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Martin Kurečka
Plumed AlphaFold
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4ad59d7b
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4ad59d7b
authored
8 years ago
by
Giovanni Bussi
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Closes #213
[makedoc]
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developer-doc/AddingAMeasure.txt
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developer-doc/AddingAMeasure.txt
developer-doc/AddingAMultColvar.txt
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developer-doc/AddingAMeasure.txt
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@@ -99,7 +99,7 @@ It is useful to think carefully about how you can reuse other parts of the code
how PLMD::OptimalRMSD and PLMD::SimpleRMSD make extensive use of the PLMD::RMSD class. Similarly notice how the PLMD::OptimalRMSD,
PLMD::SimpleRMSD and PLMD::DRMSD classes are reused in PLMD::MultiDomainRMSD.
\section
d
ocs Adding documentation for your measure
\section
AddingAMeasureD
ocs Adding documentation for your measure
To test whether you have implemented you new measure correctly you should implement a small Action that calculates the
distance between the instantaneous positions of the atoms and some read in reference configuration. The methods
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developer-doc/AddingAMultColvar.txt
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@@ -39,7 +39,7 @@ through these classes and attempt to understand the code contained within them.
provides a rather prescriptive description as to how to implement a new multicolvar. I hope this helps but I am keenly
aware that any description is bound to be incomplete so if you have questions please do email the user list to ask.
\section
d
ocs Creating documentation
\section
AddingAMultColvarD
ocs Creating documentation
The first thing you will have to change is the documentation. As discussed on the \ref usingDoxygen page
of this manual the documentation is created using Doxygen. You are implementing a cv so your PLMEDOC line
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