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This makes volumes to pseudoatoms write a proper pdb file that other programs such as prody and the rest of xmipp can read.

For example, xmipp_reduce_pseudoatoms makes a mess with the current files because of having the first digit of the residue number being in the chain field as the zeros in between then get removed. With the fix applied to the input file, the test actually gives a more sensible result.

(float)(atoms[n].location(1)*sampling),
(float)(atoms[n].location(0)*sampling),
(float)intensity);
if (n+1 < 10000)
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Why? You can print both with %5d and it will be justified to right with no leading zeros.
If you need justification to right, you can use %-5d

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ok. I'll try that

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oh, right. The reason is I wanted to use the 5th column only if I need it. Probably, that's unnecessary complexity though.

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I don't understand.
The formatting needs to follow the standard, what does the standard say about the length?

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SonarCloud Quality Gate failed.    Quality Gate failed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell B 2 Code Smells

No Coverage information No Coverage information
95.8% 95.8% Duplication

@albertmena albertmena changed the title Jmk pseudoatoms Pseudoatoms Nov 14, 2022
@jamesmkrieger jamesmkrieger marked this pull request as draft November 15, 2022 09:16
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SonarCloud Quality Gate failed.    Quality Gate failed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
95.8% 95.8% Duplication

idea Catch issues before they fail your Quality Gate with our IDE extension sonarlint SonarLint

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4 participants