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Large pdb files lead to seg fault #6
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Some valgrind output indicating a stack overflow in Command:
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Wonder if I could set recursion depth limit? Then if the program doesn't find the path just have a marker that says it's greater than x number of bonds away. This avoids a rewrite for an iterative solution or a complicated data structure to calculate a number whose value doesn't ultimately matter. |
Or, just turn off calculating the
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Have officially confirmed that the seg fault is from recursion depth from counting covalent bonds between pairs of atoms. Instead of taking a short cut, I will implement an iterative solution. It could take the following form:
The iterative list search will probably be backtracking in style but some details will have to be ironed out. |
Seg fault, with no log outputs, is the result when using
-i examples/Villin-Headpiece/villin-unfolded-conect.pdb
as an input file. Can be a memory leak or need to test on system with more system memory.The text was updated successfully, but these errors were encountered: