cxcalc output options.

Hello,

Perhaps this is a silly question: if one does not specify an output file when using cxcalc, is the output named and saved anywhere by default?

Regards,

Tim Ritchie

Hi,

If output file is not specified, then the output is written to the console.

Example 1:

$ cxcalc logp nci10.smiles
id logP
1 1,42
2 6,22
3 2,15
4 0,71
5 2,09
6 4,61
7 1,54
8 3,37
9 0,41
10 5,11

Example 2 (output is a SMILES "file"):

$ cxcalc majormicrospecies -H 4.0 nci10.smiles -f smiles
CC1=CC(=O)C=CC1=O
S(SC1=NC2=C(S1)C=CC=C2)C1=NC2=C(S1)C=CC=C2
[O-]C1=C(Cl)C=C(C=C1N(=O)=O)N(=O)=O
[NH2+]=C1NC=C(S1)N(=O)=O
NC1=CC2=C(C=C1)C(=O)C1=C(C=CC=C1)C2=O
OC1=C(Br)C2=C(C=C1)C(C1=C(C=CC=C1)C([O-])=O)=C1C=CC(=O)C(Br)=C1O2
CN(C)C1=C(Cl)C(=O)C2=C(C=CC=C2)C1=O
CC1=C(C2=C(C=C1)C(=O)C1=CC=CC=C1C2=O)N(=O)=O
CC(=NO)C(C)=NO
C1=CC=C(C=C1)P(C1=CC=CC=C1)C1=CC=CC=C1

Zsolt

OK, thanks for the clarification.

Could you confirm the syntax to specify an output file please?

Regards,

Tim Ritchie.

The

-o, --output         output file path (default: stdout)

option can be used to specify the output file.

Example:

$ cxcalc -o mmicrospecies.smiles majormicrospecies -H 4.0 nci10.smiles -f smiles

Note: "-o" is a "general option", not a "plugin option". It should be written before the name of the calculation.

See http://www.chemaxon.com/marvin/help/applications/calc.html#usage

Zsolt

Hello again,

How should I configure the output so that the calculated descriptors are appended as columns to my original file? (I am using .smi rather than .sdf).

Regards,

Tim Ritchie.

Hi,

At the moment cxcalc has options only for adding properties  to SDF and MRV files ("-S" and "-M"). You can use molconvert to convert these formats to SMILES. Use the "T" SMILES export option to specify SDF fields to export.

Example:

$ cxcalc -S -t logP logp nci10.smiles | molconvert smiles:TlogP
#SMILES logP
CC1=CC(=O)C=CC1=O 1,42
S(SC1=NC2=C(S1)C=CC=C2)C1=NC2=CC=CC=C2S1 6,22
OC1=C(Cl)C=C(C=C1[N+]([O-])=O)[N+]([O-])=O 2,15
[O-][N+](=O)C1=CNC(=N)S1 0,71
NC1=CC2=C(C=C1)C(=O)C1=C(C=CC=C1)C2=O 2,09
OC(=O)C1=C(C=CC=C1)C1=C2C=CC(=O)C(Br)=C2OC2=C1C=CC(O)=C2Br 4,61
CN(C)C1=C(Cl)C(=O)C2=C(C=CC=C2)C1=O 1,54
CC1=C(C2=C(C=C1)C(=O)C1=CC=CC=C1C2=O)[N+]([O-])=O 3,37
CC(=NO)C(C)=NO 0,41
C1=CC=C(C=C1)P(C1=CC=CC=C1)C1=CC=CC=C1 5,11

I hope this helps,

Zsolt

Is this method possible if more than one descriptor is calculated, i.e. the output would contain the smiles and multiple columns of results (with a header row).

Thanks and regards,

Tim Ritchie.

Yes, it is.

Example:

$ cxcalc -S -t logP logp nci10.smiles | cxcalc -S -t atomcount atomcount | cxcalc -S -t PSA psa | molconvert smiles:TlogP:atomcount:PSA
#SMILES logP    atomcount       PSA
CC1=CC(=O)C=CC1=O       1.42    15      34.14
S(SC1=NC2=C(S1)C=CC=C2)C1=NC2=CC=CC=C2S1        6.22    28      25.78
OC1=C(Cl)C=C(C=C1[N+]([O-])=O)[N+]([O-])=O      2.15    17      111.87
[O-][N+](=O)C1=CNC(=N)S1        0.71    12      81.70
NC1=CC2=C(C=C1)C(=O)C1=C(C=CC=C1)C2=O   2.09    26      60.16
OC(=O)C1=C(C=CC=C1)C1=C2C=CC(=O)C(Br)=C2OC2=C1C=CC(O)=C2Br      4.61    37      83.83
CN(C)C1=C(Cl)C(=O)C2=C(C=CC=C2)C1=O     1.54    26      37.38
CC1=C(C2=C(C=C1)C(=O)C1=CC=CC=C1C2=O)[N+]([O-])=O       3.37    29      79.96
CC(=NO)C(C)=NO  0.41    16      65.18
C1=CC=C(C=C1)P(C1=CC=CC=C1)C1=CC=CC=C1  5.11    34      0.00

Simpler syntax, to calculate only the properties:

$ cxcalc nci10.smiles logp atomcount psa
id      logP    Atom count      Polar surface area
1       1.42    15      34.14
2       6.22    28      25.78
3       2.15    17      111.87
4       0.71    12      81.70
5       2.09    26      60.16
6       4.61    37      83.83
7       1.54    26      37.38
8       3.37    29      79.96
9       0.41    16      65.18
10      5.11    34      0.00

Zsolt

OK. Thanks.

I will give this a try.

Regards,

Tim Ritchie.

Zsolt, thanks for the useful post. I would have an additional question:

In case where cxcalc is calculating the microspeciesdistribution (and so more than one output molecule is created for each input molecule), it would be possible to output also a molecule identifier (e.g. molcount) as an additional column for the SMILES format?

Thanks in advance

Hi, 

Yes, you can do that using cxcalc and molconvert together. This is the command you have to use:

cxcalc msdistr -t MD sildenafil adrenaline | molconvert smiles:T_MOLCOUNT:MD

MD is the tag name for microspecies distribution, while _MOLCOUNT is the default molecule ID tag. This command will both output the ID and the relevant %s. I used just 2 molecules as an example.

For further information please see the following documentation on the SMILES format:

https://docs.chemaxon.com/display/docs/SMILES+and+SMARTS+import+and+export+options

I hope this helps, 

Daniel