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> 後には、その **基準を流れ** のあるものととらえ、一緒に進む一続きの行動を表す文が来る。(part of explanation for
> ～に沿って)
>
> 俺の **とまどいを不安の表れ** と思ったのか、そんなふうに声をかけて、彼女は教室を出て行った。

I've treated the を in these sentences as の. How is を used here, and what is
the best way to interpret it? I assume it has something to do with the
と-perception verb following it, but it doesn't line up for me.
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particle-を parsing
"nounをnoun(verb stem)" expressions: ie 基準を流れ, 戸惑いを表れ etc
I think you need to look at parsing the sentences in a different way, since
you are cutting off the scope of your analysis too soon. I think the real
pattern here is "N を N と V", where V is a verb of perception. Both of these
sentences use that pattern to express perceiving one thing as another thing.

...

For the first sentence, I would split it up as follows:

> ［その基準］を
>
> ［流れのあるもの］と
>
> とらえ

The verb とらえる means something like "to perceive". What is being perceived is
"その基準", and what it is being perceived as is "流れのあるもの".

...

For the second sentence, I would split it up as follows:

> ［俺のとまどい］を
>
> ［不安の表れ］と
>
> 思った

The verb 思う means "to think". What is being thought about is "俺のとまどい", and
what it is being thought as is "不安の表れ".
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とらえる is a verb that requires を to indicate the direct object  
Example: 魚をとらえる (to catch a fish)  
[https://dictionary.goo.ne.jp/jn/160699/meaning/m0u/捕える/](https://dictionary.goo.ne.jp/jn/160699/meaning/m0u/%E6%8D%95%E3%81%88%E3%82%8B/)

One of the meanings of とらえる is "to understand", "to interpret":  
物事の本質・内容などを理解して自分のものとする。把握する。

と is particle that can be translated as "as".

So the translation becomes:  
その基準を(this standard)  
流れのあるものと(something with a flow)  
とらえる(understand)

その基準を流れのあるものととらえる  
To understand this standard as something with a flow.
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answer