samuelflores / mmb Goto Github PK

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:

• examples/parameters.csv
• include/resources/parameters.csv
• share/MMB_UI/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?