vermouth-martinize
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marrink-lab
Describe and apply transformation on molecular structures and topologies
``` WARNING - unknown-residue - Can't add bonds based on atom names for residue D-HYP13 because 'Residue HYP is not known to force field universal'. Falling back to distance criteria....
Can be done when reading the input PDB by comparing to SEQRES when it exists.
Edit: The issue is about insertion codes, not alternate location. Some PDB specify alternate conformation by specifying one conformation without the alternate indicator and the following ones with the indicator....
Let's say you have a system consisting of a polymer, a protein, and some DNA and RNA. Mix in some lipids for good measure. Generating the "basic" topology for this...
Currently repair graph will override *any* node attributes of the incoming residue with node attributes from the reference block. In #340 this changes to everything except `resid`. This causes different...
The atom names we write are fully left aligned while they should actually be split into 2 parts with the 2 first characters being the element and being right-aligned and...
Citations are prefixed by ` INFO - general - Please cite`, emitting them with a specific logging type would make them easier to filter.
The edge directive in links makes nodes, as it adds edges. However, the atoms are not treated as link atoms in the other interaction directives are. Thus this leads frequently...
The citation parser can only handle limited BibTex format. Particularly all latex type macros are not supported and also it requires separation of field values by {} not "".
If a molecule is encountered that does not have a backbone, this line fails: https://github.com/marrink-lab/vermouth-martinize/blob/b0f49b5aeac0b5d50b3978afb72a0367c93d9fc8/vermouth/processors/apply_rubber_band.py#L304 There should be a return statement, if no coordinates are found.
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Describe and apply transformation on molecular structures and topologies