19BIO201
Intelligence in Biological Systems - 3
Chemical File Formats
19BIO201
Intelligence in Biological Systems - 3
Aadharsh Aadhithya - CB.EN.U4AIE20001
Anirudh Edpuganti - CB.EN.U4AIE20005
Madhav Kishor - CB.EN.U4AIE20033
Onteddu Chaitanya Reddy - CB.EN.U4AIE20045
Pillalamarri Akshaya - CB.EN.U4AIE20049
Team-1
Types of Chemical Files
Types of Chemical Files
Chemical Markup Language
Types of Chemical Files
Chemical Markup Language
Manage Molecular Informations
Types of Chemical Files
Chemical Markup Language
Manage Molecular Informations
XML
Types of Chemical Files
Chemical Markup Language
Manage Molecular Informations
XML
Java
Types of Chemical Files
Chemical Markup Language
Chemical concepts supported
Types of Chemical Files
Chemical Markup Language
Chemical concepts supported
- Molecules
Types of Chemical Files
Chemical Markup Language
Chemical concepts supported
- Molecules
- Reactions
Types of Chemical Files
Chemical Markup Language
Chemical concepts supported
- Molecules
- Reactions
- Spectra and Analytical data
Types of Chemical Files
Chemical Markup Language
Chemical concepts supported
- Molecules
- Reactions
- Spectra and Analytical data
- Computational Chemistry
Types of Chemical Files
Chemical Markup Language
Chemical concepts supported
- Molecules
- Reactions
- Spectra and Analytical data
- Computational Chemistry
- Chemical Crstallography and Materials
Types of Chemical Files
Structure Data Format
Types of Chemical Files
Structure Data Format
Major components of SDF
Types of Chemical Files
Structure Data Format
Major components of SDF
Simplified Connection Table
Types of Chemical Files
Structure Data Format
Major components of SDF
Simplified Connection Table
Additional Information
Types of Chemical Files
Structure Data Format
Simplified Connection Table
Atom Block
Bond Block
Types of Chemical Files
Structure Data Format
Looks like this...
Types of Chemical Files
Protein Data Bank
Types of Chemical Files
Protein Data Bank
3-D structure of molecules
Types of Chemical Files
Protein Data Bank
3-D structure of molecules
Proteins
Types of Chemical Files
Protein Data Bank
3-D structure of molecules
Proteins
Nucleic Acids
Types of Chemical Files
Protein Data Bank
Viewing these 3D structures - Possible?
Types of Chemical Files
Protein Data Bank
Viewing these 3D structures
- Jmol
Types of Chemical Files
Protein Data Bank
Viewing these 3D structures
- Jmol
- Pymol
Types of Chemical Files
Protein Data Bank
Viewing these 3D structures
- Jmol
- VMD
- Pymol
Types of Chemical Files
Protein Data Bank
Viewing these 3D structures
- Jmol
- Rasmol
- VMD
- Pymol
Types of Chemical Files
SMILES
Types of Chemical Files
SMILES
Simplified Molecular Input Line Entry Specification
Types of Chemical Files
SMILES
Brief Description
Types of Chemical Files
SMILES
Brief Description
- Nature and Topology of the Molecular Structures
Types of Chemical Files
SMILES
Brief Description
- Nature and Topology of the Molecular Structures
- Structure of Chemical Molecules - ASCII strings
Types of Chemical Files
SMILES
Brief Description
- Nature and Topology of the Molecular Structures
- Structure of Chemical Molecules - ASCII strings
- Hydrogen atoms are not represented
Types of Chemical Files
SMILES
Representation
Types of Chemical Files
SMILES
Representation
- = - Double bonds
Types of Chemical Files
SMILES
Representation
- = - Double bonds
- # - Triple bonds
Types of Chemical Files
SMILES
Representation
- = - Double bonds
- () - Branching
- # - Triple bonds
Types of Chemical Files
SMILES
Representation
Types of Chemical Files
SMILES
Representation
Aspirin
Types of Chemical Files
SMILES
Representation
Aspirin
Aspirin
Types of Chemical Files
XYZ
Types of Chemical Files
X Y Z
x-coordinate
Types of Chemical Files
X Y Z
x-coordinate
y-coordinate
Types of Chemical Files
X Y Z
x-coordinate
y-coordinate
z-coordinate
Types of Chemical Files
XYZ
Represenation
Types of Chemical Files
XYZ
Represenation
<\text{number of atoms (n)}> \\
\text{comment line} \\
atom_1 \, \, \, \text{x-coord}_1 \, \, \, \text{y-coord}_1 \, \, \, \text{z-coord}_1 \\
atom_2 \, \, \, \text{x-coord}_2 \, \, \, \text{y-coord}_2 \, \, \, \text{z-coord}_2 \\
. \\
. \\
. \\
atom_n \, \, \, \text{x-coord}_n \, \, \, \text{y-coord}_n \, \, \, \text{z-coord}_n
Types of Chemical Files
XYZ
Represenation
<\text{number of atoms (n)}> \\
\text{comment line} \\
atom_1 \, \, \, \text{x-coord}_1 \, \, \, \text{y-coord}_1 \, \, \, \text{z-coord}_1 \\
atom_2 \, \, \, \text{x-coord}_2 \, \, \, \text{y-coord}_2 \, \, \, \text{z-coord}_2 \\
. \\
. \\
. \\
atom_n \, \, \, \text{x-coord}_n \, \, \, \text{y-coord}_n \, \, \, \text{z-coord}_n
Thank you sir
File Formats
File Formats
Chemical Markup Language (CML) is an open standard for representing molecular and other chemical data. The open source project includes XML Schema, source code for parsing and working with CML data, and an active community.
CML
File Formats
The Protein Data Bank Format is commonly used for proteins but it can be used for other types of molecules as well. It was originally designed as, and continues to be, a fixed-column-width format and thus officially has a built-in maximum number of atoms, of residues, and of chains; this resulted in splitting very large structures such as ribosomes into multiple files
PDB
File Formats
The Simplified Molecular Input Line Entry Specification is a line notation for molecules. SMILES strings include connectivity but do not include 2D or 3D coordinates. Hydrogen atoms are not represented. Other atoms are represented by their element symbols B, C, N, O, F, P, S, Cl, Br, and I. The symbol "=" represents double bonds and "#" represents triple bonds. Branching is indicated by (). Rings are indicated by pairs of digits.
SMILES
File Formats
The XYZ file format is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols (or atomic numbers) and cartesian coordinates.
XYZ
File Formats
SDF is one of a family of chemical-data file formats developed by MDL; it is intended especially for structural information. "SDF" stands for structure-data file, and SDF files actually wrap the molfile (MDL Molfile) format. Multiple compounds are delimited by lines consisting of four dollar signs ($$$$). A feature of the SDF format is its ability to include associated data.
SDF
IBS3_A6
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