From 10e2afc64ab565e19b5f71eb0547c6b288e22ea7 Mon Sep 17 00:00:00 2001
From: Carlo Camilloni <carlo.camilloni@gmail.com>
Date: Wed, 29 Nov 2023 16:19:57 +0100
Subject: [PATCH] closes #963

the solution is not optimal, but I think making something general is not
trivial
---
 regtest/secondarystructure/rt32/plumed.dat        | 4 ++--
 src/secondarystructure/AntibetaRMSD.cpp           | 6 +++---
 src/secondarystructure/ParabetaRMSD.cpp           | 8 ++++----
 src/secondarystructure/SecondaryStructureRMSD.cpp | 3 ++-
 4 files changed, 11 insertions(+), 10 deletions(-)

diff --git a/regtest/secondarystructure/rt32/plumed.dat b/regtest/secondarystructure/rt32/plumed.dat
index 180a6c5e80..aaf56d6e0b 100644
--- a/regtest/secondarystructure/rt32/plumed.dat
+++ b/regtest/secondarystructure/rt32/plumed.dat
@@ -1,12 +1,12 @@
 MOLINFO STRUCTURE=helix.pdb
-ALPHARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=a
+ALPHARMSD RESIDUES=ALL TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=a
 ANTIBETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=b
 PARABETARMSD RESIDUES=all TYPE=DRMSD STRANDS_CUTOFF=1.0 LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=p
 PRINT ARG=a.*,b.*,p.* STRIDE=1 FILE=colvar FMT=%8.4f
 ALPHARMSD RESIDUES=2-7 TYPE=DRMSD R_0=0.08 NN=8 MM=12 LABEL=a2
 ALPHARMSD RESIDUES=2-7 TYPE=DRMSD R_0=0.08 NN=8 MM=12 NUMERICAL_DERIVATIVES LABEL=a2num
 DUMPDERIVATIVES ARG=a2.*,a2num.*  FILE=derivatives1 FMT=%8.4f STRIDE=1
-ANTIBETARMSD RESIDUES=3-5,8-10 STYLE=inter TYPE=OPTIMAL LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=b2
+ANTIBETARMSD RESIDUES=3-5,8-10 STYLE=INTER TYPE=OPTIMAL LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} LABEL=b2
 ANTIBETARMSD RESIDUES=3-5,8-10 STYLE=inter TYPE=OPTIMAL LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12 NOSTRETCH} NUMERICAL_DERIVATIVES LABEL=b2num
 DUMPDERIVATIVES ARG=b2.*,b2num.*  FILE=derivatives2 FMT=%8.3f STRIDE=1
 RESTRAINT ARG=b.lessthan,p.lessthan,a.lessthan,a2,b2.lessthan AT=0,1,2,3,4 KAPPA=1,2,3,4,5 SLOPE=5,4,3,2,1
diff --git a/src/secondarystructure/AntibetaRMSD.cpp b/src/secondarystructure/AntibetaRMSD.cpp
index c06abc7e3c..bab794e256 100644
--- a/src/secondarystructure/AntibetaRMSD.cpp
+++ b/src/secondarystructure/AntibetaRMSD.cpp
@@ -112,11 +112,11 @@ AntibetaRMSD::AntibetaRMSD(const ActionOptions&ao):
 
   bool intra_chain(false), inter_chain(false);
   std::string style; parse("STYLE",style);
-  if( style=="all" ) {
+  if( Tools::caseInSensStringCompare(style, "all") ) {
     intra_chain=true; inter_chain=true;
-  } else if( style=="inter") {
+  } else if( Tools::caseInSensStringCompare(style, "inter") ) {
     intra_chain=false; inter_chain=true;
-  } else if( style=="intra") {
+  } else if( Tools::caseInSensStringCompare(style, "intra") ) {
     intra_chain=true; inter_chain=false;
   } else {
     error( style + " is not a valid directive for the STYLE keyword");
diff --git a/src/secondarystructure/ParabetaRMSD.cpp b/src/secondarystructure/ParabetaRMSD.cpp
index 9e2e06ea52..1ef9fc9101 100644
--- a/src/secondarystructure/ParabetaRMSD.cpp
+++ b/src/secondarystructure/ParabetaRMSD.cpp
@@ -113,11 +113,11 @@ ParabetaRMSD::ParabetaRMSD(const ActionOptions&ao):
 
   bool intra_chain(false), inter_chain(false);
   std::string style; parse("STYLE",style);
-  if( style=="all" ) {
+  if( Tools::caseInSensStringCompare(style, "all") ) {
     intra_chain=true; inter_chain=true;
-  } else if( style=="inter") {
+  } else if( Tools::caseInSensStringCompare(style, "inter") ) {
     intra_chain=false; inter_chain=true;
-  } else if( style=="intra") {
+  } else if( Tools::caseInSensStringCompare(style, "intra") ) {
     intra_chain=true; inter_chain=false;
   } else {
     error( style + " is not a valid directive for the STYLE keyword");
@@ -148,7 +148,7 @@ ParabetaRMSD::ParabetaRMSD(const ActionOptions&ao):
   }
   // This constructs all conceivable sections of antibeta sheet that form between chains
   if( inter_chain ) {
-    if( chains.size()==1 && style!="all" ) error("there is only one chain defined so cannot use inter_chain option");
+    if( chains.size()==1 && !Tools::caseInSensStringCompare(style, "all") ) error("there is only one chain defined so cannot use inter_chain option");
     std::vector<unsigned> nlist(30);
     for(unsigned ichain=1; ichain<chains.size(); ++ichain) {
       unsigned iprev=0; for(unsigned i=0; i<ichain; ++i) iprev+=chains[i];
diff --git a/src/secondarystructure/SecondaryStructureRMSD.cpp b/src/secondarystructure/SecondaryStructureRMSD.cpp
index 4b6febcefe..10b4c1db8a 100644
--- a/src/secondarystructure/SecondaryStructureRMSD.cpp
+++ b/src/secondarystructure/SecondaryStructureRMSD.cpp
@@ -115,7 +115,8 @@ void SecondaryStructureRMSD::readBackboneAtoms( const std::string& moltype, std:
   std::vector<std::string> resstrings; parseVector( "RESIDUES", resstrings );
   if( !verbose_output ) {
     if(resstrings.size()==0) error("residues are not defined, check the keyword RESIDUES");
-    else if(resstrings[0]=="all") {
+    else if( Tools::caseInSensStringCompare(resstrings[0], "all") ) {
+      resstrings[0]="all";
       log.printf("  examining all possible secondary structure combinations\n");
     } else {
       log.printf("  examining secondary structure in residue positions : %s \n",resstrings[0].c_str() );