def test_size_of_mp_geo_result():
"""This is an end-to-end test of mp_geo.
The sample file contains alternate conformations.
"""
regression_pdb = libtbx.env.find_in_repositories(
relative_path="phenix_regression/pdb/2ERL_noH.pdb",
test=os.path.isfile)
args = [
'pdb=' + regression_pdb,
'out_file=chiral_volume_validation_endtoend.out',
'outliers_only=False', 'bonds_and_angles=True'
]
mp_geo.run(args)
with open('chiral_volume_validation_endtoend.out', 'r') as f:
lines = [i.rstrip('\n\r') for i in f.readlines()]
count_bonds = 0
count_angles = 0
count_chirals = 0
for line in lines:
geom_identifier = line.split(':')[6]
if "--" in geom_identifier:
#2ERL_noH.pdb: : 1: : :ASP:C--O:1.230:0.071:PROTEIN
count_bonds += 1
elif "-" in geom_identifier:
#2ERL_noH.pdb: : 1: : :ASP:C-CA-CB:111.672:0.827:PROTEIN
count_angles += 1
elif len(geom_identifier) == 2:
#2ERL_noH.pdb: : 21: :A:GLU:CA:2.514:0.020:PROTEIN
count_chirals += 1
assert count_bonds == 327
assert count_angles == 442
assert count_chirals == 49
assert count_bonds + count_angles + count_chirals == len(
lines
), "there are lines in mp_geo output that are not bonds, angles, or chirals"
def exercise_mp_geo():
open('mp_geo.pdb', 'w').write(pdb_str_1)
args = ['pdb=mp_geo.pdb',
'out_file=mp_geo.out',
'outliers_only=False',
'bonds_and_angles=True']
mp_geo.run(args)
f = file('mp_geo.out', 'rb')
# Strip out newline and carriage return chars to
# prevent platform-specific errors.
lines = [i.rstrip('\n\r') for i in f.readlines()]
assert 'mp_geo.pdb: A: 10: :B:ASP:CG--OD1:1.839:31.054:PROTEIN' in lines
assert \
'mp_geo.pdb: A: 10: :B:ASP:OD1-CG-OD2:109.733:5.486:PROTEIN' in lines
f.close()
open('mp_geo.pdb', 'w').write(pdb_str_2)
args = ['pdb=mp_geo.pdb',
'out_file=mp_geo.out',
'rna_backbone=True']
mp_geo.run(args)
f = file('mp_geo.out', 'rb')
lines = [i.rstrip('\n\r') for i in f.readlines()]
assert lines[0] == \
' :1: B: 115: : : C:__?__:178.072:55.525:76.414:-158.236:-67.172'
assert lines[1] == \
' :1: B: 116: :A: A:-80.906:172.347:71.412:81.732:-151.720:-70.053'
assert lines[2] == \
' :1: B: 117: :A: G:-80.508:177.077:61.989:80.676:-149.321:-69.591'
assert lines[3] == \
' :1: B: 118: : : C:-62.565:164.517:69.624:78.058:__?__:__?__'
def exercise_mp_geo():
with open('mp_geo.pdb', 'w') as f:
f.write(pdb_str_1)
args = [
'pdb=mp_geo.pdb', 'out_file=mp_geo.out', 'outliers_only=False',
'bonds_and_angles=True'
]
mp_geo.run(args)
f = open('mp_geo.out', 'r')
# Strip out newline and carriage return chars to
# prevent platform-specific errors.
lines = [i.rstrip('\n\r') for i in f.readlines()]
assert 'mp_geo.pdb: A: 10: :B:ASP:CG--OD1:1.839:31.054:PROTEIN' in lines
assert \
'mp_geo.pdb: A: 10: :B:ASP:OD1-CG-OD2:109.733:5.486:PROTEIN' in lines
f.close()
with open('mp_geo.pdb', 'w') as f:
f.write(pdb_str_2)
args = ['pdb=mp_geo.pdb', 'out_file=mp_geo.out', 'rna_backbone=True']
mp_geo.run(args)
f = open('mp_geo.out', 'r')
lines = [i.rstrip('\n\r') for i in f.readlines()]
f.close()
assert lines[0] == \
' :1: B: 115: : : C:__?__:178.072:55.525:76.414:-158.236:-67.172'
assert lines[1] == \
' :1: B: 116: :A: A:-80.906:172.347:71.412:81.732:-151.720:-70.053'
assert lines[2] == \
' :1: B: 117: :A: G:-80.508:177.077:61.989:80.676:-149.321:-69.591'
assert lines[3] == \
' :1: B: 118: : : C:-62.565:164.517:69.624:78.058:__?__:__?__'
def test_misnamed_leu():
"""Atom positions for CD1 and CD2 have been swapped.
This should create a >20sigma chiral volume outlier at CG.
This is a 'pseudochiral naming error'.
Validation wants to be able to catch these naming errors."""
pdb_str = """\
ATOM 60 N LEU A 8 30.132 40.069 18.642 1.00 9.84 N
ATOM 61 CA LEU A 8 29.607 41.180 19.467 1.00 14.15 C
ATOM 62 C LEU A 8 30.075 42.538 18.984 1.00 17.37 C
ATOM 63 O LEU A 8 29.586 43.570 19.483 1.00 17.01 O
ATOM 64 CB LEU A 8 29.919 40.890 20.938 1.00 16.63 C
ATOM 65 CG LEU A 8 29.183 39.722 21.581 1.00 18.88 C
ATOM 66 CD1 LEU A 8 27.700 39.721 21.228 1.00 18.59 C
ATOM 67 CD2 LEU A 8 29.308 39.750 23.095 1.00 19.31 C
END
"""
with open('chiral_volume_validation_cases_leu_misnamed.pdb', 'w') as f:
f.write(pdb_str)
args = [
'pdb=chiral_volume_validation_cases_leu_misnamed.pdb',
'out_file=chiral_volume_validation_cases_leu_misnamed.out',
'outliers_only=False', 'bonds_and_angles=True'
]
mp_geo.run(args)
with open('chiral_volume_validation_cases_leu_misnamed.out', 'r') as f:
lines = [i.rstrip('\n\r') for i in f.readlines()]
#chiral_volume_validation_cases_leu_misnamed.pdb: A: 8: : :LEU:CA:2.369:0.707:PROTEIN
#chiral_volume_validation_cases_leu_misnamed.pdb: A: 8: : :LEU:CG:2.604:25.967:PROTEIN
ca_volume = None
ca_sigma = None
cg_volume = None
cg_sigma = None
for line in lines:
#print(line)
chiral_center = line.split(":")[6]
if chiral_center == "CA":
ca_volume = float(line.split(":")[7])
ca_sigma = float(line.split(":")[8])
elif chiral_center == "CG":
cg_volume = float(line.split(":")[7])
cg_sigma = float(line.split(":")[8])
assert approx_equal(ca_volume, 2.369, eps=0.01) #same
assert approx_equal(ca_sigma, 0.707, eps=0.01) #same
assert approx_equal(cg_volume, 2.604, eps=0.01) #sign change
assert approx_equal(cg_sigma, 25.967, eps=0.01) #>20sigma outlier
def test_misnamed_val():
"""Atom positions for CG1 and CG2 have been swapped.
This should create a >20sigma chiral volume outlier at CB.
This is a 'pseudochiral naming error'.
Validation wants to be able to catch these naming errors."""
pdb_str = """\
ATOM 37 N VAL A 5 28.260 33.943 11.096 1.00 4.44 N
ATOM 38 CA VAL A 5 28.605 33.965 12.503 1.00 3.87 C
ATOM 39 C VAL A 5 28.638 35.461 12.900 1.00 4.93 C
ATOM 40 O VAL A 5 29.522 36.103 12.320 1.00 6.84 O
ATOM 41 CB VAL A 5 29.963 33.317 12.814 1.00 2.99 C
ATOM 42 CG1 VAL A 5 29.957 31.838 12.352 1.00 9.13 C
ATOM 43 CG2 VAL A 5 30.211 33.394 14.304 1.00 5.28 C
END
"""
with open('chiral_volume_validation_cases_val_misnamed.pdb', 'w') as f:
f.write(pdb_str)
args = [
'pdb=chiral_volume_validation_cases_val_misnamed.pdb',
'out_file=chiral_volume_validation_cases_val_misnamed.out',
'outliers_only=False', 'bonds_and_angles=True'
]
mp_geo.run(args)
with open('chiral_volume_validation_cases_val_misnamed.out', 'r') as f:
lines = [i.rstrip('\n\r') for i in f.readlines()]
#chiral_volume_validation_cases_val_misnamed.pdb: A: 5: : :VAL:CA:2.628:0.932:PROTEIN
#chiral_volume_validation_cases_val_misnamed.pdb: A: 5: : :VAL:CB:2.762:26.956:PROTEIN
ca_volume = None
ca_sigma = None
cb_volume = None
cb_sigma = None
for line in lines:
#print(line)
chiral_center = line.split(":")[6]
if chiral_center == "CA":
ca_volume = float(line.split(":")[7])
ca_sigma = float(line.split(":")[8])
elif chiral_center == "CB":
cb_volume = float(line.split(":")[7])
cb_sigma = float(line.split(":")[8])
assert approx_equal(ca_volume, 2.628, eps=0.01) #same
assert approx_equal(ca_sigma, 0.932, eps=0.01) #same
assert approx_equal(cb_volume, 2.762, eps=0.01) #sign change
assert approx_equal(cb_sigma, 26.956, eps=0.01) #>20sigma outlier
def test_normal_leu():
"""Regular leucine. Chiral centers at CA and CG"""
pdb_str = """\
ATOM 60 N LEU A 8 30.132 40.069 18.642 1.00 9.84 N
ATOM 61 CA LEU A 8 29.607 41.180 19.467 1.00 14.15 C
ATOM 62 C LEU A 8 30.075 42.538 18.984 1.00 17.37 C
ATOM 63 O LEU A 8 29.586 43.570 19.483 1.00 17.01 O
ATOM 64 CB LEU A 8 29.919 40.890 20.938 1.00 16.63 C
ATOM 65 CG LEU A 8 29.183 39.722 21.581 1.00 18.88 C
ATOM 66 CD1 LEU A 8 29.308 39.750 23.095 1.00 19.31 C
ATOM 67 CD2 LEU A 8 27.700 39.721 21.228 1.00 18.59 C
TER
END
"""
with open('chiral_volume_validation_cases_leu_normal.pdb', 'w') as f:
f.write(pdb_str)
args = [
'pdb=chiral_volume_validation_cases_leu_normal.pdb',
'out_file=chiral_volume_validation_cases_leu_normal.out',
'outliers_only=False', 'bonds_and_angles=True'
]
mp_geo.run(args)
with open('chiral_volume_validation_cases_leu_normal.out', 'r') as f:
lines = [i.rstrip('\n\r') for i in f.readlines()]
#chiral_volume_validation_cases_leu_normal.pdb: A: 8: : :LEU:CA:2.369:0.707:PROTEIN
#chiral_volume_validation_cases_leu_normal.pdb: A: 8: : :LEU:CG:-2.604:0.070:PROTEIN
ca_volume = None
ca_sigma = None
cg_volume = None
cg_sigma = None
for line in lines:
#print(line)
chiral_center = line.split(":")[6]
if chiral_center == "CA":
ca_volume = float(line.split(":")[7])
ca_sigma = float(line.split(":")[8])
elif chiral_center == "CG":
cg_volume = float(line.split(":")[7])
cg_sigma = float(line.split(":")[8])
assert approx_equal(ca_volume, 2.369, eps=0.01)
assert approx_equal(ca_sigma, 0.707, eps=0.01)
assert approx_equal(cg_volume, -2.604, eps=0.01)
assert approx_equal(cg_sigma, 0.070, eps=0.01)
def test_normal_val():
"""Regular valine. Chiral centers at CA and CB."""
pdb_str = """\
ATOM 37 N VAL A 5 28.260 33.943 11.096 1.00 4.44 N
ATOM 38 CA VAL A 5 28.605 33.965 12.503 1.00 3.87 C
ATOM 39 C VAL A 5 28.638 35.461 12.900 1.00 4.93 C
ATOM 40 O VAL A 5 29.522 36.103 12.320 1.00 6.84 O
ATOM 41 CB VAL A 5 29.963 33.317 12.814 1.00 2.99 C
ATOM 42 CG1 VAL A 5 30.211 33.394 14.304 1.00 5.28 C
ATOM 43 CG2 VAL A 5 29.957 31.838 12.352 1.00 9.13 C
TER
END
"""
with open('chiral_volume_validation_cases_val_normal.pdb', 'w') as f:
f.write(pdb_str)
args = [
'pdb=chiral_volume_validation_cases_val_normal.pdb',
'out_file=chiral_volume_validation_cases_val_normal.out',
'outliers_only=False', 'bonds_and_angles=True'
]
mp_geo.run(args)
with open('chiral_volume_validation_cases_val_normal.out', 'r') as f:
lines = [i.rstrip('\n\r') for i in f.readlines()]
#chiral_volume_validation_cases_val_base.pdb: A: 5: : :VAL:CA:2.628:0.932:PROTEIN
#chiral_volume_validation_cases_val_base.pdb: A: 5: : :VAL:CB:-2.762:0.664:PROTEIN
ca_volume = None
ca_sigma = None
cb_volume = None
cb_sigma = None
for line in lines:
#print(line)
chiral_center = line.split(":")[6]
if chiral_center == "CA":
ca_volume = float(line.split(":")[7])
ca_sigma = float(line.split(":")[8])
elif chiral_center == "CB":
cb_volume = float(line.split(":")[7])
cb_sigma = float(line.split(":")[8])
assert approx_equal(ca_volume, 2.628, eps=0.01)
assert approx_equal(ca_sigma, 0.932, eps=0.01)
assert approx_equal(cb_volume, -2.762, eps=0.01)
assert approx_equal(cb_sigma, 0.664, eps=0.01)
def test_misnamed_sf4():
"""Atom positions for S2 and S3 have been swapped.
This should create a >>>20sigma chiral volume outlier at FE1.
Other FEs are affected but not tested here
This is a 'pseudochiral naming error'.
Validation wants to be able to catch these naming errors."""
pdb_str = """\
HETATM14724 FE1 SF4 E 501 0.575 47.227 37.154 1.00 44.16 FE3+
HETATM14725 FE2 SF4 E 501 1.672 45.200 38.813 1.00 42.81 FE3+
HETATM14726 FE3 SF4 E 501 0.846 44.650 36.268 1.00 41.68 FE3+
HETATM14727 FE4 SF4 E 501 -0.960 45.318 38.094 1.00 49.33 FE3+
HETATM14728 S1 SF4 E 501 0.351 43.431 38.164 1.00 42.06 S
HETATM14729 S3 SF4 E 501 -0.963 46.038 35.912 1.00 42.31 S
HETATM14730 S2 SF4 E 501 0.157 46.850 39.397 1.00 45.58 S
HETATM14731 S4 SF4 E 501 2.547 46.073 36.852 1.00 45.73 S
END
"""
with open('chiral_volume_validation_cases_sf4_misnamed.pdb', 'w') as f:
f.write(pdb_str)
args = [
'pdb=chiral_volume_validation_cases_sf4_misnamed.pdb',
'out_file=chiral_volume_validation_cases_sf4_misnamed.out',
'outliers_only=False', 'bonds_and_angles=True'
]
mp_geo.run(args)
with open('chiral_volume_validation_cases_sf4_misnamed.out', 'r') as f:
lines = [i.rstrip('\n\r') for i in f.readlines()]
#chiral_volume_validation_cases_sf4_misnamed.pdb: E: 501: : :SF4:FE1:10.788:106.712:UNK
#chiral_volume_validation_cases_sf4_misnamed.pdb: E: 501: : :SF4:FE2:14.425:19.352:UNK
#chiral_volume_validation_cases_sf4_misnamed.pdb: E: 501: : :SF4:FE3:-14.365:19.049:UNK
#chiral_volume_validation_cases_sf4_misnamed.pdb: E: 501: : :SF4:FE4:-10.148:103.512:UNK
fe1_volume = None
fe1_sigma = None
for line in lines:
#print(line)
chiral_center = line.split(":")[6]
if chiral_center == "FE1":
fe1_volume = float(line.split(":")[7])
fe1_sigma = float(line.split(":")[8])
assert approx_equal(fe1_volume, 10.788, eps=0.01) #sign changes
assert approx_equal(fe1_sigma, 106.712, eps=0.01) #>>>20 sigma outlier
def test_normal_sf4():
"""Regular sf4 iron-sulfur cluster. Chiral centers at FEs"""
pdb_str = """\
HETATM14724 FE1 SF4 E 501 0.575 47.227 37.154 1.00 44.16 FE3+
HETATM14725 FE2 SF4 E 501 1.672 45.200 38.813 1.00 42.81 FE3+
HETATM14726 FE3 SF4 E 501 0.846 44.650 36.268 1.00 41.68 FE3+
HETATM14727 FE4 SF4 E 501 -0.960 45.318 38.094 1.00 49.33 FE3+
HETATM14728 S1 SF4 E 501 0.351 43.431 38.164 1.00 42.06 S
HETATM14729 S2 SF4 E 501 -0.963 46.038 35.912 1.00 42.31 S
HETATM14730 S3 SF4 E 501 0.157 46.850 39.397 1.00 45.58 S
HETATM14731 S4 SF4 E 501 2.547 46.073 36.852 1.00 45.73 S
TER
END
"""
with open('chiral_volume_validation_cases_sf4_normal.pdb', 'w') as f:
f.write(pdb_str)
args = [
'pdb=chiral_volume_validation_cases_sf4_normal.pdb',
'out_file=chiral_volume_validation_cases_sf4_normal.out',
'outliers_only=False', 'bonds_and_angles=True'
]
mp_geo.run(args)
with open('chiral_volume_validation_cases_sf4_normal.out', 'r') as f:
lines = [i.rstrip('\n\r') for i in f.readlines()]
#chiral_volume_validation_cases_sf4_normal.pdb: E: 501: : :SF4:FE1:-10.788:1.164:UNK
#chiral_volume_validation_cases_sf4_normal.pdb: E: 501: : :SF4:FE2:11.095:2.699:UNK
#chiral_volume_validation_cases_sf4_normal.pdb: E: 501: : :SF4:FE3:-10.559:0.020:UNK
#chiral_volume_validation_cases_sf4_normal.pdb: E: 501: : :SF4:FE4:10.148:2.036:UNK
fe1_volume = None
fe1_sigma = None
for line in lines:
#print(line)
chiral_center = line.split(":")[6]
if chiral_center == "FE1":
fe1_volume = float(line.split(":")[7])
fe1_sigma = float(line.split(":")[8])
assert approx_equal(fe1_volume, -10.788, eps=0.01)
assert approx_equal(fe1_sigma, 1.164, eps=0.01)
from __future__ import division import sys from mmtbx.validation.molprobity import mp_geo if __name__ == "__main__": mp_geo.run(sys.argv[1:])
