From 991ece987d2798a09e66b945c4c30374127d0331 Mon Sep 17 00:00:00 2001
From: carlocamilloni <carlo.camilloni@gmail.com>
Date: Wed, 13 Dec 2017 10:21:16 +0100
Subject: [PATCH] ISDB: updated bibliography
---
src/isdb/CS2Backbone.cpp | 3 +--
src/isdb/EMMI.cpp | 1 +
src/isdb/FretEfficiency.cpp | 3 +++
src/isdb/Jcoupling.cpp | 17 +++++++----------
src/isdb/Metainference.cpp | 1 +
src/isdb/MetainferenceBase.cpp | 3 +--
src/isdb/MetainferenceBase.h | 2 ++
src/isdb/NOE.cpp | 3 ++-
src/isdb/PRE.cpp | 3 ++-
src/isdb/RDC.cpp | 6 +++---
src/isdb/Rescale.cpp | 3 +++
src/isdb/SAXS.cpp | 3 +--
src/isdb/Select.cpp | 2 ++
user-doc/bibliography.bib | 4 ++--
14 files changed, 31 insertions(+), 23 deletions(-)
diff --git a/src/isdb/CS2Backbone.cpp b/src/isdb/CS2Backbone.cpp
index 2970b6ff3..73d309c41 100644
--- a/src/isdb/CS2Backbone.cpp
+++ b/src/isdb/CS2Backbone.cpp
@@ -37,8 +37,6 @@
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
-#include "core/PlumedMain.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#include "tools/PDB.h"
#include "tools/Torsion.h"
@@ -658,6 +656,7 @@ CS2Backbone::CS2Backbone(const ActionOptions&ao):
<<plumed.cite("Kohlhoff K, Robustelli P, Cavalli A, Salvatella A, Vendruscolo M, J. Am. Chem. Soc. 131, 13894 (2009)");
if(camshift) log<<plumed.cite("Granata D, Camilloni C, Vendruscolo M, Laio A, Proc. Natl. Acad. Sci. USA 110, 6817 (2013)");
else log<<plumed.cite("Camilloni C, Robustelli P, De Simone A, Cavalli A, Vendruscolo M, J. Am. Chem. Soc. 134, 3968 (2012)");
+ log<<plumed.cite("Bonomi M, Camilloni C, Bioinformatics, 33, 3999 (2017)");
log<<"\n";
const string str_cs[] = {"ha_","hn_","nh_","ca_","cb_","co_"};
diff --git a/src/isdb/EMMI.cpp b/src/isdb/EMMI.cpp
index 313287ab1..5c49e5e9a 100644
--- a/src/isdb/EMMI.cpp
+++ b/src/isdb/EMMI.cpp
@@ -336,6 +336,7 @@ EMMI::EMMI(const ActionOptions&ao):
log<<" Bibliography "<<plumed.cite("Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)");
log<<plumed.cite("Hanot, Bonomi, Greenberg, Sali, Nilges, Vendruscolo, Pellarin, bioRxiv doi: 10.1101/113951 (2017)");
+ log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
log<<"\n";
}
diff --git a/src/isdb/FretEfficiency.cpp b/src/isdb/FretEfficiency.cpp
index 079ee9b7a..28dc4f676 100644
--- a/src/isdb/FretEfficiency.cpp
+++ b/src/isdb/FretEfficiency.cpp
@@ -21,6 +21,7 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "colvar/Colvar.h"
#include "colvar/ActionRegister.h"
+#include "core/PlumedMain.h"
#include "tools/Pbc.h"
#include <string>
@@ -118,6 +119,8 @@ FretEfficiency::FretEfficiency(const ActionOptions&ao):
if(pbc) log.printf(" using periodic boundary conditions\n");
else log.printf(" without periodic boundary conditions\n");
+
+ log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
addValueWithDerivatives();
setNotPeriodic();
diff --git a/src/isdb/Jcoupling.cpp b/src/isdb/Jcoupling.cpp
index bb0651e5f..c335a50ea 100644
--- a/src/isdb/Jcoupling.cpp
+++ b/src/isdb/Jcoupling.cpp
@@ -21,8 +21,6 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
-#include "core/PlumedMain.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#include "tools/Torsion.h"
@@ -212,6 +210,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
parse("SHIFT", kshift_);
}
+ log << " Bibliography ";
// Set Karplus parameters
switch (jtype_) {
@@ -221,8 +220,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
kc_ = -0.27;
kshift_ = pi / 3.0;
log.printf("J-coupling type is HAN, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
- log << " Bibliography "
- << plumed.cite("Wang A C, Bax A, J. Am. Chem. Soc. 117, 1810 (1995)") << "\n";
+ log << plumed.cite("Wang A C, Bax A, J. Am. Chem. Soc. 117, 1810 (1995)");
break;
case HAHN:
ka_ = 7.09;
@@ -230,8 +228,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
kc_ = 1.55;
kshift_ = -pi / 3.0;
log.printf("J-coupling type is HAHN, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
- log << " Bibliography "
- << plumed.cite("Hu J-S, Bax A, J. Am. Chem. Soc. 119, 6360 (1997)") << "\n";
+ log << plumed.cite("Hu J-S, Bax A, J. Am. Chem. Soc. 119, 6360 (1997)");
break;
case CCG:
ka_ = 2.31;
@@ -239,8 +236,7 @@ JCoupling::JCoupling(const ActionOptions&ao):
kc_ = 0.55;
kshift_ = (2.0 * pi) / 3.0;
log.printf("J-coupling type is CCG, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
- log << " Bibliography "
- << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)") << "\n";
+ log << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)");
break;
case NCG:
ka_ = 1.29;
@@ -248,13 +244,14 @@ JCoupling::JCoupling(const ActionOptions&ao):
kc_ = 0.37;
kshift_ = 0.0;
log.printf("J-coupling type is NCG, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
- log << " Bibliography "
- << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)") << "\n";
+ log << plumed.cite("Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)");
break;
case CUSTOM:
log.printf("J-coupling type is custom, with A: %f, B: %f, C: %f, angle shift: %f\n", ka_, kb_, kc_, kshift_);
break;
}
+ log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
+ log<<"\n";
for (unsigned i = 0; i < ncoupl_; ++i) {
log.printf(" The %uth J-Coupling is calculated from atoms : %d %d %d %d.",
diff --git a/src/isdb/Metainference.cpp b/src/isdb/Metainference.cpp
index 5bdf32c13..2536c0f50 100644
--- a/src/isdb/Metainference.cpp
+++ b/src/isdb/Metainference.cpp
@@ -752,6 +752,7 @@ Metainference::Metainference(const ActionOptions&ao):
log<<" Bibliography "<<plumed.cite("Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)");
if(do_reweight_) log<<plumed.cite("Bonomi, Camilloni, Vendruscolo, Sci. Rep. 6, 31232 (2016)");
if(do_optsigmamean_>0) log<<plumed.cite("Loehr, Jussupow, Camilloni, J. Chem. Phys. 146, 165102 (2017)");
+ log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
log<<"\n";
}
diff --git a/src/isdb/MetainferenceBase.cpp b/src/isdb/MetainferenceBase.cpp
index c192a199c..381fa96b3 100644
--- a/src/isdb/MetainferenceBase.cpp
+++ b/src/isdb/MetainferenceBase.cpp
@@ -20,9 +20,7 @@
along with plumed. If not, see <http://www.gnu.org/licenses/>.
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "MetainferenceBase.h"
-#include "core/PlumedMain.h"
#include "tools/File.h"
-#include "tools/OpenMP.h"
#include <cmath>
#include <ctime>
#include <numeric>
@@ -552,6 +550,7 @@ void MetainferenceBase::Initialise(const unsigned input)
log<<" Bibliography "<<plumed.cite("Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)");
if(do_reweight_) log<<plumed.cite("Bonomi, Camilloni, Vendruscolo, Sci. Rep. 6, 31232 (2016)");
if(do_optsigmamean_>0) log<<plumed.cite("Loehr, Jussupow, Camilloni, J. Chem. Phys. 146, 165102 (2017)");
+ log<<plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
log<<"\n";
}
diff --git a/src/isdb/MetainferenceBase.h b/src/isdb/MetainferenceBase.h
index 5fc1affa8..7594d2b98 100644
--- a/src/isdb/MetainferenceBase.h
+++ b/src/isdb/MetainferenceBase.h
@@ -25,7 +25,9 @@
#include "core/ActionWithValue.h"
#include "core/ActionAtomistic.h"
#include "core/ActionWithArguments.h"
+#include "core/PlumedMain.h"
#include "tools/Random.h"
+#include "tools/OpenMP.h"
#define PLUMED_METAINF_INIT(ao) Action(ao),MetainferenceBase(ao)
diff --git a/src/isdb/NOE.cpp b/src/isdb/NOE.cpp
index ec130d9df..64b53e8a6 100644
--- a/src/isdb/NOE.cpp
+++ b/src/isdb/NOE.cpp
@@ -22,7 +22,6 @@
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
#include "tools/NeighborList.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#include <string>
@@ -165,6 +164,8 @@ NOE::NOE(const ActionOptions&ao):
if(pbc) log.printf(" using periodic boundary conditions\n");
else log.printf(" without periodic boundary conditions\n");
+ log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
if(!getDoScore()) {
for(unsigned i=0; i<nga.size(); i++) {
string num; Tools::convert(i,num);
diff --git a/src/isdb/PRE.cpp b/src/isdb/PRE.cpp
index 83702f1d7..6b9a38feb 100644
--- a/src/isdb/PRE.cpp
+++ b/src/isdb/PRE.cpp
@@ -22,7 +22,6 @@
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
#include "tools/NeighborList.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#include <string>
@@ -205,6 +204,8 @@ PRE::PRE(const ActionOptions&ao):
if(pbc) log.printf(" using periodic boundary conditions\n");
else log.printf(" without periodic boundary conditions\n");
+ log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
if(!getDoScore()) {
for(unsigned i=0; i<nga.size(); i++) {
string num; Tools::convert(i,num);
diff --git a/src/isdb/RDC.cpp b/src/isdb/RDC.cpp
index c871c3800..a0be6cf19 100644
--- a/src/isdb/RDC.cpp
+++ b/src/isdb/RDC.cpp
@@ -21,8 +21,6 @@
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
-#include "core/PlumedMain.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#ifdef __PLUMED_HAS_GSL
@@ -287,7 +285,9 @@ RDC::RDC(const ActionOptions&ao):
log<<" Bibliography "
<<plumed.cite("Camilloni C, Vendruscolo M, J. Phys. Chem. B 119, 653 (2015)")
- <<plumed.cite("Camilloni C, Vendruscolo M, Biochemistry 54, 7470 (2015)") <<"\n";
+ <<plumed.cite("Camilloni C, Vendruscolo M, Biochemistry 54, 7470 (2015)");
+ log<< plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
if(!getDoScore()&&!svd) {
for(unsigned i=0; i<ndata; i++) {
diff --git a/src/isdb/Rescale.cpp b/src/isdb/Rescale.cpp
index 3707c1c22..f28dce8b5 100644
--- a/src/isdb/Rescale.cpp
+++ b/src/isdb/Rescale.cpp
@@ -288,6 +288,9 @@ Rescale::Rescale(const ActionOptions&ao):
log.printf(" do MC every %d steps\n", MCstride_);
log.printf("\n");
+ log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
+
// add components
addComponent("igamma"); componentIsNotPeriodic("igamma");
addComponent("accgamma"); componentIsNotPeriodic("accgamma");
diff --git a/src/isdb/SAXS.cpp b/src/isdb/SAXS.cpp
index 3f5ab61dc..2e965236b 100644
--- a/src/isdb/SAXS.cpp
+++ b/src/isdb/SAXS.cpp
@@ -27,10 +27,8 @@
#include "MetainferenceBase.h"
#include "core/ActionRegister.h"
#include "core/ActionSet.h"
-#include "core/PlumedMain.h"
#include "core/SetupMolInfo.h"
#include "tools/Communicator.h"
-#include "tools/OpenMP.h"
#include "tools/Pbc.h"
#include <string>
@@ -277,6 +275,7 @@ SAXS::SAXS(const ActionOptions&ao):
log<<plumed.cite("Fraser, MacRae, Suzuki, J. Appl. Crystallogr., 11, 693–694 (1978).");
log<<plumed.cite("Brown, Fox, Maslen, O'Keefe, Willis, International Tables for Crystallography C, 554–595 (International Union of Crystallography, 2006).");
}
+ log<< plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)");
log<<"\n";
requestAtoms(atoms);
diff --git a/src/isdb/Select.cpp b/src/isdb/Select.cpp
index de6f0ae4b..14368243a 100644
--- a/src/isdb/Select.cpp
+++ b/src/isdb/Select.cpp
@@ -95,6 +95,8 @@ Select::Select(const ActionOptions&ao):
checkRead();
log.printf(" select based on %s\n",selector_.c_str());
+ log << " Bibliography" << plumed.cite("Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)") << "\n";
+
}
void Select::calculate()
diff --git a/user-doc/bibliography.bib b/user-doc/bibliography.bib
index 2ad2f9abc..e4ca5b0eb 100644
--- a/user-doc/bibliography.bib
+++ b/user-doc/bibliography.bib
@@ -2569,8 +2569,8 @@ author = {Bonomi, Massimiliano and Camilloni, Carlo},
title = {{Integrative structural and dynamical biology with PLUMED-ISDB}},
journal = {Bioinformatics},
year = {2017},
-volume = {},
-pages = {},
+volume = {33},
+pages = {3999--4000},
}
@Article{Lelievre2007,
--
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