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fix: test details for the v1.0
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@josan82
josan82 committed Dec 18, 2020
1 parent dccb386 commit 52cd133
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Showing 6 changed files with 37 additions and 13 deletions.
2 changes: 1 addition & 1 deletion biometall/__main__.py
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Expand Up @@ -10,7 +10,7 @@ def parse_cli():
p.add_argument('--min_coordinators', type=int, default=3,
help='Minimum number of coordinating residues of a given grid probe for that probe to be considered as potentially coordinating. Default: 3')
p.add_argument('--residues', type=str, default='[ASP,HIS,GLU,CYS]',
help='Residues that are potentially coordinating. Requires a list of 3-letter aa code separated by commas. Default: [ASN,ASP,CYS,GLN,GLU,HIS,MET,SER,THR,TYR]')
help='Residues that are potentially coordinating. Requires a list of 3-letter aa code separated by commas. Default: [ASP,CYS,GLU,HIS]')
p.add_argument('--motif', type=str, default='',
help='Search for concrete potentially coordinating motifs. Check the manual for syntax (e.g. [HIS,HIS,GLU/ASP]), Default: None')
p.add_argument('--mutations', type=str, dest='propose_mutations_to', default='',
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Binary file modified biometall/tests/.DS_Store
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30 changes: 26 additions & 4 deletions biometall/tests/data/1oi0_output1.pdb
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@@ -1,4 +1,26 @@
ATOM 1 HE SLN A 1 -14.334 35.427 -41.208 1.00 0.00 HE
ATOM 2 XE SLN A 1 -14.334 35.427 -41.208 1.00 0.00 XE
ATOM 3 HE SLN A 2 -9.269 33.401 -43.234 1.00 0.00 HE
ATOM 4 XE SLN A 2 -9.269 33.401 -43.234 1.00 0.00 XE
ATOM 1 HE SLN A 1 -13.321 47.582 -40.195 1.00 0.00 HE
ATOM 2 XE SLN A 1 -14.334 46.569 -40.195 1.00 0.00 XE
ATOM 3 XE SLN A 1 -13.321 46.569 -41.208 1.00 0.00 XE
ATOM 4 XE SLN A 1 -13.321 46.569 -40.195 1.00 0.00 XE
ATOM 5 XE SLN A 1 -13.321 46.569 -39.182 1.00 0.00 XE
ATOM 6 XE SLN A 1 -13.321 47.582 -41.208 1.00 0.00 XE
ATOM 7 XE SLN A 1 -13.321 47.582 -40.195 1.00 0.00 XE
ATOM 8 XE SLN A 1 -13.321 47.582 -39.182 1.00 0.00 XE
ATOM 9 XE SLN A 1 -13.321 48.595 -41.208 1.00 0.00 XE
ATOM 10 XE SLN A 1 -13.321 48.595 -40.195 1.00 0.00 XE
ATOM 11 XE SLN A 1 -13.321 48.595 -39.182 1.00 0.00 XE
ATOM 12 XE SLN A 1 -12.308 49.608 -40.195 1.00 0.00 XE
ATOM 13 HE SLN A 2 -0.153 40.492 -59.441 1.00 0.00 HE
ATOM 14 XE SLN A 2 -0.153 40.492 -60.454 1.00 0.00 XE
ATOM 15 XE SLN A 2 -0.153 40.492 -59.441 1.00 0.00 XE
ATOM 16 XE SLN A 2 -0.153 40.492 -58.428 1.00 0.00 XE
ATOM 17 XE SLN A 2 0.86 40.492 -59.441 1.00 0.00 XE
ATOM 18 HE SLN A 3 0.86 50.621 -43.234 1.00 0.00 HE
ATOM 19 XE SLN A 3 0.86 50.621 -44.247 1.00 0.00 XE
ATOM 20 XE SLN A 3 0.86 50.621 -43.234 1.00 0.00 XE
ATOM 21 XE SLN A 3 0.86 51.634 -43.234 1.00 0.00 XE
ATOM 22 XE SLN A 3 1.873 50.621 -43.234 1.00 0.00 XE
ATOM 23 HE SLN A 4 -4.205 49.608 -41.208 1.00 0.00 HE
ATOM 24 XE SLN A 4 -5.218 49.608 -41.208 1.00 0.00 XE
ATOM 25 XE SLN A 4 -4.205 49.608 -41.208 1.00 0.00 XE
ATOM 26 XE SLN A 4 -4.205 50.621 -41.208 1.00 0.00 XE
12 changes: 7 additions & 5 deletions biometall/tests/data/1oi0_output1.txt
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@@ -1,5 +1,7 @@
# | Coordinating residues | Coordinates of center | Num. probes | Radius search | Proposed mutations
---+----------------------------+------------------------+-------------+---------------+--------------------
1 | GLU:81:A GLU:82:A ASP:83:A | -14.334 35.427 -41.208 | 1 | 0.000 |
2 | GLU:25:A GLU:82:A ASP:83:A | -9.269 33.401 -43.234 | 1 | 0.000 |
*****Calculation took 1.75 seconds
# | Coordinating residues | Coordinates of center | Num. probes | Radius search | Proposed mutations
---+-------------------------------+------------------------+-------------+---------------+--------------------
1 | TYR:109:A GLU:114:A GLU:115:A | -13.321 47.582 -40.195 | 11 | 2.265 |
2 | TYR:101:A GLU:103:A GLU:16:A | -0.153 40.492 -59.441 | 4 | 1.013 |
3 | GLU:117:A GLU:119:A TYR:93:A | 0.860 50.621 -43.234 | 4 | 1.013 |
4 | GLU:115:A GLU:117:A TYR:93:A | -4.205 49.608 -41.208 | 3 | 1.013 |
*****Calculation took 4.80 seconds
4 changes: 2 additions & 2 deletions biometall/tests/data/1oi0_output3.txt
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@@ -1,4 +1,4 @@
# | Coordinating residues | Coordinates of center | Num. probes | Radius search | Proposed mutations
# | Coordinating residues | Coordinates of center | Num. probes | Radius search | Proposed mutations
---+----------------------------+-----------------------+-------------+---------------+-------------------------------------
1 | GLU:25:A GLU:82:A ASP:83:A | -9.269 33.401 -43.234 | 1 | 0.000 | 27:A:[['TYR', 1]] 96:A:[['TYR', 1]]
*****Calculation took 10.56 seconds
*****Calculation took 51.35 seconds
2 changes: 1 addition & 1 deletion biometall/tests/test_full_calculation.py
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Expand Up @@ -14,7 +14,7 @@
'1oi0_output0.txt', 'results_biometall_1oi0.txt',
'1oi0_output0.pdb', 'probes_1oi0.pdb'),
('1oi0.pdb', 3, 2, '[ASP,HIS,GLU,CYS]', '[GLU,GLU,ASP/TYR]', 1.0,
'[]', 0.0, True, '', None, None, None, 1.0, 0.0,
'[]', 0.2, True, '', None, None, None, 1.0, 0.0,
'1oi0_output1.txt', 'results_biometall_1oi0_GLU_GLU_ASP-TYR.txt',
'1oi0_output1.pdb', 'probes_1oi0_GLU_GLU_ASP-TYR.pdb'),
('1oi0.pdb', 3, 2, '[ASP,HIS,GLU,CYS]', '', 1.0,
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