Add 'graft' command

doc/cpptraj.lyx

@@ -5701,7 +5701,7 @@ The following COORDS data set commands are available:
 \begin_layout Standard
 \align center
 \begin_inset Tabular
-<lyxtabular version="3" rows="12" columns="2">
+<lyxtabular version="3" rows="13" columns="2">
 <features tabularvalignment="middle">
 <column alignment="center" valignment="top" width="25text%">
 <column alignment="center" valignment="top" width="75text%">
@@ -5833,6 +5833,26 @@ createcrd
 <cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
 \begin_inset Text
 
+\begin_layout Plain Layout
+graft
+\end_layout
+
+\end_inset
+</cell>
+<cell alignment="center" valignment="top" topline="true" leftline="true" rightline="true" usebox="none">
+\begin_inset Text
+
+\begin_layout Plain Layout
+Graft part of one COORDS set onto another COORDS set.
+\end_layout
+
+\end_inset
+</cell>
+</row>
+<row>
+<cell alignment="center" valignment="top" topline="true" leftline="true" usebox="none">
+\begin_inset Text
+
 \begin_layout Plain Layout
 loadcrd
 \end_layout
@@ -6083,6 +6103,36 @@ For example, to calculate RMSD for a previously created COORDS data set
 crdaction crd1 rmsd first @CA out rmsd-ca.agr crdframes 1,last,10
 \end_layout
 
+\begin_layout Subsection
+crdout
+\end_layout
+
+\begin_layout LyX-Code
+crdout <crd set> <filename> [<trajout args>] [crdframes <start>,<stop>,<offset>]
+\end_layout
+
+\begin_layout Standard
+Write COORDS data set <crd set> to trajectory named <filename>.
+ A subset of frames in the COORDS data set can be specified with 'crdframes'.
+\end_layout
+
+\begin_layout Standard
+For example, to write frames 1 to 10 from a previously created COORDS data
+ set named 
+\begin_inset Quotes eld
+\end_inset
+
+crd1
+\begin_inset Quotes erd
+\end_inset
+
+ to separate PDB files:
+\end_layout
+
+\begin_layout LyX-Code
+crdout crd1 crd1.pdb multi crdframes 1,10
+\end_layout
+
 \begin_layout Subsection
 createcrd
 \end_layout
@@ -6100,33 +6150,144 @@ reference "subsec:cpptraj_createcrd"
 \end_layout
 
 \begin_layout Subsection
-crdout
+graft
 \end_layout
 
 \begin_layout LyX-Code
-crdout <crd set> <filename> [<trajout args>] [crdframes <start>,<stop>,<offset>]
+graft src <source COORDS> [srcframe <#>] [srcfitmask <mask>] [srcmask <mask>]
 \end_layout
 
-\begin_layout Standard
-Write COORDS data set <crd set> to trajectory named <filename>.
- A subset of frames in the COORDS data set can be specified with 'crdframes'.
+\begin_layout LyX-Code
+  	tgt <target COORDS> [tgtframe <#>] [tgtfitmask <mask>] [tgtmask <mask>]
 \end_layout
 
-\begin_layout Standard
-For example, to write frames 1 to 10 from a previously created COORDS data
- set named 
-\begin_inset Quotes eld
+\begin_layout LyX-Code
+  	name <output COORDS> [bond <tgt>,<src> ...]
+\end_layout
+
+\begin_deeper
+\begin_layout Description
+src
+\begin_inset space ~
 \end_inset
 
-crd1
-\begin_inset Quotes erd
+<source
+\begin_inset space ~
 \end_inset
 
- to separate PDB files:
+COORDS> Source coordinates.
 \end_layout
 
-\begin_layout LyX-Code
-crdout crd1 crd1.pdb multi crdframes 1,10
+\begin_layout Description
+[srcframe
+\begin_inset space ~
+\end_inset
+
+<#>] Frame # from source coordinates to use (default 1).
+\end_layout
+
+\begin_layout Description
+[srcfitmask
+\begin_inset space ~
+\end_inset
+
+<mask>] Atoms from source to use if RMS-fitting source onto target.
+\end_layout
+
+\begin_layout Description
+[srcmask
+\begin_inset space ~
+\end_inset
+
+<mask>] Atoms to keep from source (default all).
+\end_layout
+
+\begin_layout Description
+tgt
+\begin_inset space ~
+\end_inset
+
+<target
+\begin_inset space ~
+\end_inset
+
+COORDS> Target coordinates that will be grafted onto.
+\end_layout
+
+\begin_layout Description
+[tgtframe
+\begin_inset space ~
+\end_inset
+
+<#> Frame # from target coordinates to use (default 1).
+\end_layout
+
+\begin_layout Description
+[tgtfitmask
+\begin_inset space ~
+\end_inset
+
+<mask>] Atoms from target to use if RMS-fitting source onto target.
+\end_layout
+
+\begin_layout Description
+[tgtmask
+\begin_inset space ~
+\end_inset
+
+<mask>] Atoms to keep from target (default all).
+\end_layout
+
+\begin_layout Description
+name
+\begin_inset space ~
+\end_inset
+
+<output
+\begin_inset space ~
+\end_inset
+
+COORDS> Name of output COORDS set containing source grafted onto target.
+\end_layout
+
+\begin_layout Description
+[bond
+\begin_inset space ~
+\end_inset
+
+<tgt>,<src>] Create a bond between target atom selected by <tgt> and source
+ atoms selected by <src> in the final structure.
+ May be specified multiple times.
+\end_layout
+
+\end_deeper
+\begin_layout Standard
+Graft one COORDS set onto another.
+ If 
+\series bold
+srcfitmask
+\series default
+ and/or 
+\series bold
+tgtfitmask
+\series default
+ is specified, the source coordinates will be RMS best-fit onto target using
+ the specified atoms.
+ Only the atoms specified by 
+\series bold
+srcmask
+\series default
+ and 
+\series bold
+tgtmask
+\series default
+ will be kept.
+ The 
+\series bold
+bond
+\series default
+ keyword can be used to create bonds between target and source in the final
+ structure.
 \end_layout
 
 \begin_layout Subsection

src/Command.cpp

@@ -41,6 +41,7 @@
 #include "Exec_CrdAction.h"
 #include "Exec_CrdOut.h"
 #include "Exec_Emin.h"
+#include "Exec_Graft.h"
 #include "Exec_LoadCrd.h"
 #include "Exec_LoadTraj.h"
 #include "Exec_PermuteDihedrals.h"
@@ -249,6 +250,7 @@ void Command::Init() {
   Command::AddCmd( new Exec_CrdAction(),        Cmd::EXE, 1, "crdaction" );
   Command::AddCmd( new Exec_CrdOut(),           Cmd::EXE, 1, "crdout" );
   Command::AddCmd( new Exec_Emin(),             Cmd::EXE, 1, "emin"); // hidden
+  Command::AddCmd( new Exec_Graft(),            Cmd::EXE, 1, "graft");
   Command::AddCmd( new Exec_LoadCrd(),          Cmd::EXE, 1, "loadcrd" );
   Command::AddCmd( new Exec_LoadTraj(),         Cmd::EXE, 1, "loadtraj" );
   Command::AddCmd( new Exec_PermuteDihedrals(), Cmd::EXE, 1, "permutedihedrals" );