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Import molfile

In order to understand the Molfile format let us look at a sample file and recognize its fundamental structure. For simplicity, some less important details will be omitted in the discussion. For a complete description, users are referred to MDL s CTfile format specification [50],... [Pg.47]

A larger number of features are provided by the ACDStructure Drawing Applet (ACDLabs). Both structures and reactions can be drawn, imported, and also exported. This applet supports Molfiles and has a large, integrated collection of pre-defined templates, which are extensible by the user. Additionally, gif files can be exported. It is not possible to draw or to Lmport/export chemical reactions. [Pg.144]

The Research Collaboratory for Structural Bioinformatics Protein Data Bank (RCSB-PDB at http //www.rcsb.org/pdb/home/home.do is the online source for X-ray and NMR structural data. Many software programs mentioned in Section 4.5 include the facihty to visualize imported data however, two free software programs operate well in this regard. One is MDL Chime described previously in this section. Chime, a chemical structure visualization plug-in for Internet Explorer and Netscape Communicator, supports a wide variety of molecule coordinate formats, including PDB (protein data bank), Molfile (from ISIS/Draw), MOP (MOPAC input hies), and GAU (Gaussian Input hies). [Pg.182]

Chemist inputs a structure by either drawing the structure from scratch or importing the structure from a molfile. If the compound has salt(s), the Chemist also specifies salt type(s) from a pick fist and their coefficients) (which defaults to 1 and must be a positive integer). The salt(s) can also be included in the structure that is drawn or in the molfile that is imported. [Pg.54]

Imports data in SD file format, MDL molfile format, SMILES text strings, Daylight Chemical Information Systems Inc. s Thor Data Tree (TDT) format, and Tripos Inc. s Sybyl Line Notation (SLN) format. [Pg.68]

The workflow with DEREK starts with entering a molecnlar strnctnre via struc-tnre editor software or by importing files in one of the following formats MDL Molfile, SD file, MDL ISIS Sketch files (.skc). In the second step, the operator selects a species for which he wants to predict toxicological information. On processing... [Pg.249]

Starting with a structure entered with MDL ISlS/Draw or imported as MDL Molfile or ISIS Sketch files (.skc), the user can define constraints to restrict the reported metabolites. Unconstrained generation of metabolic pathways from a compound would lead to combinatorial explosion of the amount of metabolites. Constraints can be defined for the following ... [Pg.251]

The external representation of molecular structure is a less rigorous definition. For example, there are many programs available that can convert to and from SMILES and molfiles. These can be used when a molfile (the external representation) needs to be imported as a SMILES (the internal representation) into the database. Similarly, a SMILES can be easily exported as a SMILES or converted to a molfile or other file format. It is useful to have these conversion functions as SQL extensions. [Pg.84]

Create Or Replace Function frowns.smiles to molfile(smi Text, name Text, coords Numeric ] [] ) Returns Text As EOPY from frowns import Smiles... [Pg.192]

Create Type frowns. named j roperty As (name Text, value Text) Create Or Replace Function frowns.molfile properties(molfile Text) Returns Setof f rowns. named j roperty As EOPY from frowns import MDL import StringlO... [Pg.194]

Create Or Replace Function openbabel.molfile to smiles(molfil Text) Returns Text As EOPY import openbabel obc = openbabel.OBConversion() mol = openbabel.OBMol() obc.SetlnAndOutFormats("sdf", "can") if obc.Readstring(mol, molfil) mol.SetTitle("") return obc.WriteString(mol,1) else ... [Pg.200]

Create Or Replace Function openbabel.molfile properties(molfil Text) Returns Setof openbabel.named property As EOPY import pybel... [Pg.203]

The internal representation of molecules is accomplished using the technique developed by Wipke and Dyott (3), and later used by Molecular Design Limited (MDL) in several of their commercial programs. An MDL program, MACCS, is used to graphically input the molecular structure of the compound of interest, then save that structure into a file (molfile). The importation of this file provides CHESS with information such as the number and type of atoms and bonds, as well as stereochemical information. [Pg.48]

All these structures can be viewed. More structures can be imported. The selected structures can be exported to any of the following viz. MOLFILE, SDFILE, SMILES, JTF, RDF, Marvin Document. The stractures can be modified as well. A query of 2D structure can also be placed to be searched within the database. For querying, MarvinSketch application from the JChem package is used. [Pg.73]

Most in-house systems permit links to other database management software, in particular to relational database systems such as ORACLE, in order to integrate large amounts of textual or numeric data that already exist there with reaction databases. As many of the reaction retrieval systems mentioned here are able to import and export files in MolFile or RxnFile formats (originally proprietary file formats of MDL, later published), or in the SMD format, even exchange of reaction databases between different retrieval systems is often possible. ... [Pg.2413]

A new project on electronic publishing, financially supported by the German Ministry of Research, and worked out by Wiley-VCH/Chemical Concepts, uses JCAMP and MDL standards (Figure 1). Spectroscopic data acquired directly from the spectrometer site are converted to the JCAMP format. The software TranSpec allows structure input or import in Molfile format. Quality control modules check the reliability of the information. The files in JCAMP and MDL formats are sent to the data server by email. Special software extracts the data from the email automatically and handles the entry into the database. [Pg.2633]


See other pages where Import molfile is mentioned: [Pg.30]    [Pg.88]    [Pg.91]    [Pg.382]    [Pg.97]    [Pg.131]    [Pg.133]    [Pg.140]   
See also in sourсe #XX -- [ Pg.167 , Pg.207 ]




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