Add 'byfac' keyword to change mass/charge command (#1079)

* Add byfac to change charge/mass

* Add test for change byfac

* Add byfac to manual

* 6.25.2. Revision bump for change byfac

doc/cpptraj.lyx

@@ -14842,8 +14842,11 @@ change [parm <name> | parmindex <#> | <#> |
 \end_layout
 
 \begin_layout LyX-Code
-      {mass|charge} [of <mask>] {to <value>|by <offset>|fromset <data set>}
- |
+      {mass|charge} [of <mask>] {to <value> |by <offset> |
+\end_layout
+
+\begin_layout LyX-Code
+                                 byfac <factor> |fromset <data set>} |
 \end_layout
 
 \begin_layout LyX-Code
@@ -15171,6 +15174,14 @@ by
 <offset> Value to offset masses/charges by.
 \end_layout
 
+\begin_layout Description
+byfac
+\begin_inset space ~
+\end_inset
+
+<factor> Value to multiply masses/charges by.
+\end_layout
+
 \begin_layout Description
 fromset
 \begin_inset space ~

src/Exec_Change.cpp

@@ -18,7 +18,8 @@ void Exec_Change::Help() const
           "\t  addbond <mask1> <mask2> [req <length> <rk> <force constant>] |\n"
           "\t  removebonds <mask1> [<mask2>] [out <file>] |\n"
           "\t  bondparm <mask1> [<mask2>] {setrk|scalerk|setreq|scalereq} <value> |\n"
-          "\t  {mass|charge} [of <mask>] {to <value>|by <offset>|fromset <data set>} |\n"
+          "\t  {mass|charge} [of <mask>] {to <value> |by <offset> |\n"
+          "\t                             byfac <factor> |fromset <data set>} |\n"
           "\t  mergeres firstres <start res#> lastres <stop res#>\n"
           "\t}\n"
           "  Change specified parts of topology or topology of a COORDS data set.\n",
@@ -633,6 +634,16 @@ void Exec_Change::changeTopVal(Topology& topIn, int atnum, ChangeType typeIn, do
       mprintf("\tChanging charge of atom '%s' by %g to %g\n", topIn.AtomMaskName(atnum).c_str(), newVal, oldVal+newVal);
       currentAtom.SetCharge( oldVal + newVal );
       break;
+    case MASS_BYFAC :
+      oldVal = currentAtom.Mass();
+      mprintf("\tChanging mass of atom '%s' by factor of %g to %g\n", topIn.AtomMaskName(atnum).c_str(), newVal, oldVal*newVal);
+      currentAtom.SetMass( oldVal * newVal );
+      break;
+    case CHARGE_BYFAC :
+      oldVal = currentAtom.Charge();
+      mprintf("\tChanging charge of atom '%s' by factor of %g to %g\n", topIn.AtomMaskName(atnum).c_str(), newVal, oldVal*newVal);
+      currentAtom.SetCharge( oldVal * newVal );
+      break;
   }
 }
 
@@ -698,11 +709,15 @@ const
     ChangeType ctype;
     bool change_to = argIn.Contains("to");
     bool change_by = argIn.Contains("by");
-    if (!change_to && !change_by) {
-      mprinterr("Error: Expected either 'fromset', 'to', or 'by' for 'change %s'.\n", desc[typeIn]);
+    bool change_byfac = argIn.Contains("byfac");
+    int nchange = 0;
+    if (change_to) nchange++;
+    if (change_by) nchange++;
+    if (change_byfac) nchange++;
+    if (nchange < 1) {
+      mprinterr("Error: Expected either 'fromset', 'to', 'by', or 'byfac' for 'change %s'.\n", desc[typeIn]);
       return 1;
-    }
-    if (change_to && change_by) {
+    } else if (nchange > 1) {
       mprinterr("Error: Specify either 'to' or 'by', not both.\n");
       return 1;
     }
@@ -724,6 +739,15 @@ const
       for (AtomMask::const_iterator at = atomsToChange.begin(); at != atomsToChange.end(); ++at) {
         changeTopVal(topIn, *at, ctype, offset);
       }
+    } else if (change_byfac) {
+      if (typeIn == 0)
+        ctype = MASS_BYFAC;
+      else
+        ctype = CHARGE_BYFAC;
+      double fac = argIn.getKeyDouble("byfac", 0.0);
+      for (AtomMask::const_iterator at = atomsToChange.begin(); at != atomsToChange.end(); ++at) {
+        changeTopVal(topIn, *at, ctype, fac);
+      }
     }
   }
 

src/Exec_Change.h

@@ -10,7 +10,7 @@ class Exec_Change : public Exec {
     DispatchObject* Alloc() const { return (DispatchObject*)new Exec_Change(); }
     RetType Execute(CpptrajState&, ArgList&);
   private:
-    enum ChangeType { MASS_TO = 0, CHARGE_TO, MASS_BY, CHARGE_BY };
+    enum ChangeType { MASS_TO = 0, CHARGE_TO, MASS_BY, CHARGE_BY, MASS_BYFAC, CHARGE_BYFAC };
     /// Change mass or charge
     static inline void changeTopVal(Topology&, int, ChangeType, double);
 

src/Version.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 "V6.25.1"
+#define CPPTRAJ_INTERNAL_VERSION "V6.25.2"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif

test/Test_Change/AFV.1.byfac.dat.save

@@ -0,0 +1,13 @@
+#Atom Name  #Res Name  #Mol Type   Charge     Mass GBradius El     rVDW     eVDW
+    1 N        1 ALA      1 N3    -0.4293  30.0200   1.5500  N   1.8240   0.1700
+    2 H1       1 ALA      1 H     -0.4002   4.0160   1.3000  H   0.6000   0.0157
+    3 H2       1 ALA      1 H     -0.4002   4.0160   1.3000  H   0.6000   0.0157
+    4 H3       1 ALA      1 H     -0.4002   4.0160   1.3000  H   0.6000   0.0157
+    5 CA       1 ALA      1 CX    -0.4519  26.0200   1.7000  C   1.9080   0.1094
+    6 HA       1 ALA      1 HP    -0.4556   4.0160   1.3000  H   1.1000   0.0157
+    7 CB       1 ALA      1 CT    -0.5299  26.0200   1.7000  C   1.9080   0.1094
+    8 HB1      1 ALA      1 HC    -0.4850   4.0160   1.3000  H   1.4870   0.0157
+    9 HB2      1 ALA      1 HC    -0.4850   4.0160   1.3000  H   1.4870   0.0157
+   10 HB3      1 ALA      1 HC    -0.4850   4.0160   1.3000  H   1.4870   0.0157
+   11 C        1 ALA      1 C     -0.1918  26.0200   1.7000  C   1.9080   0.0860
+   12 O        1 ALA      1 O     -0.7861  34.0000   1.5000  O   1.6612   0.2100

test/Test_Change/RunTest.sh

@@ -4,7 +4,7 @@
 
 CleanFiles change.in ala3.mod.pdb ala3.chain.pdb crdala3.chain.pdb \
            AFV.zeroHmass.dat AFV.fluctMass.dat merged.?-?.mol2 \
-           AFV.zeroHcharge.dat AFV.1.offset.dat
+           AFV.zeroHcharge.dat AFV.1.offset.dat AFV.1.byfac.dat
 
 TESTNAME='Change command test'
 
@@ -102,9 +102,13 @@ change charge of :1 by -1.0
 change mass of :1 by 1.0
 parmstrip !:1
 atoms * out AFV.1.offset.dat
+change charge of :1 byfac 0.5
+change mass of :1 byfac 2.0
+atoms * out AFV.1.byfac.dat
 EOF
   RunCpptraj "$UNITNAME"
   DoTest AFV.1.offset.dat.save AFV.1.offset.dat
+  DoTest AFV.1.byfac.dat.save AFV.1.byfac.dat
 fi
 
 UNITNAME='Merge residues test'