Add mass and charge keywords, add test

Amber-MD · Jul 12, 2024 · 79e18e3 · 79e18e3
1 parent 6f6f3b2
commit 79e18e3
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Showing 3 changed files with 69 additions and 2 deletions.
diff --git a/src/Action_AddAtom.cpp b/src/Action_AddAtom.cpp
@@ -14,7 +14,7 @@ Action_AddAtom::~Action_AddAtom() {
 // Action_AddAtom::Help()
 void Action_AddAtom::Help() const {
   mprintf("\taname <name> [elt <element>] [rname <res name>]\n"
-          "\t[xyz <X> <Y> <Z>]\n");
+          "\t[xyz <X> <Y> <Z>] [mass <mass>] [charge <charge>]\n");
   mprintf("%s", ActionTopWriter::Keywords());
   mprintf("  Add an atom to current topology/coordinates.\n");
 }
@@ -45,6 +45,21 @@ Action::RetType Action_AddAtom::Init(ArgList& actionArgs, ActionInit& init, int
     rname.assign("TMP");
   residueName_ = NameType( rname );
 
+  bool has_mass = false;
+  double mass = 0;
+  if (actionArgs.Contains("mass")) {
+    has_mass = true;
+    mass = actionArgs.getKeyDouble("mass", 0);
+  }
+
+  bool has_charge = false;
+  double charge = 0;
+  if (actionArgs.Contains("charge")) {
+    has_charge = true;
+    charge = actionArgs.getKeyDouble("charge", 0);
+  }
+
+  // ----- Last arg to process -----
   if (actionArgs.Contains("xyz")) {
     ArgList xyzargs = actionArgs.GetNstringKey("xyz", 3);
     if (xyzargs.Nargs() != 3) {
@@ -59,9 +74,13 @@ Action::RetType Action_AddAtom::Init(ArgList& actionArgs, ActionInit& init, int
 
   // ----- No more args after here -----
   newAtom_ = Atom(atomName, elt.c_str());
+  if (has_mass) newAtom_.SetMass( mass );
+  if (has_charge) newAtom_.SetCharge( charge );
 
   mprintf("    ADDATOM: Adding atom named '%s', element %s, residue name '%s'\n",
           *atomName, elt.c_str(), *residueName_);
+  if (has_mass) mprintf("\tAtom mass = %g\n", mass);
+  if (has_charge) mprintf("\tAtom charge = %g\n", charge);
   mprintf("\tAtom will be placed at XYZ= %g %g %g\n", xyz_[0], xyz_[1], xyz_[2]);
   topWriter_.PrintOptions();
 

diff --git a/test/Test_AddAtom/RunTest.sh b/test/Test_AddAtom/RunTest.sh
@@ -2,7 +2,7 @@
 
 . ../MasterTest.sh
 
-CleanFiles addatom.in tz2.addatom.pdb tz2.mask.dat
+CleanFiles addatom.in tz2.addatom.pdb tz2.mask.dat tz2.mg.mol2
 
 TESTNAME='Add atom tests'
 
@@ -22,4 +22,14 @@ RunCpptraj "Add atom test"
 DoTest tz2.addatom.pdb.save tz2.addatom.pdb
 DoTest tz2.mask.dat.save tz2.mask.dat
 
+cat > addatom.in <<EOF
+parm ../tz2.parm7
+trajin ../tz2.pdb 1 1
+strip !:1
+addatom aname MG rname MG mass 24.3 charge 2 xyz 3 4 5
+trajout tz2.mg.mol2
+EOF
+RunCpptraj "Add atom test, MG"
+DoTest tz2.mg.mol2.save tz2.mg.mol2
+
 EndTest
diff --git a/test/Test_AddAtom/tz2.mg.mol2.save b/test/Test_AddAtom/tz2.mg.mol2.save
@@ -0,0 +1,38 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+   14    12     2     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 N          -1.8890    9.1590    7.5690 N3         1 SER      0.184900
+      2 H1         -1.0370    8.6910    7.2960 H          1 SER      0.189800
+      3 H2         -1.9000    9.2980    8.5690 H          1 SER      0.189800
+      4 H3         -2.5380    8.4470    7.2650 H          1 SER      0.189800
+      5 CA         -2.0640   10.5010    6.9930 CT         1 SER      0.056700
+      6 HA         -3.1000   10.8240    7.1020 HP         1 SER      0.078200
+      7 CB         -1.2300   11.5610    7.7070 CT         1 SER      0.259600
+      8 HB2        -1.6700   11.8110    8.6730 H1         1 SER      0.027300
+      9 HB3        -1.2480   12.5030    7.1590 H1         1 SER      0.027300
+     10 OG          0.1230   11.2160    7.9040 OH         1 SER     -0.671400
+     11 HG          0.2740   11.7280    8.7010 HO         1 SER      0.423900
+     12 C          -1.6130   10.4180    5.5420 C          1 SER      0.616300
+     13 O          -2.4980   10.4330    4.6890 O          1 SER     -0.572200
+     14 MG          3.0000    4.0000    5.0000 MG         2 MG       2.000000
+@<TRIPOS>BOND
+    1    12    13 1
+    2     7    10 1
+    3     5     7 1
+    4     5    12 1
+    5     1     5 1
+    6    10    11 1
+    7     7     8 1
+    8     7     9 1
+    9     5     6 1
+   10     1     2 1
+   11     1     3 1
+   12     1     4 1
+@<TRIPOS>SUBSTRUCTURE
+      1 SER               1 ****               0 ****  **** 
+      2 MG               14 ****               0 ****  ****