Add ability to change names in 'atommap' command (#1060)

* Add changenames keyword to change atom names in target topology during atom mapping. * Add test for changenames * Update atommap help * Update manual entry * 6.22.2. Revision bump for atommap 'changenames' keyword. * Protect in parallel * Use setup-python v5 * Try using python 3.10 to get CI working * Forgot to update the YML environment too
Amber-MD · Dec 13, 2023 · a7b1e03 · a7b1e03
1 parent dd503b2
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diff --git a/.github/workflows/merge-gate.yml b/.github/workflows/merge-gate.yml
@@ -138,10 +138,10 @@ jobs:
         sudo apt-get install clang
         sudo apt-get install cmake-data cmake    
     - uses: actions/checkout@v3
-    - name: Set up Python 3.8
-      uses: actions/setup-python@v4
+    - name: Set up Python 3.10
+      uses: actions/setup-python@v5
       with:
-        python-version: '3.8'
+        python-version: '3.10'
     - name: Add conda to system path
       run: |
         # $CONDA is an environment variable pointing to the root of the miniconda directory

diff --git a/devtools/ci/environment.yml b/devtools/ci/environment.yml
@@ -1,7 +1,7 @@
 channels:
     - conda-forge
 dependencies:
-    - python=3.8
+    - python=3.10
     - pyflakes
     - numpy
     - cython

diff --git a/doc/cpptraj.lyx b/doc/cpptraj.lyx
@@ -23367,6 +23367,10 @@ atommap
 
 \end_layout
 
+\begin_layout LyX-Code
+        [changenames]
+\end_layout
+
 \begin_deeper
 \begin_layout Description
 <target> Reference structure whose atoms will be remapped.
@@ -23427,6 +23431,11 @@ rmsout
 \end_layout
 
 \end_deeper
+\begin_layout Description
+changenames If specified, change names of mapped atoms in <target> to match
+ those in <reference>.
+\end_layout
+
 \end_deeper
 \begin_layout Standard
 Attempt to map the atoms of <target> to those of <reference> based on structural

diff --git a/src/Action_AtomMap.cpp b/src/Action_AtomMap.cpp
@@ -15,15 +15,18 @@ Action_AtomMap::Action_AtomMap() :
   mode_(ALL),
   maponly_(false),
   rmsfit_(false),
+  renameAtoms_(false),
   rmsdata_(0)
 {}
 
 void Action_AtomMap::Help() const {
   mprintf("\t<target> <reference> [mapout <filename>] [maponly]\n"
           "\t[rmsfit [ rmsout <rmsout> ]] [mode {all | byres}]\n"
+          "\t[changenames]\n"
           "  Attempt to create a map from atoms in <target> to atoms in <reference> solely\n"
           "  based on how they are bonded; remap <target> so it matches <reference>.\n"
           "  If 'rmsfit' is specified, calculate the RMSD of remapped target to reference.\n"
+          "  If 'changenames' is specified change target atom names to match reference.\n"
           "  Modes: 'all'   : try to map all atoms at once (default).\n"
           "         'byres' : map residue by residue (assumes 1 to 1 residue correspondence).\n");
 }
@@ -48,6 +51,7 @@ Action::RetType Action_AtomMap::Init(ArgList& actionArgs, ActionInit& init, int
 # endif
   maponly_ = actionArgs.hasKey("maponly");
   rmsfit_ = actionArgs.hasKey("rmsfit");
+  renameAtoms_ = actionArgs.hasKey("changenames");
   std::string modestring = actionArgs.GetStringKey("mode");
   if (!modestring.empty()) {
     if      (modestring == "all") mode_ = ALL;
@@ -92,14 +96,18 @@ Action::RetType Action_AtomMap::Init(ArgList& actionArgs, ActionInit& init, int
     mprintf("\tMap will only be written, not used to remap input trajectories.\n");
   else
     mprintf("\tAtoms in input trajectories matching target will be remapped.\n");
-  if (!maponly_ && rmsfit_) {
-    mprintf("\tWill RMS-fit mapped atoms in tgt to reference.\n");
-    if (rmsout != 0) {
-      rmsdata_ = init.DSL().AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "RMSD");
-      if (rmsdata_==0) return Action::ERR;
-      rmsout->AddDataSet(rmsdata_);
-      mprintf("\tRMSDs will be written to '%s'\n", rmsout->DataFilename().full());
+  if (!maponly_) {
+    if (rmsfit_) {
+      mprintf("\tWill RMS-fit mapped atoms in tgt to reference.\n");
+      if (rmsout != 0) {
+        rmsdata_ = init.DSL().AddSet(DataSet::DOUBLE, actionArgs.GetStringNext(), "RMSD");
+        if (rmsdata_==0) return Action::ERR;
+        rmsout->AddDataSet(rmsdata_);
+        mprintf("\tRMSDs will be written to '%s'\n", rmsout->DataFilename().full());
+      }
     }
+    if (renameAtoms_)
+      mprintf("\tTarget atom names will be renamed using reference atom names.\n");
   }
   switch (mode_) {
     case BY_RES:
@@ -206,6 +214,15 @@ Action::RetType Action_AtomMap::Init(ArgList& actionArgs, ActionInit& init, int
     newFrame_->SetupFrameM( TgtFrame_->Top().Atoms() );
     // Set up new Parm
     newParm_ = TgtFrame_->Top().ModifyByMap(AMap_);
+    if (renameAtoms_) {
+      // newParm_ is already in the correct order
+      for (int refatom = 0; refatom != (int)AMap_.size(); ++refatom) {
+        if (AMap_[refatom] != -1) {
+          //mprintf("DEBUG: ref %i name %s becomes tgt %i\n", refatom+1, *(RefFrame_->Top()[refatom].Name()), targetatom+1);
+          (*newParm_).SetAtom(refatom).SetName( RefFrame_->Top()[refatom].Name() );
+        }
+      }
+    }
   }
 
   return Action::OK;

diff --git a/src/Action_AtomMap.h b/src/Action_AtomMap.h
@@ -29,6 +29,7 @@ class Action_AtomMap : public Action {
     Frame rmsRefFrame_; ///< Ref frame for calculating RMS of remapped target to ref
     Frame rmsTgtFrame_; ///< Tgt frame for calculating RMS of remapped target to ref
     bool rmsfit_;       ///< If true, attempt to RMS-fit remapped target to ref
+    bool renameAtoms_;  ///< If true, rename target atoms to match reference
     DataSet* rmsdata_;  ///< RMS of remapped target to ref.
 };
 #endif
diff --git a/src/Version.h b/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 "V6.22.1"
+#define CPPTRAJ_INTERNAL_VERSION "V6.22.2"
 /// PYTRAJ relies on this
 #define CPPTRAJ_VERSION_STRING CPPTRAJ_INTERNAL_VERSION
 #endif
diff --git a/test/Test_AtomMap/ADD.names.mol2 b/test/Test_AtomMap/ADD.names.mol2
@@ -0,0 +1,48 @@
+@<TRIPOS>MOLECULE
+ADD
+   18    19     1     0     0
+SMALL
+resp
+
+
+@<TRIPOS>ATOM
+      1 C1          -3.0530     0.5460     0.0060 CT         1 ADD       0.063213
+      2 H1          -3.1040     1.2390    -0.8210 H1         1 ADD       0.047610
+      3 N1          -1.7830    -0.1470    -0.0030 N*         1 ADD      -0.156619
+      4 C2          -1.5590    -1.5030     0.0010 CK         1 ADD       0.121145
+      5 H2          -2.3800    -2.1940     0.0030 H5         1 ADD       0.163537
+      6 N2          -0.3010    -1.8360    -0.0000 NB         1 ADD      -0.546770
+      7 C3           0.3630    -0.6210    -0.0050 CB         1 ADD      -0.088583
+      8 C4           1.7210    -0.2690    -0.0050 CA         1 ADD       0.819921
+      9 N3           2.7060    -1.1900    -0.0320 N2         1 ADD      -0.958412
+     10 H3           3.6400    -0.8830     0.1180 H          1 ADD       0.419226
+     11 H4           2.4860    -2.1470     0.1200 H          1 ADD       0.419226
+     12 N4           2.0450     1.0240     0.0040 NC         1 ADD      -0.822741
+     13 C5           1.0670     1.9280     0.0020 CQ         1 ADD       0.619667
+     14 H5           1.3920     2.9540     0.0070 H5         1 ADD       0.056434
+     15 N5          -0.2370     1.7300    -0.0020 NC         1 ADD      -0.791023
+     16 C6          -0.5410     0.4290    -0.0040 CB         1 ADD       0.538950
+     17 H6          -3.8480    -0.1810    -0.0900 H1         1 ADD       0.047610
+     18 H7          -3.1820     1.0930     0.9310 H1         1 ADD       0.047610
+@<TRIPOS>BOND
+     1     1     2 1   
+     2     1     3 1   
+     3     1    17 1   
+     4     1    18 1   
+     5     3     4 1   
+     6     3    16 1   
+     7     4     5 1   
+     8     4     6 2   
+     9     6     7 1   
+    10     7     8 1   
+    11     7    16 2   
+    12     8     9 1   
+    13     8    12 2   
+    14     9    10 1   
+    15     9    11 1   
+    16    12    13 1   
+    17    13    14 1   
+    18    13    15 2   
+    19    15    16 1   
+@<TRIPOS>SUBSTRUCTURE
+     1 ADD         1 TEMP              0 ****  ****    0 ROOT
diff --git a/test/Test_AtomMap/RunTest.sh b/test/Test_AtomMap/RunTest.sh
@@ -5,7 +5,7 @@
 # Clean
 CleanFiles atommap.in initial.mol2 atommap.dat reordered.pdb reordered.mol2 \
            fit.mol2 rmsd.dat map.chm_to_amb.dat mapped.pdb.? rmsout.dat \
-           map.byres.chm_to_amb.dat
+           map.byres.chm_to_amb.dat map.Base.dat remap.ADD.mol2
 
 TESTNAME='Atom map tests'
 Requires maxthreads 3
@@ -78,7 +78,6 @@ EOF
   RunCpptraj "Atom map charmm->amber atom order"
   DoTest map.chm_to_amb.dat.save map.chm_to_amb.dat
 
-  # Test 4
   cat > atommap.in <<EOF
 parm cg-amb.topo
 reference cg-amb.crds
@@ -89,6 +88,27 @@ EOF
   RunCpptraj "Atom map charmm->amber atom order, by residue"
   DoTest map.chm_to_amb.dat.save map.byres.chm_to_amb.dat
 fi
+
+# Test 4
+UNITNAME='Atom map with renaming test'
+CheckFor maxthreads 1
+if [ $? -eq 0 ] ; then
+  cat > atommap.in <<EOF
+for FILE in template-base-adenine.pdb,ADD.names.mol2 NAME in Base0,Base1
+  parm \$FILE
+  reference \$FILE [\$NAME] parm \$FILE
+done
+
+atommap [Base1] [Base0] mapout map.Base.dat changenames
+
+trajin ADD.names.mol2 parm ADD.names.mol2
+trajout remap.ADD.mol2 parm ADD.names.mol2
+run
+EOF
+  RunCpptraj "$UNITNAME"
+  DoTest remap.ADD.mol2.save remap.ADD.mol2
+fi
+
 EndTest
 
 exit 0
diff --git a/test/Test_AtomMap/remap.ADD.mol2.save b/test/Test_AtomMap/remap.ADD.mol2.save
@@ -0,0 +1,48 @@
+@<TRIPOS>MOLECULE
+Cpptraj Generated mol2 file.
+   18    19     1     0     0
+SMALL
+USER_CHARGES
+
+
+@<TRIPOS>ATOM
+      1 C1'        -3.0530    0.5460    0.0060 CT         1 ADD      0.063213
+      2 1H1'       -3.1040    1.2390   -0.8210 H1         1 ADD      0.047610
+      3 2H1'       -3.8480   -0.1810   -0.0900 H1         1 ADD      0.047610
+      4 3H1'       -3.1820    1.0930    0.9310 H1         1 ADD      0.047610
+      5 N9         -1.7830   -0.1470   -0.0030 N*         1 ADD     -0.156619
+      6 C8         -1.5590   -1.5030    0.0010 CK         1 ADD      0.121145
+      7 H8         -2.3800   -2.1940    0.0030 H5         1 ADD      0.163537
+      8 N7         -0.3010   -1.8360   -0.0000 NB         1 ADD     -0.546770
+      9 C5          0.3630   -0.6210   -0.0050 CB         1 ADD     -0.088583
+     10 C6          1.7210   -0.2690   -0.0050 CA         1 ADD      0.819921
+     11 N6          2.7060   -1.1900   -0.0320 N2         1 ADD     -0.958412
+     12 H61         3.6400   -0.8830    0.1180 H          1 ADD      0.419226
+     13 H62         2.4860   -2.1470    0.1200 H          1 ADD      0.419226
+     14 N1          2.0450    1.0240    0.0040 NC         1 ADD     -0.822741
+     15 C2          1.0670    1.9280    0.0020 CQ         1 ADD      0.619667
+     16 H2          1.3920    2.9540    0.0070 H5         1 ADD      0.056434
+     17 N3         -0.2370    1.7300   -0.0020 NC         1 ADD     -0.791023
+     18 C4         -0.5410    0.4290   -0.0040 CB         1 ADD      0.538950
+@<TRIPOS>BOND
+    1     1     5 1
+    2     5     6 1
+    3     5    18 1
+    4     6     8 1
+    5     8     9 1
+    6     9    10 1
+    7     9    18 1
+    8    10    11 1
+    9    10    14 1
+   10    14    15 1
+   11    15    17 1
+   12    17    18 1
+   13     1     2 1
+   14     1     3 1
+   15     1     4 1
+   16     6     7 1
+   17    11    12 1
+   18    11    13 1
+   19    15    16 1
+@<TRIPOS>SUBSTRUCTURE
+      1 ADD               1 ****               0 ****  **** 
diff --git a/test/Test_AtomMap/template-base-adenine.pdb b/test/Test_AtomMap/template-base-adenine.pdb
@@ -0,0 +1,20 @@
+ATOM      1  C1' DAA     1       4.559   1.151   3.778  1.00  0.00           C  
+ATOM      2 1H1' DAA     1       5.072   1.095   4.737  1.00  0.00           H  
+ATOM      3 2H1' DAA     1       5.108   1.778   3.076  1.00  0.00           H  
+ATOM      4 3H1' DAA     1       3.547   1.538   3.897  1.00  0.00           H  
+ATOM      5  N9  DAA     1       4.539  -0.297   3.316  1.00  0.00           N  
+ATOM      6  C8  DAA     1       4.337  -0.846   2.077  1.00  0.00           C  
+ATOM      7  H8  DAA     1       4.152  -0.207   1.226  1.00  0.00           H  
+ATOM      8  N7  DAA     1       4.453  -2.141   2.049  1.00  0.00           N  
+ATOM      9  C5  DAA     1       4.754  -2.480   3.363  1.00  0.00           C  
+ATOM     10  C6  DAA     1       4.998  -3.708   3.989  1.00  0.00           C  
+ATOM     11  N6  DAA     1       4.977  -4.883   3.346  1.00  0.00           N  
+ATOM     12  H61 DAA     1       5.161  -5.739   3.851  1.00  0.00           H  
+ATOM     13  H62 DAA     1       4.777  -4.914   2.356  1.00  0.00           H  
+ATOM     14  N1  DAA     1       5.265  -3.689   5.302  1.00  0.00           N  
+ATOM     15  C2  DAA     1       5.285  -2.520   5.935  1.00  0.00           C  
+ATOM     16  H2  DAA     1       5.498  -2.482   6.993  1.00  0.00           H  
+ATOM     17  N3  DAA     1       5.073  -1.309   5.456  1.00  0.00           N  
+ATOM     18  C4  DAA     1       4.806  -1.356   4.133  1.00  0.00           C  
+TER
+END