python3-cactus

2014-10-12 23:17 UTC
  • Xyne

Metadata

Description:

Interface modules for CACTUS (CADD Group Chemoinformatics Tools and User Services).

Latest Version:

2012.12

Architecture:

  • any

Dependencies:

Arch Repositories:

  • [xyne-any]
  • [xyne-i686]
  • [xyne-x86_64]

AUR ID:

63994

Tags:

About

The CACTUS package provides modules for interacting with CADD Group Chemoinformatics Tools and User Services (CACTUS)

Modules

CACTUS.CIR

This module is a memoized wrapper around the Chemical Identifier Resolver (CIR). In combination with OpenBabel it is possible to access a wide variety of chemical data.

The module's main function provides a command-line interface for CIR interaction. See the ouput examples below.

TODO

Create modules for the other tools and services.

cactus-cir: Help Message

$ cactus-cir -h

usage: cactus-cir [-h] [--more-help]
                  [--format {CONFIG,CONTCAR,HISTORY,POSCAR,VASP,abinit,acesout,acr,adfout,alc,arc,axsf,bgf,box,bs,c09out,c3d1,c3d2,caccrt,can,car,castep,ccc,cdx,cdxml,cif,ck,cml,cmlr,crk2d,crk3d,ct,cub,cube,dat,dmol,dx,ent,fa,fasta,fch,fchk,fck,feat,fhiaims,fract,fs,fsa,g03,g09,g92,g94,g98,gal,gam,gamess,gamin,gamout,got,gpr,gro,gukin,gukout,gzmat,hin,inchi,inp,ins,jout,log,mcdl,mcif,mdl,ml2,mmcif,mmd,mmod,mol,mol2,mold,molden,molf,moo,mop,mopcrt,mopin,mopout,mpc,mpo,mpqc,mrv,msi,nwo,out,outmol,output,pc,pcm,pdb,pdbqt,png,pos,pqr,pqs,prep,pwscf,qcout,res,rsmi,rxn,sd,sdf,smi,smiles,sy2,t41,tdd,text,therm,tmol,txt,txyz,unixyz,vmol,xml,xsf,xtc,xyz,yob}]
                  [-o <identifier> [<identifier> ...]]
                  [-f <filepath> [<filepath> ...]]
                  [-r {hashisy,cas,stdinchikey,uuuuu,ficts,ficus,iupac_name,names} [{hashisy,cas,stdinchikey,uuuuu,ficts,ficus,iupac_name,names} ...]]
                  [-d <database path>]
                  [<identifier> [<identifier> ...]]

Query the CACTUS (CADD Group Chemoinformatics Tools and User Services:
http://cactus.nci.nih.gov/) Chemical Identifier Resolver using chemical
identifier strings or chemical files as input. Files may be in any format from
which Open Babel can obtain an InChi Key. Query results are cached in an
SQLite3 database.

positional arguments:
  <identifier>          Identifier strings. By default, these are interpretted
                        as InChi Keys. To use another string format recognized
                        by Open Babel, use the "--format" option. To use an
                        identifier only recognized by the Chemical Structure
                        Identifier, use "--other".

optional arguments:
  -h, --help            show this help message and exit
  --more-help           Display more help including descriptions of Open Babel
                        input formats and Chemical Identifier Resolver output
                        representations.
  --format {CONFIG,CONTCAR,HISTORY,POSCAR,VASP,abinit,acesout,acr,adfout,alc,arc,axsf,bgf,box,bs,c09out,c3d1,c3d2,caccrt,can,car,castep,ccc,cdx,cdxml,cif,ck,cml,cmlr,crk2d,crk3d,ct,cub,cube,dat,dmol,dx,ent,fa,fasta,fch,fchk,fck,feat,fhiaims,fract,fs,fsa,g03,g09,g92,g94,g98,gal,gam,gamess,gamin,gamout,got,gpr,gro,gukin,gukout,gzmat,hin,inchi,inp,ins,jout,log,mcdl,mcif,mdl,ml2,mmcif,mmd,mmod,mol,mol2,mold,molden,molf,moo,mop,mopcrt,mopin,mopout,mpc,mpo,mpqc,mrv,msi,nwo,out,outmol,output,pc,pcm,pdb,pdbqt,png,pos,pqr,pqs,prep,pwscf,qcout,res,rsmi,rxn,sd,sdf,smi,smiles,sy2,t41,tdd,text,therm,tmol,txt,txyz,unixyz,vmol,xml,xsf,xtc,xyz,yob}
                        Select one of the Open Babel input formats for
                        identifier strings passed on the command line. File
                        formats are determined directly from the file and are
                        not affected by this option.
  -o <identifier> [<identifier> ...], --other <identifier> [<identifier> ...]
                        Identifiers recognized by the Chemical Structure
                        Identifier server, e.g. OPSIN-parsable systematic
                        IUPAC names.
  -f <filepath> [<filepath> ...], --files <filepath> [<filepath> ...]
                        Filepaths to files that can be read by Open Babel.
                        InChi Keys will be extracted from these.
  -r {hashisy,cas,stdinchikey,uuuuu,ficts,ficus,iupac_name,names} [{hashisy,cas,stdinchikey,uuuuu,ficts,ficus,iupac_name,names} ...], --representation {hashisy,cas,stdinchikey,uuuuu,ficts,ficus,iupac_name,names} [{hashisy,cas,stdinchikey,uuuuu,ficts,ficus,iupac_name,names} ...]
                        Specify the output representation(s). See "-l" for
                        more information. If this option is not given, all
                        representations will be displayed. Multiple
                        representations may be specified.
  -d <database path>, --database <database path>
                        Set the path to the SQLite3 database of cached
                        results. If this option is not given, the database
                        will be created in "$XDG_CACHE_HOME" if it is set,
                        otherwise it will be created in the current working
                        directory. If the given path is a directory, the
                        database will be created within that directory.

cactus-cir: InChIKey Example

$ cactus-cir FPKOPBFLPLFWAD-UHFFFAOYSA-N LFQSCWFLJHTTHZ-UHFFFAOYSA-N

InChi Key: FPKOPBFLPLFWAD-UHFFFAOYSA-N
  CAS Registry Number
    602-29-9

  FICTS Identifier
    B4E4F814074DF48C-FICTS-01-4C

  FICuS Identifier
    B4E4F814074DF48C-FICuS-01-6D

  Cactvs HASHISY
    B4E4F814074DF48C

  IUPAC Name
    1-methyl-2,3,4-trinitrobenzene

  Names
    1-methyl-2,3,4-trinitrobenzene
    1-methyl-2,3,4-trinitro-benzene
    602-29-9
    2,3,4-TRINITROTOLUENE
    4-05-00-00872 (Beilstein Handbook Reference)
    BRN 1989993
    Benzene, 1-methyl-2,3,4-trinitro-
    Toluene, 2,3,4-trinitro-

  Standard InChIKey
    InChIKey=FPKOPBFLPLFWAD-UHFFFAOYSA-N

  uuuuu Identifier
    B4E4F814074DF48C-uuuuu-01-1C

InChi Key: LFQSCWFLJHTTHZ-UHFFFAOYSA-N
  CAS Registry Number
    121182-78-3
    64-17-5
    8024-45-1
    8000-16-6
    68475-56-9
    71076-86-3
    71329-38-9

  FICTS Identifier
    E174572A915E4471-FICTS-01-1A

  FICuS Identifier
    E174572A915E4471-FICuS-01-3B

  Cactvs HASHISY
    E174572A915E4471

  IUPAC Name
    ethanol

  Names
    ethanol
    121182-78-3
    64-17-5
    8024-45-1
    8000-16-6
    68475-56-9
    71076-86-3
    71329-38-9
    Ethyl alcohol & water, 50%
    Ethyl alcohol & water, 60%
    Ethyl alcohol & water, 70%
    Ethyl alcohol & water, 80%
    Ethyl alcohol & water, 95%
    Ethyl alcohol & water, 96%
    Ethyl alcohol, anhydrous
    Ethyl hydrate
    Ethyl hydroxide
    Ethylalcohol
    Etylowy alkohol
    Fermentation alcohol
    Jaysol
    Jaysol S
    Molasses alcohol
    NCI-C03134
    NSC85228
    Potato alcohol
    SD Alchol 23-hydrogen
    Spirits of wine
    Spirt
    Tecsol
    Thanol
    WLN: Q2
    Absolute ethyl alcohol
    459828_ALDRICH
    02878_FLUKA
    187380_ALDRICH
    02882_FLUKA
    02883_FLUKA
    459836_ALDRICH
    UK Industrial methylated spirit
    02884_FLUKA
    Alcare Hand Degermer
    (C6-C9)Alkyl alcohol
    Alcohols, C6-9
    02890_FLUKA
    34963_RIEDEL
    D00068
    Dehydrated ethanol (JP15)
    Dehydrated ethanol (TN)
    02891_FLUKA
    676829_SIAL
    Alcohols, C1-3
    Anti-EphB1 (ELK Receptor)-CY antibody produced in sheep
    Higher alcohol distillate
    E7517_SIGMA
    02875_FLUKA
    [CH2Me(OH)]
    c0038
    cologne spirits (alcohol)
    sd alcohol 23-hydrogen
    spirit
    D06542
    Ethanol (JP15)
    Ethanol (TN)
    EOH
    24102_RIEDEL
    41322_FLUKA
    EOX
    ETHYLOXY GROUP
    24103_RIEDEL
    39278_FLUKA
    02877_FLUKA
    CDA 19
    270741_ALDRICH
    24105_RIEDEL
    493511_SIAL
    alcohol etilico
    493538_ALDRICH
    277649_ALDRICH
    Ethanol Fixative 80% v/v
    24106_RIEDEL
    493546_ALDRICH
    AIDS006139
    OXA
    OXYDIMETHYLENE GROUP
    32294_RIEDEL
    32205_RIEDEL
    HYDROXYETHYL GROUP
    Ethicap
    02857_FLUKA
    29221_FLUKA
    40210_RIEDEL
    02858_FLUKA
    245119_ALDRICH
    Alcohols, C>30
    24194_RIEDEL
    SY Fresh M
    02870_FLUKA
    Duplicating Fluid 100C.NPA
    02860_FLUKA
    32221_RIEDEL
    AIDS-006139
    QMHAIh@
    Esumiru WK 88
    459844_SIAL
    100C.NPA
    C2H5OH
    CHEBI:16236
    C00469
    Dehydrated ethanol
    Methylcarbinol
    etanol
    spiritus vini
    48075_SUPELCO
    InChI=1/C2H6O/c1-2-3/h3H,2H2,1H
    ETOH
    absolute alcohol
    alcohol
    Alkohol
    Anhydrol
    2858_SIGMA
    Cologne spirit
    Hinetoless
    Methylated spirit
    [OEtH]
    Alcohol (USP)
    1-Hydroxyethane
    AI3-01706
    Aethanol [German]
    Aethylalkohol [German]
    Alcohol (ethyl alcohol)
    Alcohol dehydrated
    Alcohol, ethyl
    Alcool ethylique [French]
    Alcool etilico [Italian]
    Alkohol [German]
    Alkoholu etylowego [Polish]
    CCRIS 945
    Caswell No. 430
    Denatured alcohol
    Distilled spirits
    EINECS 200-578-6
    EPA Pesticide Chemical Code 001501
    Etanolo [Italian]
    Ethanol solution
    Ethanol, undenatured
    Ethyl alcohol and water
    Ethyl alcohol anhydrous
    Ethyl alcohol in alcoholic beverages
    Ethyl alcohol usp
    Ethyl alcohol, undenatured
    Ethylalcohol [Dutch]
    Etylowy alkohol [Polish]
    FEMA No. 2419
    FEMA Number 2419
    HSDB 82
    Hydroxyethane
    NSC 85228
    AHD 2000
    SDM No. 37
    Tecsol C
    Ethanol (9CI)
    02483_FLUKA
    Ethyl alcohol (6CI,7CI,8CI)
    E2385_SIGMA
    IMS 99
    Infinity Pure
    Lux
    SDA 3A
    SDA 40-2
    Ethanol standards 10% (v/v)
    Sekundasprit
    Synasol
    458600_ALDRICH
    NCGC00091458-01
    Anhydrol PM 4085
    E7023_ALDRICH
    Anhydrous alcohol
    E7148_ALDRICH
    02865_FLUKA
    02851_FLUKA
    02853_FLUKA
    34870_SIAL
    CDA 19-200
    02854_FLUKA
    Dehydrated alcohol
    02855_FLUKA
    Desinfektol EL
    02856_FLUKA
    ZINC04795012
    EINECS 270-649-4
    Absolute ethanol
    Aethanol
    Aethylalkohol
    Alcohol, anhydrous
    Alcohol, dehydrated
    Alcohol, diluted
    Alcohols
    Alcool ethylique
    Alcool etilico
    Algrain
    ethyl alcohol
    grain alcohol
    Cologne spirits
    Denatured alcohol CD-10
    Denatured alcohol CD-5
    Denatured alcohol CD-5a
    Denatured alcohol SD-1
    Denatured alcohol SD-13a
    Denatured alcohol SD-17
    Denatured alcohol SD-23a
    Denatured alcohol SD-28
    Denatured alcohol SD-30
    Denatured alcohol SD-39b
    Denatured alcohol SD-39c
    Denatured alcohol SD-3a
    Denatured alcohol SD-40m
    Denatured ethanol
    Etanolo
    Ethanol 200 proof
    Ethyl alc
    Ethyl alcohol & water, 10%
    Ethyl alcohol & water, 20%
    Ethyl alcohol & water, 30%
    Ethyl alcohol & water, 40%
    Ethyl alcohol & water, 5%

  Standard InChIKey
    InChIKey=LFQSCWFLJHTTHZ-UHFFFAOYSA-N

  uuuuu Identifier
    E174572A915E4471-uuuuu-01-EA
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