Question

我在VMD（Visual Molecular Dynamics）中使用tk控制台运行代码。我遇到的第一个问题是代码占用了太多的计算机处理能力并导致VMD关闭。我想这是因为我把它打印到文件中。我真的只需要查看距离小于20的结果。下面是导致VMD关闭的原始代码：

set seg1 [atomselect top "segname LA0 and name CA"]
set seg2 [atomselect top "segname RA0 and name CA"]

set file [open "Contact_map27.dat" w]

set list1 [$seg1 get index]
set list2 [$seg2 get index]

foreach atom1 $list1 {
    foreach atom2 $list2 {
            set index1 [atomselect top "index $atom1"]
            set index2 [atomselect top "index $atom2"]
            set resid1 [[atomselect top "index $atom1"] get resid]
            set resid2 [[atomselect top "index $atom2"] get resid]
            set resnm1 [[atomselect top "index $atom1"] get resname]
            set resnm2 [[atomselect top "index $atom2"] get resname]
 puts $file "$resnm1 $resid1 $resnm2 $resid2 [veclength [vecsub [measure center $index1] [measure center $index2]]]"
            $index1 delete
            $index2 delete
    }
}

close $file

以下是我所做的修改，只应在距离小于20时打印值：

set seg1 [atomselect top "segname LA0 and name CA"]
set seg2 [atomselect top "segname RA0 and name CA"]

set file [open "Contact_map27.dat" w]

set list1 [$seg1 get index]
set list2 [$seg2 get index]

foreach atom1 $list1 {
    foreach atom2 $list2 {
            set index1 [atomselect top "index $atom1"]
            set index2 [atomselect top "index $atom2"]
            set resid1 [[atomselect top "index $atom1"] get resid]
            set resid2 [[atomselect top "index $atom2"] get resid]
            set resnm1 [[atomselect top "index $atom1"] get resname]
            set resnm2 [[atomselect top "index $atom2"] get resname]
    set dist [[veclength [vecsub [measure center $index1] [measure center $index2]]]]
 if {$dist < 20} {
puts $file "$resnm1 $resid1 $resnm2 $resid2 $dist"}
else {puts $file " "}
            $index1 delete
            $index2 delete
    }
}

close $file

我运行第二个代码时收到的错误消息是＆＃34;无效的命令名称＆＃34; 26.774817104116487＆＃34;＆＃34;

如果有人能给我第二双眼睛让我知道发生了什么，我会非常感激！提前谢谢！

Answer 1

你对veclength的调用有一组额外的括号。

您可以通过将一些代码移出内部循环并进入外部循环来减少CPU使用量。仅依赖于atom1的调用不需要在内部循环中。

您还可以使用您设置的索引变量来减少CPU的数量。不使用变量，重复'atomselect'调用。我假设它每次都返回相同的索引。

set seg1 [atomselect top "segname LA0 and name CA"]
set seg2 [atomselect top "segname RA0 and name CA"]

set file [open "Contact_map27.dat" w]

set list1 [$seg1 get index]
set list2 [$seg2 get index]

foreach atom1 $list1 {
    set index1 [atomselect top "index $atom1"]
    set resid1 [$index1 get resid]
    set resnm1 [$index1 get resname]
    foreach atom2 $list2 {
            set index2 [atomselect top "index $atom2"]
            set resid2 [$index2 get resid]
            set resnm2 [$index2 get resname]
    set dist [veclength [vecsub [measure center $index1] [measure center $index2]]]
 if {$dist < 20} {
puts $file "$resnm1 $resid1 $resnm2 $resid2 $dist"}
else {puts $file " "}
            $index2 delete
    }
    $index1 delete
}

close $file

高CPU使用率，关机和“命令名称无效”26.774817104116487“”？

1 个答案: