#1246 - Doc for keyword *bonds* of PDBWriter is wrong - attempt at fix #1279
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jbarnoud
requested changes
Apr 3, 2017
| """Create a new PDBWriter | ||
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| Note | ||
| ____ |
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Should be dashes rather than underscores.
| *multiframe* | ||
| the value of :data:`MDAnalysis.core.flags` ['convert_lengths'] | ||
| bonds: :obj:, 'str', optional | ||
| If set to "conect", then write those bonds to the output file that were already defined in an input PDB file as PDB CONECT_ record. If set to "all", write all bonds (including guessed ones) to the file. ``None`` does not write any bonds. The default is "conect". |
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There is a large hole between "records." and "If".
| ``False``: write a single frame to the file; ``True``: create a | ||
| multi frame PDB file in which frames are written as MODEL_ ... ENDMDL_ | ||
| records. If ``None``, then the class default is chosen. [``None``] | ||
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| .. _CONECT: http://www.wwpdb.org/documentation/format32/sect10.html#CONECT |
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These lines link the occurrences of "_CONECT", "_MODEL", and "_ENDMDL" to the appropriate URL. They should not be removed.
| @@ -1000,6 +998,23 @@ def CONECT(self, conect): | |||
| self.pdbfile.write(self.fmt['CONECT'].format(conect)) | |||
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| class PrimitivePDBReader(PDBReader): | |||
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This class and the next one were removed in a previous commit. They should not be reintroduced. Please rebase your branch against the develop branch so it is up to date.
| @@ -206,7 +206,7 @@ def _check_lengths_match(*arrays): | |||
| if not all( a.shape == ref for a in arrays): | |||
| raise ValueError("Input arrays must all be same shape" | |||
| "Got {0}".format([a.shape for a in arrays])) | |||
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Please remove the trailing spaces.
orbeckst
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May 1, 2017
- fixes #1246 - supercedes and closes PR #1279 by @Shtkddud123 - added @Shtkddud123 to AUTHORS - updated CHANGELOG
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orbeckst
pushed a commit
that referenced
this pull request
May 1, 2017
- fixes #1246 - supercedes and closes PR #1279 by @Shtkddud123 - added @Shtkddud123 to AUTHORS - updated CHANGELOG
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I fixed up the PR and resubmitted as PR #1329 |
kain88-de
pushed a commit
that referenced
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May 2, 2017
- fixes #1246 - supercedes and closes PR #1279 by @Shtkddud123 - added @Shtkddud123 to AUTHORS - updated CHANGELOG
kain88-de
pushed a commit
that referenced
this pull request
May 2, 2017
- fixes #1246 - supercedes and closes PR #1279 by @Shtkddud123 - added @Shtkddud123 to AUTHORS - updated CHANGELOG
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Fixes #1246
Changes made in this Pull Request:
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