Merge branch 'master' of https://github.com/QChASM/AaronTools

Catalysis.pm

@@ -52,7 +52,6 @@ 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
@@ -1498,18 +1497,18 @@ 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);
 }
 
 
@@ -1782,15 +1781,19 @@ 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) {

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)

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 +62,29 @@ sub findJob {
                 push(@jobIDs,$array[0]);
             }
         }
+    }elsif ($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
+        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 $i (0..$#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);
+            }
+        }
     }
 
+
     if(@jobIDs) {
     	return @jobIDs;
     }
@@ -81,13 +102,15 @@ sub killJob {
         $rv = system("qdel $job");
     }elsif ($queue_type =~ /Slurm/i) {
         $rv = system("scancel $job");
+    }elsif ($queue_type =~ /SGE/i) {
+        $rv = system("qdel $job >&/dev/null");
    }
    sleep(3);
    return $rv;
 }
 
 
-#Works for LSF or PBS (default)
+#Works for LSF, PBS, Slurm, and soon SGE
 sub submit_job {
     my %params = @_;
 
@@ -131,7 +154,7 @@ 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);
@@ -164,6 +187,11 @@ sub submit_job {
 		print {*STDERR} "Submission denied for $jobname.job!\n";
                 $failed = 1;
             }
+        } elsif($queue_type =~ /SGE/i) {
+            if(system("qsub $jobname.job >& /dev/null")) {
+		print {*STDERR} "Submission denied for $jobname.job!\n";
+                $failed = 1;
+        	}
         }
         chdir($current);
     }

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

Ligands/NBD.xyz

@@ -0,0 +1,17 @@
+15
+ 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

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

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

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
+

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
+

Ligands/achiral_ligands

@@ -1,39 +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)
-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)
+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

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)

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 (still in progress!) is <a href="https://github.com/QChASM/AaronTools/wiki">available here.</a>
+Documentation on installing and using AaronTools is <a href="https://github.com/QChASM/AaronTools/wiki">available here.</a>
+
+If you have any questions, feel free to contact us at [email protected]