TOPOS 3.2 demo package (self-extracting zip, 698K)
TOPOS 3.2 suite of practical works
TOPOS 3.2 User's Manual (pdf, 1247K)
Attention! Because the new version of TOPOS 4.0 for Windows is in preparation the older version TOPOS 3.2 for DOS now is available at highly reduced price of $149. Purchasers of the DOS version then will get a reduction of $150 at purchasing the Windows version, so finally they obtain TOPOS 3.2 free of charge to become acquainted with the program package capabilities. Contact Prof. V.A.Blatov to get detailed information on new TOPOS distribution.
Attention! New service based on the IsoTest program is free of charge! Click here to know more information.
For more information contact:
 | Internet: blatov@ssu.samara.ru |
| Mail: Ac.Pavlov St. 1, 443011 Samara, Russia |
| Phone: (8462)345445 |
| Fax: (8462)345417 |
TOPOS 3.2 is a program package for multipurpose geometrical and topological analysis of crystal structures. It provides the working with crystal structure databases and the calculation of the geometrical and topological characteristics of crystal structures in these databases. TOPOS 3.2 is an integrated interactive shell including database management system (DBMS), which allows one to edit, search and retrieve crystal structure information, and a number of applied programs integrated into DBMS. The version 3.2 includes seven applied programs (see below).
What is new in the TOPOS 3.2?
In comparison with the TOPOS 3.1:
| A number of new features in the program IsoTest. The procedures of topological analysis of atomic sublattices and packings and of structure type classification are added. |
| A procedure of smart adding hydrogens in crystal structures of compounds of various nature. |
| A number of new filters in the DBMS. |
In comparison with the TOPOS 3.0:
| The new programs AutoCN and IsoTest. |
| The program ADS now can determine the molecular coordination numbers, analyzes the topology of molecular packings, gives the composition of polymeric complex groups and allows one to study the topology of complex groups with multiatomic ligands, considering them as quasi-monoatomic by means of contracting several atoms of ligands to the complexing atoms. |
| The program IsoCryst now can image non-valent interatomic contacts, allows one to construct VDPs and coordination polyhedra immediately on an image of crystal structure, performs the "growth" of a crystal structure taking into account not only valent bonds, but also non-valent. A polyhedral representation of a crystal structures in terms of VDPs or/and coordination polyhedra also is possible. |
| Now you can analyze the holes in crystal structures with the program Dirichlet. |
| A number of new filters appear in the DBMS, such as the filter on molecular fragment, the filter on atomic environment, the filter on the errors in composition of the unit cell, etc. |
| The DBMS now supports the more fast, flexible and efficient database format. |
| Free converter programs from the CSD and ICSD text formats to the TOPOS database format are available. |
| constructs Voronoi-Dirichlet polyhedra (VDPs) of atoms in crystal structures taking into account both all basis atoms and an arbitrary subset of atomic sublattices given by the user; |
| images VDPs, the corresponding Delaunay stars, coordination polyhedra and Schlegel projections; |
| calculates all the main geometric characteristics of VDPs; |
| determines the topological characteristics of VDPs and automatically forms the library of topological types of VDPs; |
| allows one to calculate VDPs of atoms in a group of crystal structures from a database and forms summary tables for the following statistical analysis. |
In the Dirichlet program a very fast "gift wrapping" algorithm of VDP calculation by means of construction of a convex hull for a set of atoms has been realized for the first time. This algorithm allows one to calculate hundreds of thousand VDPs with a reasonable outlay of machine time.
calculates an adjacent matrix of crystal structure, including atomic coordination numbers. The AutoCN program uses VDPs and an "intersecting spheres" algorithm to build an adjacent matrix.
| analyses the crystal structure topology; |
| calculates the number, composition and dimensionality of all structural groups in crystal structure and their orientation along the crystallographic directions (for chain or layer groups); |
| determines the topology of structural groups and the coordination types of ligands; |
| calculates molecular coordination numbers for the molecules of any complexity and analyzes the topology of their mutual arrangement; |
| determines the way of combination of coordination polyhedra or molecules; |
| calculates the composition of the far coordination spheres of complexing atoms or molecules. |
The program ADS uses an adjacent matrix of crystal structure calculated by the AutoCN program and realizes the representation of a crystal structure as a finite "contracted" graph. This method allows one to analyze the topology of a crystal structure as a whole.
| constructs stick, sphere-and-stick and polyhedral images of crystal structures and provides the convenient service for rotation, scaling and editing an image; |
| calculates the geometrical characteristics of crystal structure (interatomic distances, bond and torsion angles, RMS planes, etc.); |
| constructs VDPs and coordination polyhedra immediately on an image of a crystal structure; |
| differs valent and non-valent (specific or van der Waals) interatomic contacts and allows one to analyze visually the packing of polymeric or molecular structural units. |
calculates interatomic distances and bond angles for a set of atoms.
| automatically tests crystal structures on isotypism (topological similarity) and determines the degree of their similarity. You can find the relations between crystal structures, which would seem to be absolutely different! |
| provides topological analysis of atomic sublattices and detects close packings at any degree of their distortion; |
| automatically classifies crystal structures according to structure type concept. |
The IsoTest program uses the adjacent matrices, the method of "contracted" graph, the method of coordination sequences and the analytical algorithms of the ADS program.
realizes a number of standard statistical methods for processing the results of a calculation of VDP characteristics, which have been done by the program DIRICHLET.
TOPOS 3.2 also includes the converter programs from the Cambridge Structural Database and the Inorganic Crystal Structure Database text formats to the TOPOS database format.
TOPOS 3.2 requires PC/AT 80386/87 (or higher) compatible computers (MS DOS 5.0 or higher, minimum RAM 2Mb, 4Mb recommended, about 1Mb of HDD space, CGA/EGA/VGA/SVGA videoadaptors) and practically does not contain any software limits on the complexity of a crystal structure and on the number of compounds in a database during the calculation, allowing to process crystal structures including tens of thousand crystallographically independent atoms (such as proteins) and with databases containing tens of thousand compounds if the computer has necessary resources.
A free demo version of TOPOS 3.2 with a suite of practical works is available. If you have any problems, please, contact blatov@ssu.samara.ru.
Inorganic Chemistry Chair Homepage
Last update: 22 March 2002