Installation:
- Download and launch platform specific installer by following the installation instructions.
molconvert [options] outformat[:export-options] [files...]
The outformat argument must be one of the following strings:
Options:
mrv
,(document formats) mol
,rgf
,sdf
,rdf
,csmol
,csrgf
,cssdf
,csrdf
,
cml
,smiles
,sybyl
,pdb
,xyz
(molecule file formats) jpeg
,png
,pov
,ppm
,svg
,(graphics formats) gzip
,base64
(compression and encoding)
-o file |
Write output to specified file instead of standard output | ||||||||
-s string |
Read a molecule from specified SMILES string | ||||||||
-F |
Remove small fragments, keep the largest | ||||||||
-Y |
Remove explicit H atoms | ||||||||
-T f1:f2... |
Print a table containing fields from SDF separated by tab in the case of SMILES export | ||||||||
-c "f1OPvalue&f2OPvalue..." |
Filtering by the values of fields in the case of SDF import. OP may be: =,<,>,<=,>= | ||||||||
-v |
Verbose | ||||||||
-vv |
Very verbose (print stack trace at error) | ||||||||
-n |
Skip valence checking | ||||||||
-2 [: options] |
Calculate 2D coordinates (default if the input is
SMILES) Options for coordinate calculation:
| ||||||||
-3 [: options] |
Calculate 3D coordinates Options for coordinate calculation:
|
filename{options} filename{MULTISET,options} to merge molecules into one that contains multiple atom sets filename{format:} to skip automatic format recognition filename{format:options} filename{format:MULTISET,options}
molconvert smiles caffeine.mol
molconvert smiles:-a -s "c1ccccc1"
molconvert smiles:a -s "C1=CC=CC=C1"
molconvert mol caffeine.smiles -o caffeine.mol
molconvert sdf *.mol -o molecules.sdf
molconvert -2:O2e mol caffeine.smiles -o caffeine.mol
molconvert smiles "foo.xyz{xyz:}"
Note: This is just an example.
XYZ and other formats known by Marvin are always recognized
(send us a bug report otherwise), so the specification of the input format
is usually not needed. It is only relevant if a user-defined import module
is used.
molconvert smiles "foo.xyz{f1.4C4}"
molconvert smiles "foo.xyz.gz{gzip:xyz:f1.4C4}"
molconvert mol "foo.xyz.gz{gzip:xyz:MULTISET,f1.4C4}"
molconvert smiles -c "ID<=1000&logP>=-2&logP<=4" -T ID:logP foo.sdf