From 0724f13b8451f34fa9f37868cd081e31b4740dfd Mon Sep 17 00:00:00 2001 From: ajs99778 Date: Tue, 14 Aug 2018 13:09:12 -0400 Subject: [PATCH 01/15] moved chiral ligands out of the achiral ligands list --- Ligands/achiral_ligands | 3 --- Ligands/chiral_ligands | 7 +++++-- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/Ligands/achiral_ligands b/Ligands/achiral_ligands index cbf0276..79e19ad 100644 --- a/Ligands/achiral_ligands +++ b/Ligands/achiral_ligands @@ -28,9 +28,6 @@ AcAce acetyl acetone Xphos 2-Dicyclohexylphosphino-2′,4′,6′-triisopropylbiphenyl DPEphos DPEphos (from DOI: 10.1021/om201034m) Xantphos Xantphos (from DOI: 10.1021/om201034m) -JoshPhos tBu-Joshphos (from DOI: 10.1021/ol5027798) -SL-J212-1 SL-J212-1 (from DOI: 10.1021/om500329q) -SL-J212-2 SL-J212-2 (from DOI: 10.1021/om500329q) PyrOx PyrOx PymdOx PymdOx BiOX Bioxazoline (Reisman) diff --git a/Ligands/chiral_ligands b/Ligands/chiral_ligands index fdd3566..90321db 100644 --- a/Ligands/chiral_ligands +++ b/Ligands/chiral_ligands @@ -22,6 +22,9 @@ RR-Me-iPrPh-NC5C (R,R)-(N,N')-bis(2,6-diisopropylphenyl)-dimethyl imidazolidinyl SS-Me-iPrPh-NC5C (S,S)-(N,N')-bis(2,6-diisopropylphenyl)-dimethyl imidazolidinyl carbene ('7b' from DOI: 10.1021/ja202007s) RR-Me-TBF (R,R)-Me-tbf ('2b' from DOI: 10.1021/om9003797) SS-Me-TBF (S,S)-Me-tbf ('2b' from DOI: 10.1021/om9003797) +JoshPhos tBu-Joshphos (from DOI: 10.1021/ol5027798) +SL-J212-1 SL-J212-1 (from DOI: 10.1021/om500329q) +SL-J212-2 SL-J212-2 (from DOI: 10.1021/om500329q) RR-norphos (2R,3R)-(−)-2,3-Bis(diphenylphosphino)bicyclo[2.2.1]hept-5-ene ((-)-Norphos) SS-norphos (2S,3S)-(−)-2,3-Bis(diphenylphosphino)bicyclo[2.2.1]hept-5-ene ((+)-Norphos) RR-QuinoxP (R,R)-QuinoxP* (from DOI: 10.1038/s41467-018-04693-9) @@ -40,5 +43,5 @@ R-pFPh-StackPhos (R)-p-FPh-StackPhos S-pFPh-StackPhos (S)-p-FPh-StackPhos R-Me-StackPhos (R)-Me-StackPhos S-Me-StackPhos (S)-Me-StackPhos -R-Ph-Mes-NC5C (4R,5R)-(N,N′)-bis(Mesityl) imidazolidinyl carbene (from DOI: 10.1021/jo800613h) -S-Ph-Mes-NC5C (4S,5S)-(N,N′)-bis(Mesityl) imidazolidinyl carbene (from DOI: 10.1021/jo800613h) +R-Ph-Mes-NC5C (4R,5R)-(N,N′)-bis(Mesityl) imidazolidinyl carbene (from DOI: 10.1021/jo800613h) +S-Ph-Mes-NC5C (4S,5S)-(N,N′)-bis(Mesityl) imidazolidinyl carbene (from DOI: 10.1021/jo800613h) From ffe4affdc71c1e6631a93a6c5761bc386f3a76df Mon Sep 17 00:00:00 2001 From: yanfei yanfei Date: Tue, 14 Aug 2018 20:37:39 -0600 Subject: [PATCH 02/15] 8-14 debug --- test/test | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/test/test b/test/test index eafdd2b..5b00402 100755 --- a/test/test +++ b/test/test @@ -1,5 +1,4 @@ #!/usr/bin/perl -w - #This is a test script go through all cases provided in the test directory. use strict; use warnings; @@ -55,7 +54,7 @@ for my $case (@cases) { next; } - if (system('./test.pl')) { + if (system('perl ./test.pl')) { print "Case $case didn't pass the test, find error message above.\n"; push (@fail, $case); print '-' x 88 . "\n"; From f5dd304bd3067178ee24800403e612c28a6dea05 Mon Sep 17 00:00:00 2001 From: yanfei yanfei Date: Tue, 14 Aug 2018 22:43:05 -0600 Subject: [PATCH 03/15] fix issue #31 --- Catalysis.pm | 23 +++++++++++++---------- 1 file changed, 13 insertions(+), 10 deletions(-) diff --git a/Catalysis.pm b/Catalysis.pm index a30053d..714c1a8 100644 --- a/Catalysis.pm +++ b/Catalysis.pm @@ -51,7 +51,6 @@ sub new { die "Cannot assign substituents to key atoms"; } } - $self->ligand()->set_substituents($substituents->{ligand}); $self->ligand()->detect_backbone_subs( no_new_subs => $params{no_new_subs} ); #substrate subs @@ -1496,18 +1495,18 @@ sub _detect_substituent { my $self = shift; my %params = @_; - my ($start, $end) = ($params{target}, $params{end}); + my ($start, $end, $no_new_sub) = ($params{target}, $params{end}, $params{no_new_sub}); my $is_sub = $self->__detect_substituent($start, $end); - if ($is_sub) { + if ($is_sub && (! $no_new_sub)) { my $to_sub = $self->{substituents}->{$start}->{sub}; $self->{substituents}->{$start} = $self->detect_substituent( target => $start, end => $end ); $self->{substituents}->{$start}->{sub} = $to_sub; } - return $is_sub; + return $is_sub && (! $no_new_sub); } @@ -1779,15 +1778,19 @@ sub detect_backbone_subs { #backbone, if not make a new backbone my $is_sub = 1; if ($no_new_subs) { - unless (grep { $_ == $atom_connected} - keys %{ $self->{substituents} }) { - $is_sub = 0; + if (grep { $_ == $atom_connected} + keys %{ $self->{substituents} }) { + my $new_back_atoms = $self->_get_all_connected( $atom_connected, + $atom ); + for my $atom_temp (@$new_back_atoms) { + $backbone{$atom_temp} = 1; + } } } - unless ($is_sub && - $self->_detect_substituent(target => $atom_connected, - end => $atom)) { + unless($self->_detect_substituent(target => $atom_connected, + end => $atom, + no_new_sub => $no_new_subs)) { my $new_back_atoms = $self->_get_all_connected( $atom_connected, $atom ); for my $atom_temp (@$new_back_atoms) { From f31b1cc640429a905d10e75d5366da9dac4296a4 Mon Sep 17 00:00:00 2001 From: ajs99778 Date: Wed, 22 Aug 2018 11:08:23 -0400 Subject: [PATCH 04/15] added ligands --- Ligands/AcAc.xyz | 16 +++++++++ Ligands/BPY.xyz | 22 ++++++++++++ Ligands/DMBPY.xyz | 28 ++++++++++++++++ Ligands/NBD.xyz | 18 ++++++++++ Ligands/PIN.xyz | 22 ++++++++++++ Ligands/TACN.xyz | 26 +++++++++++++++ Ligands/TACN_star.xyz | 36 ++++++++++++++++++++ Ligands/Tp.xyz | 29 ++++++++++++++++ Ligands/achiral_ligands | 47 ++++++++++++++------------ Ligands/iPr-PNPEt.xyz | 58 ++++++++++++++++++++++++++++++++ Ligands/tBu-PNPPyr.xyz | 74 +++++++++++++++++++++++++++++++++++++++++ 11 files changed, 355 insertions(+), 21 deletions(-) create mode 100644 Ligands/AcAc.xyz create mode 100644 Ligands/BPY.xyz create mode 100644 Ligands/DMBPY.xyz create mode 100644 Ligands/NBD.xyz create mode 100644 Ligands/PIN.xyz create mode 100644 Ligands/TACN.xyz create mode 100644 Ligands/TACN_star.xyz create mode 100644 Ligands/Tp.xyz create mode 100644 Ligands/iPr-PNPEt.xyz create mode 100644 Ligands/tBu-PNPPyr.xyz diff --git a/Ligands/AcAc.xyz b/Ligands/AcAc.xyz new file mode 100644 index 0000000..f09f073 --- /dev/null +++ b/Ligands/AcAc.xyz @@ -0,0 +1,16 @@ +14 + K:1,2; +O -1.985120 -0.037738 -0.880122 +O -1.246030 -0.575973 1.655096 +C -4.257931 0.352017 -1.344514 +C -3.112127 0.033407 -0.437138 +C -3.472700 -0.223337 0.936276 +H -4.363881 -0.186217 1.198114 +C -2.499493 -0.520293 1.854356 +C -2.923295 -0.777037 3.280468 +H -3.929826 0.500496 -2.234599 +H -4.702240 1.143902 -1.032449 +H -4.876545 -0.381095 -1.348631 +H -2.150027 -0.984288 3.811554 +H -3.533366 -1.519429 3.304346 +H -3.355642 0.002474 3.632055 diff --git a/Ligands/BPY.xyz b/Ligands/BPY.xyz new file mode 100644 index 0000000..78277f5 --- /dev/null +++ b/Ligands/BPY.xyz @@ -0,0 +1,22 @@ +20 + K:1,11; +N -0.849888 -1.545396 -0.994456 +C -0.496569 -2.750066 -0.548988 +C -1.731028 -1.463056 -1.983569 +H -1.962653 -0.604751 -2.318839 +C -2.315906 -2.566591 -2.537900 +H -2.950606 -2.477091 -3.239829 +C -1.044791 -3.891191 -1.059907 +H -0.784960 -4.740546 -0.722634 +C -1.973340 -3.799901 -2.062378 +H -2.372629 -4.583921 -2.421691 +N 0.849888 -1.545396 0.994456 +C 0.496569 -2.750066 0.548987 +C 1.731027 -1.463056 1.983569 +H 1.962653 -0.604751 2.318838 +C 2.315905 -2.566591 2.537899 +H 2.950606 -2.477091 3.239829 +C 1.044790 -3.891191 1.059907 +H 0.784960 -4.740546 0.722633 +C 1.973340 -3.799901 2.062377 +H 2.372628 -4.583921 2.421690 diff --git a/Ligands/DMBPY.xyz b/Ligands/DMBPY.xyz new file mode 100644 index 0000000..2f971d3 --- /dev/null +++ b/Ligands/DMBPY.xyz @@ -0,0 +1,28 @@ +26 + K:1,11; +N -0.849888 -1.545311 -0.994454 +C -0.496569 -2.749981 -0.548986 +C -1.731028 -1.462971 -1.983567 +H -1.962653 -0.604666 -2.318837 +C -2.315906 -2.566506 -2.537898 +H -2.950606 -2.477006 -3.239827 +C -1.044791 -3.891106 -1.059905 +H -0.784960 -4.740461 -0.722632 +C -1.973340 -3.799816 -2.062376 +C -2.632903 -5.051861 -2.669798 +N 0.849888 -1.545311 0.994458 +C 0.496569 -2.749981 0.548989 +C 1.731027 -1.462971 1.983571 +H 1.962653 -0.604666 2.318840 +C 2.315905 -2.566506 2.537901 +H 2.950606 -2.477006 3.239831 +C 1.044790 -3.891106 1.059909 +H 0.784960 -4.740461 0.722635 +C 1.973340 -3.799816 2.062379 +C 2.632902 -5.077324 2.614241 +H -3.350162 -5.499065 -1.972213 +H -3.178774 -4.798231 -3.588896 +H -1.882957 -5.807875 -2.928833 +H 1.882955 -5.767101 3.017804 +H 3.178773 -5.607954 1.822090 +H 3.350161 -4.840866 3.408408 diff --git a/Ligands/NBD.xyz b/Ligands/NBD.xyz new file mode 100644 index 0000000..bd05dd4 --- /dev/null +++ b/Ligands/NBD.xyz @@ -0,0 +1,18 @@ +15 + K:1,2; + C -2.017031 0.652187 0.969063 + C -1.187639 1.765595 0.962747 + C -0.534768 1.816707 2.350987 + C 0.377576 0.577591 2.331227 + C -0.443981 -0.508189 2.326854 + C -1.871666 0.016743 2.355847 + C -1.688229 1.272435 3.222059 + H -2.718211 0.549963 0.452381 + H -1.256460 2.511551 0.437803 + H -0.067174 2.649691 2.608195 + H 1.322156 0.577591 2.442986 + H -0.177899 -1.287299 2.483478 + H -2.536449 -0.568971 2.580660 + H -2.472071 1.889921 3.265791 + H -1.385371 1.074895 4.117751 + diff --git a/Ligands/PIN.xyz b/Ligands/PIN.xyz new file mode 100644 index 0000000..89e4531 --- /dev/null +++ b/Ligands/PIN.xyz @@ -0,0 +1,22 @@ +20 + K:1,2; +O -0.938496 -1.630847 -1.237852 +O -0.343964 -1.270457 1.194208 +C -0.888849 -2.911605 -0.519289 +C -1.066552 -2.525945 0.986751 +C 0.473245 -3.524219 -0.794942 +C -1.983239 -3.820064 -1.059109 +C -2.522108 -2.247645 1.367209 +C -0.465507 -3.547397 1.942921 +H 1.159504 -2.946212 -0.453247 +H 0.589201 -3.633511 -1.741062 +H 0.532094 -4.380365 -0.364234 +H -2.841178 -3.429092 -0.879647 +H -1.926896 -4.678141 -0.631273 +H -1.871681 -3.928068 -2.006665 +H -2.893570 -1.602196 0.762783 +H -2.558005 -1.904801 2.263080 +H -3.027629 -3.062103 1.316960 +H 0.448012 -3.715601 1.698853 +H -0.965367 -4.365879 1.892672 +H -0.500145 -3.205357 2.838792 diff --git a/Ligands/TACN.xyz b/Ligands/TACN.xyz new file mode 100644 index 0000000..b951f1d --- /dev/null +++ b/Ligands/TACN.xyz @@ -0,0 +1,26 @@ +24 + K:1,2,3; +N -0.015037 -1.670895 -1.412810 +N 2.122668 -0.539531 0.013103 +N -0.025937 -1.673282 1.400163 +C -0.284515 -2.973081 -0.707463 +C 1.313815 -1.624471 -2.097232 +H -0.727996 -1.558385 -2.133943 +C 2.403365 -1.057745 1.386082 +C 2.447945 -1.528502 -1.073579 +H 2.722586 0.274346 -0.125536 +C -0.814426 -2.741326 0.711276 +C 1.364163 -2.108591 1.783966 +H -0.526241 -1.440291 2.258390 +H -1.004441 -3.576882 -1.272020 +H 0.642132 -3.554649 -0.679927 +H 1.471423 -2.499587 -2.744532 +H 1.308831 -0.741159 -2.746945 +H 2.360046 -0.200283 2.068158 +H 3.412823 -1.486980 1.469540 +H 3.378058 -1.253693 -1.584876 +H 2.634086 -2.505288 -0.615961 +H -1.857292 -2.403154 0.679994 +H -0.799037 -3.687308 1.271378 +H 1.424596 -2.296645 2.862203 +H 1.580031 -3.065375 1.298228 diff --git a/Ligands/TACN_star.xyz b/Ligands/TACN_star.xyz new file mode 100644 index 0000000..8573da8 --- /dev/null +++ b/Ligands/TACN_star.xyz @@ -0,0 +1,36 @@ +33 +K:1,2,3; +N -0.015037 -1.670895 -1.412810 +N 2.122668 -0.539531 0.013103 +N -0.025937 -1.673282 1.400163 +C -0.284515 -2.973081 -0.707463 +C 1.313815 -1.624471 -2.097232 +C -1.077179 -1.503282 -2.487129 +H -0.904012 -2.188220 -3.324952 +H -2.076554 -1.718321 -2.084571 +H -1.090333 -0.477951 -2.873909 +C 2.403365 -1.057745 1.386082 +C 2.447945 -1.528502 -1.073579 +C 3.016183 0.672654 -0.193385 +H 4.029394 0.485512 0.180055 +H 3.097014 0.920431 -1.260680 +H 2.613764 1.552939 0.320651 +C -0.814426 -2.741326 0.711276 +C 1.364163 -2.108591 1.783966 +C -0.771222 -1.326204 2.678633 +H -1.177244 -2.225098 3.156346 +H -0.101013 -0.840945 3.401398 +H -1.598235 -0.635262 2.479322 +H -1.004441 -3.576882 -1.272020 +H 0.642132 -3.554649 -0.679927 +H 1.471423 -2.499587 -2.744532 +H 1.308831 -0.741159 -2.746945 +H 2.360046 -0.200283 2.068158 +H 3.412823 -1.486980 1.469540 +H 3.378058 -1.253693 -1.584876 +H 2.634086 -2.505288 -0.615961 +H -1.857292 -2.403154 0.679994 +H -0.799037 -3.687308 1.271378 +H 1.424596 -2.296645 2.862203 +H 1.580031 -3.065375 1.298228 + diff --git a/Ligands/Tp.xyz b/Ligands/Tp.xyz new file mode 100644 index 0000000..09107d0 --- /dev/null +++ b/Ligands/Tp.xyz @@ -0,0 +1,29 @@ +26 +K:21,23,25; +B -3.183132 -0.062567 0.145157 +H -4.307004 -0.144333 0.187246 +C -3.455934 1.909433 -1.578502 +C -2.603811 2.848024 -2.127646 +C -1.340141 2.520958 -1.627219 +H -4.531663 1.801551 -1.717316 +H -2.855081 3.672290 -2.795141 +H -0.386257 3.008403 -1.828718 +C -3.248410 0.471724 2.722359 +C -2.296935 0.506171 3.721557 +C -1.084321 0.209383 3.093205 +H -4.323821 0.636263 2.789572 +H -2.419183 0.737123 4.779771 +H -0.103762 0.116739 3.560132 +C -3.248796 -2.612370 -0.478887 +C -2.368799 -3.499833 -1.074760 +C -1.200587 -2.758316 -1.290176 +H -4.244503 -2.791037 -0.072999 +H -2.539641 -4.547665 -1.321662 +H -0.266440 -3.090168 -1.743324 +N -1.409282 1.457271 -0.820238 +N -2.732182 1.082887 -0.787594 +N -1.274941 0.018656 1.781489 +N -2.620850 0.176387 1.558450 +N -1.353326 -1.500457 -0.853876 +N -2.636194 -1.411801 -0.380624 + diff --git a/Ligands/achiral_ligands b/Ligands/achiral_ligands index 79e19ad..d6953c6 100644 --- a/Ligands/achiral_ligands +++ b/Ligands/achiral_ligands @@ -1,36 +1,41 @@ BPE 1,2-Bis(4-pyridyl)ethane DMPE 1,2-Bis(dimethylphosphino)ethane DPPE 1,2-Bis(diphenylphosphino)ethane -Cp_star pentamethylcyclopentadiene -Cp cyclopentadiene DPPP 1,3-Bis(diphenylphosphino)propane DPPF 1,1′-Ferrocenediyl-bis(diphenylphosphine) -DMP 2,9-dimethyl phenanthroline -BenQuin Benzo[h]quinoline -COD cyclooctadiene -bpy 2,2′-bipyridine -dmb 4,4′-dimethyl-2,2′-bipyridine +Xphos 2-Dicyclohexylphosphino-2′,4′,6′-triisopropylbiphenyl PhBP3 PhBP3 (from DOI: 10.1021/ja026433e) tBu-PCP tetra(t-butyl)-2,6-bis(diphosphino)benzene (from DOI: 10.1126/science.1200514) -tBu-PNP tetra(t-butyl)-2,6-bis(diphosphino)pyridine (from DOI: 10.1021/ic901032c) -iPr-NC3C 2,3-di(bisisopropylamino) cyclopropyl carbene (′8′ from DOI: 10.1021/ja202007s) -Mes-NC5C (N,N′)-bis(mesityl) imidazolidinyl carbene (′6a′ from DOI: 10.1021/ja202007s) -iPrPh-NC5C (N,N′)-bis(2,6-diisopropylphenyl) imidazolidinyl carbene (′6b′ from DOI: 10.1021/ja202007s) -IMes 1,3-Dimesitylimidazol-2-ylidene (′5b′ from DOI: 10.1021/ja202007s) -Ad-HC5C (N,N′)-bis(adamantyl) dihydroimidazolyl carbene (′5c′ from DOI: 10.1021/ja202007s) -iPrPh-BIP (N,N′)-bis(2,6-diisoproylphenyl)imino pyridine (from DOI: 10.1039/b107490c) +tBu-PNPPyr tetra(t-butyl)-2,6-bis(diphosphino)pyridine (from DOI: 10.1021/ic901032c) +iPr-PNPEt {bis[2-(diisopropylphosphinomethyl)ethyl]amino}ethyl]amine (from DOI: 10.1021/ja504034q) +DPEphos DPEphos (from DOI: 10.1021/om201034m) +Xantphos Xantphos (from DOI: 10.1021/om201034m) +ACN acetonitrile EDA ethylene diamine +BenQuin Benzo[h]quinoline Milstein Milstein catalyst (from DOI: 10.1021/acscatal.7b01791) PHNNP amine(imine)diphosphine (from DOI: 10.1021/om500479q) -CO carbonmonoxide -iPr-PNP2 {bis[2-(diisopropylphosphinomethyl)ethyl]amino}ethyl]amine (from DOI: 10.1021/ja504034q) -AcAce acetyl acetone -Xphos 2-Dicyclohexylphosphino-2′,4′,6′-triisopropylbiphenyl -DPEphos DPEphos (from DOI: 10.1021/om201034m) -Xantphos Xantphos (from DOI: 10.1021/om201034m) +DMP 2,9-dimethyl phenanthroline +BPY 2,2′-bipyridine +DMBPY 4,4′-dimethyl-2,2′-bipyridine +iPrPh-BIP (N,N′)-bis(2,6-diisoproylphenyl)imino pyridine (from DOI: 10.1039/b107490c) +TACN 1,4,7-triazacyclononane +TACN_star (N,N′,N′′)-trimethyl-1,4,7-triazacyclononane +Tp tris(pyrazolyl)borate PyrOx PyrOx PymdOx PymdOx +CO carbonyl BiOX Bioxazoline (Reisman) BDA 2,2'-bipyridine-6,6'-dicarboxylate KASBAI 2,6-dicyclohexyl-4-(2,4,6-trimethylphenyl)-3,5-diphenyl-2,4,6-triaza-3,5-diborinanylidene (from DOI: 10.1021/ja052987g) -ACN acetonitrile +iPr-NC3C 2,3-di(bisisopropylamino) cyclopropyl carbene (′8′ from DOI: 10.1021/ja202007s) +Mes-NC5C (N,N′)-bis(mesityl) imidazolidinyl carbene (′6a′ from DOI: 10.1021/ja202007s) +iPrPh-NC5C (N,N′)-bis(2,6-diisopropylphenyl) imidazolidinyl carbene (′6b′ from DOI: 10.1021/ja202007s) +IMes 1,3-Dimesitylimidazol-2-ylidene (′5b′ from DOI: 10.1021/ja202007s) +Ad-HC5C (N,N′)-bis(adamantyl) dihydroimidazolyl carbene (′5c′ from DOI: 10.1021/ja202007s) +Cp_star pentamethylcyclopentadiene +Cp cyclopentadiene +COD cyclooctadiene +NBD 2,5-Norbornadiene +PIN pinacolate +AcAc acetyl acetone diff --git a/Ligands/iPr-PNPEt.xyz b/Ligands/iPr-PNPEt.xyz new file mode 100644 index 0000000..6dbb987 --- /dev/null +++ b/Ligands/iPr-PNPEt.xyz @@ -0,0 +1,58 @@ +56 + K:1,2,3; +P -0.913462 0.983318 1.764983 +P 1.399724 -0.741981 -1.575780 +N 0.932404 1.830902 -0.321032 +H 0.471425 2.208942 -0.894171 +C -0.377824 2.734742 1.559618 +H -1.047573 3.233174 1.028062 +H -0.295782 3.169591 2.444238 +C 0.966388 2.747873 0.847019 +H 1.173244 3.667194 0.543581 +H 1.678717 2.463272 1.473314 +C 2.287053 1.725990 -0.919671 +H 2.922113 1.363017 -0.252773 +H 2.603372 2.623611 -1.194275 +C 2.227956 0.806946 -2.129697 +H 3.140669 0.611084 -2.459419 +H 1.712169 1.231705 -2.861518 +C -0.400718 0.479772 3.482636 +C -2.757353 1.178074 1.881494 +C 2.859741 -1.725853 -0.965961 +C 0.877745 -1.597858 -3.141419 +H -1.041610 0.897205 4.127173 +C 1.006800 0.969081 3.840015 +H 1.224066 0.696782 4.754841 +H 1.039809 1.946318 3.774110 +H 1.655721 0.576528 3.219016 +C -0.471164 -1.031005 3.670544 +H -0.286961 -1.253545 4.607731 +H 0.193857 -1.463643 3.095443 +H -1.366642 -1.348918 3.428892 +H -3.046424 1.580027 1.012370 +C -3.227774 2.148124 2.968341 +H -4.185222 2.325049 2.858106 +H -2.729875 2.989902 2.893413 +H -3.068219 1.752806 3.850607 +C -3.464027 -0.164347 1.975644 +H -4.428390 -0.034418 1.855799 +H -3.295538 -0.561047 2.856145 +H -3.125269 -0.761471 1.277168 +H 3.404224 -1.083530 -0.427343 +C 3.804492 -2.238107 -2.055161 +H 4.616381 -2.597072 -1.641489 +H 4.042146 -1.500964 -2.655565 +H 3.359072 -2.945394 -2.567299 +C 2.484660 -2.850020 0.003590 +H 3.299820 -3.249485 0.370972 +H 1.971075 -3.534224 -0.474418 +H 1.941516 -2.483729 0.733842 +H 1.704144 -1.947424 -3.583337 +C 0.184120 -0.673008 -4.132350 +H -0.109795 -1.189962 -4.911247 +H 0.809037 0.023636 -4.420881 +H -0.593436 -0.258339 -3.702986 +C -0.005063 -2.790584 -2.813463 +H -0.218294 -3.275747 -3.638258 +H -0.833122 -2.478200 -2.392729 +H 0.468868 -3.387708 -2.196583 diff --git a/Ligands/tBu-PNPPyr.xyz b/Ligands/tBu-PNPPyr.xyz new file mode 100644 index 0000000..92d1077 --- /dev/null +++ b/Ligands/tBu-PNPPyr.xyz @@ -0,0 +1,74 @@ +72 + K:1,2,3; +P -1.099120 -1.399940 1.313020 +P 1.174420 1.555840 -1.049270 +N -1.051330 1.574950 0.928440 +C -1.739090 1.228630 2.044220 +C -1.915380 2.163140 3.055060 +H -2.355680 1.926010 3.862190 +C -1.437730 3.453340 2.857520 +H -1.573270 4.109250 3.531930 +C -0.771880 3.799420 1.712420 +H -0.459010 4.685190 1.579690 +C -0.569110 2.823230 0.750960 +C -2.278560 -0.179090 2.075090 +H -3.010030 -0.139770 1.394500 +C -3.041700 -0.528470 3.345200 +C -2.205500 -2.608530 0.383660 +C -0.093610 -2.184240 2.700110 +C 0.172980 3.050440 -0.548480 +H 0.776660 3.827860 -0.446620 +H -0.478510 3.260760 -1.263010 +C 2.883140 1.854730 -0.333960 +C 1.138130 1.563340 -2.900420 +H -2.441020 -0.458170 4.116830 +H -3.382380 -1.444930 3.280380 +H -3.792780 0.090810 3.457860 +C -2.626000 -1.881800 -0.892620 +H -1.831630 -1.680170 -1.429680 +H -3.082560 -1.046670 -0.658050 +H -3.232950 -2.452210 -1.409620 +C -1.389470 -3.842700 -0.008330 +H -1.246480 -4.403650 0.781830 +H -0.522880 -3.559760 -0.369460 +H -1.876010 -4.353500 -0.688910 +C -3.468260 -3.049220 1.149120 +H -3.974820 -3.689530 0.604350 +H -4.027130 -2.265290 1.335860 +H -3.207930 -3.473280 1.993290 +C 1.140390 -2.871760 2.064280 +H 1.795300 -3.079290 2.764930 +H 1.546970 -2.270520 1.405310 +H 0.861780 -3.701360 1.622910 +C -0.846990 -3.168130 3.599840 +H -0.237190 -3.520980 4.280420 +H -1.194920 -3.905660 3.058150 +H -1.592110 -2.704340 4.038120 +C 0.421530 -1.005810 3.545820 +H -0.332710 -0.573830 3.998000 +H 0.868970 -0.357470 2.964010 +H 1.055700 -1.338440 4.214060 +C 3.623050 0.500570 -0.320070 +H 3.713730 0.167770 -1.238320 +H 3.113680 -0.145270 0.212360 +H 4.512420 0.618520 0.073460 +C 2.651890 2.267530 1.127520 +H 3.510920 2.301930 1.596670 +H 2.066020 1.613620 1.562720 +H 2.228970 3.151730 1.153750 +C 3.704500 2.909910 -1.039230 +H 4.570540 3.002200 -0.590140 +H 3.228800 3.766530 -1.013000 +H 3.846240 2.643760 -1.971370 +C 1.386720 2.929650 -3.545510 +H 2.261360 3.268730 -3.266170 +H 0.687740 3.556160 -3.263090 +H 1.367420 2.837320 -4.520850 +C 2.151930 0.544060 -3.459080 +H 2.012950 0.440220 -4.423630 +H 2.024170 -0.320240 -3.014620 +H 3.063540 0.864790 -3.292410 +C -0.279980 1.073910 -3.280060 +H -0.947590 1.689520 -2.912770 +H -0.425340 0.177030 -2.912770 +H -0.363260 1.045460 -4.255410 From d0378caec31164cd045c33ad5085bf5038a87fab Mon Sep 17 00:00:00 2001 From: ajs99778 Date: Wed, 22 Aug 2018 11:10:08 -0400 Subject: [PATCH 05/15] added ligands --- Ligands/AcAce.xyz | 16 ---------- Ligands/bpy.xyz | 22 ------------- Ligands/dmb.xyz | 28 ----------------- Ligands/iPr-PNP2.xyz | 58 ---------------------------------- Ligands/tBu-PNP.xyz | 74 -------------------------------------------- 5 files changed, 198 deletions(-) delete mode 100644 Ligands/AcAce.xyz delete mode 100644 Ligands/bpy.xyz delete mode 100644 Ligands/dmb.xyz delete mode 100644 Ligands/iPr-PNP2.xyz delete mode 100644 Ligands/tBu-PNP.xyz diff --git a/Ligands/AcAce.xyz b/Ligands/AcAce.xyz deleted file mode 100644 index f09f073..0000000 --- a/Ligands/AcAce.xyz +++ /dev/null @@ -1,16 +0,0 @@ -14 - K:1,2; -O -1.985120 -0.037738 -0.880122 -O -1.246030 -0.575973 1.655096 -C -4.257931 0.352017 -1.344514 -C -3.112127 0.033407 -0.437138 -C -3.472700 -0.223337 0.936276 -H -4.363881 -0.186217 1.198114 -C -2.499493 -0.520293 1.854356 -C -2.923295 -0.777037 3.280468 -H -3.929826 0.500496 -2.234599 -H -4.702240 1.143902 -1.032449 -H -4.876545 -0.381095 -1.348631 -H -2.150027 -0.984288 3.811554 -H -3.533366 -1.519429 3.304346 -H -3.355642 0.002474 3.632055 diff --git a/Ligands/bpy.xyz b/Ligands/bpy.xyz deleted file mode 100644 index 78277f5..0000000 --- a/Ligands/bpy.xyz +++ /dev/null @@ -1,22 +0,0 @@ -20 - K:1,11; -N -0.849888 -1.545396 -0.994456 -C -0.496569 -2.750066 -0.548988 -C -1.731028 -1.463056 -1.983569 -H -1.962653 -0.604751 -2.318839 -C -2.315906 -2.566591 -2.537900 -H -2.950606 -2.477091 -3.239829 -C -1.044791 -3.891191 -1.059907 -H -0.784960 -4.740546 -0.722634 -C -1.973340 -3.799901 -2.062378 -H -2.372629 -4.583921 -2.421691 -N 0.849888 -1.545396 0.994456 -C 0.496569 -2.750066 0.548987 -C 1.731027 -1.463056 1.983569 -H 1.962653 -0.604751 2.318838 -C 2.315905 -2.566591 2.537899 -H 2.950606 -2.477091 3.239829 -C 1.044790 -3.891191 1.059907 -H 0.784960 -4.740546 0.722633 -C 1.973340 -3.799901 2.062377 -H 2.372628 -4.583921 2.421690 diff --git a/Ligands/dmb.xyz b/Ligands/dmb.xyz deleted file mode 100644 index 2f971d3..0000000 --- a/Ligands/dmb.xyz +++ /dev/null @@ -1,28 +0,0 @@ -26 - K:1,11; -N -0.849888 -1.545311 -0.994454 -C -0.496569 -2.749981 -0.548986 -C -1.731028 -1.462971 -1.983567 -H -1.962653 -0.604666 -2.318837 -C -2.315906 -2.566506 -2.537898 -H -2.950606 -2.477006 -3.239827 -C -1.044791 -3.891106 -1.059905 -H -0.784960 -4.740461 -0.722632 -C -1.973340 -3.799816 -2.062376 -C -2.632903 -5.051861 -2.669798 -N 0.849888 -1.545311 0.994458 -C 0.496569 -2.749981 0.548989 -C 1.731027 -1.462971 1.983571 -H 1.962653 -0.604666 2.318840 -C 2.315905 -2.566506 2.537901 -H 2.950606 -2.477006 3.239831 -C 1.044790 -3.891106 1.059909 -H 0.784960 -4.740461 0.722635 -C 1.973340 -3.799816 2.062379 -C 2.632902 -5.077324 2.614241 -H -3.350162 -5.499065 -1.972213 -H -3.178774 -4.798231 -3.588896 -H -1.882957 -5.807875 -2.928833 -H 1.882955 -5.767101 3.017804 -H 3.178773 -5.607954 1.822090 -H 3.350161 -4.840866 3.408408 diff --git a/Ligands/iPr-PNP2.xyz b/Ligands/iPr-PNP2.xyz deleted file mode 100644 index 6dbb987..0000000 --- a/Ligands/iPr-PNP2.xyz +++ /dev/null @@ -1,58 +0,0 @@ -56 - K:1,2,3; -P -0.913462 0.983318 1.764983 -P 1.399724 -0.741981 -1.575780 -N 0.932404 1.830902 -0.321032 -H 0.471425 2.208942 -0.894171 -C -0.377824 2.734742 1.559618 -H -1.047573 3.233174 1.028062 -H -0.295782 3.169591 2.444238 -C 0.966388 2.747873 0.847019 -H 1.173244 3.667194 0.543581 -H 1.678717 2.463272 1.473314 -C 2.287053 1.725990 -0.919671 -H 2.922113 1.363017 -0.252773 -H 2.603372 2.623611 -1.194275 -C 2.227956 0.806946 -2.129697 -H 3.140669 0.611084 -2.459419 -H 1.712169 1.231705 -2.861518 -C -0.400718 0.479772 3.482636 -C -2.757353 1.178074 1.881494 -C 2.859741 -1.725853 -0.965961 -C 0.877745 -1.597858 -3.141419 -H -1.041610 0.897205 4.127173 -C 1.006800 0.969081 3.840015 -H 1.224066 0.696782 4.754841 -H 1.039809 1.946318 3.774110 -H 1.655721 0.576528 3.219016 -C -0.471164 -1.031005 3.670544 -H -0.286961 -1.253545 4.607731 -H 0.193857 -1.463643 3.095443 -H -1.366642 -1.348918 3.428892 -H -3.046424 1.580027 1.012370 -C -3.227774 2.148124 2.968341 -H -4.185222 2.325049 2.858106 -H -2.729875 2.989902 2.893413 -H -3.068219 1.752806 3.850607 -C -3.464027 -0.164347 1.975644 -H -4.428390 -0.034418 1.855799 -H -3.295538 -0.561047 2.856145 -H -3.125269 -0.761471 1.277168 -H 3.404224 -1.083530 -0.427343 -C 3.804492 -2.238107 -2.055161 -H 4.616381 -2.597072 -1.641489 -H 4.042146 -1.500964 -2.655565 -H 3.359072 -2.945394 -2.567299 -C 2.484660 -2.850020 0.003590 -H 3.299820 -3.249485 0.370972 -H 1.971075 -3.534224 -0.474418 -H 1.941516 -2.483729 0.733842 -H 1.704144 -1.947424 -3.583337 -C 0.184120 -0.673008 -4.132350 -H -0.109795 -1.189962 -4.911247 -H 0.809037 0.023636 -4.420881 -H -0.593436 -0.258339 -3.702986 -C -0.005063 -2.790584 -2.813463 -H -0.218294 -3.275747 -3.638258 -H -0.833122 -2.478200 -2.392729 -H 0.468868 -3.387708 -2.196583 diff --git a/Ligands/tBu-PNP.xyz b/Ligands/tBu-PNP.xyz deleted file mode 100644 index 92d1077..0000000 --- a/Ligands/tBu-PNP.xyz +++ /dev/null @@ -1,74 +0,0 @@ -72 - K:1,2,3; -P -1.099120 -1.399940 1.313020 -P 1.174420 1.555840 -1.049270 -N -1.051330 1.574950 0.928440 -C -1.739090 1.228630 2.044220 -C -1.915380 2.163140 3.055060 -H -2.355680 1.926010 3.862190 -C -1.437730 3.453340 2.857520 -H -1.573270 4.109250 3.531930 -C -0.771880 3.799420 1.712420 -H -0.459010 4.685190 1.579690 -C -0.569110 2.823230 0.750960 -C -2.278560 -0.179090 2.075090 -H -3.010030 -0.139770 1.394500 -C -3.041700 -0.528470 3.345200 -C -2.205500 -2.608530 0.383660 -C -0.093610 -2.184240 2.700110 -C 0.172980 3.050440 -0.548480 -H 0.776660 3.827860 -0.446620 -H -0.478510 3.260760 -1.263010 -C 2.883140 1.854730 -0.333960 -C 1.138130 1.563340 -2.900420 -H -2.441020 -0.458170 4.116830 -H -3.382380 -1.444930 3.280380 -H -3.792780 0.090810 3.457860 -C -2.626000 -1.881800 -0.892620 -H -1.831630 -1.680170 -1.429680 -H -3.082560 -1.046670 -0.658050 -H -3.232950 -2.452210 -1.409620 -C -1.389470 -3.842700 -0.008330 -H -1.246480 -4.403650 0.781830 -H -0.522880 -3.559760 -0.369460 -H -1.876010 -4.353500 -0.688910 -C -3.468260 -3.049220 1.149120 -H -3.974820 -3.689530 0.604350 -H -4.027130 -2.265290 1.335860 -H -3.207930 -3.473280 1.993290 -C 1.140390 -2.871760 2.064280 -H 1.795300 -3.079290 2.764930 -H 1.546970 -2.270520 1.405310 -H 0.861780 -3.701360 1.622910 -C -0.846990 -3.168130 3.599840 -H -0.237190 -3.520980 4.280420 -H -1.194920 -3.905660 3.058150 -H -1.592110 -2.704340 4.038120 -C 0.421530 -1.005810 3.545820 -H -0.332710 -0.573830 3.998000 -H 0.868970 -0.357470 2.964010 -H 1.055700 -1.338440 4.214060 -C 3.623050 0.500570 -0.320070 -H 3.713730 0.167770 -1.238320 -H 3.113680 -0.145270 0.212360 -H 4.512420 0.618520 0.073460 -C 2.651890 2.267530 1.127520 -H 3.510920 2.301930 1.596670 -H 2.066020 1.613620 1.562720 -H 2.228970 3.151730 1.153750 -C 3.704500 2.909910 -1.039230 -H 4.570540 3.002200 -0.590140 -H 3.228800 3.766530 -1.013000 -H 3.846240 2.643760 -1.971370 -C 1.386720 2.929650 -3.545510 -H 2.261360 3.268730 -3.266170 -H 0.687740 3.556160 -3.263090 -H 1.367420 2.837320 -4.520850 -C 2.151930 0.544060 -3.459080 -H 2.012950 0.440220 -4.423630 -H 2.024170 -0.320240 -3.014620 -H 3.063540 0.864790 -3.292410 -C -0.279980 1.073910 -3.280060 -H -0.947590 1.689520 -2.912770 -H -0.425340 0.177030 -2.912770 -H -0.363260 1.045460 -4.255410 From 77af81e0eaee19958fcda17d91bac162c386f978 Mon Sep 17 00:00:00 2001 From: ajs99778 Date: Wed, 22 Aug 2018 12:07:26 -0400 Subject: [PATCH 06/15] fixed coordinates --- Ligands/NBD.xyz | 33 ++++++++++++++++----------------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/Ligands/NBD.xyz b/Ligands/NBD.xyz index bd05dd4..d750a79 100644 --- a/Ligands/NBD.xyz +++ b/Ligands/NBD.xyz @@ -1,18 +1,17 @@ 15 - K:1,2; - C -2.017031 0.652187 0.969063 - C -1.187639 1.765595 0.962747 - C -0.534768 1.816707 2.350987 - C 0.377576 0.577591 2.331227 - C -0.443981 -0.508189 2.326854 - C -1.871666 0.016743 2.355847 - C -1.688229 1.272435 3.222059 - H -2.718211 0.549963 0.452381 - H -1.256460 2.511551 0.437803 - H -0.067174 2.649691 2.608195 - H 1.322156 0.577591 2.442986 - H -0.177899 -1.287299 2.483478 - H -2.536449 -0.568971 2.580660 - H -2.472071 1.889921 3.265791 - H -1.385371 1.074895 4.117751 - + K:1,2,4,5; +C -2.017031 0.652187 0.969063 +C -1.187639 1.765595 0.962747 +C -0.534768 1.816707 2.350987 +C 0.377576 0.577591 2.331227 +C -0.443981 -0.508189 2.326854 +C -1.871666 0.016743 2.355847 +C -1.688229 1.272435 3.222059 +H -2.718211 0.549963 0.452381 +H -1.256460 2.511551 0.437803 +H -0.067174 2.649691 2.608195 +H 1.322156 0.577591 2.442986 +H -0.177899 -1.287299 2.483478 +H -2.536449 -0.568971 2.580660 +H -2.472071 1.889921 3.265791 +H -1.385371 1.074895 4.117751 From 5f1c781cd25f7842eb8fb92ef1b79577167a7024 Mon Sep 17 00:00:00 2001 From: "Steven E. Wheeler" Date: Wed, 22 Aug 2018 16:13:03 -0500 Subject: [PATCH 07/15] Adjusting geometry --- Ligands/BiOX.xyz | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Ligands/BiOX.xyz b/Ligands/BiOX.xyz index b66adc2..5a6db5c 100644 --- a/Ligands/BiOX.xyz +++ b/Ligands/BiOX.xyz @@ -1,6 +1,6 @@ 18 K:4,13; -C 0.903816 0.000000 2.400507 +C 0.803816 0.000000 2.400507 C 3.177037 0.000000 2.550514 C 2.813944 0.000000 1.201250 N 1.427688 0.000000 1.117375 @@ -9,7 +9,7 @@ H 3.145268 -1.094449 0.829914 O 1.966020 0.000000 3.310760 H 3.690859 0.903215 2.876592 H 3.145268 1.094449 0.829914 -C -0.903816 0.000000 2.400507 +C -0.803816 0.000000 2.400507 C -3.177037 0.000000 2.550514 C -2.813944 0.000000 1.201250 N -1.427688 0.000000 1.117375 From 803d7d1f53fd6760672b62456eb1b2c58fe47b07 Mon Sep 17 00:00:00 2001 From: "Steven E. Wheeler" Date: Thu, 23 Aug 2018 08:09:53 -0500 Subject: [PATCH 08/15] Cleaning up printing --- FileReader.pm | 4 +++- JobControl.pm | 2 +- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/FileReader.pm b/FileReader.pm index 293660e..fa0c7f7 100644 --- a/FileReader.pm +++ b/FileReader.pm @@ -86,7 +86,9 @@ sub grab_coords { $constraints = [@constraints]; } if ($_ =~ /\s+L:(\S+)/ || ($_ =~ /^L:(\S+)/)) { #Ligand atoms (L:14-26) - my @temp = map { $_ - 1 } split(/-/, $1); + my $temp = $1; + $temp =~ s/;$//g; #strip off trailing semicolon + my @temp = map { $_ - 1 } split(/-/, $temp); $ligand = [$temp[0]..$temp[1]]; } if ($_ =~ /\s+C:(\S+)/ || ($_ =~ /^C:(\S+)/)) { #Reaction Center (C:13) diff --git a/JobControl.pm b/JobControl.pm index 652e012..385acb4 100644 --- a/JobControl.pm +++ b/JobControl.pm @@ -131,7 +131,7 @@ sub submit_job { if ($job_found) { - print "Submitting $jobfile\n"; + print " Submitting $jobfile\n"; open JOB, ">$jobfile" or die "cannot open $jobfile\n"; print JOB $job_content; close (JOB); From ee44d46120d205bcd1a424c8186aeb95cfd9d7f3 Mon Sep 17 00:00:00 2001 From: "Steven E. Wheeler" Date: Fri, 24 Aug 2018 09:12:53 -0500 Subject: [PATCH 09/15] Preparing for SGE --- JobControl.pm | 12 ++++++++++-- 1 file changed, 10 insertions(+), 2 deletions(-) diff --git a/JobControl.pm b/JobControl.pm index 385acb4..fd01c24 100644 --- a/JobControl.pm +++ b/JobControl.pm @@ -17,7 +17,7 @@ my $queue_type = $ENV{'QUEUE_TYPE'}; #Returns jobIDs of all jobs (queued or running) in current directory, returns 0 if no jobs in queue match current directory #This could be improved by searching for $Path more carefully! -#Works for PBS (default) or LSF +#Works for PBS, LSF, Slurm and soon SGE sub findJob { my $Path = $_[0]; chomp($Path); @@ -62,8 +62,11 @@ sub findJob { push(@jobIDs,$array[0]); } } + }elsif ($queue_type =~ /SGE/i) { + die "SGE not supported yet!"; } + if(@jobIDs) { return @jobIDs; } @@ -81,13 +84,15 @@ sub killJob { $rv = system("qdel $job"); }elsif ($queue_type =~ /Slurm/i) { $rv = system("scancel $job"); + }elsif ($queue_type =~ /SGE/i) { + die "SGE not supported yet!"; } sleep(3); return $rv; } -#Works for LSF or PBS (default) +#Works for LSF, PBS, Slurm, and soon SGE sub submit_job { my %params = @_; @@ -165,6 +170,9 @@ sub submit_job { $failed = 1; } } + } elsif($queue_type =~ /SGE/i) { + die "SGE not yet supported!"; + } chdir($current); } return $failed; From 38f029a8d0537e6b318d345bd9d6911929736804 Mon Sep 17 00:00:00 2001 From: ajs99778 Date: Fri, 24 Aug 2018 11:59:57 -0400 Subject: [PATCH 10/15] added SGE subroutines --- JobControl.pm | 26 ++++++++++++++++++++++---- 1 file changed, 22 insertions(+), 4 deletions(-) diff --git a/JobControl.pm b/JobControl.pm index fd01c24..0a81402 100644 --- a/JobControl.pm +++ b/JobControl.pm @@ -63,7 +63,23 @@ sub findJob { } } }elsif ($queue_type =~ /SGE/i) { - die "SGE not supported yet!"; + my $qstat1 = `qstat -s pr -u $ENV{USER}`; #get qstat output for this user's jobs that are running/pending + + my @jobs = ($qstat1 =~ m/^\s*?(\w+)/gm); #get the first column of qstat data, which contains job IDs + shift(@jobs); #the first line's first column is the header 'job-ID', so remove that + my $jlist = join(',', @jobs); #join these on commas so we can ask qstat for more info about them + my $qstat2 = `qstat -j $jlist`; #call qstat again, but this time get more info + + foreach my $job (@jobs) { + if ( $qstat2 =~ m/job_number:\s+?($job)[\D\d]+?sge_o_workdir:\s+(.*)/gm ) { #look for a job_number followed by a sge_o_workdir + if ($2 =~ /$Path/) { #if the string after sge_o_workdir is the same as PWD, this job is running in this directory + #this is split up into two if statements instead of looking for a job_number followed by sge_o_workdir:\s+$pwd because of reasons + #the main reason is that it would find a job ID, and then look all the way ahead to find sge_o_workdir:\s+$pwd even if there's another job_number in between + #I tried using (?!job_number), but that didn't stop it from looking too far ahead + push(@jobIDs, $job); + } + } + } } @@ -85,7 +101,7 @@ sub killJob { }elsif ($queue_type =~ /Slurm/i) { $rv = system("scancel $job"); }elsif ($queue_type =~ /SGE/i) { - die "SGE not supported yet!"; + $rv = system("qdel $job >&/dev/null"); } sleep(3); return $rv; @@ -169,9 +185,11 @@ sub submit_job { print {*STDERR} "Submission denied for $jobname.job!\n"; $failed = 1; } - } } elsif($queue_type =~ /SGE/i) { - die "SGE not yet supported!"; + if(system("qsub $jobname.job >& /dev/null")) { + print {*STDERR} "Submission denied for $jobname.job!\n"; + $failed = 1; + } } chdir($current); } From 53a7ecd31d65a21c2787723572ec77a691c86afd Mon Sep 17 00:00:00 2001 From: ajs99778 Date: Fri, 24 Aug 2018 12:34:11 -0400 Subject: [PATCH 11/15] fixed issue with finding jobs on SGE --- JobControl.pm | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/JobControl.pm b/JobControl.pm index 0a81402..26969f0 100644 --- a/JobControl.pm +++ b/JobControl.pm @@ -71,12 +71,13 @@ sub findJob { my $qstat2 = `qstat -j $jlist`; #call qstat again, but this time get more info foreach my $job (@jobs) { - if ( $qstat2 =~ m/job_number:\s+?($job)[\D\d]+?sge_o_workdir:\s+(.*)/gm ) { #look for a job_number followed by a sge_o_workdir - if ($2 =~ /$Path/) { #if the string after sge_o_workdir is the same as PWD, this job is running in this directory + if ( $qstat2 =~ m/job_number:\s+?(\d+)[\D\d]+?sge_o_workdir:\s+(.*)/gm ) { #look for a job_number followed by a sge_o_workdir + my $j = $1; + if ($2 =~ /$Path/) { #if the string after sge_o_workdir is the same as PWD, this job is running in this directory #this is split up into two if statements instead of looking for a job_number followed by sge_o_workdir:\s+$pwd because of reasons #the main reason is that it would find a job ID, and then look all the way ahead to find sge_o_workdir:\s+$pwd even if there's another job_number in between #I tried using (?!job_number), but that didn't stop it from looking too far ahead - push(@jobIDs, $job); + push(@jobIDs, $j); } } } From 1e3da6b7155119681187b2238e2dfbbe9912c8fc Mon Sep 17 00:00:00 2001 From: ajs99778 Date: Fri, 24 Aug 2018 12:39:31 -0400 Subject: [PATCH 12/15] fixed issue with finding jobs on SGE --- JobControl.pm | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/JobControl.pm b/JobControl.pm index 26969f0..e2d5a96 100644 --- a/JobControl.pm +++ b/JobControl.pm @@ -73,7 +73,7 @@ sub findJob { foreach my $job (@jobs) { if ( $qstat2 =~ m/job_number:\s+?(\d+)[\D\d]+?sge_o_workdir:\s+(.*)/gm ) { #look for a job_number followed by a sge_o_workdir my $j = $1; - if ($2 =~ /$Path/) { #if the string after sge_o_workdir is the same as PWD, this job is running in this directory + if ($2 =~ /$Path$/) { #if the string after sge_o_workdir is the same as PWD, this job is running in this directory #this is split up into two if statements instead of looking for a job_number followed by sge_o_workdir:\s+$pwd because of reasons #the main reason is that it would find a job ID, and then look all the way ahead to find sge_o_workdir:\s+$pwd even if there's another job_number in between #I tried using (?!job_number), but that didn't stop it from looking too far ahead From 44f6f59d8aa95012e2a3dcf46e13051832d18b91 Mon Sep 17 00:00:00 2001 From: ajs99778 Date: Sat, 25 Aug 2018 11:30:37 -0400 Subject: [PATCH 13/15] made SGE findjob better --- JobControl.pm | 25 +++++++++++++------------ 1 file changed, 13 insertions(+), 12 deletions(-) diff --git a/JobControl.pm b/JobControl.pm index e2d5a96..281e700 100644 --- a/JobControl.pm +++ b/JobControl.pm @@ -64,23 +64,24 @@ sub findJob { } }elsif ($queue_type =~ /SGE/i) { my $qstat1 = `qstat -s pr -u $ENV{USER}`; #get qstat output for this user's jobs that are running/pending - my @jobs = ($qstat1 =~ m/^\s*?(\w+)/gm); #get the first column of qstat data, which contains job IDs - shift(@jobs); #the first line's first column is the header 'job-ID', so remove that + shift(@jobs); #the first line's first column is the header 'job-ID', so remove that my $jlist = join(',', @jobs); #join these on commas so we can ask qstat for more info about them + my $qstat2 = `qstat -j $jlist`; #call qstat again, but this time get more info + my @lines = split(/\n/, $qstat2); #split each line into an array + my $job; - foreach my $job (@jobs) { - if ( $qstat2 =~ m/job_number:\s+?(\d+)[\D\d]+?sge_o_workdir:\s+(.*)/gm ) { #look for a job_number followed by a sge_o_workdir - my $j = $1; - if ($2 =~ /$Path$/) { #if the string after sge_o_workdir is the same as PWD, this job is running in this directory - #this is split up into two if statements instead of looking for a job_number followed by sge_o_workdir:\s+$pwd because of reasons - #the main reason is that it would find a job ID, and then look all the way ahead to find sge_o_workdir:\s+$pwd even if there's another job_number in between - #I tried using (?!job_number), but that didn't stop it from looking too far ahead - push(@jobIDs, $j); - } + foreach my $i (0..$#lines) { + #it looks like job_number is always before the corresponding sge_o_workdir + if( $lines[$i] =~ m/job_number:\s+(\d+)/ ) { + $job = $1; + } + if( $lines[$i] =~ m/sge_o_workdir:\s+[\S]+$Path$/ ) { + #this will return all your jobs if you run it in your home directory because $Path is '' + push(@jobIDs, $job); } - } + } } From 75925f452d9812fc26ec738b699d0af5f92eebd5 Mon Sep 17 00:00:00 2001 From: "Steven E. Wheeler" Date: Mon, 27 Aug 2018 08:22:52 -0400 Subject: [PATCH 14/15] Update README.md --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index f86b1db..ff0f34c 100644 --- a/README.md +++ b/README.md @@ -3,4 +3,4 @@ AaronTools provides a collection of tools for automating routine tasks encounter These tools can be used either directly within a Perl script using AaronTools objects, or via a series of command-line scripts. -Documentation (still in progress!) is available here. +Documentation is available here. From 71e2fd19276ff69091acf60e9ee61c05a7fe509e Mon Sep 17 00:00:00 2001 From: "Steven E. Wheeler" Date: Mon, 27 Aug 2018 09:44:52 -0400 Subject: [PATCH 15/15] Update README.md --- README.md | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index ff0f34c..47d88ae 100644 --- a/README.md +++ b/README.md @@ -3,4 +3,6 @@ AaronTools provides a collection of tools for automating routine tasks encounter These tools can be used either directly within a Perl script using AaronTools objects, or via a series of command-line scripts. -Documentation is available here. +Documentation on installing and using AaronTools is available here. + +If you have any questions, feel free to contact us at catalysttrends@uga.edu