Merge branch 'master' of https://github.com/asad/SMSD

README.md

@@ -53,6 +53,75 @@ java -Xms500M -Xmx512M -cp smsd.jar: uk.ac.ebi.smsd.cmd.SMSDcmd $@
 ```
 ===================
 
+--------------------
+Options
+--------------------
+
+```
+Single SMILES query vs single SMILES target:
+
+java -Xms500M -Xmx512M -cp smsd.jar: uk.ac.ebi.smsd.cmd.SMSDcmd -Q SMI -q "CCN" -T SMI -t "CCCNC"
+
+Single SMILES query vs single MOL target:
+
+java -Xms500M -Xmx512M -cp smsd.jar: uk.ac.ebi.smsd.cmd.SMSDcmd -Q SMI -q "CCN" -T MOL -t Data/ATP.mol
+
+Signature query vs smiles target, outputting the subgraph to stdout:
+
+java -Xms500M -Xmx512M -cp smsd.jar: uk.ac.ebi.smsd.cmd.SMSDcmd -Q SIG -q "[C]([C][C])" -T SMI -t "C(C)CC" -O SMI -o --
+
+Multiway N-MCS, outputing the subgraph as a smiles to stdout:
+
+java -Xms500M -Xmx512M -cp smsd.jar: uk.ac.ebi.smsd.cmd.SMSDcmd -T SDF -t Data/arom.sdf -N -O SMI -o --
+
+Just use ./SMSD -I to list all the image options.
+
+Few more options:
+
+++++++++++++++++++++++++++++++++++++++++++++++
+NOTE: The graph matching is performed by removing
+the Hydrogens
+++++++++++++++++++++++++++++++++++++++++++++++
+
+usage:
+       
+ -A                  Appends output to existing files, else creates new
+                     files
+ -a                  Add Hydrogen
+ -b                  Match Bond types (Single, Double etc)
+ -d <WIDTHxHEIGHT>   Dimension of the image in pixels
+ -f <number>         Default: 0, Stereo: 1, Stereo+Fragment: 2,
+                     Stereo+Fragment+Energy: 3
+ -g                  create png of the mapping
+ -h,--help           Help page for command usage
+ -I <option=value>   Image options
+ -m                  Report all Mappings
+ -N                  Do N-way MCS on the target SD file
+ -o <filename>       Output the substructure to a file
+ -O <type>           Output type
+ -Q <type>           Query type (MOL, SMI, etc)
+ -q <filepath>       Query filename
+ -r                  Remove Hydrogen
+ -s                  SubStructure detection
+ -S <suffix>         Add suffix to the files
+ -T <type>           Target type (MOL, SMI, etc)
+ -t <filepath>       Target filename
+ -z                  Ring Match
+
+++++++++++++++++++++++++++++++++++++++++++++++
+
+Allowed types for single-molecules (query or target):
+MOL	MDL V2000 format
+ML2	MOL2 Tripos format
+PDB	Protein Databank Format
+CML	Chemical Markup Language
+SMI	SMILES string format
+SIG	Signature string format
+
+Allowed types for multiple-molecules (targets only):
+SDF	SD file format
+```
+
 THIRD PARTY TOOL
 ---------------
 You need the CDK (https://github.com/cdk/cdk) as SMSD depends on the CDK for processing the Chemical information.