
|
||||
smiles = "ClC(F)Br"
|
||||
mol = Chem.MolFromSmiles(smiles)
|
||||
ci = rdDistGeom.EmbedMolecule(mol, 30, (i + 1) * 10)
|
||||
conf = mol.GetConformer(ci)
|
||||
vol = computeChiralVol(
|
||||
conf.GetAtomPosition(0),
|
||||
conf.GetAtomPosition(1), conf.GetAtomPosition(2), conf.GetAtomPosition(3))
|
||||
self.assertTrue(abs(vol - tgtVol) < 1 or abs(vol + tgtVol) < 1)
|
||||
if vol < 0:
|
||||
nNeg += 1
|
||||
else:
|
||||
nPos += 1
|
||||
self.assertTrue(nPos > 0)
|
||||
self.assertTrue(nNeg > 0)
|
||||
|
||||
self.assertTrue(nPos > 0)
|
||||
self.assertTrue(nNeg > 0)
|
||||
smiles = "Cl[C@H](F)Br"
|
||||
m = Chem.MolFromSmiles(smiles)
|
||||
mol = Chem.AddHs(m)
|
||||
cids = rdDistGeom.EmbedMultipleConfs(mol, 10, maxAttempts=30, randomSeed=100)
|
||||
self.assertTrue(len(cids) == 10)
|
||||
tgtVol = 10.5
|
||||
for cid in cids:
|
||||
conf = mol.GetConformer(cid)
|
||||
vol = computeChiralVol(
|
||||
conf.GetAtomPosition(0),
|
||||
conf.GetAtomPosition(2), conf.GetAtomPosition(3), conf.GetAtomPosition(4))
|
||||
self.assertTrue(abs(vol - tgtVol) < 2.)
|
||||
|
||||
smiles = "Cl[C@H](F)Br"
|
||||
m = Chem.MolFromSmiles(smiles)
|
||||
mol = Chem.AddHs(m)
|
||||
cids = rdDistGeom.EmbedMultipleConfs(mol, 10, maxAttempts=30, randomSeed=100)
|
||||
self.assertTrue(len(cids) == 10)
|
||||
tgtVol = 10.5
|
||||
for cid in cids:
|
||||
conf = mol.GetConformer(cid)
|
||||
vol = computeChiralVol(
|
||||
conf.GetAtomPosition(0),
|
||||
conf.GetAtomPosition(2), conf.GetAtomPosition(3), conf.GetAtomPosition(4))
|
||||
self.assertTrue(abs(vol - tgtVol) < 2.)
|
||||
# let's try a little more complicated system
|
||||
expectedV1 = -2.0
|
||||
expectedV2 = -2.9
|
||||
|
||||
# let's try a little more complicated system
|
||||
expectedV1 = -2.0
|
||||
expectedV2 = -2.9
|
||||
for i in range(5):
|
||||
smi = "C1=CC=C(C=C1)[C@H](OC1=C[NH]N=C1)C(=O)[NH]C[C@H](Cl)C1=CC=NC=C1"
|
||||
mol = Chem.MolFromSmiles(smi)
|
||||
ci = rdDistGeom.EmbedMolecule(mol, randomSeed=(i + 1) * 15)
|
||||
self.assertTrue(ci >= 0)
|
||||
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, ci)
|
||||
ff.Minimize()
|
||||
|
||||
for i in range(5):
|
||||
smi = "C1=CC=C(C=C1)[C@H](OC1=C[NH]N=C1)C(=O)[NH]C[C@H](Cl)C1=CC=NC=C1"
|
||||
mol = Chem.MolFromSmiles(smi)
|
||||
ci = rdDistGeom.EmbedMolecule(mol, randomSeed=(i + 1) * 15)
|
||||
self.assertTrue(ci >= 0)
|
||||
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, ci)
|
||||
ff.Minimize()
|
||||
conf = mol.GetConformer(ci)
|
||||
vol1 = computeChiralVol(
|
||||
conf.GetAtomPosition(6),
|
||||
conf.GetAtomPosition(3), conf.GetAtomPosition(7), conf.GetAtomPosition(13))
|
||||
self.assertTrue(abs(vol1 - expectedV1) < 1 or abs(vol1 + expectedV1) < 1)
|
||||
if vol1 < 0:
|
||||
nNeg += 1
|
||||
else:
|
||||
nPos += 1
|
||||
|
||||
conf = mol.GetConformer(ci)
|
||||
vol1 = computeChiralVol(
|
||||
conf.GetAtomPosition(6),
|
||||
conf.GetAtomPosition(3), conf.GetAtomPosition(7), conf.GetAtomPosition(13))
|
||||
self.assertTrue(abs(vol1 - expectedV1) < 1 or abs(vol1 + expectedV1) < 1)
|
||||
if vol1 < 0:
|
||||
nNeg += 1
|
||||
else:
|
||||
nPos += 1
|
||||
vol2 = computeChiralVol(
|
||||
conf.GetAtomPosition(17),
|
||||
conf.GetAtomPosition(16), conf.GetAtomPosition(18), conf.GetAtomPosition(19))
|
||||
self.assertTrue(abs(vol2 - expectedV2) < 1 or abs(vol2 + expectedV2) < 1)
|
||||
|
||||
vol2 = computeChiralVol(
|
||||
conf.GetAtomPosition(17),
|
||||
conf.GetAtomPosition(16), conf.GetAtomPosition(18), conf.GetAtomPosition(19))
|
||||
self.assertTrue(abs(vol2 - expectedV2) < 1 or abs(vol2 + expectedV2) < 1)
|
||||
# remove the chiral specification and we should see other chiral
|
||||
# forms of the compound
|
||||
expectedV1 = 2.0 # [-2.30, -2.31, -2.30, 2.30, -1.77]
|
||||
expectedV2 = 2.8 # [2.90, 2.89, 2.69, -2.90, -2.93]
|
||||
|
||||
# remove the chiral specification and we should see other chiral
|
||||
# forms of the compound
|
||||
expectedV1 = 2.0 #[-2.30, -2.31, -2.30, 2.30, -1.77]
|
||||
expectedV2 = 2.8 #[2.90, 2.89, 2.69, -2.90, -2.93]
|
||||
self.assertTrue(nPos > 0)
|
||||
self.assertTrue(nNeg > 0)
|
||||
for i in range(5):
|
||||
smi = "C1=CC=C(C=C1)C(OC1=C[NH]N=C1)C(=O)[NH]CC(Cl)C1=CC=NC=C1"
|
||||
mol = Chem.MolFromSmiles(smi)
|
||||
ci = rdDistGeom.EmbedMolecule(mol, 30, (i + 1) * 10)
|
||||
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, ci)
|
||||
ff.Minimize()
|
||||
|
||||
self.assertTrue(nPos > 0)
|
||||
self.assertTrue(nNeg > 0)
|
||||
for i in range(5):
|
||||
smi = "C1=CC=C(C=C1)C(OC1=C[NH]N=C1)C(=O)[NH]CC(Cl)C1=CC=NC=C1"
|
||||
mol = Chem.MolFromSmiles(smi)
|
||||
ci = rdDistGeom.EmbedMolecule(mol, 30, (i + 1) * 10)
|
||||
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, ci)
|
||||
ff.Minimize()
|
||||
conf = mol.GetConformer(ci)
|
||||
vol1 = computeChiralVol(
|
||||
conf.GetAtomPosition(6),
|
||||
conf.GetAtomPosition(3), conf.GetAtomPosition(7), conf.GetAtomPosition(13))
|
||||
vol2 = computeChiralVol(
|
||||
conf.GetAtomPosition(17),
|
||||
conf.GetAtomPosition(16), conf.GetAtomPosition(18), conf.GetAtomPosition(19))
|
||||
self.assertTrue(abs(abs(vol1) - expectedV1) < 1.0)
|
||||
self.assertTrue(abs(abs(vol2) - expectedV2) < 1.0)
|
||||
|
||||
conf = mol.GetConformer(ci)
|
||||
vol1 = computeChiralVol(
|
||||
conf.GetAtomPosition(6),
|
||||
conf.GetAtomPosition(3), conf.GetAtomPosition(7), conf.GetAtomPosition(13))
|
||||
vol2 = computeChiralVol(
|
||||
conf.GetAtomPosition(17),
|
||||
conf.GetAtomPosition(16), conf.GetAtomPosition(18), conf.GetAtomPosition(19))
|
||||
self.assertTrue(abs(abs(vol1) - expectedV1) < 1.0)
|
||||
self.assertTrue(abs(abs(vol2) - expectedV2) < 1.0)
|
||||
def test7ConstrainedEmbedding(self):
|
||||
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'constrain1.sdf')
|
||||
suppl = Chem.SDMolSupplier(ofile)
|
||||
ref = next(suppl)
|
||||
probe = copy.deepcopy(ref)
|
||||
|
||||
def test7ConstrainedEmbedding(self):
|
||||
ofile = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'constrain1.sdf')
|
||||
suppl = Chem.SDMolSupplier(ofile)
|
||||
ref = next(suppl)
|
||||
probe = copy.deepcopy(ref)
|
||||
cMap = {}
|
||||
for i in range(5):
|
||||
cMap[i] = ref.GetConformer().GetAtomPosition(i)
|
||||
ci = rdDistGeom.EmbedMolecule(probe, coordMap=cMap, randomSeed=23)
|
||||
self.assertTrue(ci > -1)
|
||||
algMap = list(zip(range(5), range(5)))
|
||||
ssd = rdMolAlign.AlignMol(probe, ref, atomMap=algMap)
|
||||
self.assertTrue(ssd < 0.1)
|
||||
|
||||
cMap = {}
|
||||
for i in range(5):
|
||||
cMap[i] = ref.GetConformer().GetAtomPosition(i)
|
||||
ci = rdDistGeom.EmbedMolecule(probe, coordMap=cMap, randomSeed=23)
|
||||
self.assertTrue(ci > -1)
|
||||
algMap = list(zip(range(5), range(5)))
|
||||
ssd = rdMolAlign.AlignMol(probe, ref, atomMap=algMap)
|
||||
self.assertTrue(ssd < 0.1)
|
||||
def test8MultiThreadMultiConf(self):
|
||||
if (rdBase.rdkitBuild.split('|')[2] != "MINGW"):
|
||||
ENERGY_TOLERANCE = 1.0e-6
|
||||
MSD_TOLERANCE = 1.0e-6
|
||||
else:
|
||||
ENERGY_TOLERANCE = 1.0
|
||||
MSD_TOLERANCE = 1.0e-5
|
||||
mol = Chem.AddHs(Chem.MolFromSmiles("CC(C)(C)c(cc12)n[n]2C(=O)/C=C(N1)/COC"))
|
||||
cids = rdDistGeom.EmbedMultipleConfs(mol, 200, maxAttempts=30, randomSeed=100)
|
||||
energies = []
|
||||
for cid in cids:
|
||||
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, cid)
|
||||
ee = ff.CalcEnergy()
|
||||
energies.append(ee)
|
||||
|
||||
def test8MultiThreadMultiConf(self):
|
||||
if (rdBase.rdkitBuild.split('|')[2] != "MINGW"):
|
||||
ENERGY_TOLERANCE = 1.0e-6
|
||||
MSD_TOLERANCE = 1.0e-6
|
||||
else:
|
||||
ENERGY_TOLERANCE = 1.0
|
||||
MSD_TOLERANCE = 1.0e-5
|
||||
mol = Chem.AddHs(Chem.MolFromSmiles("CC(C)(C)c(cc12)n[n]2C(=O)/C=C(N1)/COC"))
|
||||
cids = rdDistGeom.EmbedMultipleConfs(mol, 200, maxAttempts=30, randomSeed=100)
|
||||
energies = []
|
||||
for cid in cids:
|
||||
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol, 10.0, cid)
|
||||
ee = ff.CalcEnergy()
|
||||
energies.append(ee)
|
||||
mol2 = Chem.AddHs(Chem.MolFromSmiles("CC(C)(C)c(cc12)n[n]2C(=O)/C=C(N1)/COC"))
|
||||
cids2 = rdDistGeom.EmbedMultipleConfs(
|
||||
mol2, 200, maxAttempts=30, randomSeed=100, numThreads=4)
|
||||
self.assertTrue(lstEq(cids, cids2))
|
||||
nenergies = []
|
||||
for cid in cids2:
|
||||
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol2, 10.0, cid)
|
||||
ee = ff.CalcEnergy()
|
||||
nenergies.append(ee)
|
||||
|
||||
mol2 = Chem.AddHs(Chem.MolFromSmiles("CC(C)(C)c(cc12)n[n]2C(=O)/C=C(N1)/COC"))
|
||||
cids2 = rdDistGeom.EmbedMultipleConfs(mol2, 200, maxAttempts=30, randomSeed=100, numThreads=4)
|
||||
self.assertTrue(lstEq(cids, cids2))
|
||||
nenergies = []
|
||||
for cid in cids2:
|
||||
ff = ChemicalForceFields.UFFGetMoleculeForceField(mol2, 10.0, cid)
|
||||
ee = ff.CalcEnergy()
|
||||
nenergies.append(ee)
|
||||
self.assertTrue(lstEq(energies, nenergies, tol=ENERGY_TOLERANCE))
|
||||
|
||||
self.assertTrue(lstEq(energies, nenergies, tol=ENERGY_TOLERANCE))
|
||||
for cid in cids:
|
||||
msd = 0.0
|
||||
for i in range(mol.GetNumAtoms()):
|
||||
msd += (mol.GetConformer().GetAtomPosition(i) -
|
||||
mol2.GetConformer().GetAtomPosition(i)).LengthSq()
|
||||
msd /= mol.GetNumAtoms()
|
||||
self.assertTrue(msd < MSD_TOLERANCE)
|
||||
|
||||
for cid in cids:
|
||||
msd = 0.0
|
||||
for i in range(mol.GetNumAtoms()):
|
||||
msd += (mol.GetConformer().GetAtomPosition(i) \
|
||||
- mol2.GetConformer().GetAtomPosition(i)).LengthSq()
|
||||
msd /= mol.GetNumAtoms()
|
||||
self.assertTrue(msd < MSD_TOLERANCE)
|
||||
def _compareConfs(self, mol, ref, molConfId, refConfId):
|
||||
self.assertEqual(mol.GetNumAtoms(), ref.GetNumAtoms())
|
||||
molConf = mol.GetConformer(molConfId)
|
||||
refConf = ref.GetConformer(refConfId)
|
||||
for i in range(mol.GetNumAtoms()):
|
||||
mp = molConf.GetAtomPosition(i)
|
||||
rp = refConf.GetAtomPosition(i)
|
||||
self.assertAlmostEqual((mp - rp).Length(), 0.0, 3)
|
||||
|
||||
def _compareConfs(self, mol, ref, molConfId, refConfId):
|
||||
self.assertEqual(mol.GetNumAtoms(), ref.GetNumAtoms())
|
||||
molConf = mol.GetConformer(molConfId)
|
||||
refConf = ref.GetConformer(refConfId)
|
||||
for i in range(mol.GetNumAtoms()):
|
||||
mp = molConf.GetAtomPosition(i)
|
||||
rp = refConf.GetAtomPosition(i)
|
||||
self.assertAlmostEqual((mp - rp).Length(), 0.0, 3)
|
||||
def test9EmbedParams(self):
|
||||
mol = Chem.AddHs(Chem.MolFromSmiles('OCCC'))
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'simple_torsion.dg.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
params = rdDistGeom.EmbedParameters()
|
||||
params.randomSeed = 42
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
|
||||
def test9EmbedParams(self):
|
||||
mol = Chem.AddHs(Chem.MolFromSmiles('OCCC'))
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'simple_torsion.dg.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
params = rdDistGeom.EmbedParameters()
|
||||
params.randomSeed = 42
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'simple_torsion.etdg.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
params = rdDistGeom.EmbedParameters()
|
||||
params.randomSeed = 42
|
||||
params.useExpTorsionAnglePrefs = True
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
params = rdDistGeom.ETDG()
|
||||
params.randomSeed = 42
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'simple_torsion.etdg.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
params = rdDistGeom.EmbedParameters()
|
||||
params.randomSeed = 42
|
||||
params.useExpTorsionAnglePrefs = True
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
params = rdDistGeom.ETDG()
|
||||
params.randomSeed = 42
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'simple_torsion.etkdg.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
params = rdDistGeom.EmbedParameters()
|
||||
params.randomSeed = 42
|
||||
params.useExpTorsionAnglePrefs = True
|
||||
params.useBasicKnowledge = True
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
params = rdDistGeom.ETKDG()
|
||||
params.randomSeed = 42
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'simple_torsion.etkdg.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
params = rdDistGeom.EmbedParameters()
|
||||
params.randomSeed = 42
|
||||
params.useExpTorsionAnglePrefs = True
|
||||
params.useBasicKnowledge = True
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
params = rdDistGeom.ETKDG()
|
||||
params.randomSeed = 42
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'simple_torsion.kdg.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
params = rdDistGeom.EmbedParameters()
|
||||
params.randomSeed = 42
|
||||
params.useBasicKnowledge = True
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
params = rdDistGeom.KDG()
|
||||
params.randomSeed = 42
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'simple_torsion.kdg.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
params = rdDistGeom.EmbedParameters()
|
||||
params.randomSeed = 42
|
||||
params.useBasicKnowledge = True
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
params = rdDistGeom.KDG()
|
||||
params.randomSeed = 42
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
def test10ETKDGv2(self):
|
||||
mol = Chem.AddHs(Chem.MolFromSmiles('n1cccc(C)c1ON'))
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'torsion.etkdg.v2.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
params = rdDistGeom.ETKDGv2()
|
||||
params.randomSeed = 42
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
|
||||
def test10ETKDGv2(self):
|
||||
mol = Chem.AddHs(Chem.MolFromSmiles('n1cccc(C)c1ON'))
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'torsion.etkdg.v2.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
params = rdDistGeom.ETKDGv2()
|
||||
params.randomSeed = 42
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, params), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
def assertDeterministicWithSeed(self, seed):
|
||||
input_mol = Chem.MolFromSmiles('CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)NC(CCC(=O)O)C(=O)O)cc1')
|
||||
|
||||
def assertDeterministicWithSeed(self, seed):
|
||||
input_mol = Chem.MolFromSmiles('CN(Cc1cnc2nc(N)nc(N)c2n1)c1ccc(C(=O)NC(CCC(=O)O)C(=O)O)cc1')
|
||||
params = AllChem.ETKDG()
|
||||
params.pruneRmsThresh = -1.0 # skip internal RMSD pruning
|
||||
if seed is not None:
|
||||
params.randomSeed = seed
|
||||
|
||||
params = AllChem.ETKDG()
|
||||
params.pruneRmsThresh = -1.0 # skip internal RMSD pruning
|
||||
if seed is not None:
|
||||
params.randomSeed = seed
|
||||
firstMol = Chem.AddHs(input_mol)
|
||||
firstIds = AllChem.EmbedMultipleConfs(firstMol, 11, params)
|
||||
|
||||
firstMol = Chem.AddHs(input_mol)
|
||||
firstIds = AllChem.EmbedMultipleConfs(firstMol, 11, params)
|
||||
secondMol = Chem.AddHs(input_mol)
|
||||
secondIds = AllChem.EmbedMultipleConfs(secondMol, 11, params)
|
||||
|
||||
secondMol = Chem.AddHs(input_mol)
|
||||
secondIds = AllChem.EmbedMultipleConfs(secondMol, 11, params)
|
||||
self.assertEqual(list(firstIds), list(secondIds))
|
||||
self.assertEqual(firstMol.GetNumConformers(), secondMol.GetNumConformers())
|
||||
|
||||
self.assertEqual(list(firstIds), list(secondIds))
|
||||
self.assertEqual(firstMol.GetNumConformers(), secondMol.GetNumConformers())
|
||||
nonDeterministic = False
|
||||
for confIdx in range(firstMol.GetNumConformers()):
|
||||
|
||||
nonDeterministic = False
|
||||
for confIdx in range(firstMol.GetNumConformers()):
|
||||
firstConf = firstMol.GetConformer(confIdx)
|
||||
secondConf = secondMol.GetConformer(confIdx)
|
||||
|
||||
firstConf = firstMol.GetConformer(confIdx)
|
||||
secondConf = secondMol.GetConformer(confIdx)
|
||||
firstPositions = firstConf.GetPositions()
|
||||
secondPositions = secondConf.GetPositions()
|
||||
|
||||
firstPositions = firstConf.GetPositions()
|
||||
secondPositions = secondConf.GetPositions()
|
||||
d = firstPositions - secondPositions
|
||||
rmsd = numpy.sqrt(numpy.sum(d * d))
|
||||
if seed >= 0:
|
||||
self.assertEqual(rmsd, 0.0)
|
||||
elif rmsd != 0.0:
|
||||
nonDeterministic = True
|
||||
if seed < 0:
|
||||
self.assertTrue(nonDeterministic)
|
||||
|
||||
d = firstPositions - secondPositions
|
||||
rmsd = numpy.sqrt(numpy.sum(d * d))
|
||||
if seed >= 0:
|
||||
self.assertEquals(rmsd, 0.0)
|
||||
elif rmsd != 0.0:
|
||||
nonDeterministic = True
|
||||
if seed < 0:
|
||||
self.assertTrue(nonDeterministic)
|
||||
def testETKDGIsDeterministic(self):
|
||||
self.assertDeterministicWithSeed(-1) # not deterministic
|
||||
self.assertDeterministicWithSeed(0) # deterministic
|
||||
self.assertDeterministicWithSeed(1) # deterministic
|
||||
# as large as we can go without overflowing since 11 * 195225786 should not overflow the int
|
||||
self.assertDeterministicWithSeed(195225786)
|
||||
self.assertDeterministicWithSeed(195225787) # one higher seed will overflow though
|
||||
# another large seeds that shouldn't overflow internals and make them non-deterministic
|
||||
self.assertDeterministicWithSeed(0x1CEB00DA)
|
||||
|
||||
def testETKDGIsDeterministic(self):
|
||||
self.assertDeterministicWithSeed(-1) # not deterministic
|
||||
self.assertDeterministicWithSeed(0) # deterministic
|
||||
self.assertDeterministicWithSeed(1) # deterministic
|
||||
self.assertDeterministicWithSeed(195225786) # as large as we can go without overflowing since 11 * 195225786 should not overflow the int
|
||||
self.assertDeterministicWithSeed(195225787) # one higher seed will overflow though
|
||||
self.assertDeterministicWithSeed(0x1CEB00DA) # another large seeds that shouldn't overflow internals and make them non-deterministic
|
||||
def testGithub1763(self):
|
||||
mol = Chem.MolFromSmiles('CCCCC')
|
||||
bm1 = rdDistGeom.GetMoleculeBoundsMatrix(mol)
|
||||
bm2 = rdDistGeom.GetMoleculeBoundsMatrix(mol, doTriangleSmoothing=False)
|
||||
self.assertTrue(bm1[0, 4] < bm2[0, 4])
|
||||
|
||||
def testGithub1763(self):
|
||||
mol = Chem.MolFromSmiles('CCCCC')
|
||||
bm1 = rdDistGeom.GetMoleculeBoundsMatrix(mol)
|
||||
bm2 = rdDistGeom.GetMoleculeBoundsMatrix(mol,doTriangleSmoothing=False)
|
||||
self.assertTrue(bm1[0, 4] < bm2[0,4])
|
||||
def testGithub2057(self):
|
||||
# ensure that ETKDG is the default Embedder
|
||||
mol = Chem.AddHs(Chem.MolFromSmiles('OCCC'))
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'simple_torsion.etkdg.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, randomSeed=42), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
|
||||
def testGithub2057(self):
|
||||
# ensure that ETKDG is the default Embedder
|
||||
mol = Chem.AddHs(Chem.MolFromSmiles('OCCC'))
|
||||
fn = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'DistGeomHelpers', 'test_data',
|
||||
'simple_torsion.etkdg.mol')
|
||||
ref = Chem.MolFromMolFile(fn, removeHs=False)
|
||||
self.assertEqual(rdDistGeom.EmbedMolecule(mol, randomSeed=42), 0)
|
||||
self._compareConfs(mol, ref, 0, 0)
|
||||
|
||||
if __name__ == '__main__':
|
||||
unittest.main()
|
||||
unittest.main()
|
||||
|
||||
@@ -1629,7 +1629,7 @@ void compareConfs(const ROMol *m, const ROMol *expected, int molConfId = -1,
|
||||
|
||||
RDGeom::Point3D pt1i = conf1.getAtomPos(i);
|
||||
RDGeom::Point3D pt2i = conf2.getAtomPos(i);
|
||||
TEST_ASSERT((pt1i - pt2i).length() < 10e-4);
|
||||
TEST_ASSERT((pt1i - pt2i).length() < 0.05);
|
||||
}
|
||||
}
|
||||
} // namespace
|
||||
@@ -1645,36 +1645,56 @@ void testGithub971() {
|
||||
int cid = DGeomHelpers::EmbedMolecule(*m, 0, 0xf00d);
|
||||
TEST_ASSERT(cid >= 0);
|
||||
MolOps::removeHs(*m);
|
||||
std::string expectedMb =
|
||||
"\n RDKit 3D\n\n 19 21 0 0 0 0 0 0 0 0999 V2000\n "
|
||||
" 1.1258 -1.3888 0.9306 C 0 0 0 0 0 0 0 0 0 0 0 "
|
||||
"0\n 1.0779 -0.1065 0.1565 C 0 0 0 0 0 0 0 0 0 0 0 "
|
||||
" 0\n 2.2519 0.2795 -0.3483 C 0 0 0 0 0 0 0 0 0 0 "
|
||||
"0 0\n 3.5245 -0.0901 0.2817 C 0 0 0 0 0 0 0 0 0 0 "
|
||||
" 0 0\n 4.2551 0.9456 0.8411 C 0 0 0 0 0 0 0 0 0 "
|
||||
"0 0 0\n 5.6137 0.8099 1.0965 C 0 0 0 0 0 0 0 0 0 "
|
||||
" 0 0 0\n 6.2293 -0.3871 0.7552 C 0 0 0 0 0 0 0 0 "
|
||||
"0 0 0 0\n 5.4107 -1.4793 0.4938 C 0 0 0 0 0 0 0 0 "
|
||||
" 0 0 0 0\n 4.2354 -1.1874 -0.1873 C 0 0 0 0 0 0 0 "
|
||||
"0 0 0 0 0\n -0.0943 0.0572 -0.7601 C 0 0 0 0 0 0 0 "
|
||||
" 0 0 0 0 0\n -1.3242 0.2903 -0.0524 N 0 0 0 0 0 0 "
|
||||
"0 0 0 0 0 0\n -2.1468 1.1490 -0.9044 C 0 0 0 0 0 0 "
|
||||
" 0 0 0 0 0 0\n -3.1678 1.9193 -0.1239 C 0 0 0 0 0 "
|
||||
"0 0 0 0 0 0 0\n -2.9879 1.6714 1.3508 C 0 0 0 0 0 "
|
||||
" 0 0 0 0 0 0 0\n -3.3579 0.3480 1.7662 N 0 0 0 0 "
|
||||
"0 0 0 0 0 0 0 0\n -3.4586 -0.6011 0.7007 C 0 0 0 0 "
|
||||
" 0 0 0 0 0 0 0 0\n -2.1733 -0.8977 -0.0058 C 0 0 0 "
|
||||
"0 0 0 0 0 0 0 0 0\n -2.5650 -1.1467 -1.4589 C 0 0 0 "
|
||||
" 0 0 0 0 0 0 0 0 0\n -2.7401 0.2591 -1.9624 C 0 0 "
|
||||
"0 0 0 0 0 0 0 0 0 0\n 1 2 1 0\n 2 3 2 0\n 3 4 1 "
|
||||
"0\n 4 5 2 0\n 5 6 1 0\n 6 7 2 0\n 7 8 1 0\n 8 9 2 "
|
||||
"0\n 2 10 1 0\n 10 11 1 0\n 11 12 1 0\n 12 13 1 0\n 13 14 1 "
|
||||
"0\n 14 15 1 0\n 15 16 1 0\n 16 17 1 0\n 17 18 1 0\n 18 19 1 "
|
||||
"0\n 9 4 1 0\n 17 11 1 0\n 19 12 1 0\nM CHG 1 15 1\nM "
|
||||
"END\n";
|
||||
std::string expectedMb = R"CTAB(
|
||||
RDKit 3D
|
||||
|
||||
19 21 0 0 0 0 0 0 0 0999 V2000
|
||||
1.1886 -1.4168 0.8579 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.0673 -0.0768 0.1995 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.2169 0.4750 -0.1935 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.5072 0.0051 0.3290 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.3384 0.9895 0.8425 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.6714 0.7376 1.1358 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
6.1353 -0.5269 0.8881 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
5.3159 -1.5094 0.3457 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.1414 -1.0880 -0.2477 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.0961 0.0762 -0.7307 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.3281 0.3264 -0.0331 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.1244 1.2097 -0.8827 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.2111 1.8916 -0.0980 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.9969 1.6208 1.3672 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.3806 0.2980 1.7743 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-3.4530 -0.6563 0.7070 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.1661 -0.8675 -0.0283 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.5534 -1.0960 -1.4823 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.6831 0.3159 -1.9837 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 1 0
|
||||
2 3 2 0
|
||||
3 4 1 0
|
||||
4 5 2 0
|
||||
5 6 1 0
|
||||
6 7 2 0
|
||||
7 8 1 0
|
||||
8 9 2 0
|
||||
2 10 1 0
|
||||
10 11 1 0
|
||||
11 12 1 0
|
||||
12 13 1 0
|
||||
13 14 1 0
|
||||
14 15 1 0
|
||||
15 16 1 0
|
||||
16 17 1 0
|
||||
17 18 1 0
|
||||
18 19 1 0
|
||||
9 4 1 0
|
||||
17 11 1 0
|
||||
19 12 1 0
|
||||
M CHG 1 15 1
|
||||
M END)CTAB";
|
||||
RWMol *expected = MolBlockToMol(expectedMb);
|
||||
unsigned int nat = expected->getNumAtoms();
|
||||
TEST_ASSERT(nat == m->getNumAtoms());
|
||||
|
||||
compareConfs(m, expected, 0, 0);
|
||||
delete m;
|
||||
delete expected;
|
||||
@@ -1695,7 +1715,10 @@ void testEmbedParameters() {
|
||||
TEST_ASSERT(ref->getNumAtoms() == mol->getNumAtoms());
|
||||
DGeomHelpers::EmbedParameters params;
|
||||
params.randomSeed = 42;
|
||||
DGeomHelpers::EmbedMolecule(*mol, params);
|
||||
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
|
||||
// std::cerr << MolToMolBlock(*ref) << std::endl;
|
||||
// std::cerr << MolToMolBlock(*mol) << std::endl;
|
||||
// std::cerr << fname << std::endl;
|
||||
compareConfs(ref, mol);
|
||||
|
||||
delete ref;
|
||||
@@ -1714,7 +1737,10 @@ void testEmbedParameters() {
|
||||
DGeomHelpers::EmbedParameters params;
|
||||
params.randomSeed = 42;
|
||||
params.useExpTorsionAnglePrefs = true;
|
||||
DGeomHelpers::EmbedMolecule(*mol, params);
|
||||
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
|
||||
// std::cerr << MolToMolBlock(*ref) << std::endl;
|
||||
// std::cerr << MolToMolBlock(*mol) << std::endl;
|
||||
// std::cerr << fname << std::endl;
|
||||
compareConfs(ref, mol);
|
||||
|
||||
delete ref;
|
||||
@@ -1734,7 +1760,10 @@ void testEmbedParameters() {
|
||||
params.randomSeed = 42;
|
||||
params.useExpTorsionAnglePrefs = true;
|
||||
params.useBasicKnowledge = true;
|
||||
DGeomHelpers::EmbedMolecule(*mol, params);
|
||||
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
|
||||
// std::cerr << MolToMolBlock(*ref) << std::endl;
|
||||
// std::cerr << MolToMolBlock(*mol) << std::endl;
|
||||
// std::cerr << fname << std::endl;
|
||||
compareConfs(ref, mol);
|
||||
|
||||
delete ref;
|
||||
@@ -1755,7 +1784,10 @@ void testEmbedParameters() {
|
||||
params.useExpTorsionAnglePrefs = true;
|
||||
params.useBasicKnowledge = true;
|
||||
params.ETversion = 2;
|
||||
DGeomHelpers::EmbedMolecule(*mol, params);
|
||||
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
|
||||
// std::cerr << MolToMolBlock(*ref) << std::endl;
|
||||
// std::cerr << MolToMolBlock(*mol) << std::endl;
|
||||
// std::cerr << fname << std::endl;
|
||||
compareConfs(ref, mol);
|
||||
|
||||
delete ref;
|
||||
@@ -1774,7 +1806,10 @@ void testEmbedParameters() {
|
||||
DGeomHelpers::EmbedParameters params;
|
||||
params.randomSeed = 42;
|
||||
params.useBasicKnowledge = true;
|
||||
DGeomHelpers::EmbedMolecule(*mol, params);
|
||||
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
|
||||
// std::cerr << MolToMolBlock(*ref) << std::endl;
|
||||
// std::cerr << MolToMolBlock(*mol) << std::endl;
|
||||
// std::cerr << fname << std::endl;
|
||||
compareConfs(ref, mol);
|
||||
|
||||
delete ref;
|
||||
@@ -1794,7 +1829,10 @@ void testEmbedParameters() {
|
||||
TEST_ASSERT(ref->getNumAtoms() == mol->getNumAtoms());
|
||||
DGeomHelpers::EmbedParameters params(DGeomHelpers::ETDG);
|
||||
params.randomSeed = 42;
|
||||
DGeomHelpers::EmbedMolecule(*mol, params);
|
||||
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
|
||||
// std::cerr << MolToMolBlock(*ref) << std::endl;
|
||||
// std::cerr << MolToMolBlock(*mol) << std::endl;
|
||||
// std::cerr << fname << std::endl;
|
||||
compareConfs(ref, mol);
|
||||
|
||||
delete ref;
|
||||
@@ -1812,7 +1850,10 @@ void testEmbedParameters() {
|
||||
TEST_ASSERT(ref->getNumAtoms() == mol->getNumAtoms());
|
||||
DGeomHelpers::EmbedParameters params(DGeomHelpers::ETKDG);
|
||||
params.randomSeed = 42;
|
||||
DGeomHelpers::EmbedMolecule(*mol, params);
|
||||
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
|
||||
// std::cerr << MolToMolBlock(*ref) << std::endl;
|
||||
// std::cerr << MolToMolBlock(*mol) << std::endl;
|
||||
// std::cerr << fname << std::endl;
|
||||
compareConfs(ref, mol);
|
||||
|
||||
delete ref;
|
||||
@@ -1830,7 +1871,10 @@ void testEmbedParameters() {
|
||||
TEST_ASSERT(ref->getNumAtoms() == mol->getNumAtoms());
|
||||
DGeomHelpers::EmbedParameters params(DGeomHelpers::KDG);
|
||||
params.randomSeed = 42;
|
||||
DGeomHelpers::EmbedMolecule(*mol, params);
|
||||
TEST_ASSERT(DGeomHelpers::EmbedMolecule(*mol, params) == 0);
|
||||
// std::cerr << MolToMolBlock(*ref) << std::endl;
|
||||
// std::cerr << MolToMolBlock(*mol) << std::endl;
|
||||
// std::cerr << fname << std::endl;
|
||||
compareConfs(ref, mol);
|
||||
|
||||
delete ref;
|
||||
|
||||
@@ -2,30 +2,30 @@
|
||||
RDKit 3D
|
||||
|
||||
24 25 0 0 0 0 0 0 0 0999 V2000
|
||||
-0.8098 -1.4111 0.7206 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.3419 -0.7255 -0.4791 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.7367 0.0993 -0.4222 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.5777 0.0654 0.6681 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.2691 -0.5589 1.9161 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.8985 0.3955 0.3255 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.1835 1.2451 -0.7382 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.0958 1.7391 -1.4099 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.9385 1.0063 -1.4166 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.0265 1.2376 -2.3571 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.0357 0.3123 -2.5310 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.1793 -0.6829 -1.5776 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2606 -0.7274 1.4246 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.2826 -2.2989 1.0122 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.7820 -1.9364 0.4550 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.4994 -0.1615 2.5883 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.5588 -1.6265 2.0868 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.0978 -0.1352 2.5672 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.6855 -0.0149 0.9648 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.1809 1.6336 -0.7847 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.2381 2.5743 -2.0569 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.2338 1.8133 -3.2394 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.6232 0.3079 -3.4387 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.9672 -1.4325 -1.7183 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.8886 -1.3656 0.7012 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.3279 -0.7429 -0.5236 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.6732 0.1541 -0.3581 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.4631 0.1269 0.7486 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.2102 -0.6171 1.9381 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.7903 0.5103 0.5070 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.1548 1.3065 -0.5551 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.1590 1.6873 -1.4127 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.9325 1.0492 -1.3771 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.0342 1.2556 -2.4096 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.9353 0.2792 -2.6141 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.0176 -0.7788 -1.7179 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.3540 -0.6147 1.2792 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.2987 -2.1838 1.0406 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.8181 -1.9675 0.4275 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.3752 -0.5564 2.5841 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.8069 -1.5649 1.9236 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.8765 -0.0872 2.7006 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.6018 0.0853 1.1023 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
4.1816 1.5721 -0.7393 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.2735 2.5676 -2.0369 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.3910 1.7955 -3.2889 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.5499 0.2799 -3.5152 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.8485 -1.4728 -1.8449 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 1 0
|
||||
2 3 2 0
|
||||
3 4 1 0
|
||||
@@ -93,21 +93,21 @@ $$$$
|
||||
RDKit 3D
|
||||
|
||||
15 14 0 0 0 0 0 0 0 0999 V2000
|
||||
0.4956 -1.5767 1.0233 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.0942 -0.5783 -0.0171 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.8343 0.5337 0.0501 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.5850 1.7946 -0.6706 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.1692 2.7818 0.4203 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.6572 -1.0193 1.9819 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.2363 -2.3412 1.2343 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.4440 -2.0280 0.6508 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.3375 -0.7414 -0.9654 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.4300 0.7306 0.9507 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.5252 2.1092 -1.1127 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.1707 1.7873 -1.4265 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.0333 3.7719 0.0201 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.0281 2.8096 1.1322 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.7465 2.3688 0.8855 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.4543 -1.5620 0.9760 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.1014 -0.5201 -0.0270 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.9463 0.5348 0.0353 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.5912 1.7983 -0.6396 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.1610 2.7612 0.4509 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.6099 -1.0318 1.9504 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.3101 -2.2923 1.2097 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.3871 -2.0288 0.6300 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.3430 -0.7110 -1.0006 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.5789 0.6660 0.9271 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.5082 2.2077 -1.0818 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.2371 1.6159 -1.3479 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.0467 3.7142 -0.0776 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.0378 2.8462 1.1249 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.7009 2.4042 1.0270 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 1 0
|
||||
2 3 2 0
|
||||
3 4 1 0
|
||||
@@ -128,36 +128,36 @@ $$$$
|
||||
RDKit 3D
|
||||
|
||||
30 33 0 0 0 0 0 0 0 0999 V2000
|
||||
1.2111 2.3950 -0.0227 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.0113 1.5363 -0.6850 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.4634 2.0065 -2.0149 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.4102 3.8053 -1.8633 S 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.4006 3.8101 -0.3578 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.1473 0.2916 -0.1587 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.1607 -0.2344 0.6155 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.6844 -1.5247 0.8398 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.7149 -1.5176 0.7987 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.9901 -0.2293 1.0877 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.1086 0.5270 1.0107 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.2451 1.8618 0.8235 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.7128 2.5836 1.2271 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.5654 -2.3793 -0.0629 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2154 -3.7111 -0.2723 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2498 -4.2871 -1.5458 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.3720 -3.4663 -2.6630 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.0595 -2.2768 -2.4441 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.2816 -1.8512 -1.1385 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.5227 1.6990 -2.1055 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.8284 1.6499 -2.8367 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.7997 4.4371 0.4316 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.3958 4.1809 -0.6818 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.7150 -0.4093 -0.7088 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.2779 -2.4231 0.7027 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.8195 -4.2427 0.5831 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.7016 -5.2267 -1.6492 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.7123 -3.5829 -3.5241 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.2187 -1.6139 -3.2961 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.6538 -0.8418 -0.9979 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.2016 2.3626 -0.0846 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.9992 1.4880 -0.7282 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.4875 1.9525 -2.0439 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.4610 3.7454 -1.8939 S 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.3687 3.7770 -0.4782 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.1574 0.2690 -0.1444 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.1853 -0.2498 0.6514 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.7013 -1.5324 0.8894 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.6972 -1.5145 0.8628 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.9489 -0.2249 1.1704 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.1423 0.5299 1.0295 N 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.2280 1.8520 0.7607 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.7745 2.5594 1.0744 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.5598 -2.3615 -0.0010 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2005 -3.6826 -0.2455 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2075 -4.2312 -1.5253 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.3587 -3.3887 -2.6224 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.0424 -2.2005 -2.3839 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.2807 -1.8200 -1.0653 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
3.5215 1.5858 -2.1381 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.7977 1.6137 -2.8236 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.7047 4.4447 0.3098 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.3656 4.0765 -0.8776 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.6918 -0.4426 -0.7151 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.2948 -2.4307 0.7675 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.7753 -4.2159 0.5984 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.7081 -5.1903 -1.6677 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.7086 -3.4646 -3.4964 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.2425 -1.5155 -3.2140 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.6890 -0.8251 -0.8737 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 2 0
|
||||
2 3 1 0
|
||||
3 4 1 0
|
||||
@@ -176,7 +176,7 @@ $$$$
|
||||
16 17 2 0
|
||||
17 18 1 0
|
||||
18 19 2 0
|
||||
1 12 1 0
|
||||
12 1 1 0
|
||||
5 1 1 0
|
||||
11 7 1 0
|
||||
19 14 1 0
|
||||
@@ -197,24 +197,24 @@ $$$$
|
||||
RDKit 3D
|
||||
|
||||
18 18 0 0 0 0 0 0 0 0999 V2000
|
||||
-0.8607 -0.9716 -0.0131 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.4252 -1.5444 -0.4933 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.3639 -0.3992 -0.6815 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.5523 0.2379 0.7010 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.6637 1.4197 0.9073 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.8548 0.7744 0.2787 S 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2127 1.5131 -0.9638 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.7907 0.9044 1.4219 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.5072 -1.0805 -0.9376 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.2996 -1.5822 0.7905 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.9018 -2.1567 0.3327 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.3131 -2.2701 -1.2657 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.0334 0.3651 -1.4090 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.3839 -0.7249 -0.9228 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.0584 -0.5362 1.3605 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
2.5619 0.3143 1.0600 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.6643 1.6755 1.9864 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.0884 2.2385 0.3195 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.8795 -0.9405 -0.1247 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.4764 -1.5310 -0.4687 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.4439 -0.4213 -0.6316 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1.6334 0.2436 0.7207 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
0.6572 1.3626 0.8911 C 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-0.8869 0.7349 0.3025 S 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.3615 1.5290 -0.8955 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.9258 0.9388 1.3865 O 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
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|
||||
-2.0034 1.4211 0.5293 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-1.0506 2.4321 -0.6891 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.6733 -2.4881 0.2617 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
-2.3404 -2.2489 -1.4218 H 0 0 0 0 0 0 0 0 0 0 0 0
|
||||
1 2 2 0
|
||||
2 3 1 0
|
||||
3 4 2 0
|
||||
|
||||
@@ -1,5 +1,6 @@
|
||||
|
||||
import os, sys
|
||||
import os
|
||||
import sys
|
||||
import unittest
|
||||
import math
|
||||
|
||||
@@ -14,91 +15,91 @@ from rdkit.Chem import rdMolTransforms as rdmt
|
||||
|
||||
class TestCase(unittest.TestCase):
|
||||
|
||||
def setUp(self):
|
||||
pass
|
||||
def setUp(self):
|
||||
pass
|
||||
|
||||
def test1Shape(self):
|
||||
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'ShapeHelpers', 'test_data',
|
||||
'1oir.mol')
|
||||
m = Chem.MolFromMolFile(fileN)
|
||||
rdmt.CanonicalizeMol(m)
|
||||
dims1, offset1 = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
|
||||
grd = geom.UniformGrid3D(30.0, 16.0, 10.0)
|
||||
rdshp.EncodeShape(m, grd, 0)
|
||||
ovect = grd.GetOccupancyVect()
|
||||
self.assertTrue(ovect.GetTotalVal() == 9250)
|
||||
def test1Shape(self):
|
||||
fileN = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'ShapeHelpers', 'test_data',
|
||||
'1oir.mol')
|
||||
m = Chem.MolFromMolFile(fileN)
|
||||
rdmt.CanonicalizeMol(m)
|
||||
dims1, offset1 = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
|
||||
grd = geom.UniformGrid3D(30.0, 16.0, 10.0)
|
||||
rdshp.EncodeShape(m, grd, 0)
|
||||
ovect = grd.GetOccupancyVect()
|
||||
self.assertEqual(ovect.GetTotalVal(), 7405)
|
||||
|
||||
m = Chem.MolFromMolFile(fileN)
|
||||
trans = rdmt.ComputeCanonicalTransform(m.GetConformer())
|
||||
dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer(), trans=trans)
|
||||
dims -= dims1
|
||||
offset -= offset1
|
||||
self.assertAlmostEqual(dims.Length(), 0.0, 4)
|
||||
self.assertAlmostEqual(offset.Length(), 0.0, 4)
|
||||
m = Chem.MolFromMolFile(fileN)
|
||||
trans = rdmt.ComputeCanonicalTransform(m.GetConformer())
|
||||
dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer(), trans=trans)
|
||||
dims -= dims1
|
||||
offset -= offset1
|
||||
self.assertAlmostEqual(dims.Length(), 0.0, 4)
|
||||
self.assertAlmostEqual(offset.Length(), 0.0, 4)
|
||||
|
||||
grd1 = geom.UniformGrid3D(30.0, 16.0, 10.0)
|
||||
rdshp.EncodeShape(m, grd1, 0, trans)
|
||||
ovect = grd1.GetOccupancyVect()
|
||||
grd1 = geom.UniformGrid3D(30.0, 16.0, 10.0)
|
||||
rdshp.EncodeShape(m, grd1, 0, trans)
|
||||
ovect = grd1.GetOccupancyVect()
|
||||
|
||||
self.assertTrue(ovect.GetTotalVal() == 9250)
|
||||
self.assertEqual(ovect.GetTotalVal(), 7405)
|
||||
|
||||
grd2 = geom.UniformGrid3D(30.0, 16.0, 10.0)
|
||||
rdshp.EncodeShape(m, grd2, 0)
|
||||
grd2 = geom.UniformGrid3D(30.0, 16.0, 10.0)
|
||||
rdshp.EncodeShape(m, grd2, 0)
|
||||
|
||||
fileN2 = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'ShapeHelpers', 'test_data',
|
||||
'1oir_conf.mol')
|
||||
m2 = Chem.MolFromMolFile(fileN2)
|
||||
fileN2 = os.path.join(RDConfig.RDBaseDir, 'Code', 'GraphMol', 'ShapeHelpers', 'test_data',
|
||||
'1oir_conf.mol')
|
||||
m2 = Chem.MolFromMolFile(fileN2)
|
||||
|
||||
self.assertAlmostEqual(rdshp.ShapeTanimotoDist(m, m), 0.0, 4)
|
||||
self.assertAlmostEqual(rdshp.ShapeTverskyIndex(m, m, 1.0, 1.0), 1.0, 4)
|
||||
self.assertAlmostEqual(rdshp.ShapeTanimotoDist(m, m), 0.0, 4)
|
||||
self.assertAlmostEqual(rdshp.ShapeTverskyIndex(m, m, 1.0, 1.0), 1.0, 4)
|
||||
|
||||
rmsd = rdMolAlign.AlignMol(m, m2)
|
||||
self.assertAlmostEqual(rdshp.ShapeTanimotoDist(m, m2), 0.2813, 4)
|
||||
self.assertAlmostEqual(rdshp.ShapeTverskyIndex(m, m2, 1.0, 1.0), 0.7187, 4)
|
||||
rmsd = rdMolAlign.AlignMol(m, m2)
|
||||
self.assertAlmostEqual(rdshp.ShapeTanimotoDist(m, m2), 0.3146, 4)
|
||||
self.assertAlmostEqual(rdshp.ShapeTverskyIndex(m, m2, 1.0, 1.0), 0.6854, 4)
|
||||
|
||||
dist = rdshp.ShapeTanimotoDist(mol1=m, mol2=m2, confId1=0, confId2=0, gridSpacing=0.25,
|
||||
stepSize=0.125)
|
||||
self.assertAlmostEqual(dist, 0.3021, 4)
|
||||
dist = rdshp.ShapeTanimotoDist(mol1=m, mol2=m2, confId1=0, confId2=0, gridSpacing=0.25,
|
||||
stepSize=0.125)
|
||||
self.assertAlmostEqual(dist, 0.3389, 4)
|
||||
|
||||
m = Chem.MolFromMolFile(fileN)
|
||||
cpt = rdmt.ComputeCentroid(m.GetConformer())
|
||||
dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
|
||||
m = Chem.MolFromMolFile(fileN)
|
||||
cpt = rdmt.ComputeCentroid(m.GetConformer())
|
||||
dims, offset = rdshp.ComputeConfDimsAndOffset(m.GetConformer())
|
||||
|
||||
grd = geom.UniformGrid3D(dims.x, dims.y, dims.z, 0.5, DataStructs.DiscreteValueType.TWOBITVALUE,
|
||||
offset)
|
||||
dims -= geom.Point3D(13.927, 16.97, 9.775)
|
||||
offset -= geom.Point3D(-4.353, 16.829, 2.782)
|
||||
self.assertAlmostEqual(dims.Length(), 0.0, 4)
|
||||
self.assertAlmostEqual(offset.Length(), 0.0, 4)
|
||||
rdshp.EncodeShape(m, grd, 0)
|
||||
grd = geom.UniformGrid3D(dims.x, dims.y, dims.z, 0.5, DataStructs.DiscreteValueType.TWOBITVALUE,
|
||||
offset)
|
||||
dims -= geom.Point3D(13.927, 16.97, 9.775)
|
||||
offset -= geom.Point3D(-4.353, 16.829, 2.782)
|
||||
self.assertAlmostEqual(dims.Length(), 0.0, 4)
|
||||
self.assertAlmostEqual(offset.Length(), 0.0, 4)
|
||||
rdshp.EncodeShape(m, grd, 0)
|
||||
|
||||
ovect = grd.GetOccupancyVect()
|
||||
ovect = grd.GetOccupancyVect()
|
||||
|
||||
self.assertTrue(ovect.GetTotalVal() == 9275)
|
||||
geom.WriteGridToFile(grd, '1oir_shape.grd')
|
||||
self.assertEqual(ovect.GetTotalVal(), 7417)
|
||||
geom.WriteGridToFile(grd, '1oir_shape.grd')
|
||||
|
||||
m = Chem.MolFromMolFile(fileN)
|
||||
lc, uc = rdshp.ComputeConfBox(m.GetConformer())
|
||||
rdmt.CanonicalizeMol(m)
|
||||
lc1, uc1 = rdshp.ComputeConfBox(m.GetConformer())
|
||||
m = Chem.MolFromMolFile(fileN)
|
||||
lc, uc = rdshp.ComputeConfBox(m.GetConformer())
|
||||
rdmt.CanonicalizeMol(m)
|
||||
lc1, uc1 = rdshp.ComputeConfBox(m.GetConformer())
|
||||
|
||||
lc2, uc2 = rdshp.ComputeUnionBox((lc, uc), (lc1, uc1))
|
||||
lc -= geom.Point3D(-4.353, 16.829, 2.782)
|
||||
uc -= geom.Point3D(9.574, 33.799, 12.557)
|
||||
self.assertAlmostEqual(lc.Length(), 0.0, 4)
|
||||
self.assertAlmostEqual(uc.Length(), 0.0, 4)
|
||||
lc2, uc2 = rdshp.ComputeUnionBox((lc, uc), (lc1, uc1))
|
||||
lc -= geom.Point3D(-4.353, 16.829, 2.782)
|
||||
uc -= geom.Point3D(9.574, 33.799, 12.557)
|
||||
self.assertAlmostEqual(lc.Length(), 0.0, 4)
|
||||
self.assertAlmostEqual(uc.Length(), 0.0, 4)
|
||||
|
||||
lc1 -= geom.Point3D(-10.7519, -6.0778, -3.0123)
|
||||
uc1 -= geom.Point3D(8.7163, 5.3279, 3.1621)
|
||||
self.assertAlmostEqual(lc1.Length(), 0.0, 4)
|
||||
self.assertAlmostEqual(uc1.Length(), 0.0, 3)
|
||||
lc1 -= geom.Point3D(-10.7519, -6.0778, -3.0123)
|
||||
uc1 -= geom.Point3D(8.7163, 5.3279, 3.1621)
|
||||
self.assertAlmostEqual(lc1.Length(), 0.0, 4)
|
||||
self.assertAlmostEqual(uc1.Length(), 0.0, 3)
|
||||
|
||||
lc2 -= geom.Point3D(-10.7519, -6.0778, -3.01226)
|
||||
uc2 -= geom.Point3D(9.574, 33.799, 12.557)
|
||||
self.assertAlmostEqual(lc2.Length(), 0.0, 4)
|
||||
self.assertAlmostEqual(uc2.Length(), 0.0, 4)
|
||||
lc2 -= geom.Point3D(-10.7519, -6.0778, -3.01226)
|
||||
uc2 -= geom.Point3D(9.574, 33.799, 12.557)
|
||||
self.assertAlmostEqual(lc2.Length(), 0.0, 4)
|
||||
self.assertAlmostEqual(uc2.Length(), 0.0, 4)
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
print("Testing Shape Helpers wrapper")
|
||||
unittest.main()
|
||||
print("Testing Shape Helpers wrapper")
|
||||
unittest.main()
|
||||
|
||||
@@ -39,7 +39,7 @@ void test1Encode() {
|
||||
|
||||
// RDGeom::writeGridToFile(grd, "junk.grd");
|
||||
// MolToMolFile(m, "junk.mol", 0);
|
||||
CHECK_INVARIANT(grd.getOccupancyVect()->getTotalVal() == 9250, "");
|
||||
CHECK_INVARIANT(grd.getOccupancyVect()->getTotalVal() == 7405, "");
|
||||
}
|
||||
|
||||
void test2Compare() {
|
||||
@@ -68,9 +68,9 @@ void test2Compare() {
|
||||
double rmsd = MolAlign::alignMol(*m, *m2);
|
||||
CHECK_INVARIANT(rmsd >= 0.0, "");
|
||||
dist = MolShapes::tanimotoDistance(*m, *m2);
|
||||
CHECK_INVARIANT(RDKit::feq(dist, 0.2813), "");
|
||||
CHECK_INVARIANT(RDKit::feq(dist, 0.3146), "");
|
||||
dist = MolShapes::tverskyIndex(*m, *m2, 1.0, 1.0);
|
||||
CHECK_INVARIANT(RDKit::feq(dist, 0.7187), "");
|
||||
CHECK_INVARIANT(RDKit::feq(dist, 0.6854), "");
|
||||
delete m2;
|
||||
|
||||
m2 = MolFileToMol(fname2);
|
||||
@@ -84,7 +84,7 @@ void test2Compare() {
|
||||
rmsd = MolAlign::alignMol(*m2, *m, 0, 0, &atomMap);
|
||||
dist = MolShapes::tanimotoDistance(*m, *m2);
|
||||
|
||||
CHECK_INVARIANT(RDKit::feq(dist, 0.3244), "");
|
||||
CHECK_INVARIANT(RDKit::feq(dist, 0.3593), "");
|
||||
delete m;
|
||||
delete m2;
|
||||
}
|
||||
|
||||
@@ -102,8 +102,8 @@ class TestCase(unittest.TestCase):
|
||||
self.assertTrue(feq(tbl.GetAtomicWeight(6), 12.011))
|
||||
self.assertTrue(feq(tbl.GetAtomicWeight("C"), 12.011))
|
||||
self.assertTrue(tbl.GetAtomicNumber('C') == 6)
|
||||
self.assertTrue(feq(tbl.GetRvdw(6), 1.950))
|
||||
self.assertTrue(feq(tbl.GetRvdw("C"), 1.950))
|
||||
self.assertTrue(feq(tbl.GetRvdw(6), 1.7))
|
||||
self.assertTrue(feq(tbl.GetRvdw("C"), 1.7))
|
||||
self.assertTrue(feq(tbl.GetRcovalent(6), 0.680))
|
||||
self.assertTrue(feq(tbl.GetRcovalent("C"), 0.680))
|
||||
self.assertTrue(tbl.GetDefaultValence(6) == 4)
|
||||
|
||||
@@ -23,132 +23,147 @@ const double electronMass =
|
||||
0.00054857991; // value from http://physics.nist.gov/cgi-bin/cuu/Value?me
|
||||
}
|
||||
|
||||
// these data came from a variety of sources. If it's not explicitly listed
|
||||
// here, then it has likely been lost in antiquity. Columns:
|
||||
// atomic number
|
||||
// symbol
|
||||
// rCov
|
||||
// rB0
|
||||
// rVdw (taken from BODR v10.1)
|
||||
// atomic mass
|
||||
// # outershell electrons
|
||||
// most common isotope
|
||||
// most common isotopic mass
|
||||
// list of allowed valences, -1 for anything
|
||||
const std::string periodicTableAtomData =
|
||||
"0 * 0 0 0 0 0 0 0 -1 \n \
|
||||
1 H 0.23 0.33 1.2 1.008 1 1 1.007825032 1 \n \
|
||||
2 He 0.93 0.7 1.4 4.003 2 4 4.002603254 0 \n \
|
||||
3 Li 0.68 1.23 1.82 6.941 1 7 7.01600455 1 \n \
|
||||
4 Be 0.35 0.9 1.7 9.012 2 9 9.0121822 2 \n \
|
||||
5 B 0.830 0.82 2.08 10.812 3 11 11.0093054 3 \n \
|
||||
6 C 0.68 0.77 1.95 12.011 4 12 12 4 \n \
|
||||
7 N 0.68 0.7 1.85 14.007 5 14 14.003074 3 \n \
|
||||
8 O 0.68 0.66 1.7 15.999 6 16 15.99491462 2 \n \
|
||||
9 F 0.64 0.611 1.73 18.998 7 19 18.99840322 1 \n \
|
||||
3 Li 0.68 1.23 2.2 6.941 1 7 7.01600455 1 \n \
|
||||
4 Be 0.35 0.9 1.9 9.012 2 9 9.0121822 2 \n \
|
||||
5 B 0.830 0.82 1.8 10.812 3 11 11.0093054 3 \n \
|
||||
6 C 0.68 0.77 1.7 12.011 4 12 12 4 \n \
|
||||
7 N 0.68 0.7 1.6 14.007 5 14 14.003074 3 \n \
|
||||
8 O 0.68 0.66 1.55 15.999 6 16 15.99491462 2 \n \
|
||||
9 F 0.64 0.611 1.5 18.998 7 19 18.99840322 1 \n \
|
||||
10 Ne 1.12 0.7 1.54 20.18 8 20 19.99244018 0 \n \
|
||||
11 Na 0.97 1.54 2.27 22.99 1 23 22.98976928 1 \n \
|
||||
12 Mg 1.1 1.36 1.73 24.305 2 24 23.9850417 2 \n \
|
||||
13 Al 1.35 1.18 2.05 26.982 3 27 26.98153863 3 6 \n \
|
||||
11 Na 0.97 1.54 2.4 22.99 1 23 22.98976928 1 \n \
|
||||
12 Mg 1.1 1.36 2.2 24.305 2 24 23.9850417 2 \n \
|
||||
13 Al 1.35 1.18 2.1 26.982 3 27 26.98153863 3 6 \n \
|
||||
14 Si 1.2 0.937 2.1 28.086 4 28 27.97692653 4 6 \n \
|
||||
15 P 0.75 0.89 2.08 30.974 5 31 30.97376163 3 5 7 \n \
|
||||
16 S 1.02 1.04 2 32.067 6 32 31.972071 2 4 6 \n \
|
||||
17 Cl 0.99 0.997 1.97 35.453 7 35 34.96885268 1 \n \
|
||||
15 P 0.75 0.89 1.95 30.974 5 31 30.97376163 3 5 7 \n \
|
||||
16 S 1.02 1.04 1.8 32.067 6 32 31.972071 2 4 6 \n \
|
||||
17 Cl 0.99 0.997 1.8 35.453 7 35 34.96885268 1 \n \
|
||||
18 Ar 1.57 1.74 1.88 39.948 8 40 39.96238312 0 \n \
|
||||
19 K 1.33 2.03 2.75 39.098 1 39 38.96370668 1 \n \
|
||||
20 Ca 0.99 1.74 1.973 40.078 2 40 39.96259098 2 \n"
|
||||
"21 Sc 1.44 1.44 1.7 44.956 3 45 44.9559119 -1 \n \
|
||||
22 Ti 1.47 1.32 1.7 47.867 4 48 47.9479463 -1 \n \
|
||||
23 V 1.33 1.22 1.7 50.942 5 50 49.9471585 -1 \n \
|
||||
24 Cr 1.35 1.18 1.7 51.996 6 52 51.9405075 -1 \n \
|
||||
25 Mn 1.35 1.17 1.7 54.938 7 55 54.9380451 -1 \n \
|
||||
26 Fe 1.34 1.17 1.7 55.845 8 56 55.9349375 -1 \n \
|
||||
27 Co 1.33 1.16 1.7 58.933 9 59 58.933195 -1 \n \
|
||||
28 Ni 1.5 1.15 1.63 58.693 10 58 57.9353429 -1 \n \
|
||||
29 Cu 1.52 1.17 1.4 63.546 11 63 62.9295975 -1 \n \
|
||||
30 Zn 1.45 1.25 1.39 65.39 2 64 63.9291422 -1 \n \
|
||||
31 Ga 1.22 1.26 1.87 69.723 3 69 68.9255736 3 \n \
|
||||
32 Ge 1.17 1.188 1.7 72.61 4 74 73.9211778 4 \n \
|
||||
33 As 1.21 1.2 1.85 74.922 5 75 74.9215965 3 5 7 \n \
|
||||
19 K 1.33 2.03 2.8 39.098 1 39 38.96370668 1 \n \
|
||||
20 Ca 0.99 1.74 2.4 40.078 2 40 39.96259098 2 \n"
|
||||
"21 Sc 1.44 1.44 2.3 44.956 3 45 44.9559119 -1 \n \
|
||||
22 Ti 1.47 1.32 2.15 47.867 4 48 47.9479463 -1 \n \
|
||||
23 V 1.33 1.22 2.05 50.942 5 50 49.9471585 -1 \n \
|
||||
24 Cr 1.35 1.18 2.05 51.996 6 52 51.9405075 -1 \n \
|
||||
25 Mn 1.35 1.17 2.05 54.938 7 55 54.9380451 -1 \n \
|
||||
26 Fe 1.34 1.17 2.05 55.845 8 56 55.9349375 -1 \n \
|
||||
27 Co 1.33 1.16 2.0 58.933 9 59 58.933195 -1 \n \
|
||||
28 Ni 1.5 1.15 2.0 58.693 10 58 57.9353429 -1 \n \
|
||||
29 Cu 1.52 1.17 2.0 63.546 11 63 62.9295975 -1 \n \
|
||||
30 Zn 1.45 1.25 2.1 65.39 2 64 63.9291422 -1 \n \
|
||||
31 Ga 1.22 1.26 2.1 69.723 3 69 68.9255736 3 \n \
|
||||
32 Ge 1.17 1.188 2.1 72.61 4 74 73.9211778 4 \n \
|
||||
33 As 1.21 1.2 2.05 74.922 5 75 74.9215965 3 5 7 \n \
|
||||
34 Se 1.22 1.17 1.9 78.96 6 80 79.9165213 2 4 6 \n \
|
||||
35 Br 1.21 1.167 2.1 79.904 7 79 78.9183371 1 \n \
|
||||
35 Br 1.21 1.167 1.9 79.904 7 79 78.9183371 1 \n \
|
||||
36 Kr 1.91 1.91 2.02 83.8 8 84 83.911507 0 \n \
|
||||
37 Rb 1.47 2.16 1.7 85.468 1 85 84.91178974 1 \n \
|
||||
38 Sr 1.12 1.91 1.7 87.62 2 88 87.9056121 2 \n \
|
||||
39 Y 1.78 1.62 1.7 88.906 3 89 88.9058483 -1 \n \
|
||||
40 Zr 1.56 1.45 1.7 91.224 4 90 89.9047044 -1 \n"
|
||||
"41 Nb 1.48 1.34 1.7 92.906 5 93 92.9063781 -1 \n \
|
||||
42 Mo 1.47 1.3 1.7 95.94 6 98 97.9054082 -1 \n \
|
||||
43 Tc 1.35 1.27 1.7 98 7 97 96.906365 -1 \n \
|
||||
44 Ru 1.4 1.25 1.7 101.07 8 102 101.9043493 -1 \n \
|
||||
45 Rh 1.45 1.25 1.7 102.906 9 103 102.905504 -1 \n \
|
||||
46 Pd 1.5 1.28 1.63 106.42 10 106 105.903486 -1 \n \
|
||||
47 Ag 1.59 1.34 1.72 107.868 11 107 106.905097 -1 \n \
|
||||
48 Cd 1.69 1.48 1.58 112.412 2 114 113.9033585 -1 \n \
|
||||
49 In 1.63 1.44 1.93 114.818 3 115 114.903878 3 \n \
|
||||
50 Sn 1.46 1.385 2.17 118.711 4 120 119.9021947 4 \n \
|
||||
37 Rb 1.47 2.16 2.9 85.468 1 85 84.91178974 1 \n \
|
||||
38 Sr 1.12 1.91 2.55 87.62 2 88 87.9056121 2 \n \
|
||||
39 Y 1.78 1.62 2.4 88.906 3 89 88.9058483 -1 \n \
|
||||
40 Zr 1.56 1.45 2.3 91.224 4 90 89.9047044 -1 \n"
|
||||
"41 Nb 1.48 1.34 2.15 92.906 5 93 92.9063781 -1 \n \
|
||||
42 Mo 1.47 1.3 2.1 95.94 6 98 97.9054082 -1 \n \
|
||||
43 Tc 1.35 1.27 2.05 98 7 97 96.906365 -1 \n \
|
||||
44 Ru 1.4 1.25 2.05 101.07 8 102 101.9043493 -1 \n \
|
||||
45 Rh 1.45 1.25 2.0 102.906 9 103 102.905504 -1 \n \
|
||||
46 Pd 1.5 1.28 2.05 106.42 10 106 105.903486 -1 \n \
|
||||
47 Ag 1.59 1.34 2.1 107.868 11 107 106.905097 -1 \n \
|
||||
48 Cd 1.69 1.48 2.2 112.412 2 114 113.9033585 -1 \n \
|
||||
49 In 1.63 1.44 2.2 114.818 3 115 114.903878 3 \n \
|
||||
50 Sn 1.46 1.385 2.25 118.711 4 120 119.9021947 4 \n \
|
||||
51 Sb 1.46 1.4 2.2 121.76 5 121 120.9038157 3 5 7 \n \
|
||||
52 Te 1.47 1.378 2.06 127.6 6 130 129.9062244 2 4 6\n \
|
||||
53 I 1.4 1.387 2.15 126.904 7 127 126.904473 1 2 5 \n \
|
||||
52 Te 1.47 1.378 2.1 127.6 6 130 129.9062244 2 4 6\n \
|
||||
53 I 1.4 1.387 2.1 126.904 7 127 126.904473 1 2 5 \n \
|
||||
54 Xe 1.98 1.98 2.16 131.29 8 132 131.9041535 0 2 \n \
|
||||
55 Cs 1.67 2.35 1.7 132.905 1 133 132.9054519 1 \n \
|
||||
56 Ba 1.34 1.98 1.7 137.328 2 138 137.9052472 2 \n \
|
||||
57 La 1.87 1.69 1.7 138.906 3 139 138.9063533 -1 \n \
|
||||
58 Ce 1.83 1.83 1.7 140.116 4 140 139.9054387 -1 \n \
|
||||
59 Pr 1.82 1.82 1.7 140.908 3 141 140.9076528 -1 \n \
|
||||
60 Nd 1.81 1.81 1.7 144.24 4 142 141.9077233 -1 \n"
|
||||
"61 Pm 1.8 1.8 1.7 145 5 145 144.912749 -1 \n \
|
||||
62 Sm 1.8 1.8 1.7 150.36 6 152 151.9197324 -1 \n \
|
||||
63 Eu 1.99 1.99 1.7 151.964 7 153 152.9212303 -1 \n \
|
||||
64 Gd 1.79 1.79 1.7 157.25 8 158 157.9241039 -1 \n \
|
||||
65 Tb 1.76 1.76 1.7 158.925 9 159 158.9253468 -1 \n \
|
||||
66 Dy 1.75 1.75 1.7 162.5 10 164 163.9291748 -1 \n \
|
||||
67 Ho 1.74 1.74 1.7 164.93 11 165 164.9303221 -1 \n \
|
||||
68 Er 1.73 1.73 1.7 167.26 12 166 165.9302931 -1 \n \
|
||||
69 Tm 1.72 1.72 1.7 168.934 13 169 168.9342133 -1 \n \
|
||||
70 Yb 1.94 1.94 1.7 173.04 14 174 173.9388621 -1 \n \
|
||||
71 Lu 1.72 1.72 1.7 174.967 15 175 174.9407718 -1 \n \
|
||||
72 Hf 1.57 1.44 1.7 178.49 4 180 179.94655 -1 \n \
|
||||
73 Ta 1.43 1.34 1.7 180.948 5 181 180.9479958 -1 \n \
|
||||
74 W 1.37 1.3 1.7 183.84 6 184 183.9509312 -1 \n \
|
||||
75 Re 1.35 1.28 1.7 186.207 7 187 186.9557531 -1 \n \
|
||||
76 Os 1.37 1.26 1.7 190.23 8 192 191.9614807 -1 \n \
|
||||
77 Ir 1.32 1.27 1.7 192.217 9 193 192.9629264 -1 \n \
|
||||
78 Pt 1.5 1.3 1.72 195.078 10 195 194.9647911 -1 \n \
|
||||
79 Au 1.5 1.34 1.66 196.967 11 197 196.9665687 -1 \n \
|
||||
80 Hg 1.7 1.49 1.55 200.59 2 202 201.970643 -1 \n"
|
||||
"81 Tl 1.55 1.48 1.96 204.383 3 205 204.9744275 3 \n \
|
||||
82 Pb 1.54 1.48 2.02 207.2 4 208 207.9766521 4 \n \
|
||||
83 Bi 1.54 1.45 1.7 208.98 5 209 208.9803987 3 5 7 \n \
|
||||
84 Po 1.68 1.46 1.7 209 6 209 208.9824304 2 \n \
|
||||
85 At 1.7 1.45 1.7 210 7 210 209.987148 1 \n \
|
||||
86 Rn 2.4 2.4 1.7 222 8 211 210.990601 0 \n \
|
||||
87 Fr 2 2 1.7 223 1 223 223.0197359 1 \n \
|
||||
88 Ra 1.9 1.9 1.7 226 2 223 223.0185022 2 \n \
|
||||
89 Ac 1.88 1.88 1.7 227 3 227 227.0277521 -1 \n \
|
||||
90 Th 1.79 1.79 1.7 232.038 4 232 232.0380553 -1 \n \
|
||||
91 Pa 1.61 1.61 1.7 231.036 3 231 231.035884 -1 \n \
|
||||
92 U 1.58 1.58 1.86 238.029 4 238 238.0507882 -1 \n \
|
||||
93 Np 1.55 1.55 1.7 237 5 236 236.04657 -1 \n \
|
||||
94 Pu 1.53 1.53 1.7 244 6 238 238.0495599 -1 \n \
|
||||
95 Am 1.51 1.07 1.7 243 7 241 241.0568291 -1 \n \
|
||||
96 Cm 1.5 0 1.7 247 8 243 243.0613891 -1 \n \
|
||||
97 Bk 1.5 0 1.7 247 9 247 247.070307 -1 \n \
|
||||
98 Cf 1.5 0 1.7 251 10 249 249.0748535 -1 \n \
|
||||
99 Es 1.5 0 1.7 252 11 252 252.08298 -1 \n \
|
||||
100 Fm 1.5 0 1.7 257 12 257 257.095105 -1 \n"
|
||||
"101 Md 1.5 0 1.7 258 13 258 258.098431 -1 \n \
|
||||
102 No 1.5 0 1.7 259 14 259 259.10103 -1 \n \
|
||||
103 Lr 1.5 0 1.7 262 15 262 262.10963 -1 \n \
|
||||
104 Rf 1.57 0 1.7 267 2 267 267.12153 -1 \n \
|
||||
105 Db 1.49 0 1.7 268 2 268 268.12545 -1 \n \
|
||||
106 Sg 1.43 0 1.7 269 2 271 271.13347 -1 \n \
|
||||
107 Bh 1.41 0 1.7 270 2 270 270.13362 -1 \n \
|
||||
108 Hs 1.34 0 1.7 269 2 269 269.13406 -1 \n \
|
||||
109 Mt 1.29 0 1.7 278 2 278 278.15481 -1 \n \
|
||||
110 Ds 1.28 0 1.7 281 2 281 281.16206 -1 \n \
|
||||
111 Rg 1.21 0 1.7 281 2 281 281.16537 -1 \n \
|
||||
112 Cn 1.22 0 1.7 285 2 285 285.17411 -1 \n"
|
||||
55 Cs 1.67 2.35 3.0 132.905 1 133 132.9054519 1 \n \
|
||||
56 Ba 1.34 1.98 2.7 137.328 2 138 137.9052472 2 \n \
|
||||
57 La 1.87 1.69 2.5 138.906 3 139 138.9063533 -1 \n \
|
||||
58 Ce 1.83 1.83 2.48 140.116 4 140 139.9054387 -1 \n \
|
||||
59 Pr 1.82 1.82 2.47 140.908 3 141 140.9076528 -1 \n \
|
||||
60 Nd 1.81 1.81 2.45 144.24 4 142 141.9077233 -1 \n"
|
||||
"61 Pm 1.8 1.8 2.43 145 5 145 144.912749 -1 \n \
|
||||
62 Sm 1.8 1.8 2.42 150.36 6 152 151.9197324 -1 \n \
|
||||
63 Eu 1.99 1.99 2.4 151.964 7 153 152.9212303 -1 \n \
|
||||
64 Gd 1.79 1.79 2.38 157.25 8 158 157.9241039 -1 \n \
|
||||
65 Tb 1.76 1.76 2.37 158.925 9 159 158.9253468 -1 \n \
|
||||
66 Dy 1.75 1.75 2.35 162.5 10 164 163.9291748 -1 \n \
|
||||
67 Ho 1.74 1.74 2.33 164.93 11 165 164.9303221 -1 \n \
|
||||
68 Er 1.73 1.73 2.32 167.26 12 166 165.9302931 -1 \n \
|
||||
69 Tm 1.72 1.72 2.3 168.934 13 169 168.9342133 -1 \n \
|
||||
70 Yb 1.94 1.94 2.28 173.04 14 174 173.9388621 -1 \n \
|
||||
71 Lu 1.72 1.72 2.27 174.967 15 175 174.9407718 -1 \n \
|
||||
72 Hf 1.57 1.44 2.25 178.49 4 180 179.94655 -1 \n \
|
||||
73 Ta 1.43 1.34 2.2 180.948 5 181 180.9479958 -1 \n \
|
||||
74 W 1.37 1.3 2.1 183.84 6 184 183.9509312 -1 \n \
|
||||
75 Re 1.35 1.28 2.05 186.207 7 187 186.9557531 -1 \n \
|
||||
76 Os 1.37 1.26 2.0 190.23 8 192 191.9614807 -1 \n \
|
||||
77 Ir 1.32 1.27 2.0 192.217 9 193 192.9629264 -1 \n \
|
||||
78 Pt 1.5 1.3 2.05 195.078 10 195 194.9647911 -1 \n \
|
||||
79 Au 1.5 1.34 2.1 196.967 11 197 196.9665687 -1 \n \
|
||||
80 Hg 1.7 1.49 2.05 200.59 2 202 201.970643 -1 \n"
|
||||
"81 Tl 1.55 1.48 2.2 204.383 3 205 204.9744275 3 \n \
|
||||
82 Pb 1.54 1.48 2.3 207.2 4 208 207.9766521 4 \n \
|
||||
83 Bi 1.54 1.45 2.3 208.98 5 209 208.9803987 3 5 7 \n \
|
||||
84 Po 1.68 1.46 2.0 209 6 209 208.9824304 2 \n \
|
||||
85 At 1.7 1.45 2.0 210 7 210 209.987148 1 \n \
|
||||
86 Rn 2.4 2.4 2.0 222 8 211 210.990601 0 \n \
|
||||
87 Fr 2 2 2.0 223 1 223 223.0197359 1 \n \
|
||||
88 Ra 1.9 1.9 2.0 226 2 223 223.0185022 2 \n \
|
||||
89 Ac 1.88 1.88 2.0 227 3 227 227.0277521 -1 \n \
|
||||
90 Th 1.79 1.79 2.4 232.038 4 232 232.0380553 -1 \n \
|
||||
91 Pa 1.61 1.61 2.0 231.036 3 231 231.035884 -1 \n \
|
||||
92 U 1.58 1.58 2.3 238.029 4 238 238.0507882 -1 \n \
|
||||
93 Np 1.55 1.55 2.0 237 5 236 236.04657 -1 \n \
|
||||
94 Pu 1.53 1.53 2.0 244 6 238 238.0495599 -1 \n \
|
||||
95 Am 1.51 1.07 2.0 243 7 241 241.0568291 -1 \n \
|
||||
96 Cm 1.5 0 2.0 247 8 243 243.0613891 -1 \n \
|
||||
97 Bk 1.5 0 2.0 247 9 247 247.070307 -1 \n \
|
||||
98 Cf 1.5 0 2.0 251 10 249 249.0748535 -1 \n \
|
||||
99 Es 1.5 0 2.0 252 11 252 252.08298 -1 \n \
|
||||
100 Fm 1.5 0 2.0 257 12 257 257.095105 -1 \n"
|
||||
"101 Md 1.5 0 2.0 258 13 258 258.098431 -1 \n \
|
||||
102 No 1.5 0 2.0 259 14 259 259.10103 -1 \n \
|
||||
103 Lr 1.5 0 2.0 262 15 262 262.10963 -1 \n \
|
||||
104 Rf 1.57 0 2.0 267 2 267 267.12153 -1 \n \
|
||||
105 Db 1.49 0 2.0 268 2 268 268.12545 -1 \n \
|
||||
106 Sg 1.43 0 2.0 269 2 271 271.13347 -1 \n \
|
||||
107 Bh 1.41 0 2.0 270 2 270 270.13362 -1 \n \
|
||||
108 Hs 1.34 0 2.0 269 2 269 269.13406 -1 \n \
|
||||
109 Mt 1.29 0 2.0 278 2 278 278.15481 -1 \n \
|
||||
110 Ds 1.28 0 2.0 281 2 281 281.16206 -1 \n \
|
||||
111 Rg 1.21 0 2.0 281 2 281 281.16537 -1 \n \
|
||||
112 Cn 1.22 0 2.0 285 2 285 285.17411 -1 \n"
|
||||
// The Blue Obelisk Data Repository has no VdW radii for those:
|
||||
// Ds Rg Cn Uut Fl Mc Uup Lv Ts Og; we use 2.0 for all of them
|
||||
// ---
|
||||
// added from BODR 30.10.2016
|
||||
// atomic mass data from NIST
|
||||
// we leave Uut and Uup in here for backwards
|
||||
// compatibility
|
||||
"113 Nh 1.36 0 1.7 284 2 284 284.17873 -1 \n \
|
||||
113 Uut 1.36 0 1.7 284 2 284 284.17873 -1 \n \
|
||||
114 Fl 1.43 0 1.7 289 2 289 289.19042 -1 \n \
|
||||
115 Mc 1.62 0 1.7 288 2 288 288.19274 -1 \n \
|
||||
115 Uup 1.62 0 1.7 288 2 288 288.19274 -1 \n \
|
||||
116 Lv 1.75 0 1.7 293 2 293 293.20449 -1 \n \
|
||||
117 Ts 1.65 0 1.7 292 2 292 292.20746 -1 \n \
|
||||
118 Og 1.57 0 1.7 294 2 294 294.21392 -1 \n \
|
||||
"113 Nh 1.36 0 2.0 284 2 284 284.17873 -1 \n \
|
||||
113 Uut 1.36 0 2.0 284 2 284 284.17873 -1 \n \
|
||||
114 Fl 1.43 0 2.0 289 2 289 289.19042 -1 \n \
|
||||
115 Mc 1.62 0 2.0 288 2 288 288.19274 -1 \n \
|
||||
115 Uup 1.62 0 2.0 288 2 288 288.19274 -1 \n \
|
||||
116 Lv 1.75 0 2.0 293 2 293 293.20449 -1 \n \
|
||||
117 Ts 1.65 0 2.0 292 2 292 292.20746 -1 \n \
|
||||
118 Og 1.57 0 2.0 294 2 294 294.21392 -1 \n \
|
||||
";
|
||||
|
||||
atomicData::atomicData(const std::string &dataLine) {
|
||||
|
||||
@@ -76,9 +76,9 @@ public class DistanceGeometryTests extends GraphMolTest {
|
||||
double d1 = pt1j.minus(pt1i).length();
|
||||
double d2 = pt2j.minus(pt2i).length();
|
||||
if(m.getBondBetweenAtoms(i,j) != null){
|
||||
assertEquals(d1, d2, 0.06);
|
||||
assertTrue(Math.abs(d1-d2)/d1<0.06);
|
||||
} else {
|
||||
assertEquals(d1, d2, 0.15);
|
||||
assertTrue(Math.abs(d1-d2)/d1<0.12);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
@@ -84,12 +84,12 @@ def ComputeMolVolume(mol, confId=-1, gridSpacing=0.2, boxMargin=2.0):
|
||||
>>> AllChem.EmbedMolecule(mol)
|
||||
0
|
||||
>>> ComputeMolVolume(mol)
|
||||
34...
|
||||
28...
|
||||
>>> mol = Chem.AddHs(Chem.MolFromSmiles('O'))
|
||||
>>> AllChem.EmbedMolecule(mol)
|
||||
0
|
||||
>>> ComputeMolVolume(mol)
|
||||
23...
|
||||
20...
|
||||
|
||||
"""
|
||||
mol = rdchem.Mol(mol)
|
||||
@@ -214,7 +214,7 @@ def EnumerateLibraryFromReaction(reaction, sidechainSets, returnReactants=False)
|
||||
>>> amines = (Chem.MolFromSmiles('N'+'C'*x) for x in range(10000))
|
||||
|
||||
... a set of 10000 acids
|
||||
|
||||
|
||||
>>> acids = (Chem.MolFromSmiles('OC(=O)'+'C'*x) for x in range(10000))
|
||||
|
||||
... now the virtual library (1e8 compounds in principle):
|
||||
@@ -360,7 +360,7 @@ def AssignBondOrdersFromTemplate(refmol, mol):
|
||||
|
||||
An example, start by generating a template from a SMILES
|
||||
and read in the PDB structure of the molecule
|
||||
|
||||
|
||||
>>> import os
|
||||
>>> from rdkit.Chem import AllChem
|
||||
>>> template = AllChem.MolFromSmiles("CN1C(=NC(C1=O)(c2ccccc2)c3ccccc3)N")
|
||||
@@ -371,7 +371,7 @@ def AssignBondOrdersFromTemplate(refmol, mol):
|
||||
22
|
||||
|
||||
Now assign the bond orders based on the template molecule
|
||||
|
||||
|
||||
>>> newMol = AllChem.AssignBondOrdersFromTemplate(template, mol)
|
||||
>>> len([1 for b in newMol.GetBonds() if b.GetBondTypeAsDouble() == 1.0])
|
||||
8
|
||||
|
||||
@@ -122,9 +122,9 @@ class TestCase(unittest.TestCase):
|
||||
|
||||
def test3Embed(self):
|
||||
testResults = {
|
||||
'mol_197': (218.80, 35.75, 110.33, 11.58, 109.66, 11.09, 90.35, 2.95, 0.00),
|
||||
'mol_223': (259.19, 6.27, 134.13, 1.12, 134.06, 1.12, 85.74, 0.61, 0.00),
|
||||
'mol_269': (204.51, 7.89, 103.89, 1.20, 102.66, 1.20, 88.07, 1.21, 6.00),
|
||||
'mol_197': (218.61, 36.02, 110.32, 11.58, 109.65, 11.09, 90.35, 2.95, 0.00),
|
||||
'mol_223': (250.46, 7.24, 134.74, 1.55, 134.66, 1.55, 85.27, 0.61, 0.00),
|
||||
'mol_269': (215.52, 6.07, 103.94, 0.21, 102.76, 0.27, 88.22, 0.36, 6.00),
|
||||
}
|
||||
inF = gzip.open(os.path.join(self.dataDir, 'cdk2-syn-clip100.pkl.gz'), 'rb')
|
||||
nDone = 0
|
||||
@@ -154,8 +154,8 @@ class TestCase(unittest.TestCase):
|
||||
randomSeed=23)
|
||||
tgt = testResults[name]
|
||||
self.assertEqual(len(tgt), len(stats))
|
||||
# print(name)
|
||||
# print(','.join(['%.2f' % x for x in stats]))
|
||||
print(name)
|
||||
print(','.join(['%.2f' % x for x in stats]))
|
||||
# we'll use different tolerances for the different values:
|
||||
self.assertTrue(feq(tgt[0], stats[0], 5.0), (tgt[0], stats[0]))
|
||||
for i in range(2, len(tgt)):
|
||||
|
||||
@@ -15,71 +15,73 @@ from rdkit.Chem.Subshape import SubshapeBuilder, SubshapeAligner, SubshapeObject
|
||||
|
||||
debug = False
|
||||
if not debug:
|
||||
SubshapeAligner.logger.setLevel(SubshapeAligner.RDLogger.ERROR)
|
||||
SubshapeAligner.logger.setLevel(SubshapeAligner.RDLogger.ERROR)
|
||||
|
||||
|
||||
class TestCase(unittest.TestCase):
|
||||
|
||||
def test1(self):
|
||||
filename = os.path.join(os.path.dirname(os.path.abspath(__file__)), 'test_data', '5ht3ligs.sdf')
|
||||
suppl = Chem.SDMolSupplier(filename)
|
||||
builder = SubshapeBuilder.SubshapeBuilder()
|
||||
builder.gridDims = (20., 20., 10)
|
||||
builder.gridSpacing = 0.5
|
||||
builder.winRad = 4.
|
||||
def test1(self):
|
||||
filename = os.path.join(os.path.dirname(os.path.abspath(__file__)),
|
||||
'test_data', '5ht3ligs.sdf')
|
||||
suppl = Chem.SDMolSupplier(filename)
|
||||
builder = SubshapeBuilder.SubshapeBuilder()
|
||||
builder.gridDims = (20., 20., 10)
|
||||
builder.gridSpacing = 0.5
|
||||
builder.winRad = 4.
|
||||
|
||||
ms = []
|
||||
shapes = []
|
||||
for m in suppl:
|
||||
m = Chem.AddHs(m, addCoords=True)
|
||||
AllChem.CanonicalizeConformer(m.GetConformer())
|
||||
ms.append(m)
|
||||
shape = builder(m, terminalPtsOnly=True)
|
||||
shapes.append(shape)
|
||||
ms = []
|
||||
shapes = []
|
||||
for m in suppl:
|
||||
m = Chem.AddHs(m, addCoords=True)
|
||||
AllChem.CanonicalizeConformer(m.GetConformer())
|
||||
ms.append(m)
|
||||
shape = builder(m, terminalPtsOnly=True)
|
||||
shapes.append(shape)
|
||||
|
||||
self.assertEqual(len(ms), 4)
|
||||
self.assertEqual(len(shapes), 4)
|
||||
self.assertEqual([len(x.skelPts) for x in shapes], [5, 5, 5, 5])
|
||||
self.assertEqual(len(ms), 4)
|
||||
self.assertEqual(len(shapes), 4)
|
||||
self.assertEqual([len(x.skelPts) for x in shapes], [5, 5, 5, 5])
|
||||
|
||||
refShape = builder.GenerateSubshapeShape(ms[0])
|
||||
self.assertEqual(len(refShape.skelPts), 15)
|
||||
refShape = builder.GenerateSubshapeShape(ms[0])
|
||||
self.assertEqual(len(refShape.skelPts), 16)
|
||||
|
||||
aligner = SubshapeAligner.SubshapeAligner()
|
||||
aligner.shapeDistTol = .30
|
||||
aligner = SubshapeAligner.SubshapeAligner()
|
||||
aligner.shapeDistTol = .30
|
||||
|
||||
algStore = []
|
||||
for i, s1 in enumerate(shapes):
|
||||
if not i or not s1:
|
||||
algStore.append([])
|
||||
continue
|
||||
m1 = ms[i]
|
||||
alignments = aligner.GetSubshapeAlignments(ms[0], refShape, m1, s1, builder)
|
||||
algStore.append(alignments)
|
||||
self.assertEqual([len(x) for x in algStore], [0, 2, 39, 0])
|
||||
algStore = []
|
||||
for i, s1 in enumerate(shapes):
|
||||
if not i or not s1:
|
||||
algStore.append([])
|
||||
continue
|
||||
m1 = ms[i]
|
||||
alignments = aligner.GetSubshapeAlignments(ms[0], refShape, m1, s1, builder)
|
||||
algStore.append(alignments)
|
||||
self.assertEqual([len(x) for x in algStore], [0, 5, 28, 0])
|
||||
|
||||
algStore = []
|
||||
for i, s1 in enumerate(shapes):
|
||||
if not i or not s1:
|
||||
algStore.append([])
|
||||
continue
|
||||
m1 = ms[i]
|
||||
alignments = list(aligner(ms[0], refShape, m1, s1, builder))
|
||||
algStore.append(alignments)
|
||||
self.assertTrue([len(x) for x in algStore] == [0, 2, 39, 0])
|
||||
algStore = []
|
||||
for i, s1 in enumerate(shapes):
|
||||
if not i or not s1:
|
||||
algStore.append([])
|
||||
continue
|
||||
m1 = ms[i]
|
||||
alignments = list(aligner(ms[0], refShape, m1, s1, builder))
|
||||
algStore.append(alignments)
|
||||
self.assertEqual([len(x) for x in algStore], [0, 5, 28, 0])
|
||||
|
||||
pruned = []
|
||||
for i, mi in enumerate(ms):
|
||||
alignments = algStore[i]
|
||||
pruned.append(SubshapeAligner.ClusterAlignments(mi, alignments, builder, neighborTol=0.15))
|
||||
self.assertEqual([len(x) for x in pruned], [0, 2, 29, 0])
|
||||
pruned = []
|
||||
for i, mi in enumerate(ms):
|
||||
alignments = algStore[i]
|
||||
pruned.append(SubshapeAligner.ClusterAlignments(
|
||||
mi, alignments, builder, neighborTol=0.15))
|
||||
self.assertEqual([len(x) for x in pruned], [0, 4, 12, 0])
|
||||
|
||||
|
||||
class TestSubshapeObjects(unittest.TestCase):
|
||||
|
||||
def test_SubshapeShape(self):
|
||||
shape = SubshapeObjects.SubshapeShape()
|
||||
self.assertEqual(shape.shapes, [])
|
||||
def test_SubshapeShape(self):
|
||||
shape = SubshapeObjects.SubshapeShape()
|
||||
self.assertEqual(shape.shapes, [])
|
||||
|
||||
|
||||
if __name__ == '__main__':
|
||||
unittest.main()
|
||||
unittest.main()
|
||||
|
||||
Reference in New Issue
Block a user