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Miscellaneous improvements to 'makestructure', 'dssp', 'change', and 'bonds'; small DSSP fix. #811

Merged
merged 40 commits into from
Apr 22, 2020
Merged

Miscellaneous improvements to 'makestructure', 'dssp', 'change', and 'bonds'; small DSSP fix. #811

merged 40 commits into from
Apr 22, 2020

Commits on Apr 15, 2020

  1. Add charmm HIS residue names

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    drroe committed Apr 15, 2020
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  2. Add 'nointrares' keyword to 'bonds' command.

    @drroe
    drroe committed Apr 15, 2020
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  3. Start adding a remove bond function

    @drroe
    drroe committed Apr 15, 2020
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  4. Ensure erased bond indices are removed from atoms as well.

    @drroe
    drroe committed Apr 15, 2020
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Commits on Apr 16, 2020

  1. Add new formatted name routine

    @drroe
    drroe committed Apr 16, 2020
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  2. Add a removebonds command

    @drroe
    drroe committed Apr 16, 2020
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  3. Use a copy of the bonds array since it will be modified. Have RemoveB… 

    …ond return a status
    @drroe
    drroe committed Apr 16, 2020
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  4. Ensure molecule info is redetermined.

    @drroe
    drroe committed Apr 16, 2020
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  5. Fix print of command line to the log

    @drroe
    drroe committed Apr 16, 2020
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  6. Add outfile to removebonds

    @drroe
    drroe committed Apr 16, 2020
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  7. Add a command that can be used to create leap input for a given set o… 

    …f COORDS. Currently only looks for disulfides.
    @drroe
    drroe committed Apr 16, 2020
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  8. Change name of cys residues involved in disulfide bonds

    @drroe
    drroe committed Apr 16, 2020
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Commits on Apr 17, 2020

  1. Get rid of 'if' statement inside loop reading residue numbers

    @drroe
    drroe committed Apr 17, 2020
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  2. The last atom of residues is already being set after the atom is added.

    @drroe
    drroe committed Apr 17, 2020
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  3. Have atom/residue/molecule info print out the number or atoms/residue… 

    …s/molecules.
    @drroe
    drroe committed Apr 17, 2020
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Commits on Apr 18, 2020

  1. Add back the concept of "offset" when searching for dihedrals. In wei… 

    …rd structures or structures where bond information has been incorrectly assigned (e.g. some PDBs) the old code was sometimes finding dihedrals it shouldnt have.
    @drroe
    drroe committed Apr 18, 2020
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  2. Add option to print reference values to a file

    @drroe
    drroe committed Apr 18, 2020
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  3. Add founddihout option; makes for easier debugging

    @drroe
    drroe committed Apr 18, 2020
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Commits on Apr 19, 2020

  1. More info

    @drroe
    drroe committed Apr 19, 2020
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  2. Add crdset keyword to GetTopByIndex

    @drroe
    drroe committed Apr 19, 2020
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  3. Add the PSI-O dihedral

    @drroe
    drroe committed Apr 19, 2020
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Commits on Apr 20, 2020

  1. DRR - If an action was skipped, do not make it an error.

    @drroe
    drroe committed Apr 20, 2020
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  2. Allow multiple args for removedata

    @drroe
    drroe committed Apr 20, 2020
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  3. Go back to making a single skipped action an error for crdaction

    @drroe
    drroe committed Apr 20, 2020
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Commits on Apr 22, 2020

  1. Merge branch 'master' into debug

    @drroe
    drroe committed Apr 22, 2020
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  2. Improve DSSP help. Add "SG" atom name so that disulfides are not foll… 

    …owed when looking for previous/next residues.
    @drroe
    drroe committed Apr 22, 2020
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  3. Add namesg keyword.

    @drroe
    drroe committed Apr 22, 2020
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  4. DRR - Skip residues for which no atoms are selected.

    @drroe
    drroe committed Apr 22, 2020
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  5. DRR - Nonsense assignment no longer made.

    @drroe
    drroe committed Apr 22, 2020
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  6. DRR - Do not follow bonds to unselected atoms

    @drroe
    drroe committed Apr 22, 2020
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  7. Hide command for now

    @drroe
    drroe committed Apr 22, 2020
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  8. Remove the "psi-o" dihedral

    @drroe
    drroe committed Apr 22, 2020
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  9. Update makestructure

    @drroe
    drroe committed Apr 22, 2020
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  10. Add namesg keyword to manual

    @drroe
    drroe committed Apr 22, 2020
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  11. Note that residues with no selected atoms in dssp are now skipped.

    @drroe
    drroe committed Apr 22, 2020
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  12. Add change removebonds to manual

    @drroe
    drroe committed Apr 22, 2020
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  13. Add bonds nointrares to manual

    @drroe
    drroe committed Apr 22, 2020
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  14. Add change removebonds out keyword to manual

    @drroe
    drroe committed Apr 22, 2020
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  15. Version change for makestructure additional keywords, change removebo… 

    …nds, dssp namesg, bonds nointrares. Minor version bump since dssp now skips residues that have no selected atoms.
    @drroe
    drroe committed Apr 22, 2020
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  16. Fix up change removebonds help

    @drroe
    drroe committed Apr 22, 2020
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