GreenPolyProducts/openbabel
5
0
Fork 0
mirror of https://github.com/openbabel/openbabel.git synced 2026-08-27 05:37:38 -05:00
Code Issues Packages Projects Releases Wiki Activity

fix firstonly logic and extend man page

Browse Source
This commit is contained in:
David Koes
2019-04-25 16:35:48 -04:00
parent f124c6e50e
commit 85ccd84950
2 changed files with 29 additions and 6 deletions
Download Patch File Download Diff File Expand all files Collapse all files
doc/obrms.1
+24 -3
View File
@@ -3,20 +3,41 @@
.Dt obrms 1 URM
.Sh NAME
.Nm obrms
.Nd "calculate the RMSD between two chemically identical structures"
.Nd "Calculate the heavy-atom RMSD between two chemically identical structures"
.Sh SYNOPSIS
.Nm
.Op Ar -firstonly
.Op -fmxso
.Ar filename1
.Ar filename2
.Sh DESCRIPTION
Computes the heavy-atom RMSD of identical compound structures.
Structures in multi-structure files are compared one-by-one unless -firstonly
is passed, in which case only the first structure in the reference file is used.
.Sh OPTIONS
.Bl -tag -width flag
.It Fl f, -firstonly
use only the first structure in the reference file (otherwise the nth molecule
in the reference file is compared to the nth molecule in the test file)
.It Fl m, -minimize
Compute the minimum RMSD achievable by applying a rigid-body transformation to
the test molecule
.It Fl x, -cross
Compute all n^2 RMSDs between molecules of the reference file. Test file is ignored.
.It Fl s, -separate
Separate reference file into constituent molecules (disconnected fragments)
and report best RMSD
.It Fl o, -out
Re-oriented test structure output (used with -m)
.Sh EXAMPLES
.Dl "obrms ref.sdf test.sdf"
.Pp
Calculate the RMSD between ref.sdf and test.sdf
Calculate the RMSD between ref.sdf and test.sdf. Both files should have the
same number of molecules.
.Dl "obrms -f ref.sdf test.sdf"
.Pp
Calculate the RMSD between the first molecule in ref.sdf and each molecule in
test.sdf.
.Sh SEE ALSO
.Xr obfit 1 .
.Pp
tools/obrms.cpp
+5 -3
View File
@@ -139,7 +139,7 @@ class Matcher
}
qtrfit(refcoord, testcoord, N, rmatrix);
rotate_coords(testcoord, rmatrix, N);
rotate_coords(testcoord, rmatrix, N);
for (unsigned i = 0; i < N; i++)
{
@@ -226,7 +226,7 @@ int main(int argc, char **argv)
"Usage: obrms reference_file [test_file]\n"
"Options:\n"
"\t -o, --out re-oriented test structure output\n"
"\t -f, --firstonly use only the first structure in the test file\n"
"\t -f, --firstonly use only the first structure in the reference file\n"
"\t -m, --minimize compute minimum RMSD\n"
"\t -x, --cross compute all n^2 RMSDs between molecules of reference file\n"
"\t -s, --separate separate reference file into constituent molecules and report best RMSD\n"
@@ -373,9 +373,11 @@ int main(int argc, char **argv)
{
outconv.Write(&moltest, &out);
}
if (firstOnly)
if (!firstOnly) //one test molecule will be read for each reference molecule
break;
}
if(firstOnly) //done with first reference mol
break;
}
}
return (0);