GreenPolyProducts/openbabel
5
0
Fork 0
mirror of https://github.com/openbabel/openbabel.git synced 2026-08-26 21:27:29 -05:00
Code Issues Packages Projects Releases Wiki Activity

Merge pull request #1970 from e-kwsm/improve-python

Browse Source 
Improve python script
This commit is contained in:
Noel O'Boyle
2019-04-18 08:26:25 +01:00
committed by GitHub
parent d28440de93 6b57788a05
commit 532ca37c32
17 changed files with 508 additions and 515 deletions
Download Patch File Download Diff File Expand all files Collapse all files
doc/examples/obconversion_readstring.py
+3 -2
View File
@@ -1,13 +1,14 @@
from __future__ import print_function
import openbabel as ob
# Initialize the OBConversion object
conv = ob.OBConversion()
if not conv.SetInFormat('smi'):
print 'could not find smiles format'
print('could not find smiles format')
# Read the smiles string
mol = ob.OBMol()
if not conv.ReadString(mol, 'CCCC'):
print 'could not read the smiles string'
print('could not read the smiles string')
# ... Use OBMol object ...
scripts/python/examples/dalke_test.py
+369 -375
View File
File diff suppressed because it is too large Load Diff
scripts/python/examples/energy.py
+7 -6
View File
@@ -4,6 +4,7 @@
#
######################################################################
from __future__ import print_function
import openbabel
import sys
@@ -11,7 +12,7 @@ import sys
try:
filename = sys.argv[1]
except:
print "Usage: python energy.py filename"
print("Usage: python energy.py filename")
sys.exit(1)
# Read the file.
@@ -24,19 +25,19 @@ conv.ReadFile(mol, filename)
# Find the MMFF94 force field.
ff = openbabel.OBForceField.FindForceField("MMFF94")
if ff == 0:
print "Could not find forcefield"
print("Could not find forcefield")
# Set the log level to high since we want to print out individual
# interactions.
ff.SetLogLevel(openbabel.OBFF_LOGLVL_HIGH)
ff.SetLogLevel(openbabel.OBFF_LOGLVL_HIGH)
# python specific, python doesn't have std::ostream so the SetLogFile()
# function is replaced by SetLogToStdOut and SetLogToStdErr in the SWIG
# interface file
ff.SetLogToStdErr()
ff.SetLogToStdErr()
# Setup the molecule. This assigns atoms types, charges and parameters
# Setup the molecule. This assigns atoms types, charges and parameters
if ff.Setup(mol) == 0:
print "Could not setup forcefield"
print("Could not setup forcefield")
# Calculate the energy
ff.Energy()
scripts/python/examples/examples.py
+11 -10
View File
@@ -1,16 +1,17 @@
from __future__ import print_function
import openbabel
mol = openbabel.OBMol()
print 'Should print 0 (atoms)'
print mol.NumAtoms()
print('Should print 0 (atoms)')
print(mol.NumAtoms())
a = mol.NewAtom()
b = mol.NewAtom()
mol.AddBond(1, 2, 1)
print 'Should print 2 (atoms)'
print mol.NumAtoms()
print 'Should print 1 (bond)'
print mol.NumBonds()
print('Should print 2 (atoms)')
print(mol.NumAtoms())
print('Should print 1 (bond)')
print(mol.NumBonds())
obConversion = openbabel.OBConversion()
obConversion.SetInAndOutFormats("smi", "mdl")
@@ -18,12 +19,12 @@ obConversion.SetInAndOutFormats("smi", "mdl")
mol.Clear()
obConversion.ReadString(mol, "C1=CC=CS1")
print 'Should print 5 (atoms)'
print mol.NumAtoms()
print('Should print 5 (atoms)')
print(mol.NumAtoms())
mol.AddHydrogens()
print 'Should print 9 (atoms) after adding hydrogens'
print mol.NumAtoms()
print('Should print 9 (atoms) after adding hydrogens')
print(mol.NumAtoms())
outMDL = obConversion.WriteString(mol)
scripts/python/examples/minSimple.py
+8 -7
View File
@@ -4,6 +4,7 @@
#
######################################################################
from __future__ import print_function
import openbabel
import sys
@@ -11,7 +12,7 @@ import sys
try:
filename = sys.argv[1]
except:
print "Usage: python energy.py filename"
print("Usage: python energy.py filename")
sys.exit(1)
# Read the file.
@@ -24,19 +25,19 @@ conv.ReadFile(mol, filename)
# Find the MMFF94 force field.
ff = openbabel.OBForceField.FindForceField("MMFF94")
if ff == 0:
print "Could not find forcefield"
print("Could not find forcefield")
# Set the log level to low since we only want to print out the minimization
# Set the log level to low since we only want to print out the minimization
# steps and not all individual interactions for each call to Energy()
ff.SetLogLevel(openbabel.OBFF_LOGLVL_LOW)
ff.SetLogLevel(openbabel.OBFF_LOGLVL_LOW)
# python specific, python doesn't have std::ostream so the SetLogFile()
# function is replaced by SetLogToStdOut and SetLogToStdErr in the SWIG
# interface file
ff.SetLogToStdErr()
ff.SetLogToStdErr()
# Setup the molecule. This assigns atoms types, charges and parameters
# Setup the molecule. This assigns atoms types, charges and parameters
if ff.Setup(mol) == 0:
print "Could not setup forcefield"
print("Could not setup forcefield")
# Minimize using steepest descent for 2000 steps
ff.SteepestDescent(2000)
scripts/python/examples/testpybel.py
+5 -5
View File
@@ -62,8 +62,8 @@ class TestToolkit(myTestCase):
def testattributes(self):
"""Test attributes like informats, descs and so on"""
informats, outformats = self.toolkit.informats, self.toolkit.outformats
self.assertNotEqual(len(self.toolkit.informats.keys()), 0)
self.assertNotEqual(len(self.toolkit.outformats.keys()), 0)
self.assertNotEqual(len(list(self.toolkit.informats.keys())), 0)
self.assertNotEqual(len(list(self.toolkit.outformats.keys())), 0)
self.assertNotEqual(len(self.toolkit.descs), 0)
self.assertNotEqual(len(self.toolkit.forcefields), 0)
self.assertNotEqual(len(self.toolkit.fps), 0)
@@ -278,7 +278,7 @@ M END
def testMDglobalaccess(self):
"""Check out the keys"""
data = self.head[0].data
self.assertFalse(data.has_key('Noel'))
self.assertFalse('Noel' in data)
self.assertEqual(len(data), len(self.datakeys))
for key in data:
self.assertEqual(key in self.datakeys, True)
@@ -288,9 +288,9 @@ M END
def testMDdelete(self):
"""Delete some keys"""
data = self.head[0].data
self.assertTrue(data.has_key('NSC'))
self.assertTrue('NSC' in data)
del data['NSC']
self.assertFalse(data.has_key('NSC'))
self.assertFalse('NSC' in data)
data.clear()
self.assertEqual(len(data), 0)
scripts/python/examples/wgtRotorSrch.py
+8 -7
View File
@@ -4,6 +4,7 @@
#
######################################################################
from __future__ import print_function
import openbabel
import sys
@@ -11,7 +12,7 @@ import sys
try:
filename = sys.argv[1]
except:
print "Usage: python energy.py filename"
print("Usage: python energy.py filename")
sys.exit(1)
# Read the file.
@@ -24,21 +25,21 @@ conv.ReadFile(mol, filename)
# Find the MMFF94 force field.
ff = openbabel.OBForceField.FindForceField("MMFF94")
if ff == 0:
print "Could not find forcefield"
print("Could not find forcefield")
# Set the log level to low since we only want to print out the conformer search
# steps and not all individual interactions for each call to Energy()
ff.SetLogLevel(openbabel.OBFF_LOGLVL_LOW)
ff.SetLogLevel(openbabel.OBFF_LOGLVL_LOW)
# python specific, python doesn't have std::ostream so the SetLogFile()
# function is replaced by SetLogToStdOut and SetLogToStdErr in the SWIG
# interface file
ff.SetLogToStdErr()
ff.SetLogToStdErr()
# Setup the molecule. This assigns atoms types, charges and parameters
# Setup the molecule. This assigns atoms types, charges and parameters
if ff.Setup(mol) == 0:
print "Could not setup forcefield"
print("Could not setup forcefield")
# Weighted rotor search: generate 25 conformers, optimize each conformer for
# Weighted rotor search: generate 25 conformers, optimize each conformer for
# 500 steps.
ff.WeightedRotorSearch(25, 500)
scripts/python/setup.py
+1 -1
View File
@@ -44,7 +44,7 @@ def locate_ob():
ob_ver = StrictVersion(pkgconfig('openbabel-2.0', '--modversion'))
py_ver = StrictVersion(find_version())
if not ob_ver.version[:2] == py_ver.version[:2]:
print('Warning: Open Babel %s.%s.x is required. Your version (%s) may not be compatible.'
print('Warning: Open Babel %s.%s.x is required. Your version (%s) may not be compatible.'
% (py_ver.version[0], py_ver.version[1], ob_ver))
include_dirs = pkgconfig('openbabel-2.0', '--variable=pkgincludedir')
library_dirs = pkgconfig('openbabel-2.0', '--variable=libdir')
test/testRInChI.py
+1 -1
View File
@@ -36,7 +36,7 @@ class TestReactionInChIWriter(BaseTest):
# Example: esterification of acetic acid
("OCC.CC(=O)O>S(=O)(=O)(O)O>CC(=O)OCC.O", "RInChI=1.00.1S/C2H4O2/c1-2(3)4/h1H3,(H,3,4)!C2H6O/c1-2-3/h3H,2H2,1H3<>C4H8O2/c1-3-6-4(2)5/h3H2,1-2H3!H2O/h1H2<>H2O4S/c1-5(2,3)4/h(H2,1,2,3,4)/d+"),
# Example: alkaline ring opening
("CC[C@]1(C)O[C@H]1C.[OH-]>>CC[C@](C)(O)[C@@H](C)O", "RInChI=1.00.1S/C6H12O/c1-4-6(3)5(2)7-6/h5H,4H2,1-3H3/t5-,6-/m0/s1!H2O/h1H2/p-1<>C6H14O2/c1-4-6(3,8)5(2)7/h5,7-8H,4H2,1-3H3/t5-,6+/m1/s1/d+"),
("CC[C@]1(C)O[C@H]1C.[OH-]>>CC[C@](C)(O)[C@@H](C)O", "RInChI=1.00.1S/C6H12O/c1-4-6(3)5(2)7-6/h5H,4H2,1-3H3/t5-,6-/m0/s1!H2O/h1H2/p-1<>C6H14O2/c1-4-6(3,8)5(2)7/h5,7-8H,4H2,1-3H3/t5-,6+/m1/s1/d+"),
# Partial reactions
(">>C1CC=C(O)CC1", "RInChI=1.00.1S/<>C6H10O/c7-6-4-2-1-3-5-6/h4,7H,1-3,5H2/d+"),
("C1CC=C(O)CC1>>", "RInChI=1.00.1S/<>C6H10O/c7-6-4-2-1-3-5-6/h4,7H,1-3,5H2/d-"),
test/testbabel.py
+3 -4
View File
@@ -71,9 +71,8 @@ def log(text):
The log file (log.txt) is created in build/test
"""
output = open("log.txt", "a")
print >> output, text
output.close()
with open("log.txt", "a") as output:
output.write(text + "\n")
class BaseTest(unittest.TestCase):
"""A base class for test classes that adds additional
@@ -269,7 +268,7 @@ TORSDOF 5
'O=[S@@](c1nc2c([nH]1)cccc2)Cc1nccc(c1C)OCC(F)(F)F',
'C#C[C@]1(O)CC[C@@H]2[C@]1(C)CC[C@H]1[C@H]2CCc2c1ccc(c2)O',
]
for cofname, CAN in zip(listCOFnames, listCANexpected):
for cofname, CAN in zip(listCOFnames, listCANexpected):
coffilename = cofname + '.cof'
if(cofname == 'culgi_06'):
cofname = 'mol24' # Special case: 'internal name' not the same as file name
test/testbindings.py
-1
View File
@@ -19,7 +19,6 @@ and so you can quickly develop the tests and try them out.
"""
import os
import re
import sys
import unittest
import itertools
test/testfastsearch.py
+4 -5
View File
@@ -14,7 +14,6 @@ In both cases, the test file is run directly from the source folder,
and so you can quickly develop the tests and try them out.
"""
import os
import unittest
from testbabel import run_exec, BaseTest
@@ -38,22 +37,22 @@ S(N1[CH](c2ccccc2C=C1)C#N)(c1ccc(cc1)C)(=O)=O
c12c(c(OC)c3c(c1OC)occ3)ccc(o2)=O
c12c(O[CH](C1=O)C(C)C)cc1c(c2)ccc(=O)o1
c12[C]3([C@H]4([N@@](CCc1c1ccccc1[nH]2)C[C@H](C=C4CC)C3))C(=O)OC"""
outputfile = open("ten.smi", "w")
outputfile.write(smiles)
outputfile.close()
output, error = run_exec("babel ten.smi ten.fs")
self.canFindFile("ten.fs")
self.assertConverted(error, 10)
query = "Nc2nc(c1ccccc1)nc3ccccc23"
output, error = run_exec("babel ten.fs -ifs -s %s -osmi" % query)
self.assertConverted(error, 1)
output, error = run_exec("babel ten.fs -ifs -s %s -at 0.5 -aa -osmi" % query)
self.assertConverted(error, 1)
if __name__ == "__main__":
test/testkekule.py
+1 -1
View File
@@ -16,7 +16,7 @@ and so you can quickly develop the tests and try them out.
import unittest
from testbabel import run_exec, executable, log, BaseTest
from testbabel import run_exec, executable, BaseTest
class TestKekuleAssignment(BaseTest):
"""A series of tests relating to aromaticity/kekule"""
test/testpdbformat.py
+71 -71
View File
@@ -17,7 +17,7 @@ and so you can quickly develop the tests and try them out.
import unittest
from testbabel import run_exec, executable, log, BaseTest
from testbabel import run_exec, executable, BaseTest
class TestPDBFormat(BaseTest):
"""A series of tests relating to PDB"""
@@ -29,76 +29,76 @@ class TestPDBFormat(BaseTest):
"""
self.canFindExecutable("babel")
self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
ATOM 407 CA VAL L 29 57.124 18.088 47.170 1.00 0.00 C
ATOM 408 C VAL L 29 55.739 17.571 47.538 1.00 0.00 C
ATOM 409 O VAL L 29 55.535 16.362 47.550 1.00 0.00 O
ATOM 410 CB VAL L 29 57.580 17.456 45.842 1.00 0.00 C
ATOM 411 CG1 VAL L 29 56.571 17.743 44.741 1.00 0.00 C
ATOM 412 CG2 VAL L 29 58.957 17.973 45.450 1.00 0.00 C
ATOM 413 H VAL L 29 58.603 16.959 48.212 1.00 0.00 H
ATOM 414 HA VAL L 29 57.012 19.163 47.024 1.00 0.00 H
ATOM 415 HB VAL L 29 57.674 16.378 45.977 1.00 0.00 H
ATOM 416 1HG1 VAL L 29 56.909 17.289 43.809 1.00 0.00 H
ATOM 417 2HG1 VAL L 29 55.603 17.327 45.016 1.00 0.00 H
ATOM 418 3HG1 VAL L 29 56.479 18.821 44.604 1.00 0.00 H
ATOM 419 1HG2 VAL L 29 59.263 17.515 44.510 1.00 0.00 H
ATOM 420 2HG2 VAL L 29 58.917 19.055 45.331 1.00 0.00 H
ATOM 421 3HG2 VAL L 29 59.676 17.719 46.229 1.00 0.00 H
ATOM 422 N SER L 30 54.838 18.500 47.837 1.00 0.00 N
ATOM 423 CA SER L 30 53.494 18.162 48.273 1.00 0.00 C
ATOM 424 C SER L 30 52.725 17.364 47.221 1.00 0.00 C
ATOM 425 O SER L 30 52.723 17.697 46.056 1.00 0.00 O
ATOM 426 CB SER L 30 52.734 19.429 48.610 1.00 0.00 C
ATOM 427 OG SER L 30 51.403 19.143 48.941 1.00 0.00 O
ATOM 428 H SER L 30 55.100 19.472 47.757 1.00 0.00 H
ATOM 429 HA SER L 30 53.471 17.585 49.199 1.00 0.00 H
ATOM 430 1HB SER L 30 53.219 19.934 49.445 1.00 0.00 H
ATOM 431 2HB SER L 30 52.761 20.107 47.758 1.00 0.00 H
ATOM 432 HG SER L 30 50.919 19.965 48.828 1.00 0.00 H
ATOM 433 N SER L 30A 52.170 16.303 47.698 1.00 0.00 N
ATOM 434 CA SER L 30A 51.329 15.409 46.920 1.00 0.00 C
ATOM 435 C SER L 30A 52.015 14.812 45.685 1.00 0.00 C
ATOM 436 O SER L 30A 51.350 14.366 44.764 1.00 0.00 O
ATOM 437 CB SER L 30A 50.082 16.156 46.488 1.00 0.00 C
ATOM 438 OG SER L 30A 49.348 16.592 47.599 1.00 0.00 O
ATOM 439 H SER L 30A 52.421 16.046 48.642 1.00 0.00 H
ATOM 440 HA SER L 30A 50.943 14.567 47.497 1.00 0.00 H
ATOM 441 1HB SER L 30A 50.364 17.013 45.876 1.00 0.00 H
ATOM 442 2HB SER L 30A 49.463 15.505 45.873 1.00 0.00 H
ATOM 443 HG SER L 30A 49.931 17.176 48.090 1.00 0.00 H
ATOM 444 N SER L 31 53.347 14.792 45.683 1.00 0.00 N
ATOM 445 CA SER L 31 54.094 14.259 44.549 1.00 0.00 C
ATOM 446 C SER L 31 53.734 14.959 43.242 1.00 0.00 C
ATOM 447 O SER L 31 53.703 14.356 42.179 1.00 0.00 O
ATOM 448 CB SER L 31 53.835 12.771 44.418 1.00 0.00 C
ATOM 449 OG SER L 31 54.240 12.087 45.572 1.00 0.00 O
ATOM 450 H SER L 31 53.852 15.150 46.480 1.00 0.00 H
ATOM 451 HA SER L 31 55.175 14.292 44.689 1.00 0.00 H
ATOM 452 1HB SER L 31 52.774 12.600 44.243 1.00 0.00 H
ATOM 453 2HB SER L 31 54.375 12.383 43.555 1.00 0.00 H
ATOM 454 HG SER L 31 53.773 11.248 45.560 1.00 0.00 H
ATOM 455 N TYR L 32 53.460 16.259 43.402 1.00 0.00 N
ATOM 456 CA TYR L 32 53.176 17.161 42.301 1.00 0.00 C
ATOM 457 C TYR L 32 54.489 17.641 41.668 1.00 0.00 C
ATOM 458 O TYR L 32 54.910 18.762 41.892 1.00 0.00 O
ATOM 459 CB TYR L 32 52.342 18.352 42.780 1.00 0.00 C
ATOM 460 CG TYR L 32 50.880 18.031 42.990 1.00 0.00 C
ATOM 461 CD1 TYR L 32 50.294 16.936 42.371 1.00 0.00 C
ATOM 462 CD2 TYR L 32 50.089 18.824 43.807 1.00 0.00 C
ATOM 463 CE1 TYR L 32 48.958 16.639 42.559 1.00 0.00 C
ATOM 464 CE2 TYR L 32 48.751 18.535 44.002 1.00 0.00 C
ATOM 465 CZ TYR L 32 48.190 17.441 43.376 1.00 0.00 C
ATOM 466 OH TYR L 32 46.859 17.150 43.569 1.00 0.00 O
ATOM 467 H TYR L 32 53.456 16.618 44.347 1.00 0.00 H
ATOM 468 HA TYR L 32 52.651 16.625 41.509 1.00 0.00 H
ATOM 469 1HB TYR L 32 52.778 18.693 43.721 1.00 0.00 H
ATOM 470 2HB TYR L 32 52.439 19.136 42.030 1.00 0.00 H
ATOM 471 HD1 TYR L 32 50.908 16.305 41.727 1.00 0.00 H
ATOM 472 HD2 TYR L 32 50.537 19.687 44.299 1.00 0.00 H
ATOM 473 HE1 TYR L 32 48.512 15.775 42.066 1.00 0.00 H
ATOM 474 HE2 TYR L 32 48.145 19.172 44.648 1.00 0.00 H
ATOM 475 HH TYR L 32 46.462 17.658 44.280 1.00 0.00 H
self.entryPDBwithInsertioncodes="""ATOM 406 N VAL L 29 58.041 17.797 48.254 1.00 0.00 N
ATOM 407 CA VAL L 29 57.124 18.088 47.170 1.00 0.00 C
ATOM 408 C VAL L 29 55.739 17.571 47.538 1.00 0.00 C
ATOM 409 O VAL L 29 55.535 16.362 47.550 1.00 0.00 O
ATOM 410 CB VAL L 29 57.580 17.456 45.842 1.00 0.00 C
ATOM 411 CG1 VAL L 29 56.571 17.743 44.741 1.00 0.00 C
ATOM 412 CG2 VAL L 29 58.957 17.973 45.450 1.00 0.00 C
ATOM 413 H VAL L 29 58.603 16.959 48.212 1.00 0.00 H
ATOM 414 HA VAL L 29 57.012 19.163 47.024 1.00 0.00 H
ATOM 415 HB VAL L 29 57.674 16.378 45.977 1.00 0.00 H
ATOM 416 1HG1 VAL L 29 56.909 17.289 43.809 1.00 0.00 H
ATOM 417 2HG1 VAL L 29 55.603 17.327 45.016 1.00 0.00 H
ATOM 418 3HG1 VAL L 29 56.479 18.821 44.604 1.00 0.00 H
ATOM 419 1HG2 VAL L 29 59.263 17.515 44.510 1.00 0.00 H
ATOM 420 2HG2 VAL L 29 58.917 19.055 45.331 1.00 0.00 H
ATOM 421 3HG2 VAL L 29 59.676 17.719 46.229 1.00 0.00 H
ATOM 422 N SER L 30 54.838 18.500 47.837 1.00 0.00 N
ATOM 423 CA SER L 30 53.494 18.162 48.273 1.00 0.00 C
ATOM 424 C SER L 30 52.725 17.364 47.221 1.00 0.00 C
ATOM 425 O SER L 30 52.723 17.697 46.056 1.00 0.00 O
ATOM 426 CB SER L 30 52.734 19.429 48.610 1.00 0.00 C
ATOM 427 OG SER L 30 51.403 19.143 48.941 1.00 0.00 O
ATOM 428 H SER L 30 55.100 19.472 47.757 1.00 0.00 H
ATOM 429 HA SER L 30 53.471 17.585 49.199 1.00 0.00 H
ATOM 430 1HB SER L 30 53.219 19.934 49.445 1.00 0.00 H
ATOM 431 2HB SER L 30 52.761 20.107 47.758 1.00 0.00 H
ATOM 432 HG SER L 30 50.919 19.965 48.828 1.00 0.00 H
ATOM 433 N SER L 30A 52.170 16.303 47.698 1.00 0.00 N
ATOM 434 CA SER L 30A 51.329 15.409 46.920 1.00 0.00 C
ATOM 435 C SER L 30A 52.015 14.812 45.685 1.00 0.00 C
ATOM 436 O SER L 30A 51.350 14.366 44.764 1.00 0.00 O
ATOM 437 CB SER L 30A 50.082 16.156 46.488 1.00 0.00 C
ATOM 438 OG SER L 30A 49.348 16.592 47.599 1.00 0.00 O
ATOM 439 H SER L 30A 52.421 16.046 48.642 1.00 0.00 H
ATOM 440 HA SER L 30A 50.943 14.567 47.497 1.00 0.00 H
ATOM 441 1HB SER L 30A 50.364 17.013 45.876 1.00 0.00 H
ATOM 442 2HB SER L 30A 49.463 15.505 45.873 1.00 0.00 H
ATOM 443 HG SER L 30A 49.931 17.176 48.090 1.00 0.00 H
ATOM 444 N SER L 31 53.347 14.792 45.683 1.00 0.00 N
ATOM 445 CA SER L 31 54.094 14.259 44.549 1.00 0.00 C
ATOM 446 C SER L 31 53.734 14.959 43.242 1.00 0.00 C
ATOM 447 O SER L 31 53.703 14.356 42.179 1.00 0.00 O
ATOM 448 CB SER L 31 53.835 12.771 44.418 1.00 0.00 C
ATOM 449 OG SER L 31 54.240 12.087 45.572 1.00 0.00 O
ATOM 450 H SER L 31 53.852 15.150 46.480 1.00 0.00 H
ATOM 451 HA SER L 31 55.175 14.292 44.689 1.00 0.00 H
ATOM 452 1HB SER L 31 52.774 12.600 44.243 1.00 0.00 H
ATOM 453 2HB SER L 31 54.375 12.383 43.555 1.00 0.00 H
ATOM 454 HG SER L 31 53.773 11.248 45.560 1.00 0.00 H
ATOM 455 N TYR L 32 53.460 16.259 43.402 1.00 0.00 N
ATOM 456 CA TYR L 32 53.176 17.161 42.301 1.00 0.00 C
ATOM 457 C TYR L 32 54.489 17.641 41.668 1.00 0.00 C
ATOM 458 O TYR L 32 54.910 18.762 41.892 1.00 0.00 O
ATOM 459 CB TYR L 32 52.342 18.352 42.780 1.00 0.00 C
ATOM 460 CG TYR L 32 50.880 18.031 42.990 1.00 0.00 C
ATOM 461 CD1 TYR L 32 50.294 16.936 42.371 1.00 0.00 C
ATOM 462 CD2 TYR L 32 50.089 18.824 43.807 1.00 0.00 C
ATOM 463 CE1 TYR L 32 48.958 16.639 42.559 1.00 0.00 C
ATOM 464 CE2 TYR L 32 48.751 18.535 44.002 1.00 0.00 C
ATOM 465 CZ TYR L 32 48.190 17.441 43.376 1.00 0.00 C
ATOM 466 OH TYR L 32 46.859 17.150 43.569 1.00 0.00 O
ATOM 467 H TYR L 32 53.456 16.618 44.347 1.00 0.00 H
ATOM 468 HA TYR L 32 52.651 16.625 41.509 1.00 0.00 H
ATOM 469 1HB TYR L 32 52.778 18.693 43.721 1.00 0.00 H
ATOM 470 2HB TYR L 32 52.439 19.136 42.030 1.00 0.00 H
ATOM 471 HD1 TYR L 32 50.908 16.305 41.727 1.00 0.00 H
ATOM 472 HD2 TYR L 32 50.537 19.687 44.299 1.00 0.00 H
ATOM 473 HE1 TYR L 32 48.512 15.775 42.066 1.00 0.00 H
ATOM 474 HE2 TYR L 32 48.145 19.172 44.648 1.00 0.00 H
ATOM 475 HH TYR L 32 46.462 17.658 44.280 1.00 0.00 H
"""
output, error = run_exec(self.entryPDBwithInsertioncodes,
"babel -ipdb -ofasta")
test/testsmartssym.py
+3 -5
View File
@@ -14,11 +14,9 @@ In both cases, the test file is run directly from the source folder,
and so you can quickly develop the tests and try them out.
"""
import os
import unittest
import pdb
from testbabel import run_exec, executable, log, BaseTest
from testbabel import run_exec, BaseTest
def checkmatch(query, molecules):
result = []
@@ -69,7 +67,7 @@ class TestSmartsSym(BaseTest):
self.assertEqual(fastcheckmatch(data[2], data[0:6]),
[False, True, True, False, False, False])
self.assertEqual(fastcheckmatch(data[4], data[0:6]), [True]*6)
def testTetStereoImplicitH(self):
data = ['[C@H](Br)(Cl)I',
'[C@@H](Br)(Cl)I',
@@ -99,7 +97,7 @@ class TestSmartsSym(BaseTest):
self.assertEqual(fastcheckmatch(data[2], data[0:6]),
[False, True, True, False, False, False])
self.assertEqual(fastcheckmatch(data[5], data[0:6]), [True]*6)
if __name__ == "__main__":
testsuite = []
test/testsym.py
+12 -12
View File
@@ -17,7 +17,7 @@ and so you can quickly develop the tests and try them out.
import os
import unittest
from testbabel import run_exec, executable, log, BaseTest
from testbabel import run_exec, BaseTest
class TestSym(BaseTest):
"""Base class for a series of tests relating to symmetry"""
@@ -95,7 +95,7 @@ class TestCisTransSym(TestSym):
self.inchi = "InChI=1S/C4H4BrCl/c5-3-1-2-4-6/h1-4H/b3-1-,4-2+"
self.smiles = [
"C(=C\C=C/Br)/Cl",
"Cl/C=C/C=C\Br",
"Cl/C=C/C=C\Br",
"Br/C=C\C=C\Cl",
"C(=C\Cl)/C=C\Br",
"C(=C\C=C\Cl)\Br",
@@ -136,7 +136,7 @@ class TestRingBondCisTransSym(TestSym):
class TestConversions(BaseTest):
"""A series of tests relating to file format conversions and symmetry"""
def setUp(self):
self.canFindExecutable("babel")
self.data = [
@@ -154,7 +154,7 @@ class TestConversions(BaseTest):
(r"I/C=C\1/NC1", r"I/C=C/1\CN1", "InChI=1S/C3H4IN/c4-1-3-2-5-3/h1,5H,2H2/b3-1+"),
(r"I/C=C/1\NC1", r"I/C=C\1/CN1", "InChI=1S/C3H4IN/c4-1-3-2-5-3/h1,5H,2H2/b3-1-"),
]
def testSMILEStoInChI(self):
# Tests interconversions between the SMILES on the left versus
# the InChI on the right.
@@ -164,7 +164,7 @@ class TestConversions(BaseTest):
self.assertEqual(output.rstrip(), inchi)
output, error = run_exec(inchi, "babel -iinchi -ocan")
self.assertEqual(output.rstrip(), can)
def parseMDL(self, text):
lines = text.split("\n")
broken = lines[3].split()
@@ -186,7 +186,7 @@ class TestConversions(BaseTest):
output, error = run_exec(smi, "obabel -ismi --gen2d -omdl")
output, error = run_exec(output.rstrip(), "obabel -imdl -ocan")
self.assertEqual(can, output.rstrip())
def testSMILESto3DMDL(self):
"""Test interconversion between SMILES and 3D MDL"""
data = [
@@ -247,10 +247,10 @@ class TestConversions(BaseTest):
smiles, can = self.data[i][0:2]
output, error = run_exec(smiles, "babel -ismi -oxyz --gen3d")
canoutput, error = run_exec(output, "babel -ixyz -ocan")
self.assertEqual(canoutput.rstrip(), can)
sdfoutput, error = run_exec(output, "babel -ixyz -osdf")
atoms, bonds = self.parseMDL(sdfoutput)
parities = [atom['parity'] for atom in atoms]
@@ -266,7 +266,7 @@ class TestConversions(BaseTest):
# The following file was created using RDKit starting from
# the SMILES strings in data[x][0] below.
filename = self.getTestFile("testsym_2Dtests.sdf")
output, error = run_exec("babel -isdf %s -ocan" % filename)
for i, smiles in enumerate(output.rstrip().split("\n")):
self.assertEqual(smiles.rstrip(), self.data[i][1])
@@ -302,7 +302,7 @@ class TestConversions(BaseTest):
finaloutput, error = run_exec(output, "obabel -isdf -ocan")
for line in finaloutput.rstrip().split("\n"):
result, correct_answer = line.split()
self.assertEqual(result, correct_answer)
self.assertEqual(result, correct_answer)
def testSMILESto0DMDL(self):
"""Test interconversion between SMILES and 0D MDL"""
@@ -339,7 +339,7 @@ class TestStereoConversion(BaseTest):
test_inchi = 'InChI=1S/C10H10/c1-2-3-7-10-8-5-4-6-9-10/h2-9H,1H2/b7-3+'
output, error = run_exec(test_inchi, "babel -iinchi -osmi")
self.assertEqual(output.rstrip(), "C=C/C=C/c1ccccc1")
test_smiles = "C=C\C=C/c1ccccc1"
output, error = run_exec(test_smiles, "babel -ismi -oinchi")
self.assertEqual(output.rstrip(), "InChI=1S/C10H10/c1-2-3-7-10-8-5-4-6-9-10/h2-9H,1H2/b7-3-")
@@ -359,6 +359,6 @@ class TestStereoConversion(BaseTest):
self.assertEqual(output.rstrip(), smi)
del TestSym # remove base class to avoid tests
if __name__ == "__main__":
unittest.main()
test/testunique.py
+1 -2
View File
@@ -14,7 +14,6 @@ In both cases, the test file is run directly from the source folder,
and so you can quickly develop the tests and try them out.
"""
import os
import unittest
from testbabel import run_exec, BaseTest
@@ -52,6 +51,6 @@ C([2H])([2H])([2H])[2H] deuteromethane"""
output, error = run_exec(self.smiles,
"babel -ismi -osmi --unique %s" % param[0])
self.assertConverted(error, param[1])
if __name__ == "__main__":
unittest.main()