Ensure all PDB-related Amber Topology sections are read and written#853
Merged
drroe merged 15 commits intoAmber-MD:masterfrom Oct 16, 2020
Merged
Ensure all PDB-related Amber Topology sections are read and written#853drroe merged 15 commits intoAmber-MD:masterfrom
drroe merged 15 commits intoAmber-MD:masterfrom
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…. This situation usually occurs when alternate sites are present (which is allowable), and there is no reason why a residue cannot be part of 2 molecules. The less cpptraj alters topology without user input the better.
…r to detect if the arrays are actually present or not, and hence whether they should be written to an output topology.
…. Add "AddX" routines for the extra arrays.
…ere, but makes it so that the flag isnt lost when reading/writing.
…r, occupancy, serial numbers
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The PGI build in Jenkins failed. |
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This pull request fixes 2 alerts when merging eaa1e74 into 9e5c2e3 - view on LGTM.com fixed alerts:
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This was referenced Oct 17, 2020
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Adds support for reading/writing the
ATOM_BFACTOR,ATOM_OCCUPANCY, andATOM_NUMBERflags from Amber Topology files. Under the hood, the arrays that store such variables which were previously in a combined "extra" array are now all separate to make it easier to know when a topology has e.g. B-factors. Adds a test underTest_Stripto make sure this info is properly handled.Also, now residues can now correspond to separate molecules - this can happen when e.g. alternate sites are present. Previously, residues in topologies were automatically renumbered when this happened - this is now controlled by the new
renumresidueskeyword to theparmcommand.