using Calculator Plugins

How can I use the Calculator Plugins?

ChemAxon's Calculator Plugins are part of all of our software packages (Marvin Beans, Marvin Applets, and JChem). You don't need to install the Plugins separately, but you do need license keys to activate them.





The documentation is available at http://www.chemaxon.com/marvin/chemaxon/marvin/help/calculator-plugins.html





I suggest to download one of these packages and try the plugin you are interested in.





You can access these tools from

• GUI
  
  
  MarvinSketch: http://www.chemaxon.com/marvin/chemaxon/marvin/help/sketch-index.html
  
  
  MarvinView: http://www.chemaxon.com/marvin/chemaxon/marvin/help/view-index.html
• Java API
  
  
  http://www.chemaxon.com/marvin/doc/api/chemaxon/marvin/calculations/package-summary.html
• command line
  
  
  Calculator: http://www.chemaxon.com/marvin/doc/user/calc.html
  
  
  Evaluator: http://www.jchem.com/doc/user/Evaluator.html
• SQL statements using the JChem Cartridge for Oracle
  
  
  http://www.jchem.com/doc/guide/cartridge/index.html
• chemical expressions using our tools (for example Reactor, structure searching, etc.)
  
  
  http://www.jchem.com/doc/user/
  
  
  

Users can develop their own plugins.

Hello.





How can I obtain those licence keys and what will the charge be?





greets,


AV

AV wrote:

How can I obtain those licence keys and what will the charge be?

We will contact you by email about the licensing issues.


(The email address of Sales is available at http://www.chemaxon.com/contactus.html )

Is it possible to run plugins in batch mode?

We have the cxcalc tool for plugin calculations in batch mode.


For example,

Code:

cxcalc logd test.smiles

will write logD values for the series of pH-s in the default pH range


[0, 14] with default step 1.0:

Code:

id      pH=0.00 pH=1.00 pH=2.00 pH=3.00 pH=4.00 pH=5.00 pH=6.00 pH=7.00 pH=8.00pH=9.00  pH=10.00     pH=11.00        pH=12.00        pH=13.00        pH=14.001       -2.05   -2.05   -2.05   -2.05  -2.04   -1.94   -1.46   -0.59   0.24   0.56     0.19    -0.58   -1.07   -1.17   -1.18

Different command line options can alter the output, type

Code:

cxcalc logd -h

for help on logD options, type

Code:

cxcalc -h

on general options and available calculations.


Note, that general options should be written between "cxcalc" and "logd" while logd specific


options should be written after "logd". The input file(s)/SMILES string(s) can be placed


at either place.


General cxcalc documentation:


http://www.chemaxon.hu/marvin/doc/user/calc.html





You can have just the numbers without the header and molecule ID by:

Code:

cxcalc -N hi logd test.smiles -2.05   -2.05   -2.05   -2.05   -2.04   -1.94   -1.46   -0.59   0.24    0.56   0.19     -0.58 -1.07   -1.17   -1.18

You can alter the pH range and step size by:

Code:

cxcalc logd -l 2.0 -u 4.5 -s 0.5 test.smiles id      pH=2.00 pH=2.50 pH=3.00 pH=3.50 pH=4.00 pH=4.50 1       -2.05   -2.05   -2.05   -2.04   -2.04   -2.01

You can always type the SMILES instead of the file name


and you can give more input SMILES / files:

Code:

cxcalc logd -l 2.0 -u 4.5 -s 0.5 "NCC1=CC=C(Cl)C=C1O" "NCC1=C(CCCl)C=C(Cl)C=C1O" id      pH=2.00 pH=2.50 pH=3.00 pH=3.50 pH=4.00 pH=4.50 1       -2.05   -2.05   -2.05   -2.04   -2.04   -2.01 2       -1.18   -1.18   -1.18   -1.18   -1.17   -1.15

You can calculate the logD value at a specific pH:

Code:

cxcalc logd -H 5.4 test.smiles id      logD(pH=5.4) 1       -1.81

pKa calculation





help on options:

Code:

cxcalc pka -h

Strongest acidic and basic pKa values with atom indexes:

Code:

cxcalc pka test.sdf id      apKa1   apKa2   bpKa1   bpKa2   atoms 1       3.65    8.68    9.76            10,7,12 2       3.39    8.75    9.50            17,12,14

pKa values for each atom, stored in SDF tag in output file result.sdf:

Code:

cxcalc -S -o result.sdf pka test.sdf

The strongest acidic and basic micro pKa values:

Code:

cxcalc pka -a 1 -b 1 -m micro test.sdf id      apKa1   bpKa1   atoms 1       3.83    9.01    10,12 2       3.70    9.05    17,14

logP calculation





help on options:

Code:

cxcalc logp -h

logP values:

Code:

cxcalc logp test.sdf id      logP 1       -2.53 2       -0.48

micro logP with atomic increments:

Code:

cxcalc logp -t logPMicro,increments test.sdf id      logP of ionic species   increments 1       0.40    -0.10;0.16;0.01;0.01;0.16;0.01;0.49;-0.11;-0.35;0.49;-0.84;0.12 2       1.92    0.16;0.01;0.16;0.16;0.01;0.16;0.01;-0.10;0.01;-0.10;0.96;0.49;-0.84;0.12;-0.11;-0.35;0.49

SDF output with logP values in SDF tags:

Code:

cxcalc -S logp test.sdf

TPSA calculation





help on options:

Code:

cxcalc psa -h

TPSA values:

Code:

cxcalc psa test.sdf id      PSA 1       83.55 2       83.55

TPSA values of major microspecies at pH=3.4:

Code:

cxcalc psa -H 3.4 test.sdf id      PSA 1       85.17 2       88.00

Results written in SDF tag:

Code:

cxcalc -S psa -H 3.4 test.sdf

HBDA calculation





There are more calculations here:





acc/don: Hydrogen bond acceptor/donor multiplicity calculation on atoms.


acceptorcount/donorcount: Hydrogen bond acceptor/donor atom count in molecule.


accsitecount/donsitecount: Hydrogen bond acceptor/donor multiplicity in molecule.


msacc/msdon: Hydrogen bond acceptor/donor average multiplicity over microspecies by pH.





Combinations (more calculations in one keyword):


acceptor: acc, acceptorcount, accsitecount, msacc


donor: don, donorcount, donsitecount, msdon


hbda: acc, don, accsitecount, donsitecount








Acceptor and donor atom counts:

Code:

cxcalc acceptorcount donorcount test.sdf id      acceptorcount   donorcount 1       4       3 2       5       3

Acceptor and donor atom counts with multiplicity:

Code:

cxcalc accsitecount donsitecount test.sdf id      accsitecount    donsitecount 1       5       4 2       6       4

Take major microspecies at pH=7.4:

Code:

cxcalc acceptorcount -H 7.4 donorcount -H 7.4 test.sdf id      acceptorcount   donorcount 1       3       2 2       4       2 cxcalc accsitecount -H 7.4 donsitecount -H 7.4 test.sdf id      accsitecount    donsitecount 1       4       4 2       5       4

Average acceptor/donor multiplicity over microspecies by pH


(in the [4.0, 8.0] interval, with step 0.5):

Code:

cxcalc msacc -l 4.0 -u 8.0 -s 0.5 msdon -l 4.0 -u 8.0 -s 0.5 test.sdf id      pH=4.00 pH=4.50 pH=5.00 pH=5.50 pH=6.00 pH=6.50 pH=7.00 pH=7.50 pH=8.00 pH=4.00  pH=4.50 pH=5.00 pH=5.50 pH=6.00 pH=6.50 pH=7.00 pH=7.50 pH=8.00 1       4.00    4.00    4.00    4.00    4.00    4.00    4.01    4.02    4.06   4.31     4.12    4.04    4.01    4.00    3.99    3.98    3.94    3.82 2       5.00    5.00    5.00    5.00    5.00    5.00    5.00    5.01    5.04   4.20     4.07    4.02    4.01    4.00    4.00    3.98    3.95    3.84

Note, that the options should be listed for each calculation keyword separately. All of the above can be written to SDF tags by setting the -S global option right after cxcalc, as in case of the other calculations above.

From Marvin 4.0. there is a new cxcalc option: -M which produces MRV output of a result molecule containing the molecular results in molecule properties, atomic results in atom labels. This is the decorated molecule that is displayed in the Marvin GUI (when plugins are run from MarvinView / MarvinSketch Tools menu).


This option is useful when you want to show the results visually.





Examples:

Code:

cxcalc -M -o result.mrv charge test.sdf cxcalc -M -o result.mrv pka test.sdf cxcalc -M -o result.mrv logp -t logPTrue,increments test.sdf

Then you can see the atomic results in atom labels,


moleular values in tags:

Code:

mview result.mrv