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Arg fix #2504

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Arg fix #2504

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baa02d9
Fix issue with protonating charged ARG
dkoes Jul 1, 2022
523c775
tests for ARG fix
dkoes Jul 1, 2022
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3 changes: 2 additions & 1 deletion data/bondtyp.txt
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Expand Up @@ -97,7 +97,8 @@

# if three N are present in R-N-guanidine-ish, prefer double bond to the
# non-terminal N (i.e. D2 if present)
[#6D3^2;!R]([#7D2;!R])([#7D1;!R])~[#7D1;!R] 0 1 2 0 2 1 0 3 1
[#6D3^2;!R]([#7D2;!R])([#7D1;!R])~[#7D1;!R;+0] 0 1 2 0 2 1 0 3 1
[#6D3^2;!R]([#7D2;!R])([#7D1;!R])~[#7D1;!R;+] 0 1 1 0 2 1 0 3 2
# guanidinium and amidine -C(=NH)NH2 without hydrogens
[#6D3^2;!R]([#7D1H0;!R])([#7;!R])* 0 1 2 0 2 1 0 3 1
# and also with hydrogens
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4 changes: 2 additions & 2 deletions data/resdata.txt
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Expand Up @@ -52,8 +52,8 @@ BOND CB CG 1
BOND CG CD 1
BOND CD NE 1
BOND NE CZ 1
BOND CZ NH2 2
BOND CZ NH1 1
BOND CZ NH2 1
BOND CZ NH1 2
BOND N H 1
BOND HN N 1
BOND NH1 1HH1 1
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26 changes: 23 additions & 3 deletions src/data.cpp
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Expand Up @@ -21,6 +21,7 @@ GNU General Public License for more details.
#pragma warning (disable : 4786)
#endif
#include <cstdlib>
#include <algorithm>
#include <openbabel/babelconfig.h>
#include <openbabel/data.h>
#include <openbabel/data_utilities.h>
Expand Down Expand Up @@ -614,14 +615,30 @@ namespace OpenBabel
return(false);
}

static std::string trim(const std::string &s)
{
auto start = s.begin();
while (start != s.end() && std::isspace(*start)) {
start++;
}

auto end = s.end();
do {
end--;
} while (std::distance(start, end) > 0 && std::isspace(*end));

return std::string(start, end + 1);
}

int OBResidueData::LookupBO(const string &s)
{
if (_resnum == -1)
return(0);

string strim = trim(s);
unsigned int i;
for (i = 0;i < _resbonds[_resnum].size();++i)
if (_resbonds[_resnum][i].first == s)
if (_resbonds[_resnum][i].first == strim)
return(_resbonds[_resnum][i].second);

return(0);
Expand All @@ -633,12 +650,15 @@ namespace OpenBabel
return(0);
string s;

s = (s1 < s2) ? s1 + " " + s2 : s2 + " " + s1;
string s1strip = trim(s1);
string s2strip = trim(s2);

s = (s1strip < s2strip) ? s1strip + " " + s2strip : s2strip + " " + s1strip;
unsigned int i;
for (i = 0;i < _resbonds[_resnum].size();++i)
if (_resbonds[_resnum][i].first == s)
if (_resbonds[_resnum][i].first == s) {
return(_resbonds[_resnum][i].second);
}

return(0);
}
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2 changes: 1 addition & 1 deletion test/files/gzip.in
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Expand Up @@ -6,7 +6,7 @@ CC(Cn1cnc2c1c(=O)n(C)c(=O)n2C)O
CN(CCc1c[nH]c2c1c(O)ccc2)C
COc1c2oc(=O)ccc2c(c2c1occ2)CC(C(O)(C)C)O
#1ubq.pdb.gz
CC(C[C@@H](C(=O)N[C@H](C(=O)NCC(=O)NCC(=O)[O-])CCC/N=C(\[NH3+])/N)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](C(C)C)NC(=O)[C@H](CC(C)C)N)CC(C)C)CCC/N=C(\[NH3+])/N)C.[NH3+]CCCC[C@@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)N1CCC[C@H]1C(=O)N1CCC[C@H]1C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@@H](CC(C)C)CO)[C@H](O)C)CO)CCC(=[O-])O)CCCC[NH3+])CCC(=O)N)[C@H](CC)C)CC(=O)N)Cc1ccc(cc1)O)CC(=[O-])O)CO)CC(C)C)[C@H](O)C)CCC/N=C(\[NH3+])/N)CC(=[O-])O)CCC(=[O-])O)CC(C)C)CCC(=O)N)CCCC[NH3+])C)Cc1ccccc1)[C@H](CC)C)CC(C)C)CCC/N=C(\[NH3+])/N)CCC(=O)N)CCC(=O)N)CC(=O)[O-])[C@H](CC)C)CCC(=[O-])O)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H]([C@H](CC)C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H](C(C)C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H]([C@H](CC)C)NC(=O)[C@H]([C@H](O)C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@@H]1CCCN1C(=O)[C@@H](NC(=O)[C@H](C(C)C)NC(=O)[C@@H](NC(=O)[C@@H](NC(=O)[C@H]([C@H](O)C)NC(=O)[C@H]([C@H](CC)C)NC(=O)[C@H]([C@H](O)C)NC(=O)[C@@H](NC(=O)CNC(=O)[C@H]([C@H](O)C)NC(=O)[C@@H](NC(=O)[C@H]([C@H](O)C)NC(=O)[C@@H](NC(=O)[C@H](C(C)C)NC(=O)[C@@H](NC(=O)[C@H]([C@H](CC)C)NC(=O)[C@@H](NC(=O)[C@H](CCSC)N)CCC(=O)N)Cc1ccccc1)CCCC[NH3+])CC(C)C)CCCC[NH3+])CC(C)C)CCC(=O)[O-])CCC(=[O-])O)CO)CC(=[O-])O)CCC(=O)[O-])CC(=O)N)CCCC[NH3+])C)CCCC[NH3+])CCC(=O)N)CC(=[O-])O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O
N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N1[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)N2[C@H](C(=O)N3[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)NCC(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C=O)CC(C)C)[C@@H](C)O)CO)CCC(=O)[O-])CCCC[NH3+])CCC(=O)N)[C@H](CC)C)CC(=O)N)Cc4ccc(cc4)O)CC(=[O-])O)CO)CC(C)C)[C@@H](C)O)CCCNC(=[NH2+])N)CC(=[O-])O)CCC(=O)[O-])CC(C)C)CCC(=O)N)CCCC[NH3+])C)Cc4ccccc4)[C@H](CC)C)CC(C)C)CCCNC(=[NH2+])N)CCC(=O)N)CCC(=O)N)CC(=[O-])O)CCC3)CCC2)[C@H](CC)C)CCC(=O)[O-])CCCC[NH3+])CC(=[O-])O)CCC(=O)N)[C@H](CC)C)CCCC[NH3+])C)CCCC[NH3+])C(C)C)CC(=O)N)CCC(=O)[O-])[C@H](CC)C)[C@@H](C)O)CC(=[O-])O)CO)CCC1)CCC(=O)[O-])C(C)C)CCC(=O)[O-])CC(C)C)[C@@H](C)O)[C@H](CC)C)[C@@H](C)O)CCCC[NH3+])[C@@H](C)O)CC(C)C)[C@@H](C)O)CCCC[NH3+])C(C)C)Cc1ccccc1)[C@H](CC)C)CCC(=O)N)CCSC.N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)N[C@H](C(=O)NCC(=O)NCC(=O)[O-])CCCNC(=[NH2+])N)CC(C)C)CCCNC(=[NH2+])N)CC(C)C)C(C)C)CC(C)C.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O.O ../test/files/1ubq.pdb.gz
# tencmpds.sdf.gz
[O-]C(=O)CC(C[N+](C)(C)C)OC(=O)C
OC(=O)CC(C[N+](C)(C)C)OC(=O)C
Expand Down
149 changes: 149 additions & 0 deletions test/testbabel.py
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Expand Up @@ -235,6 +235,155 @@ def testPDBQT(self):
output, error = run_exec(pdb, "obabel -ipdb -opdbqt")
self.assertEqual(output.replace("\r", ""), pdbqt.replace("\r", ""))

def testARG(self):
'''Get correct protonation of arginine'''
self.canFindExecutable("obabel")
arg1 = '''ATOM 1213 N ARG B 57 -19.748 -9.497 -12.692 1.00 13.96 B N
ATOM 1214 CA ARG B 57 -20.874 -10.021 -13.461 1.00 14.94 B C
ATOM 1215 C ARG B 57 -20.773 -9.510 -14.886 1.00 15.07 B C
ATOM 1216 O ARG B 57 -20.694 -8.309 -15.108 1.00 15.56 B O
ATOM 1217 CB ARG B 57 -22.204 -9.574 -12.843 1.00 16.31 B C
ATOM 1218 CG ARG B 57 -22.372 -9.987 -11.398 1.00 18.33 B C
ATOM 1219 CD ARG B 57 -23.782 -9.756 -10.880 1.00 21.63 B C
ATOM 1220 NE ARG B 57 -24.302 -8.403 -11.085 1.00 23.91 B N
ATOM 1221 CZ ARG B 57 -24.000 -7.334 -10.350 1.00 25.07 B C
ATOM 1222 NH1 ARG B 57 -23.127 -7.409 -9.347 1.00 26.54 B N1+
ATOM 1223 NH2 ARG B 57 -24.573 -6.169 -10.630 1.00 27.50 B N
'''
arg1sdf = '''
OpenBabel07012217113D

26 25 0 0 1 0 0 0 0 0999 V2000
-19.7480 -9.4970 -12.6920 N 0 0 0 0 0 0 0 0 0 0 0 0
-20.8740 -10.0210 -13.4610 C 0 0 2 0 0 0 0 0 0 0 0 0
-20.7730 -9.5100 -14.8860 C 0 0 0 0 0 0 0 0 0 0 0 0
-20.6940 -8.3090 -15.1080 O 0 0 0 0 0 0 0 0 0 0 0 0
-22.2040 -9.5740 -12.8430 C 0 0 0 0 0 0 0 0 0 0 0 0
-22.3720 -9.9870 -11.3980 C 0 0 0 0 0 0 0 0 0 0 0 0
-23.7820 -9.7560 -10.8800 C 0 0 0 0 0 0 0 0 0 0 0 0
-24.3020 -8.4030 -11.0850 N 0 0 0 0 0 0 0 0 0 0 0 0
-24.0000 -7.3340 -10.3500 C 0 0 0 0 0 0 0 0 0 0 0 0
-23.1270 -7.4090 -9.3470 N 0 3 0 0 0 0 0 0 0 0 0 0
-24.5730 -6.1690 -10.6300 N 0 0 0 0 0 0 0 0 0 0 0 0
-18.8734 -9.8043 -13.1175 H 0 0 0 0 0 0 0 0 0 0 0 0
-19.8001 -9.8432 -11.7340 H 0 0 0 0 0 0 0 0 0 0 0 0
-20.8414 -11.0905 -13.4505 H 0 0 0 0 0 0 0 0 0 0 0 0
-20.7709 -10.1786 -15.6721 H 0 0 0 0 0 0 0 0 0 0 0 0
-23.0021 -10.0032 -13.4120 H 0 0 0 0 0 0 0 0 0 0 0 0
-22.2157 -8.5043 -12.8659 H 0 0 0 0 0 0 0 0 0 0 0 0
-21.6904 -9.4201 -10.7989 H 0 0 0 0 0 0 0 0 0 0 0 0
-22.1744 -11.0369 -11.3378 H 0 0 0 0 0 0 0 0 0 0 0 0
-23.7869 -9.9579 -9.8292 H 0 0 0 0 0 0 0 0 0 0 0 0
-24.4176 -10.4090 -11.4408 H 0 0 0 0 0 0 0 0 0 0 0 0
-24.9301 -8.2717 -11.8317 H 0 0 0 0 0 0 0 0 0 0 0 0
-22.6971 -8.2681 -9.1318 H 0 0 0 0 0 0 0 0 0 0 0 0
-22.9116 -6.6053 -8.8208 H 0 0 0 0 0 0 0 0 0 0 0 0
-25.2196 -6.1036 -11.3695 H 0 0 0 0 0 0 0 0 0 0 0 0
-24.3512 -5.3709 -10.0980 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 12 1 0 0 0 0
1 13 1 0 0 0 0
2 3 1 0 0 0 0
2 5 1 0 0 0 0
2 14 1 6 0 0 0
3 4 2 0 0 0 0
3 15 1 0 0 0 0
5 6 1 0 0 0 0
5 16 1 0 0 0 0
5 17 1 0 0 0 0
6 7 1 0 0 0 0
6 18 1 0 0 0 0
6 19 1 0 0 0 0
7 8 1 0 0 0 0
7 20 1 0 0 0 0
7 21 1 0 0 0 0
8 9 1 0 0 0 0
8 22 1 0 0 0 0
9 10 2 0 0 0 0
9 11 1 0 0 0 0
10 23 1 0 0 0 0
10 24 1 0 0 0 0
11 25 1 0 0 0 0
11 26 1 0 0 0 0
M CHG 1 10 1
M END
$$$$
'''
arg0 = '''ATOM 1213 N ARG B 57 -19.748 -9.497 -12.692 1.00 13.96 B N
ATOM 1214 CA ARG B 57 -20.874 -10.021 -13.461 1.00 14.94 B C
ATOM 1215 C ARG B 57 -20.773 -9.510 -14.886 1.00 15.07 B C
ATOM 1216 O ARG B 57 -20.694 -8.309 -15.108 1.00 15.56 B O
ATOM 1217 CB ARG B 57 -22.204 -9.574 -12.843 1.00 16.31 B C
ATOM 1218 CG ARG B 57 -22.372 -9.987 -11.398 1.00 18.33 B C
ATOM 1219 CD ARG B 57 -23.782 -9.756 -10.880 1.00 21.63 B C
ATOM 1220 NE ARG B 57 -24.302 -8.403 -11.085 1.00 23.91 B N
ATOM 1221 CZ ARG B 57 -24.000 -7.334 -10.350 1.00 25.07 B C
ATOM 1222 NH1 ARG B 57 -23.127 -7.409 -9.347 1.00 26.54 B N
ATOM 1223 NH2 ARG B 57 -24.573 -6.169 -10.630 1.00 27.50 B N
'''
arg0sdf = '''
OpenBabel07012217123D

25 24 0 0 1 0 0 0 0 0999 V2000
-19.7480 -9.4970 -12.6920 N 0 0 0 0 0 0 0 0 0 0 0 0
-20.8740 -10.0210 -13.4610 C 0 0 2 0 0 0 0 0 0 0 0 0
-20.7730 -9.5100 -14.8860 C 0 0 0 0 0 0 0 0 0 0 0 0
-20.6940 -8.3090 -15.1080 O 0 0 0 0 0 0 0 0 0 0 0 0
-22.2040 -9.5740 -12.8430 C 0 0 0 0 0 0 0 0 0 0 0 0
-22.3720 -9.9870 -11.3980 C 0 0 0 0 0 0 0 0 0 0 0 0
-23.7820 -9.7560 -10.8800 C 0 0 0 0 0 0 0 0 0 0 0 0
-24.3020 -8.4030 -11.0850 N 0 0 0 0 0 0 0 0 0 0 0 0
-24.0000 -7.3340 -10.3500 C 0 0 0 0 0 0 0 0 0 0 0 0
-23.1270 -7.4090 -9.3470 N 0 0 0 0 0 0 0 0 0 0 0 0
-24.5730 -6.1690 -10.6300 N 0 0 0 0 0 0 0 0 0 0 0 0
-18.8734 -9.8043 -13.1175 H 0 0 0 0 0 0 0 0 0 0 0 0
-19.8001 -9.8432 -11.7340 H 0 0 0 0 0 0 0 0 0 0 0 0
-20.8414 -11.0905 -13.4505 H 0 0 0 0 0 0 0 0 0 0 0 0
-20.7709 -10.1786 -15.6721 H 0 0 0 0 0 0 0 0 0 0 0 0
-23.0021 -10.0032 -13.4120 H 0 0 0 0 0 0 0 0 0 0 0 0
-22.2157 -8.5043 -12.8659 H 0 0 0 0 0 0 0 0 0 0 0 0
-21.6904 -9.4201 -10.7989 H 0 0 0 0 0 0 0 0 0 0 0 0
-22.1744 -11.0369 -11.3378 H 0 0 0 0 0 0 0 0 0 0 0 0
-23.7869 -9.9579 -9.8292 H 0 0 0 0 0 0 0 0 0 0 0 0
-24.4176 -10.4090 -11.4408 H 0 0 0 0 0 0 0 0 0 0 0 0
-22.6971 -8.2681 -9.1318 H 0 0 0 0 0 0 0 0 0 0 0 0
-22.9116 -6.6053 -8.8208 H 0 0 0 0 0 0 0 0 0 0 0 0
-25.2196 -6.1036 -11.3695 H 0 0 0 0 0 0 0 0 0 0 0 0
-24.3512 -5.3709 -10.0980 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 12 1 0 0 0 0
1 13 1 0 0 0 0
2 3 1 0 0 0 0
2 5 1 0 0 0 0
2 14 1 6 0 0 0
3 4 2 0 0 0 0
3 15 1 0 0 0 0
5 6 1 0 0 0 0
5 16 1 0 0 0 0
5 17 1 0 0 0 0
6 7 1 0 0 0 0
6 18 1 0 0 0 0
6 19 1 0 0 0 0
7 8 1 0 0 0 0
7 20 1 0 0 0 0
7 21 1 0 0 0 0
8 9 2 0 0 0 0
9 10 1 0 0 0 0
9 11 1 0 0 0 0
10 22 1 0 0 0 0
10 23 1 0 0 0 0
11 24 1 0 0 0 0
11 25 1 0 0 0 0
M END
$$$$
'''
self.maxDiff = None
#skip subtitle
output, error = run_exec(arg1, "obabel -ipdb -osdf -h")
self.assertEqual(output[24:].replace("\r", ""), arg1sdf[24:].replace("\r", ""))
output, error = run_exec(arg0, "obabel -ipdb -osdf -h")
self.assertEqual(output[24:].replace("\r", ""), arg0sdf[24:].replace("\r", ""))

def testMissingPlugins(self):
if sys.platform.startswith("win32"):
return
Expand Down