Haha, are you studying Turkish literature or something?
"gece yarısı şehre sessizce gelip giden trenler gibi gönlüme sessizce gelip geçtin..."
For starters, I´d say this sentence is wrong. It should be "gönlümden". FROM my heart. Not TO my heart. Because "geçmek", "going away" is not something you do to something. You go away from something. I guess "gönlüme" is written with a TO because of the "gelip" part. Because you come TO a place. But see, there is a discrepancy between how you´d choose the suffix for "gönül". This is and example of what we call "anlatım bozukluğu". "gelip", here, is like an adjective for "geçmek", so the object ("gönül") should behave according to "geçmek".
Having said that, I don´t think I could give a good translation. This is artsy stuff, you know...
The best I could do is,
"Just as quiet as those trains at midnight, silently passing by; only briefly, were you in my heart."
