1. Andrew Dalke
  2. fmcs

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dalke  committed 7715506

changed --output-all-structures to --output-all
Minor updates and corrections to the text

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             [--ring-matches-ring-only] [--complete-rings-only]
             [--select SELECT] [--timeout SECONDS] [--output FILENAME]
             [--output-format {smarts,fragment-smiles,fragment-sdf,complete-sdf}]
-            [--output-all-structures] [--save-atom-class-tag TAG]
+            [--output-all] [--save-atom-class-tag TAG]
             [--save-counts-tag TAG] [--save-atom-indices-tag TAG]
             [--save-smarts-tag TAG] [--save-smiles-tag TAG] [--times] [-v]
             [--version]
                         'complete-sdf' writes the entire SD file with the
                         fragment information stored in the tag specified by
                         --save-fragment-indices-tag. (Default: smarts)
-  --output-all-structures
-                        By default the structure output formats only show an
+  --output-all          By default the structure output formats only show an
                         MCS for the first input structure. If this option is
                         enabled then an MCS for all of the structures are
                         shown.
 You can easily see that the elements match but that bond types were ignored.
 
 
-Independently specify --atom-compare and --bond-compare options
+Separately specify --atom-compare and --bond-compare options
 ---------------------------------------------------------------
 
-You can specify the base atom and bond comparisons 
-
-The "--compare" option is a shortcut. You can specify the atom and
-bond comparison directly using "--atom-compare" and "--bond-compare".
+The "--compare" option is a shortcut for common, chemically reasonable
+comparisons. You can specify the atom and bond comparison separately
+using "--atom-compare" and "--bond-compare", which means you can do
+some pretty strange (or interesting!) MCS searches.
 
 Here I explicitly use the default of "--atom-compare elements":
 
 Generating SD files and SD tags
 -------------------------------
 
-So far I've shown examples of 
-You can get the result as an SD file in one of two forms, either a "fragmenet-sdf":
+So far I've shown examples of generates SMILES output files. You can
+get the result as an SD file in one of two forms, either a "fragment-sdf":
 
 % python fmcs.py sample_files/na_clustered_3D_MM_1.sdf --output-format fragment-sdf
 ZINC03581099
 CCN(C(=O)OC)C(c1ccc(O)cc1)c1ccc(OC)cc1 CHEMBL311765
 Total time 1.01 seconds: load 0.00 fragment 0.00 select 0.00 enumerate 1.00
 
+
 Verbosity
 ---------
 
 #################
 
 
-When I run this program I get:
+When I run this program I get (also available as test/smsd_arom_isotopes.smi):
 
 % python halogen_classes.py sample_files/smsd_arom.smi test.smi
 % cat test.smi 
 
 And here you see that it made a difference.
 
-% fmcs sample_files/smsd_arom.smi 
+% fmcs sample_files/smsd_arom.smi
 [#6]-1-[#6]-[#6]-[#6]-[#6]-[#6]-1 6 atoms 6 bonds (complete search)
 
 % fmcs --atom-compare isotopes test.smi