Add new options to resinfo short (#1158)

* Fix maxwidth behavior

* Add groupsize keyword

* 6.30.1 - revision bump for resinfo short groupsize keyword

* Add nucleic keyword

* Update resinfo manual entry

* Update manual

* Add test

Author: drroe

doc/CpptrajManual.pdf

@@ -1,3 +1,3 @@
 b37726e7a841f6fc695ecd7fb040ffbf  CpptrajDevelopmentGuide.lyx
-70869c8569e7bd44d1669bc9ba6d68d8  cpptraj.lyx
+30abc9d08551e23061abcb780f78b02a  cpptraj.lyx
 5d9b5b5ed47a3ded57b6464df99b3585  CpptrajManual.lyx

doc/DocumentChecksums.txt

@@ -16684,7 +16684,11 @@ parmresinfo
 
 \end_inset
 
- [parm <name> | parmindex <#> | <#>] <mask> [short [maxwidth <#res>]]
+ [parm <name> | parmindex <#> | <#>] <mask>
+\end_layout
+
+\begin_layout LyX-Code
+        [short {nucleic|[maxwidth <#res>] [groupsize <#res>]}]
 \end_layout
 
 \begin_layout LyX-Code
@@ -16738,6 +16742,19 @@ parmindex
 <#res>] Max # of residues to print in one line (default 50).
 \end_layout
 
+\begin_layout Description
+[groupsize
+\begin_inset space ~
+\end_inset
+
+<#res>] Max # of residues to put in a group (default 10).
+\end_layout
+
+\begin_layout Description
+[nucleic] Do a printout suitable for nucleic acid residues (maxwidth 45,
+ groupsize 3).
+\end_layout
+
 \end_deeper
 \begin_layout Description
 [out

doc/cpptraj.lyx

@@ -174,18 +174,24 @@ Exec::RetType Exec_AtomInfo::Execute(CpptrajState& State, ArgList& argIn) {
 
 // -----------------------------------------------------------------------------
 void Exec_ResInfo::Help() const {
-  mprintf("\t[%s] <mask> [short [maxwidth <#res>]]\n\t[out <file>]\n", DataSetList::TopIdxArgs);
+  mprintf("\t[%s] <mask> \n\t[short {nucleic|[maxwidth <#res>] [groupsize <#res>]}]\n\t[out <file>]\n", DataSetList::TopIdxArgs);
   mprintf("  Print info for residues in <mask> for specified topology (first by default).\n"
           "  If 'short' is specified print residue info in shorter form.\n");
 }
 
 Exec::RetType Exec_ResInfo::Execute(CpptrajState& State, ArgList& argIn) {
   bool printShort = argIn.hasKey("short");
+  int maxwidth = argIn.getKeyInt("maxwidth", 50);
+  int groupsize = argIn.getKeyInt("groupsize", 10);
+  if (argIn.hasKey("nucleic")) {
+    maxwidth = 45;
+    groupsize = 3;
+  }
   TopInfo info;
   if (CommonSetup(info, State, argIn, "Residue info")) return CpptrajState::ERR;
   int err;
   if (printShort)
-    err = info.PrintShortResInfo( argIn.GetMaskNext(), argIn.getKeyInt("maxwidth",50) );
+    err = info.PrintShortResInfo( argIn.GetMaskNext(), maxwidth, groupsize );
   else
     err = info.PrintResidueInfo( argIn.GetMaskNext() );
   if (err != 0) return CpptrajState::ERR;

src/Exec_Top.cpp

@@ -218,7 +218,7 @@ int TopInfo::PrintResidueInfo(std::string const& maskExpression) const {
 }
 
 /** Print residue info using single char names. */ // TODO use Topology::ResnumsSelectedBy
-int TopInfo::PrintShortResInfo(std::string const& maskString, int maxChar) const {
+int TopInfo::PrintShortResInfo(std::string const& maskString, int maxChar, int groupSize) const {
   if (maskString.empty()) {
     mprinterr("Error: No valid mask given for short residue info.\n");
     return 1;
@@ -261,7 +261,7 @@ int TopInfo::PrintShortResInfo(std::string const& maskString, int maxChar) const
           if (current_res == max_res) break;
           startRes = -1;
           resLine.clear();
-        } else if ((total % 10) == 0)
+        } else if ((total % groupSize) == 0)
           resLine += ' ';
         rn = current_res;
       }

src/TopInfo.cpp

@@ -19,7 +19,7 @@ class TopInfo {
     int SetupTopInfo(Topology const* p, DataSet_Coords* c) { return SetupTopInfo(0, p, c); }
 
     int PrintAtomInfo(std::string const&) const;
-    int PrintShortResInfo(std::string const&, int) const;
+    int PrintShortResInfo(std::string const&, int, int) const;
     int PrintResidueInfo(std::string const&) const;
     int PrintMoleculeInfo(std::string const&) const;
     int PrintShortMolInfo(std::string const&) const;

src/TopInfo.h

@@ -12,7 +12,7 @@
  * Whenever a number that precedes <revision> is incremented, all subsequent
  * numbers should be reset to 0.
  */
-#define CPPTRAJ_INTERNAL_VERSION "V6.30.0"
+#define CPPTRAJ_INTERNAL_VERSION "V6.30.1"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif

src/Version.h

@@ -4,7 +4,7 @@
 
 CleanFiles info.in atoms.dat residues.dat bonds.dat angles.dat dihedrals.dat \
            molecules.dat masscharge.dat values.dat molshort.dat molselect.dat \
-           molselect2.dat ChargeMass.dat
+           molselect2.dat ChargeMass.dat ftu.res.out ftu.nucleic.out
 
 INPUT="-i info.in"
 cat > info.in <<EOF
@@ -43,6 +43,10 @@ molinfo short 1 *
 molinfo short out molshort.dat 1 *
 resinfo ^2,5-7,100 out molselect.dat parm dna30.parm7
 atoms ^1:DC@P,O?P out molselect2.dat parmindex 1
+
+parm ../FtuFabI.NAD.TCL.parm7
+resinfo parmindex 2 ^1 short maxwidth 45 groupsize 3 out ftu.res.out
+resinfo parmindex 2 ^1 short nucleic out ftu.nucleic.out
 quit
 EOF
 RunCpptraj "Topology info print test."
@@ -57,6 +61,8 @@ DoTest molshort.dat.save molshort.dat
 DoTest molselect.dat.save molselect.dat
 DoTest molselect2.dat.save molselect2.dat
 DoTest ChargeMass.dat.save ChargeMass.dat
+DoTest ftu.res.out.save ftu.res.out
+DoTest ftu.res.out.save ftu.nucleic.out
 
 UNITNAME='Topology info with reference coords test'
 CheckFor netcdf

test/Test_TopInfo/RunTest.sh

@@ -0,0 +1,6 @@
+1        MGF LAG KKI LIT GLL SNK SIA YGI AKA MHR EGA ELA FTY VGQ FKD
+46       RVE KLC AEF NPA AVL PCD VIS DQE IKD LFV ELG KVW DGL DAI VHS
+91       IAF APR DQL EGN FID CVT REG FSI AHD ISA YSF AAL AKE GRS MMK
+136      NRN ASM VAL TYI GAE KAM PSY NTM GVA KAS LEA TVR YTA LAL GED
+181      GIK VNA VSA GPI KTL AAS GIS NFK KML DYN AMV SPL KKN VDI MEV
+226      GNT VAF LCS DMA TGI TGE VVH VDA GYH CVS MGN VLL EHH HHH H