def test_backtrace_param():
lisp = cl4py.Lisp(backtrace=True)
assert lisp.eval(Symbol("*BACKTRACE*", "CL4PY"))
assert lisp.backtrace
lisp = cl4py.Lisp(backtrace=False)
assert not lisp.eval(Symbol("*BACKTRACE*", "CL4PY"))
assert not lisp.backtrace
def test_produce_backtrace_type_error(stock_lisp, backtrace_lisp):
with pytest.raises(RuntimeError):
load_sample_program(stock_lisp)
stock_lisp.find_package("COMMON-LISP-USER").make_type_error()
lisp = cl4py.Lisp(backtrace=True, quicklisp=True)
load_sample_program(lisp)
try:
lisp.find_package("COMMON-LISP-USER").make_type_error()
except RuntimeError as e:
msg = e.args[0]
backtrace_re = re.compile('Backtrace', re.MULTILINE)
assert re.search(backtrace_re, msg)
else:
pytest.fail("Should have seen a RuntimeError")
def lisp():
return cl4py.Lisp()
def backtrace_lisp():
return cl4py.Lisp(backtrace=True)
def stock_lisp():
return cl4py.Lisp()
import cl4py
lisp = cl4py.Lisp([
"/Users/meister/Development/cando-dev/build/boehm/icando-boehm", "-N",
"--load"
])
cl = lisp.find_package('CL')
chem = lisp.find_package('CHEM')
leap = lisp.find_package('LEAP')
tirun = lisp.find_package("TIRUN")
cando = lisp.find_package("CANDO")
cu = lisp.find_package('CANDO-USER')
cu.setup_default_paths()
cu.load_atom_type_rules("ATOMTYPE_GFF.DEF")
leap.source("leaprc.ff14SB.redq")
leap.source("leaprc.gaff")
tiruns = tirun.make_tirun()
sk = leap.load_sketch("ligands.cdxml")
tirun.setup_ligands(tiruns, sk)
tests_list = cl.read_from_string(
"""(list (cons :c1 (lambda (a) (eq (chem:get-name a) :c1))) (cons :c3 (lambda (a) (eq (chem:get-name a) :c3))) (cons :c5 (lambda (a) (eq (chem:get-name a) :c5))))"""
)
tests = cl.eval(cl.first(tests_list))
pick = chem.compile_smarts("[C:6]1~[C<c1>:1]~[C:2]~[C<c3>:3]~[C:4]~[C<c5>:5]1",
tests=tests)
lysozyme = cu.load_pdb("181L_mod.pdb")
cando.build_unbuilt_hydrogens(cl.first(lysozyme))
cu.simple_build_unbuilt_atoms(cl.first(lysozyme))
tirun.add_receptor(tiruns, cl.first(lysozyme))
cu.load_off("phen.lib")
cu.load_off("benz.lib")
ligs = cu.load_pdb("bnz_phn.pdb")
import glob
import random
import sys
import unittest
import atheris
import cl4py
import os
import emoji
from speac_library.speac.speac_settings import SpeacSettings
from speac_library.speac.top_level import get_the_levels
lisp = cl4py.Lisp()
cl = lisp.function("find-package")("CL")
def load_files():
path = os.path.join(os.path.dirname(__file__), "lisp_files/*.lisp")
for file_name in glob.glob(path):
file_name = file_name.replace("\\", "/")
lisp.eval(("load", '"' + file_name + '"'))
def cl4py_elements_to_python(cl4py_element):
if isinstance(cl4py_element, cl4py.Symbol):
return str(cl4py_element.name).lower()
elif isinstance(cl4py_element, cl4py.Cons):
