def setUpClass(cls):
cls.my_emap = pyemap.parse(
os.path.join(sys.path[0], "pyemap/tests/test_pdbs/2oal.pdb"))
if platform == "linux":
pyemap.process(cls.my_emap, sdef=0)
elif platform == "darwin":
pyemap.process(cls.my_emap)
def test_save_functions():
my_emap = pyemap.parse(
os.path.join(sys.path[0], "pyemap/tests/test_pdbs/4DJA.pdb"))
#cluster
fout = tempfile.NamedTemporaryFile(suffix=".png")
''' commented out for now until we can find a solution with newer RDKit
#aromatic eta moiety
my_emap.residue_to_Image("SF4603(A)")
my_emap.residue_to_file("SF4603(A)",dest=fout.name)
my_emap.residue_to_Image("FAD601(A)-1")
my_emap.residue_to_file("FAD601(A)-1",dest=fout.name)
'''
#after file is processed
pyemap.process(my_emap)
#standard residue
''' commented out for now until we can find a solution with newer RDKit
my_emap.residue_to_Image("Y443(A)")
my_emap.residue_to_file("Y443(A)",dest=fout.name)
'''
#init graph
my_emap.init_graph_to_Image()
my_emap.init_graph_to_file(dest=fout.name)
pyemap.find_paths(my_emap, "Y443(A)")
#paths graph
my_emap.paths_graph_to_Image()
my_emap.paths_graph_to_file(dest=fout.name)
#check that report does something
assert my_emap.report() != None
def test_distance_options(self):
pyemap.process(self.my_emap)
com_weight = self.my_emap.init_graph["W385(A)"]["Y53(A)"]['weight']
assert isclose(com_weight,6.18,abs_tol=1e-2)
pyemap.process(self.my_emap,dist_def=1)
closest_atom_weight = self.my_emap.init_graph["W385(A)"]["Y53(A)"]['weight']
assert isclose(closest_atom_weight,3.97,abs_tol=1e-2)
def test_custom_atom_range(self):
#custom residues
pyemap.process(self.my_emap,eta_moieties=[], custom = "(134-140),(109-117)")
resnames=[]
for residue in self.my_emap.residues.values():
resnames.append(residue.resname)
assert all(elem in resnames for elem in ["CUST-1","CUST-2"])
#example for bad custom residues, shoud raise exception
try:
pyemap.process(self.my_emap, custom = "(28-41)")
assert False
except Exception as e:
assert True
def test_chains(self):
#default all chains on
pyemap.process(self.my_emap)
labels=[]
for residue in self.my_emap.residues.values():
labels.append(residue.node_label)
assert all(elem in labels for elem in ["W18(A)" and 'Y298(B)'])
#B chain off
pyemap.process(self.my_emap,chains=["A"])
labels=[]
for residue in self.my_emap.residues.values():
labels.append(residue.node_label)
assert "W18(A)" in labels
assert 'Y298(B)' not in labels
def test_choose_eta_moieties(self):
pyemap.process(self.my_emap)
eta_moieties_resnames = []
for res in self.my_emap.eta_moieties:
eta_moieties_resnames.append(res)
#default
resnames=[]
for residue in self.my_emap.residues.values():
resnames.append(residue.resname)
assert all(elem in resnames for elem in eta_moieties_resnames)
#deselected eta moiety
pyemap.process(self.my_emap,eta_moieties=eta_moieties_resnames[:-1])
resnames=[]
for residue in self.my_emap.residues.values():
resnames.append(residue.resname)
assert all(elem in resnames for elem in eta_moieties_resnames[:-1])
assert eta_moieties_resnames[-1] not in resnames
def test_aromatic_amino_acid_options(self):
pyemap.process(self.my_emap)
##default, tryptophan and tyrosine on
resnames=[]
for residue in self.my_emap.residues.values():
resnames.append(residue.resname)
assert "TYR" in resnames
assert "TRP" in resnames
assert "PHE" not in resnames
assert "HIS" not in resnames
#phenylalanine on
pyemap.process(self.my_emap,phe=True)
resnames=[]
for residue in self.my_emap.residues.values():
resnames.append(residue.resname)
assert "TYR" in resnames
assert "TRP" in resnames
assert "PHE" in resnames
assert "HIS" not in resnames
#histidine on
resnames=[]
pyemap.process(self.my_emap,his=True)
for residue in self.my_emap.residues.values():
resnames.append(residue.resname)
assert "TYR" in resnames
assert "TRP" in resnames
assert "PHE" not in resnames
assert "HIS" in resnames
#tyrosine off
resnames=[]
pyemap.process(self.my_emap,tyr=False)
for residue in self.my_emap.residues.values():
resnames.append(residue.resname)
assert "TYR" not in resnames
assert "TRP" in resnames
assert "PHE" not in resnames
assert "HIS" not in resnames
#tryptophan off
resnames=[]
pyemap.process(self.my_emap,trp=False)
for residue in self.my_emap.residues.values():
resnames.append(residue.resname)
assert "TYR" in resnames
assert "TRP" not in resnames
assert "PHE" not in resnames
assert "HIS" not in resnames
def test_surface_options(self):
rd_check = 'Y53(A)'
asa_check = 'W61(A)'
#residue depth
pyemap.process(self.my_emap)
G = self.my_emap.init_graph
rd_ser = []
for n, d in G.nodes(data=True):
if d['shape'] == "box":
rd_ser.append(n)
#solvent accessibility
pyemap.process(self.my_emap, sdef=1)
G = self.my_emap.init_graph
asa_ser = []
for n, d in G.nodes(data=True):
if d['shape'] == "box":
asa_ser.append(n)
assert rd_check in rd_ser
assert asa_check not in rd_ser
assert rd_check not in asa_ser
assert asa_check in asa_ser
def test_graph_parameters(self):
pyemap.process(self.my_emap,num_st_dev_edges=5,percent_edges=3)
g1 = self.my_emap.init_graph
# check st_dev_edges works
pyemap.process(self.my_emap,num_st_dev_edges=1,percent_edges=3)
g2 = self.my_emap.init_graph
assert g1.edges() != g2.edges()
#check distance cutoff works
pyemap.process(self.my_emap,num_st_dev_edges=5,percent_edges=3,distance_cutoff=30)
g3 = self.my_emap.init_graph
assert g1.edges() != g3.edges()
#check percent edges works
pyemap.process(self.my_emap,num_st_dev_edges=5,percent_edges=1,distance_cutoff=30)
g4 = self.my_emap.init_graph
assert g1.edges() != g4.edges()
def test_surface_options(self):
#residue depth
asa_ser = []
rd_ser = []
pyemap.process(self.my_emap,sdef=0)
G = self.my_emap.init_graph
for n, d in G.nodes(data=True):
if d['shape'] == "box":
rd_ser.append(n)
#solvent accessibility
pyemap.process(self.my_emap,sdef=1)
G = self.my_emap.init_graph
for n, d in G.nodes(data=True):
if d['shape'] == "box":
asa_ser.append(n)
import subprocess
try:
cmd = "msms"
output = subprocess.check_output(cmd, shell=True)
assert rd_ser
except:
pass
assert asa_ser
assert rd_ser != asa_ser
def test_penalty_function_parameters(self):
#alpha
pyemap.process(self.my_emap,coef_alpha=0.5)
alpha_weight = self.my_emap.init_graph["W385(A)"]["Y53(A)"]['weight']
assert isclose(alpha_weight,6.48,abs_tol=1e-2)
#Roffset
pyemap.process(self.my_emap,r_offset=1)
alpha_weight = self.my_emap.init_graph["W385(A)"]["Y53(A)"]['weight']
assert isclose(alpha_weight,5.18,abs_tol=1e-2)
#Roffset
pyemap.process(self.my_emap,exp_beta=5)
beta_weight = self.my_emap.init_graph["W385(A)"]["Y53(A)"]['weight']
assert isclose(beta_weight,13.44,abs_tol=1e-2)
def setUpClass(cls):
cls.my_emap = pyemap.parse(os.path.join(sys.path[0],"pyemap/tests/test_pdbs/2oal.pdb"))
pyemap.process(cls.my_emap)
# PyeMap: A python package for automatic identification of electron and hole transfer pathways in proteins.
# Copyright(C) 2017-2020 Ruslan Tazhigulov, James Gayvert, Ksenia Bravaya (Boston University, USA)
import pyemap
my_emap = pyemap.fetch_and_parse("1u3d")
# view residue
my_emap.residue_to_Image("FAD510(A)-2").show()
# process file
pyemap.process(my_emap)
my_emap.init_graph_to_Image().show()
# find paths
pyemap.find_paths(my_emap,"FAD510(A)-2")
my_emap.paths_graph_to_Image().show()
# print report
print(my_emap.report())
