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アメリカやヨーロッパなど6つの国は、イランが核兵器をつくろうとしているのではないかと考えて、経済制裁(=貿易などを禁止すること)を続けていました。

America and Europe etc plus 6 countries (this is the topic)
Iran is trying to make nuclear weapons
Since it is not prohibited economic sanctions (the thing that prohibits international trade) are continuing.

I get the basic gist but I don't really understand lots of the grammar.

Especially:

  • What is it really saying about America? It seems the topic of individual clauses changes lots
  • I understand the つくろうとしている。But not the のではないかとかんがえて。 Does it mean since it is not prohibited? I don't understand how the grammar works here. ~ので? ~かと?

Cheers

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To break down:

  • The main topic remains the same throughout the sentence: アメリカやヨーロッパなど6つの国 (lit. "six countries including America and Europe"). As I said elsewhere, this phrase seems a bit odd, but I think the author wanted to say "America and five European countries".
  • And those 6つの国 serves as the subject of the following two verbs: 考えて and 続けていました。 So the basic structure of the sentence is 「6つの国は、~と考えて、~を続けてきました。」("The six countries thought [something], and have continued [something]").
  • ~と考える is "think ~", and と here is the quotative particle. イランが核兵器をつくろうとしているのではないか is what と refers to, so this is what the six countries thought. I think you failed to catch this part.
  • In 「イランが核兵器をつくろうとしているのではないか」,
    • You're understanding of イランが核兵器をつくろうとしている is perfect.
    • ~のではないか is a very common pattern you should be familiar with, and is asked and answered here: ではないか Grammar translation
      Basically it's "Isn't it that ~?", "I wonder ~", or "[I'm/they're/etc] afraid that ~". Lots of examples here.
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(My Japanese and my linguistics are both pretty rusty, so grammar geeks may want to correct some of the details in comments.)

The sentence is simpler than it looks. A literal translation (often a good step on the way toward an idiomatic one) would be something like:

As for the six countries such as America and Europe, thinking “might not Iran be trying to make a nuclear weapon?”, they were continuing the sanctions (i.e., the prohibition on trading and such).

Breaking it down:

アメリカやヨーロッパなど6つの国は、

  • 「AやBなど」is a construction meaning “A, B, and so on” or “such as A and B”.
  • 「6つの国」is “six countries” or “the six countries”. (Personally I would have stuck another の in there to join the two noun phrases,「アメリカやヨーロッパなどの6つの国」, but I'm not a native speaker.)
  • 「は」(“As for…” in the heavy-handed literal translation) is the topic marker, as of course you know.

イランが核兵器をつくろうとしているのではないかと考えて

  • 「イランが核兵器をつくる」would be “Iran makes nuclear weapons” or “Iran makes a nuclear weapon.” 「つくろうとする」would be “tries to make”, so「つくろうとしている」gives us “is trying to make.”
  • 「の」here turns the preceding clause this into a noun phrase (similar to こと, see below), which we could render in English as “Iran's attempt to make a nuclear weapon”, but in context it's closer to “that Iran is trying to make a nuclear weapon”, or even “the fact that Iran is trying to make a nuclear weapon”. I say “fact,” but—
  • —the「ではないか」casts doubt on that (it's equivalent to「じゃないか?」). “Might it not be the case that Iran is trying to make a nuclear weapon?”
  • The「と」here is the quotative「と」(you can tell because it's followed by「考える」, just as if it were「思う」or, what you're most likely to encounter first when studying Japanese,「言う」), indicating that the whole preceding phrase about Iran is what the six countries are thinking. (Thus the heavy-handed quotation marks in my literal translation.)
  • The verb「考える」is in what's called the gerund form here, 「考えて」— “thinking”.

経済制裁を続けていました

  • I've translated 「続けていました」 literally as “they were continuing”, but as discussed in this answer the ~ている form indicates the continuation of a state as well as the continuation of an action. Just “continued the sanctions” is probably closer. (It's extra-confusing because we're dealing with the verb「続ける」, ‘continue’. “Continued to continue” would be over the top as a translation, but that sort of implication is probably in there. An English-language article would probably say something like “agreed—” or decided, or determined— “to leave the sanctions in place.”)

=貿易などを禁止すること

  • Backtracking: as before, ~など means “such as” or “etc.”「こと」(事) literally means “thing” or “fact”, but here it just acts to turn「禁止する」into a noun phrase—“the prohibition of”.

All that gives us:

The six nations—America, Europe, and so on—suspecting Iran might [still] be trying to make a nuclear weapon, continued the sanctions (i.e. prohibition of trade and such).

When in doubt, work backwards. 考えて, ~と考えて, ~か, ~ないか, ~ではないか… if you start from the verb you're much less likely to accidentally invent new particles like かと and ので.

I hope that helps!

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The sentence

アメリカやヨーロッパなど6つの国は、イランが核兵器をつくろうとしているのではないかと考えて、経済制裁(=貿易などを禁止すること)を続けていました。

translates to

"America and five European countries have wondered whether Iran has been planning on making atomic weapons and continued economic sanctions (such as cessation of trade)."

イランが核兵器をつくろうとしている means "Iran is trying to make atomic weapons".

The rest of the sentence consists of three parts

アメリカやヨーロッパなど6つの国は、~しているのではないかと考えて、~続けていました。

which is just "American and five European nations have wondered whether or not <something is happening>, and continued <to do something>."

のではないかと考えて means "wondering whether or not <something>". The の nominalizes the preceding verbal phrase; ではない is the typical way of negating something.

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    「アメリカやヨーロッパなど6つの国」 literally translates to "six countries such as / including America and Europe", although Europe is not the name of a country. I think it can be rephrased as "America and five European countries" or "six countries in America and Europe". – naruto Jan 20 '16 at 4:50
  • I understand what it means but I don't understand the grammar behind it is basically what I'm saying. Especially the bits I highlighted. Thanks for your replies. You guys have helped. If there is anyway you could explain the grammar better I would be grateful. – Gidday Jan 20 '16 at 5:00
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    "wondering whether or not" >>「~しているのではないかと考える」って「~してるのではないかと疑う」"suspect" のほうが近いのでは… – Chocolate Jan 20 '16 at 5:17
  • @choco Yeah, I thought of that but it seems to be a stretching the meaning of 考える a bit. – A.Ellett Jan 20 '16 at 5:18

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