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mubingnan银虫 (小有名气)
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[求助]
MS perl code 交联键的建立
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各位大神，我最近用MS模拟研究蛋白质上自由巯基形成二硫键交联键。如下是我的perl code。目前的问题 Type mismatch in CreateBond (function/property "CreateBond", parameter 1) at -e line 60 Can't call method "My" on an undefined value at -e line 64. 请问如何解决？ 大家有什么想法敬请发言。 #use strict; use Getopt::Long; use MaterialsScript qw(:all); my $doc = $Documents{"peptide.xsd"}; my $sets = $doc->UnitCell->Sets; foreach my $set (@$sets) { $set->Delete; } $doc->UnitCell->Atoms; my $atoms = $doc->UnitCell->Atoms; foreach my $atom (@$atoms){ if($atom->ElementSymbol eq "S"  {$atom->Name = "RS"; foreach my $atom1 (@{$atom->AttachedAtoms}){ if( $atom1->ElementSymbol eq "H" {$atom1->Name = "RH";}} } } my @reactive_S; my @reactive_H; foreach my $atom (@$atoms){ if ($atom -> Name eq "RS" {push (@reactive_S, $atoms);} elsif($atom->Name eq "RH" {push (@reactive_H, $atom);}} #my $reactive_S_set=$doc->CreateSet("reactive_S",\@reactive_S); #my $reactive_H_set=$doc->CreateSet("reactive_H",\@reactive_H); Tools->BondCalculation->ChangeSettings([ExclusionMode => 'Set']); Tools->BondCalculation->ChangeSettings(Settings( DistanceCriterionMode =>"Absolute", MinAbsoluteDistance => 0.0, MaxAbsoluteDistance => 3)); $doc->CalculateCloseContacts; my $CloseContacts = $doc->UnitCell ->CloseContacts; my @GoodCloseContacts; foreach my $CloseContact (@$CloseContacts){ my $Name1=$CloseContact->Atom1->Name; my $Name2=$CloseContact->Atom2->Name; my $Atom1=$CloseContact->Atom1; my $Atom2=$CloseContact->Atom2; if(($Name1 eq "RS" && ($Name2 eq "RS") {push(@GoodCloseContacts,[1,$Name1,$Name2,$Atom1->X, $Atom1->Y, $Atom1->Z, $Atom2->X, $Atom2->Y, $Atom2->Z, $CloseContact->Length,$CloseContact->Atom1,$CloseContact->Atom2]);}} if($Name1 eq "RS" {$S=$Atom1; foreach my $at1 (@{$Atom1->AttachedAtoms}){ if($at1->Name eq "RS" {$S=$at1;push(@reactive_S,$S);} else{ $H=$at1;}}} $doc->CreateBond($S, $S, "Single" ;push(@AtomsToDelete,$H); $CloseContacts->Delete; My$AtomsToDelete_Set=$doc->CreateSet("AtomsToDelete",\@AtomsToDelete); $AtomsToDelete_Set->Items->Delete; my @atomsToDelete; my $AtomsToDelete_Set=$doc->CreateSet("AtomsToDelete",\@AtomsToDelete); $AtomsToDelete_Set->Items->Delete; my $j=0; foreach my $b(@reactive_S){ $j=+2;} |
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2楼2021-10-28 09:21:48
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