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Updated tests
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@jlgelpi
jlgelpi committed Aug 14, 2024
1 parent 6f259bf commit a82ad97
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2 changes: 1 addition & 1 deletion biobb_structure_checking/test/Makefile
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Original file line number Diff line number Diff line change
Expand Up @@ -117,7 +117,7 @@ chiral:
mutateside:
@echo "Running mutateside on 2ki5"
${COMMON};${APPBIN} -v -i pdb:2ki5 -o 2ki5_mutateside_test.pdb --json 2ki5_mutateside_test.json mutateside --mut Leu49Ile,B:arg51Lys > 2ki5_mutateside_test.log
${COMMON};${APPBIN} -v -i pdb:2ki5 -o 2ki5_mutateside_test.pdb --json 2ki5_mutateside_rb_test.json mutateside --mut Leu49Ile,B:arg51Lys --rebuild> 2ki5_mutateside_rb_test.log
${COMMON};${APPBIN} -v -i pdb:2ki5 -o 2ki5_mutateside_rb_test.pdb --json 2ki5_mutateside_rb_test.json mutateside --mut Leu49Ile --rebuild> 2ki5_mutateside_rb_test.log

fixside:
@echo "Running fixside on 2ki5"
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140 changes: 16 additions & 124 deletions biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.json
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Original file line number Diff line number Diff line change
Expand Up @@ -6,14 +6,14 @@
{
"A": {
"DNA": 0.0,
"Other": 0.006557377049180357,
"Protein": 0.9934426229508196,
"Other": 0.006535947712418277,
"Protein": 0.9934640522875817,
"RNA": 0.0
},
"B": {
"DNA": 0.0,
"Other": 0.00649350649350644,
"Protein": 0.9935064935064936,
"Other": 0.006451612903225823,
"Protein": 0.9935483870967742,
"RNA": 0.0
}
}
Expand All @@ -30,9 +30,9 @@
],
"nmodels": 1,
"stats": {
"num_ats": 4934,
"num_ats": 4961,
"num_h": 0,
"num_res": 905,
"num_res": 908,
"num_wat": 292,
"res_h": 0,
"res_hetats": 296,
Expand All @@ -51,131 +51,23 @@
"loaded_structure": "pdb:2ki5",
"modified_structure": true,
"mutateside": {
"opts": "--mut Leu49Ile,B:arg51Lys --rebuild"
"opts": "--mut Leu49Ile --rebuild"
},
"mutateside_clashes": {
"apolar": [
{
"at1": "GLY A61.O",
"at2": "THR A65.CG2",
"dist": 2.799
},
{
"at1": "MET A85.CG",
"at2": "GLU A374.OE1",
"dist": 2.8571
},
{
"at1": "ARG A89.CD",
"at2": "GLU A95.OE1",
"dist": 2.7757
},
{
"at1": "LEU A232.O",
"at2": "ARG A236.CG",
"dist": 2.7414
},
{
"at1": "MET A372.SD",
"at2": "VAL B307.CG1",
"dist": 2.7769
},
{
"at1": "HIS B58.CD2",
"at2": "TYR B172.OH",
"dist": 2.6749
},
{
"at1": "LYS B62.O",
"at2": "THR B66.CG2",
"dist": 2.8778
},
{
"at1": "THR B66.OG1",
"at2": "TYR B80.CE1",
"dist": 2.8901
},
{
"at1": "THR B86.OG1",
"at2": "GLU B374.CB",
"dist": 2.8918
},
{
"at1": "HIS B105.CE1",
"at2": "GLN B109.OE1",
"dist": 2.773
},
{
"at1": "GLU B210.O",
"at2": "ILE B214.CG1",
"dist": 2.8417
},
{
"at1": "ARG B212.CZ",
"at2": "ASP B330.OD1",
"dist": 2.8754
},
{
"at1": "SER B357.O",
"at2": "ILE B361.CG1",
"dist": 2.8614
"at1": "ILE A49.CD1",
"at2": "ILE A143.CD1",
"dist": 2.8151
}
],
"negative": [],
"polar_acceptor": [
{
"at1": "ASP A55.O",
"at2": "VAL A204.O",
"dist": 3.0347
},
{
"at1": "ARG B89.O",
"at2": "GLU B95.OE1",
"dist": 2.7924
},
{
"at1": "ASP B211.O",
"at2": "ASP B215.OD2",
"dist": 2.9139
},
{
"at1": "ALA B334.O",
"at2": "ASP B338.OD2",
"dist": 3.0997
},
{
"at1": "PRO B359.O",
"at2": "ASP B363.OD2",
"dist": 3.0725
}
],
"polar_donor": [
{
"at1": "LYS A62.NZ",
"at2": "ARG A163.NH1",
"dist": 2.5779
},
{
"at1": "ARG A212.NH2",
"at2": "ARG A216.NH2",
"dist": 3.075
}
],
"positive": [
{
"at1": "LYS A62.NZ",
"at2": "ARG A163.NH1",
"dist": 2.5779
},
{
"at1": "ARG A212.NH2",
"at2": "ARG A216.NH2",
"dist": 3.075
}
],
"polar_acceptor": [],
"polar_donor": [],
"positive": [],
"severe": []
},
"saved_structure": "2ki5_mutateside_test.pdb",
"saved_structure": "2ki5_mutateside_rb_test.pdb",
"stats": {
"biounit": false,
"ca_only": false,
Expand Down Expand Up @@ -207,9 +99,9 @@
],
"nmodels": 1,
"stats": {
"num_ats": 4934,
"num_ats": 4961,
"num_h": 0,
"num_res": 905,
"num_res": 908,
"num_wat": 292,
"res_h": 0,
"res_hetats": 296,
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94 changes: 55 additions & 39 deletions biobb_structure_checking/test/ref/2ki5_mutateside_rb_test.log
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Original file line number Diff line number Diff line change
@@ -1,11 +1,11 @@
================================================================================
= BioBB structure checking utility v3.13.3 =
= BioBB structure checking utility v3.13.5 =
= P. Andrio, A. Hospital, G. Bayarri, J.L. Gelpi 2018-23 =
================================================================================

Structure exists: 'tmpPDB/ki/2ki5.cif'
Structure exists: 'tmpPDB/ki/2ki5.cif'
Structure pdb:2ki5 loaded
PDB id: 2KI5
PDB id: 2KI5
Title: HERPES SIMPLEX TYPE-1 THYMIDINE KINASE IN COMPLEX WITH THE DRUG ACICLOVIR AT 1.9A RESOLUTION
Experimental method: X-RAY DIFFRACTION
Keywords: TRANSFERASE
Expand All @@ -25,17 +25,16 @@ SO4 A4
AC2 A1
SO4 B3
AC2 B2
Running mutateside. Options: --mut Leu49Ile,B:arg51Lys --rebuild
Running mutateside. Options: --mut Leu49Ile --rebuild
Mutations to perform
*:LEU49ILE
B:ARG51LYS

MODELLER 10.1, 2021/03/12, r12156
MODELLER 10.4, 2022/10/28, r12463

PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


Copyright(c) 1989-2021 Andrej Sali
Copyright(c) 1989-2022 Andrej Sali
All Rights Reserved

Written by A. Sali
Expand All @@ -51,53 +50,70 @@ B:ARG51LYS
Birkbeck College, University of London, London, UK


Kind, OS, HostName, Kernel, Processor: 4, Linux jlgclnx 5.14.21-150400.24.60-default x86_64
Date and time of compilation : 2021/03/12 00:04:35
Kind, OS, HostName, Kernel, Processor: 4, Linux jlgclnx 5.14.21-150500.55.68-default x86_64
Date and time of compilation : 2022/10/28 20:54:52
MODELLER executable type : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2023/05/23 13:01:38
Job starting time (YY/MM/DD HH:MM:SS): 2024/08/14 18:44:02

Fixing chain/model A/0
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
>> Model assessment by DOPE potential
DOPE score : -37238.417969

>> Summary of successfully produced models:
Filename molpdf DOPE score GA341 score
----------------------------------------------------------------------
target.B99990001.pdb 1307.28101 -37238.41797 1.00000

Fixing THR A48 - LEU A50
Adding THR A48
Adding ILE A49
Adding LEU A50

Fixing chain/model B/0
0 atoms in HETATM/BLK residues constrained
to protein atoms within 2.30 angstroms
and protein CA atoms within 10.00 angstroms
0 atoms in residues without defined topology
constrained to be rigid bodies
>> Model assessment by DOPE potential
DOPE score : -38093.339844

>> Summary of successfully produced models:
Filename molpdf DOPE score GA341 score
----------------------------------------------------------------------
target.B99990001.pdb 1530.76526 -38093.33984 1.00000

Fixing THR B48 - LEU B50
Adding THR B48
Adding ILE B49
Adding LEU B50

Checking for steric clashes
No severe clashes detected
13 Steric apolar clashes detected
GLY A61.O THR A65.CG2 2.799 A
MET A85.CG GLU A374.OE1 2.857 A
ARG A89.CD GLU A95.OE1 2.776 A
LEU A232.O ARG A236.CG 2.741 A
MET A372.SD VAL B307.CG1 2.777 A
HIS B58.CD2 TYR B172.OH 2.675 A
LYS B62.O THR B66.CG2 2.878 A
THR B66.OG1 TYR B80.CE1 2.890 A
THR B86.OG1 GLU B374.CB 2.892 A
HIS B105.CE1 GLN B109.OE1 2.773 A
GLU B210.O ILE B214.CG1 2.842 A
ARG B212.CZ ASP B330.OD1 2.875 A
SER B357.O ILE B361.CG1 2.861 A
5 Steric polar_acceptor clashes detected
ASP A55.O VAL A204.O 3.035 A
ARG B89.O GLU B95.OE1 2.792 A
ASP B211.O ASP B215.OD2 2.914 A
ALA B334.O ASP B338.OD2 3.100 A
PRO B359.O ASP B363.OD2 3.073 A
2 Steric polar_donor clashes detected
LYS A62.NZ ARG A163.NH1 2.578 A
ARG A212.NH2 ARG A216.NH2 3.075 A
2 Steric positive clashes detected
LYS A62.NZ ARG A163.NH1 2.578 A
ARG A212.NH2 ARG A216.NH2 3.075 A
1 Steric apolar clashes detected
ILE A49.CD1 ILE A143.CD1 2.815 A
No polar_acceptor clashes detected
No polar_donor clashes detected
No positive clashes detected
No negative clashes detected
Final Num. models: 1
Final Num. chains: 2 (A: Protein, B: Protein)
Final Num. residues: 905
Final Num. residues: 908
Final Num. residues with ins. codes: 0
Final Num. residues with H atoms: 0
Final Num. HETATM residues: 296
Final Num. ligands or modified residues: 4
Final Num. water mol.: 292
Final Num. atoms: 4934
Final Num. atoms: 4961
Small mol ligands found
SO4 A4
AC2 A1
SO4 B3
AC2 B2
Structure saved on 2ki5_mutateside_test.pdb
Structure saved on 2ki5_mutateside_rb_test.pdb
Summary data saved on 2ki5_mutateside_rb_test.json
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