samuelflores / mmb Goto Github PK
View Code? Open in Web Editor NEWMMB (MacroMolecule Builder)
License: Other
MMB (MacroMolecule Builder)
License: Other
MMB v4.0.0 built successfully with Gemmi v0.5.7, but due to changes in v0.5.8 it does no longer build:
src/CifOutput.cpp: In function 'void SimTK::CIFOut::reWriteOutCif(const gemmi::Model&, const std::string&, const std::string&, ParameterReader&, const SimTK::CompoundSystem&, bool)':
src/CifOutput.cpp:113:81: error: cannot bind rvalue reference of type 'gemmi::cif::Document&&' to lvalue of type 'gemmi::cif::Document'
113 | gemmi::Structure myTrajectoryOutputFile = gemmi::make_structure ( doc );
This is not very serious, but at some point I would like to upgrade Gemmi to v0.5.8 in Debian.
Gemmi no longer contains gemmi::GridSetup
, causing failures to build MMB from source. Next Debian/Ubuntu releases will have Gemmi 0.5.3 or later, thus I would suggest adapting MMB to the change in Gemmi's API.
The repository contains three different variants of parameters.csv
:
First two are nearly identical:
$ diff examples/parameters.csv include/resources/parameters.csv
98c98
< ,RECORD,DG ,DA ,WatsonCrick,Hoogsteen,Cis,N9,C4,C8,,N9,C4,C8,,0,,,,-3,,,,5,-0.722461,-0.531117,0.0419362,1.69488,-0.0662644,-0.136665,-0.988399,baseInteraction,1.11,,
---
> ,RECORD,DG ,DA ,WatsonCrick,Hoogsteen,Cis,N9,C4,C8,,N9,C4,C8,,0,,,,-3,,,,5,-0.354536,0.885708,0.126182,1.57101,-0.00846233,-0.186297,0.982457 ,baseInteraction,1.16,,
100c100
< ,RECORD,DA ,DG ,WatsonCrick,Hoogsteen,Cis,N9,C4,C8,,N9,C4,C8,,0,,,,-3,,,,5,-0.459764,0.728308,0.0665503,1.46754,0.0669876,-0.24912,0.966153,baseInteraction,1.05,,
---
> ,RECORD,DA ,DG ,WatsonCrick,Hoogsteen,Cis,N9,C4,C8,,N9,C4,C8,,0,,,,-3,,,,5,-0.354536,0.885708,0.126182,1.57101,-0.00846233,-0.186297,0.982457 ,baseInteraction,1.16,,
Third one is 100 times smaller in size than the first two.
I wonder why they are different, and which of them should be used by default?
It seems that v3.4 has been released, but there are no git tags past v3.2. Could you please push the missing tags?
I am building MMB v3.5 on Debian unstable. Lepton headers are not found unless I patch CMakeLists.txt
:
--- a/CMakeLists.txt
+++ b/CMakeLists.txt
@@ -45,7 +45,7 @@
SET(OpenMM_INSTALL_DIR "" CACHE PATH
"OpenMM install directory. Used to find libs.")
#Add the OpenMM library
-SET(Lepton_INCLUDE_DIR "/3rdparty/Lepton1.3/include/" CACHE PATH
+SET(Lepton_INCLUDE_DIR "3rdparty/Lepton1.3/include/" CACHE PATH
"Where to find Lepton includes")
#Add the Gemmi library path
SET(GEMMI_INCLUDE_DIR "" CACHE PATH
Seemingly, /
is understood as filesystem root on Debian (all Linux?) systems. It may also be true that the problem is related to newer CMake version (v3.22.0 in Debian unstable right now). Could you please check whether the patch works in your builds as well?
A declarative, efficient, and flexible JavaScript library for building user interfaces.
๐ Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. ๐๐๐
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google โค๏ธ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.