using Calculator Plugins

08-10-2004 14:15:33

How can I use the Calculator Plugins?

ChemAxon 43e6884a7a

08-10-2004 14:39:55

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

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

You can access these tools fromUsers can develop their own plugins.

ChemAxon 587f88acea

11-12-2004 13:44:00


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



ChemAxon 43e6884a7a

11-12-2004 16:11:03

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 )

07-07-2005 10:07:48

Is it possible to run plugins in batch mode?

ChemAxon fb166edcbd

07-07-2005 10:11:51

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

For example,


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:


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


cxcalc logd -h

for help on logD options, type


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:

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


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:


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:


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:


cxcalc logd -H 5.4 test.smiles

id      logD(pH=5.4)

1       -1.81

ChemAxon fb166edcbd

19-07-2005 22:16:56

pKa calculation

help on options:


cxcalc pka -h

Strongest acidic and basic pKa values with atom indexes:


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:


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

The strongest acidic and basic micro pKa values:


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:


cxcalc logp -h

logP values:


cxcalc logp test.sdf

id      logP

1       -2.53

2       -0.48

micro logP with atomic increments:


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:


cxcalc -S logp test.sdf

TPSA calculation

help on options:


cxcalc psa -h

TPSA values:


cxcalc psa test.sdf

id      PSA

1       83.55

2       83.55

TPSA values of major microspecies at pH=3.4:


cxcalc psa -H 3.4 test.sdf

id      PSA

1       85.17

2       88.00

Results written in SDF tag:


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:


cxcalc acceptorcount donorcount test.sdf

id      acceptorcount   donorcount

1       4       3

2       5       3

Acceptor and donor atom counts with multiplicity:


cxcalc accsitecount donsitecount test.sdf

id      accsitecount    donsitecount

1       5       4

2       6       4

Take major microspecies at pH=7.4:


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):


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.

ChemAxon fb166edcbd

19-07-2005 22:29:30

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.



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:


mview result.mrv