Babel issue, pull request #58
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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
.pdb may contain additional lines irrelevant to the Kabsch test than previously considered, especially if written with openbabel [1] from file formats with a connection table (e.g., .mol, .mol2, .sdf). Considered here are 'CONECT' and 'MASTER' in a reformulated conditional. They appear earlier than the already considered 'TER' and 'END' which is why the conditional is not in alphabetic order. [1] www.openbabel.org
Additional test data in the .pdb format passing successfully a Kabsch test (while --reorder instruction engaged). Derived from the corresponding .cif entries in the CCDC database; BZAMID00*.pdb corresponding to entry BZAMID, BZAMID01*.pdb corresponding to entry BZAMID01 [1]. Re-exported either with Olex2 [2], or with openbabel [3] to yield the corresponding .pdb [1] https://www.ccdc.cam.ac.uk/structures/ [2] https://www.olexsys.org/ [3] http://openbabel.org/wiki/Main_Page
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Comment to ease code-scrutiny: The suggested code starts from the current master |
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RMSD needs to a standardized PDB reader since PDB is col based. There are probably other PDB readers out there that can be used with the rmsd package. You added files for testing but they are not included in the tests. For those reasons, I will not merge this pull request. |
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There was the need to pass a small batche of structural related model data,
initially described in crystallographic models as a
.ciftocalculate_rmsd.py.There are other tools around with similar functionality (e.g., CCDC's full-version
of Mercury) but it is possible to convert these
.cifby the already popularopenbabelinto.pdbto amend them, eventually successfully, to the handyscript, too.
Since
openbabel's conversions may include lines headed byHETATOM, thevaluable suggestion by @nabraham47 deposit in issue #56 naturally was taken
into consideration, and implemented. The manual, pairwise scrutin with test
data equally deposit passes smoothly for either of the two types of
.pdbwrittencalling for the default Kabsch test with engaged
--reorderinstruction to yield thesame numerical result.