.pdb coordinate reader can be improved #56
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Hi @nabraham47 , I am very rarely a .pdb format user but there seems to be one or more issues with the PDB reader. (like #57 ) If you open up a pullrequest with the changes I will accept the changes. |
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As by [1] as by experience writing .pdb with openbabel [2], lines about atom coordinates may start by either 'ATOM', or 'HETATOM' as keyword. The addition of the later widens the scope of calculate_rmsd.py, an additional condition to work well with e.g. openbabel-written .pdb. The idea however was deposit earlier by 'nabraham47' as issue charnley#56 (2019-May-30) to the general attention. [1] http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM [2] www.openbabel.org
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Hi @nabraham47 , your very valuable suggestion contributed to widen the potential scope of the script, |
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The get_coordinates_pdb function in calculate_rmsd.py would benefit from the inclusion of 'HETATM' when reading in coordinates and atoms.
rmsd/rmsd/calculate_rmsd.py
Line 688 in cd8af49
I was able to change line 688 to:
if line.startswith("ATOM") or line.startswith("HETATM"):This allowed the program to also read in .pdb's formatted with HETATM
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