canvasMolDescriptors Command Help
Command: $SCHRODINGER/utilities/canvasMolDescriptors
canvasMolDescriptors - Calculates molecular descriptors.
Usage 1: canvasMolDescriptors [<job control options>] <program options>
Usage 2: canvasMolDescriptors [<job control options>] -commandFile <filename>
where <filename> is a line-delimited list of commands. Under job
control, the output file must be specified on the command line as
<program options>.
Job Control Options: [-JOB <jobName> [-HOST <host>[:<n>]]
[-MINREC <nrec>]
[-LOCAL]
[-TMPDIR <dir>]
[-WAIT]
[-INTERVAL <n>]
[-NICE]]
-JOB <jobName> - Job name. If omitted, no other job control options are
permitted.
-HOST <host>[:<n>] - Run job on <host>. Include ":<n>" to split across
<n> CPUs.
-MINREC <nrec> - Minimum number of records per CPU. Prevents
submission of a large number of subjobs that each
contains only a small number of records. The default
is 100.
-LOCAL - Store temporary job files in current directory.
-TMPDIR <dir> - Store temporary job files in <dir>.
-WAIT - Do not return prompt until job completes.
-INTERVAL <n> - Update log file every <n> seconds.
-NICE - Run job at reduced priority.
Program Options: -ismi <smiFile>
| -isd <sdFile> [-fieldAsName <field>]
| -imae <maeFile> [-fieldAsName <field>]
| -icsv <csvFile> [-noHeader]
[-d <delimiter>]
[-smi <SMILESCol>]
[-name <nameCol>]
[-AlogP [-method <method>] ]
[-Estate]
[-EstateKey]
[-EstateCnt]
[-EstateSum [-maxPath <n>]
[-pow <fallOffPower>] ]
[-EstateAvg [-maxPath <n>]
[-pow <fallOffPower>] ]
[-HBA [-HBAfile <filename>] ]
[-HBD [-HBDfile <filename>] [-distinct]]
[-MR]
[-MW]
[-Polar]
[-PSA]
[-RB [-RBfile <filename>] [-use_ligparse_def] ]
[-HAC]
[-CC]
[-CCU]
[-RC]
[-All [-maxPath <length> ]
[-pow <fallOffPower>] ]
[-Custom <customFile> [-CustomName <customPropName>]
[-CustomKey]
[-CustomCnt]
[-CustomSum]
[-CustomAvg] ]
[-helpHBA]
[-helpHBD]
[-helpRB]
[-smiles]
[-fill]
[-n <structureRange> [-file]]
[-o<fmt> <outputFile>
[-odata [-fieldOnly <fields>] [-uniform]]]
[-obad <badMolFile>]
-ismi <smiFile> - Input SMILES file. One SMILES string per line.
-isd <sdFile> - Input SD file, either compressed or uncompressed.
-imae <maeFile> - Input MAE file, either compressed or uncompressed.
-icsv <csvFile> - Input CSV file, SMILES string as the first column,
followed by delimited properties, header required.
-noHeader - Specify if no header line in the above <csvFile>.
-d <delimiter> - Delimiter used in the csvFile. Default is ','.
-smi <SMILESCol> - User specified field of SMILES strings, either by
name or by column index starting at 1. By default,
SMILES column is the first column.
-name <nameCol> - User specified field to use as molecule name, either
by name or by column index. By default, it is the
second column.
-AlogP - Calculates atomic logP.
-method - AlogP assignment method [last, sum, mean].
default is 'last'.
-Estate - Calculates electrotopological states.
-EstateKey - Print out the presence or absence of each Estate
atom type inside a given molecule.
-EstateCnt - Print out the count of each Estate atom type.
-EstateSum - Calculates the total sum of each Estate atom type
according to -maxPath and -pow values.
-EstateAvg - Calculates the average of each Estate atom type
(sum/count) based on -maxPath and -pow values.
-maxPath <n> - If set, only neighboring atoms within <n> bonds
are considered. By default, all neighboring atoms
are taken into account.
-pow <fallOffPower> - Sets how fast the perturbation falls. Default is 2.
-HBD - Counts hydrogen bond donors.
-HBDfile <filename> - User-defined SMARTS patterns to overwrite Canvas
default definition of hydrogen bond donors.
-distinct - Count each hydrogen as a distinct donor. By default
a given atom that bears one or more donatable
hydrogens is counted as one donor.
-HBA - Counts hydrogen bond acceptors.
-HBAfile <filename> - User-defined SMARTS patterns to overwrite Canvas
default definition of hydrogen bond acceptors.
-MR - Calculates molar refractivity.
-Polar - Calculates Miller polarizability.
-MW - Molecular weight.
-PSA - Calculates polar surface area.
-RB - Returns the number of rotatable bonds.
-HAC - Heavy atom count
-CC - Chiral center Count (includes unspecificied)
-CCU - Chiral center Count (CC + undefined)
-RC - Ring count (SSSR)
-RBfile <filename> - User-defined SMARTS patterns to modify or overwrite
Canvas default definition of rotatable bonds. See
the end of this usage page to find sample SMARTS
patterns.
-use_ligparse_def - Use the same set of rules as in MacroModel LigParse.
-All - All the above, but not including custom descriptors
(Default).
-Custom <customFile> - Calculate molecular property based on a user-specified
atom typing file. By default, this property will be
named "Custom".
-CustomName <name> - Uses <name> as the custom property name.
-CustomKey - Print out the presence or absence of each custom atom
type inside a given molecule. Must be used with
-Custom <customFile>.
-CustomCnt - Print out the count of each custom atom type. Must be
used with -Custom <customFile>.
-CustomSum - Print out the total sum of each custom atom type. Must
be used with -Custom <customFile>.
-CustomAvg - Print out the average of each custom atom type. Must
be used with -Custom <customFile>.
-helpHBD - Print out Canvas default definition of hydrogen bond
donors. Users can use this as a template to specify
their own definitions, and supply to -HBDfile option.
-helpHBA - Similar as -helpHBD, for acceptors.
-helpRB - Print out a file (with no SMARTS patterns) for users
to modify.
-smiles - Include SMILES string as the 1st column for each
molecule in <outputFile>.
-fill - Fill in a comma-separated blank line for a molecule
that fails to generate descriptors. If omitted,
skips and continues with the next molecule.
-n <structureRange> - The set of input structures to process:
1,4 - structures 1 and 4
1:10,14 - structures 1 through 10 and 14
2: - structures 2 through the end of file
:5,13:18 - structures 1 through 5 and 13 through 18
All structures are processed by default.
-file - Interpret <structureRange> as a file name. Each
line in this file should contain a valid row
range specification.
-fieldAsName <field> - Field or property title in a SD or a MAE file that
can be used as the name of a molecule. If -imae
option is used, <field> must start with "s_" or
"i_". Cannot use with -ismi or -icsv
option.
-o<fmt> - Output format: -ocsv --> CSV
-osd --> SD
-omae --> Maestro
The default is CSV. If -osd or -omae is used
with -icsv, or -ismi option, it takes
longer to finish because 2D coordinates are
generated on the fly.
<outputFile> - Output file name. May be omitted with -ocsv,
in which case standard output is used. Ignored
with -JOB, in which case the output file name is
assigned automatically: <jobName>_desc.csv,
<jobName>_desc.maegz, or <jobName>_desc.sdf.gz.
-odata - Copy data fields from input Maestro/SD file to
output file. Only available with -isd or -imae.
-v3 - Output MDL version 3 SD Format.
-fieldOnly <fields> - Copy only specific input data fields. <fields>
is a space-delimited list of property names.
-uniform - All input structures have the same data fields.
-obad <badMolFile> - Save the molecules that failed to calculate
to a file. By default, an error message goes
to standard error.
-u - Use unique SMILES for all SMILES output.
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Using user-specified SMARTS patterns to define rotatable bonds:
By default, a rotatable bond in Canvas is defined as a single, non-ring bond,
bounded to a non-terminal heavy atom (non-hydrogen). Amide bond (C-N) and a
bond next to a triple bond are excluded because of the high energy barrier.
To include or exclude a user-defined bond type, one must specify both atoms
connected to the bond with valid SMARTS. A positive integer value (>0) must
follow each SMARTS by a ">" character. Within each file, this integer value
must be unique. Only heavy atoms may be specified, and one SMARTS per line.
A line staring with ";" is treated as comment.
For example, the following two lines allows a user to include secondary
amide bond:
C(=O)N[!#1] > 1
N([!#1])C=O > 2
If, in addition, a user wants to include bonds between OH and SP3 Carbon,
one can include the following two lines in "include" section the above
file:
C(*)(*)(*)-[OH] > 3
[OH]-C(*)(*)* > 4
If a user wants to exclude single bonds connecting a Carbon attached to a
Halogen atom, one can copy the following two lines to the "exclude"
section of the file.
*-C[I,Br,Cl,F] > 5
C([I,Br,Cl,F])-* > 6
Other SMARTS patterns may be considered in counting rotatable bonds:
[OH]-C=O > 100
C(=O)-[OH] > 200