Getting backbone info

[cgoliver]

What would be the best way of recovering the full backbone connections and their direction (previously B53 and B35).

I tried for PDBID: 1F5U with the following arguments:

 python NA_pairwise_interactions.py -i ../../ 1f5u  -c basepair,backbone,covalent,sugar_ribose -o 1f5u 
Attempting to create output path 1f5u
Reading file ../../1f5u, which is number 1 out of 1
1F5U|1|A|A|9	1F5U|1|B|A|9	n0BPh	0.0000	0.0000	0.0000		=hyperlink("http://rna.bgsu.edu/rna3dhub/display3D/unitid/1F5U|1|A|A|9,1F5U|1|B|A|9")
Base-backbone calculation failed for 1F5U|1|A|G|2,1F5U|1|A|G|1
Base-backbone calculation failed for 1F5U|1|A|G|4,1F5U|1|A|G|1
Base-backbone calculation failed for 1F5U|1|A|U|3,1F5U|1|A|G|1
Base-backbone calculation failed for 1F5U|1|B|A|16,1F5U|1|B|G|1
Base-backbone calculation failed for 1F5U|1|B|C|15,1F5U|1|B|G|1
Base-backbone calculation failed for 1F5U|1|B|C|17,1F5U|1|B|G|1
Base-backbone calculation failed for 1F5U|1|B|G|4,1F5U|1|B|G|1
Base-backbone calculation failed for 1F5U|1|B|U|3,1F5U|1|B|G|1
Base-backbone calculation failed for 1F5U|1|B|C|18,1F5U|1|B|G|1
  Found 19 nucleotide-nucleotide interactions
  Recording interactions in 1f5u
Summary of time taken:
start                          :      0.001 seconds      0.000 minutes      0.810% of total
Reading CIF files              :      0.035 seconds      0.001 minutes     25.013% of total
Building cubes                 :      0.000 seconds      0.000 minutes      0.092% of total
Annotating interactions        :      0.000 seconds      0.000 minutes      0.040% of total
Check sugar ribose             :      0.003 seconds      0.000 minutes      1.940% of total
Check backbone interactions    :      0.060 seconds      0.001 minutes     43.129% of total
Check basepairing              :      0.038 seconds      0.001 minutes     27.691% of total
Calculate crossing             :      0.000 seconds      0.000 minutes      0.220% of total
Recording interactions         :      0.001 seconds      0.000 minutes      1.064% of total
Total                          :      0.138 seconds      0.002 minutes    100.000% of total
All files read successfully
Basepair annotations are not yet finalized

And the backbone file only has 3 annotations

❯ cat 1f5u/1f5u_backbone.txt 
1F5U|1|A|A|9	 n2BR	1F5U|1|B|C|13	0
1F5U|1|A|C|10	9BR	1F5U|1|A|G|8	0
1F5U|1|A|A|9	n0BPh	1F5U|1|B|A|9	0

It seems like covalent.txt would have the right info but the annotation of p_1 is new to me:

❯ cat 1f5u/1f5u_covalent.txt
1F5U|1|A|G|1	p_1	1F5U|1|A|G|2	None
1F5U|1|A|G|2	p_1	1F5U|1|A|U|3	None
1F5U|1|A|U|3	p_1	1F5U|1|A|G|4	None
1F5U|1|A|G|4	p_1	1F5U|1|A|G|5	None
1F5U|1|A|G|5	p_1	1F5U|1|A|G|6	None
1F5U|1|A|G|6	p_1	1F5U|1|A|A|7	None
1F5U|1|A|A|7	p_1	1F5U|1|A|G|8	None
1F5U|1|A|G|8	p_1	1F5U|1|A|A|9	None
1F5U|1|A|A|9	p_1	1F5U|1|A|C|10	None
1F5U|1|A|C|10	p_1	1F5U|1|A|G|11	None
1F5U|1|A|G|11	p_1	1F5U|1|A|U|12	None
1F5U|1|A|U|12	p_1	1F5U|1|A|C|13	None
1F5U|1|A|C|13	p_1	1F5U|1|A|C|14	None
1F5U|1|A|C|14	p_1	1F5U|1|A|C|15	None
1F5U|1|A|C|15	p_1	1F5U|1|A|A|16	None
1F5U|1|A|A|16	p_1	1F5U|1|A|C|17	None
1F5U|1|A|C|17	p_1	1F5U|1|A|C|18	None
1F5U|1|B|G|1	p_1	1F5U|1|B|G|2	None
1F5U|1|B|G|2	p_1	1F5U|1|B|U|3	None
1F5U|1|B|U|3	p_1	1F5U|1|B|G|4	None
1F5U|1|B|G|4	p_1	1F5U|1|B|G|5	None
1F5U|1|B|G|5	p_1	1F5U|1|B|G|6	None
1F5U|1|B|G|6	p_1	1F5U|1|B|A|7	None
1F5U|1|B|A|7	p_1	1F5U|1|B|G|8	None
1F5U|1|B|G|8	p_1	1F5U|1|B|A|9	None
1F5U|1|B|A|9	p_1	1F5U|1|B|C|10	None
1F5U|1|B|C|10	p_1	1F5U|1|B|G|11	None
1F5U|1|B|G|11	p_1	1F5U|1|B|U|12	None
1F5U|1|B|U|12	p_1	1F5U|1|B|C|13	None
1F5U|1|B|C|13	p_1	1F5U|1|B|C|14	None
1F5U|1|B|C|14	p_1	1F5U|1|B|C|15	None
1F5U|1|B|C|15	p_1	1F5U|1|B|A|16	None
1F5U|1|B|A|16	p_1	1F5U|1|B|C|17	None
1F5U|1|B|C|17	p_1	1F5U|1|B|C|18	None

Would covalent.txt contain the backbone connections? If so, can we assume that the annotations are in some kind of 5'->3' order?

Thanks!