helper_pdb2vol - PDB files to atom coord list and volume

版本 1.0.8 (3.0 KB) 作者: Carson Purnell
Generates a density volume from a PDB, and provides intermediate list of atom coordinates. Dramatically faster than pdbread.
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更新时间 2022/6/29

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This function was made to bypass the incredibly slow speed and significant limitations of matlab's pdbread function for the purpose of generating density maps of protein(s). It uses the most optimized text read functions available.
It is highly simplified and does not provide any pdb record information except a coordinate list from the atom records (not hetatm currently) and the element ID for those coordinates. The density map is output at a pixel resolution specified in angstroms, and stored in a cell array. For multi-model pdbs, each model is output separately into its own cell with the same bounding box, allowing the volumes to be easily summed or otherwise operated on.

引用格式

Carson Purnell (2024). helper_pdb2vol - PDB files to atom coord list and volume (https://www.mathworks.com/matlabcentral/fileexchange/113470-helper_pdb2vol-pdb-files-to-atom-coord-list-and-volume), MATLAB Central File Exchange. 检索来源 .

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创建方式 R2019b
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版本 已发布 发行说明
1.0.8

added a fix for when numbers in the PDB are not space-separated
1.0.6

further speed increases from improved vectorization and text/string parsing.
1.0.5

yet greater speed advantages from vectorized computations, memory optimizations, and faster read functions
1.0.2

cleaned up comments
1.0.0