I am going to post an answer that is maybe not helpful for the exact goals, but which will maybe help restate the problem to be easier. As commenters noted it is super big and complex, many whole careers have been devoted to solving very small parts of this problem.
Possible problems with premise
I think that this question starts from this statement as a premise:
DNA are blueprints that describes an organism
This premise is not correct. Or rather, it is a way of explaining what DNA is doing in very simple terms. I do not think that you will be able to simulate with any precision cell structure based on DNA sequence. But at the end of the answer I suggest some things that are a little more focused that I know you can do.
More specifically, DNA is not a blueprint because DNA does not have instructions for how to build a cell. DNA is more like instructions for how to maintain and repair a cell. A manual for a car may tell you how to keep your car in good working order and how to replace every piece of the car, but it does not tell you how to build a car.
A quick example: cells are enveloped in the plasma membrane, which has as its fundamental component a bunch of phospholipids. DNA has instructions for these steps:
- how to make new phospholipids
- how to insert phospholipids into an existing plasma membrane
DNA does not have instructions for this step:
- how to make a new plasma membrane de novo
DNA is always assuming the pre-existence of a cell. Cells won't work without DNA, but DNA is useless without an existing cell.
Some things you might be able to do
There are specific genes that are related to some cell compartments, like e.g. endoplasmic reticulum (ER). Eukaryotic cells have ER and prokaryotic cells do not. If you see genes for ER, you can guess that your cell should have ER. You would need to infer the presence of such genes, but there are existing tools that do this gene prediction from DNA sequence, e.g. https://en.wikipedia.org/wiki/List_of_gene_prediction_software
For your bacteriophage example, it seems like you are interested in macromolecular structure of a phage particle. (Note, bacteriophage are not cells). There do exist a lot of programs for predicting protein structures from protein sequence. You can often infer protein sequence from the DNA sequences of genes. Proteins are important building blocks of cells, and there is a lot of work on figuring out their structure (field is called "structural biology", loosely). I would recommend looking at some of the existing software in this field, e.g. https://www.rosettacommons.org/software.
I would recommend looking into existing cell simulators, which exist. For example: https://en.wikipedia.org/wiki/Virtual_Cell, https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1005991. I am sure there are more that you will be able to find.
Hope that helps.
I realized afterwards that when I say that that DNA doesn't tell you how to make a cell that could be considered confusing, because cells divide to make more cells. However, The process of cell division is not making a new cell "de novo" (out of nothing)- rather it's taking an existing cell and reforming it into 2 cells.
In other words DNA does this:
1 cell --> 2 cells
But DNA does not do this:
materials of a cell --> a functional cell