Comprehensive Descriptors
Contents
1. List Logic x m Sub List Type C Structures Descriptors Properties Models Close m The First List The Second List Operation AND o C NOT Atomic Typed Bond Typed Selected 147 items Max partial charge Zefirow for aton Max partial charge Zefirow for ato Max partial charge Zefirow for aton Max partial charge Zefirow for aton Max partial charge Zefirow for aton ha Selected 36 items Max partial charge Zefirow f a Max partial charge Zefirow f Max partial charge Zefirow f Max partial charge Zefirow f Max partial charge Zefirow f Max partial charge Zefirow f Max partial charge Zefirow f Max partial charge Zefirow f Max partial charge Zefirow f Max partial charge Zefirov f Max partial charge Zefirow f Max partial charge Zefirow f Max partial charae Zefirov h External Constitutional Constitutional Topological Topological Geometrical yo DE a C XOR Geometrical Charge Related Semi Empirical Semi Empirical Thermodynamical Result Thermodynamical Molecular Typed Relation 9 Molecular Typed Bond Typed Selected 1226 items Max partial charge Zefirov for aton Max partial charge Zefirow for ato Max partial charge Zefirow for aton Max partial charge Zefirov for aton Max partial charge Zefirov for aton iy 28 CODESSA PRO User s Manual The List Logic module in CO2. Manual 2 2 2 Work Area 2 2 2 1 Structure View Window Dipheny sulfone Wire Double clicking on a structure artifact in the structures folder opens a structure view window in the work area Structures are 3 dimensional and can be viewed as wire frame ball and stick CPK surface solvent accessible surface SASA Zefirov s charges on SASA solvent accessible surface area and MOPAC charges on SASA solvent accessible surface Right clicking inside the window opens the view and label context pop up menu Selecting view provides the six options mentioned above and the label identifies the number or the type of each atom When the pointer is positioned over the view window it changes to a 4 sided arrow that can be dragged to rotate the structure 19 CODESSA PRO User s Manual 2 2 2 2 Correlation View Window N 35 n 5 R2 0 950961 R2cv 0 931197 F 112 473 s2 0 00862279 Observed vs predicted logL for thioxanthen 9 one T D E 3 EL Double clicking on a correlation artifact opens the correlation view window The graph shows the observed experimental values versus the predicted values of the property in question When the window is first opened all the points for outliers will be blue rather than yellow The color of the points will change to blue to indicate they have been selected Clicking once on a point will display its properties and their associated values in the properties window Double clicking on a point will open
3. Windows 2000 Windows NT and Windows 9xs are trademarks of Microsoft Corporation All other brand and product names are trademarks or registered trademarks of their respective holders CODESSA PRO User s Manual Table of contents INTRODUCTION iocinooninncainicin di A RN 5 CODESSA PRO RELEASE CANDIDATE RC2 LICENSE AGREEMENT FOR ENDUSERS e 6 CHAPTER 1 INSTALLING CODESSA PRO oonccccccnnnoccccninoccccocroncccocncnccccconnnccccnononocss 11 1 1 SYSTEM REQUIREMENTS uaar 11 1 2 INSTALLATION INSTRUCTIONS srrsrrrcrrcerionicosieneceneseoneorionicosionecenenere 12 CHAPTER 2 DESCRIPTION OF CODESSA PRO verrrerrrrrrerererenerioneoneseso 13 2 1 CONCEPTS AND DEFINITIONS socios ies 13 AIR nea 13 CORA See ace ada eos slo ili ei i il 13 Shapshot Cache File sli alano 13 Workspace enai reap aaa 13 O EOE N 13 DIU Ac 14 becca 14 O iii lol eli ia i na 14 Descriptor Property Materie ei ana 14 Current Analysis DIMENSIONS siriani s 15 CORTE TAT ONE a AA bo 15 A eee I RIA E E NE 15 2 2 CODESSA PRO VISUAL INTERFACE ssrscererreercosinienernecenescenonicenconioneee 16 ARA OA A E iee Sates eo Rsa rosko basi oaS 17 22 2 WORK AREA asian 19 2 2 2 1 Structure View O O 19 2 2 2 2 Correlation View IN eat 20 2 2 3 PROPERTY WINDOW sti 21 IZA LOG WINDOW ii nice nasses ENS 22 CHAPTER 3 USING CODESSA PRO TO START A NEW PROJECT 0 23 3 1 CREATING A NEW FOLDER FOR THE NEW PROJECT o cconiccnincinoconsiocsoooss 23 3
4. in the work area a structure view window for the structure that corresponds to that point Right clicking the window will open a context pop up menu that will give the opportunity to show structures show descriptors create Sublists mark outliers and mark non outliers as desired Double clicking on a descriptor artifact will also open a correlation view window The window will show the relationship between the descriptor and the property dimension selected The value predicted according to any model chosen maybe viewed by selecting that model clicking the view pull down menu and then choosing predicted properties This will display the observed property values predicted property value and errors 20 CODESSA PRO User s Manual 2 2 3 Property Window The item selected determines the contents of the property window If a folder or list is selected in the workspace the number of artifacts contained is displayed If an artifact is selected the property window will provide varying information depending on the type of artifact Number of experimental properties 45 F Property Yalue The picture on the left shows the as ee information given in the property File name 50000001 mol window when a structure artifact is Number of atoms 21 selected It will also show the Number of bonds 30 x Number of calculated descriptors 220 experimental value and calculated value of the property of the current structure whic
5. 2 CREATING A STORAGE LIST paglia 23 3 3 PREPARING STORAGE ci iii 24 CODESSA PRO User s Manual 34 CALCULATING CORRELA TION cvsscscsssssesiasueisssscostsusnespsesscesststbeceesecsssbetvbocnsases 27 3 5 VIEW ING CORRELA TIONS sssssivasscessstnssossencsesssrvsysdeussetuosasbedsanveonsnsssssaheassvaceuases 27 3 6 PRINTING YOUR RESULT Spi nie ai 27 3 7 MANIPULATING LISTS siii da 28 CODESSA PRO User s Manual CODESSA PRO is an entirely new software package which performs tasks similar to CODESSA but with many distinct advantages over the previous software package In particular its add in mechanism makes CODESSA PRO expandable its calculation engine has been optimized at the assembly language level for Pentium Pentium Pro Pentium II Pentium III and Pentium IV processors and finally it has been designed to run in 32 bit Windows environments CODESSA Comprehensive Descriptors for Structural and Statistical Analysis PRO is a comprehensive program for developing quantitative structure property relationships QSPR integrating all necessary mathematical and computational tools to i calculate a large variety of molecular descriptors on the basis of the 3D geometrical and or quantum chemical structural input of chemical compounds ii develop multi linear and non linear QSPR models of the chemical physical or biological properties of individual compounds non linear QSPR models are still in preparation 111 perform cluster analyses of t
6. CODESSA PRO User s Manual Comprehensive Descriptors For Structural and Statistical Analysis CODESSA PRO User s manual by Alan R Katritzky Ruslan Petrukhin and Hongfang Yang University of Florida Mati Karelson University of Tartu Estonia CODESSA PRO User s Manual Copyright 02002 University of Florida All rights reserved The contents of this manual and the associated software are the property of University of Florida and are copyrighted This publication or parts thereof may not be reproduced in any form by any method for any purpose UNIVERSITY OF FLORIDA PROVIDES MATERIALS AS IS WITHOUT WARRANTY OF ANY KIND EITHER EXPRESSED OR IMPLIED INCLUDING BUT NOT LIMITED TO ANY IMPLIED WARRANTIES OR CONDITIONS OF MERCHANTABILITY OR FITNESS FOR A PARTICULAR PURPOSE IN NO EVENT SHALL UNIVERSITY OF FLORIDA BE LIABLE TO ANYONE FOR SPECIAL COLLATERAL INCIDENTAL OR CONSEQUENTIAL DAMAGES IN CONNECTION WITH OR ARISING OUT OF PURCHASE OR USE OF THESE MATERIALS EVEN IF UNIVERSITY OF FLORIDA HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGE ARISING FROM ANY DEFECT OR ERROR IN THESE MATERIALS THE SOLE AND EXCLUSIVE LIABILITY TO UNIVERSITY OF FLORIDA REGARDLESS OF THE FORM OF ACTION SHALL NOT EXCEED THE PURCHASE PRICE OF THE MATERIALS DESCRIBED HEREIN University of Florida reserves the right to revise and improve its products as it sees fit Third Party Trademarks Microsoft is a registered trademark and Windows XP
7. DESSA PRO compares the artifacts contained in two lists and can be opened by clicking any artifact right clicking to show the context pop up menu and choosing lists logic or just using the F4 keyboard shortcut instead Choose the type of artifact that will be contained by the list by clicking on the appropriate button in the Sub List Type box descriptors is selected in the example above Choose the desired lists for comparison and the appropriate Operation The artifacts from the two lists that meet the criteria of the operation will be displayed in the Results box The results can then be copied to a new list Create or be selected Select for further comparison When comparing three or more lists first compare two of the lists click on Select restart List Logic select Current Selection in The First List box then select the remaining list in The Second List box 29
8. Menu and choose Run The RUN dialog box opens Enter the following command in the open text box assuming D is your CD ROM D setup exe Choose OK The CODESSA PRO setup program initializes and the CODESSA PRO setup dialog box opens Follow the on screen instructions for product choice and installation The CODESSA PRO setup program will detect an existing CODESSA PRO installation and offer you the choice of uninstalling or keeping the older version of the program 12 CODESSA PRO User s Manual Chapter 2 Description of CODESSA PRO 2 1 Concepts and definitions The use of CODESSA PRO requires an understanding of the following concepts Artifacts These are the individual files or items used by CODESSA PRO There are four types of artifacts structures descriptors properties and models Using the CODESSA PRO program will frequently require manipulation of single artifacts or lists of artifacts CODESSA PRO names explicitly most artifacts e g descriptors and models Storage All items that are connected with a project are stored in a single location within the file system in the storage To change a storage location click Option on the main menu bar and select Storage The box that opens allows the user to control the storage location of structure files correlations descriptors lists etc Snapshot Cache File The snapshot CODESSA PRO cache file is a binary compressed representation of all items in storag
9. any third party CODESSA PRO User s Manual VIII Export control regulation This software may not be used in or transferred to other countries or used for any purposes except in accordance with the applicable export control regulations of the United States of America IX General The Terms are governed by the law of the State of Florida The invalidity or unenforceability of any provision of this Agreement including the Terms under applicable law shall not affect the validity or enforceability of any other provisions of this Agreement This Agreement and any other UFRF Documents incorporated by reference for the Software constitutes the entire agreement between Licensee and UFRF They may be amended only by a written agreement signed by authorized representatives of both Licensee and UFRF X CODESSA PRO Release Candidate RC2 services 1 Online documentation is provided on www codessa pro com 2 One set of Software will be supplied on CD ROM or can be downloaded from the prescribed internet site 3 Technical support support service to Licensee by telephone fax or email for inquiries XI Payment ANNUAL LICENSE CODESSA PRO Software licensed on an annual basis must be renewed each year by Licensee to retain right for use of the Software The term of the annual license begins on the first day of the month following shipment of the Software The annual license fee is due within 30 days of invoice If Licensee fails to ma
10. are despite this prohibition the altered Software is not eligible for technical support and shall then become subject to these Terms and the title to such altered Software shall vest in UFRF 11 publish or otherwise publicize information regarding the Software the performance or accuracy of the Software or other experiences with the Software without the express prior written consent of UFRF ili allow home use III Fees taxes and payment After signing this license agreement and sending credit card information or an appropriate check or money order made out to the University of Florida Research bis CODESSA PRO User s Manual Foundation Inc a compact disk CD containing the CODESSA PRO Release Candidate RC2 executables will be sent to The Licensee 1 The cost of the CODESSA PRO Release Candidate RC2 program executables for non profit and academic organizations for the first year is 800 00 Eight Hundred Dollars those having already licensed CODESSA PRO Release Candidate RC2 will pay 400 00 Four Hundred Dollars for each subsequent year 11 The cost of the Site license of CODESSA PRO Release Candidate RC2 program executables for for profit and commercial organizations for the first year is 20 000 00 Twenty Thousand Dollars those having already licensed CODESSA PRO Release Candidate RC2 will pay 10 000 00 Ten Thousand Dollars for each subsequent year The single user license for for profit and commercial organiz
11. ations for the first year is 10 000 00 Ten Thousand Dollars those having already licensed CODESSA PRO Release Candidate RC2 will pay 5 000 00 Five Thousand Dollars for each subsequent year 111 US federal or US state governments can license CODESSA PRO Release Candidate RC2 and make executable code available to their users from non profit organizations under the same conditions as for other non profit and academic organizations For foreign governments the license fee should be paid under the same conditions as for for profit and commercial organizations II iii unless a viewer is obtained 1v For multi Site multinational for profit companies there should be a license fee paid per Site although subsequent Sites will need to pay only 75 seventy five percent of the fee v The academic fee may be reduced or waived in special circumstances Please explain your request and need for a waiver or reduction to sales codessa pro com For the License Licensee will pay to UFRF any shipping and handling charge associated sales use excise or similar taxes imposed upon UFRF IV Period of license The period of the License will i begin on the date UFRF signs the CODESSA PRO Release Candidate RC2 License Agreement 11 end on the date of the first occurrence of any of the following events a the expiration of 365 days from the date UFRF signs the CODESSA PRO Release Candidate RC2 License Agreement b the expiration of ni
12. ave the data and then make a new folder which can be named either by project number or any other way of your choosing 3 2 Creating a storage list You have two choices for creating a storage list either one for many projects or just for one individual project If you decide to use a single storage list for many projects you must keep an index of the structure and molecule names Although a general storage for many projects allows a research group to avoid repeating the calculations of structures and descriptors as well as to minimize the amount of storage space used we strongly recommended the use of separate storage list for each project To create storage for a new project click the option pull down menu click storage and browse to find the folder that has just been created for your storage Then click OK to close the window Now in the project folder you will find a subfolder list an example of which appears in the following picture You can name each folder in many desired manner or use the default names which shown in the shaded area oe CODESSA PRO User s Manual Project Parameters Ed Root Folder CM 268 testl Browse MOL Subfolder 3D MOL Molecular Mechanic Subfolder SCF Subfolder MOPAC Optimization step 1 Subfolder ERMO Subfolder MOPAC Optimization step 2 Subfolder work Subfolder 3D MOL MOPAC Subfolder Lists Subfolder Descriptors Subfolder Properties Sibtalder Canelatians Subtaldec Can
13. cel All the storage subfolders should be empty before starting any optimization or calculation First you need to prepare mol files of your structures and save them either in the MOL subfolder or in a location of your choosing Keep in mind no matter how you name your mol files whenever you run CODESSA PRO the program will automatically name the files as Sddddddd mol 3 3 Preparing storage Compared with old CODESSA a major enhancement achieved by CODESSA PRO is that CODESSA PRO is highly automatic and this obviates manual storage preparation Since you already have all the mol files of all the structures if you save your mol files in the MOL Subfolder pressing F5 keyboard shortcut automatically prepares all the data which are necessary for doing correlation If the location of your mol files is different then select the edit pull down menu choose add structure browse for the folder where your mol files are located and click ok The process through which CODESSA PRO prepares all the data except property files is divided into 11 stages Each of these 11 stages is performed automatically in sequence by CODESSA PRO Stage 1 This is the first model building stage The program applies simple molecular mechanics preoptimization and transfers the 2 dimensional structures from the MOL subfolder to the 3 dimensional structures that will be stored in the 3D MOL Molecular Mechanic subfolder Missing hydrogen atoms are added according
14. culates the molecular properties using the Hessian matrix force calculation The state of the molecule is determined using the signs of eigenvalues of the Hessian matrix If the molecule are in a transition state than the program goes back to Stage 1 and restarts by using stochastic addition again If the molecule is in its ground state then go to Stage 10 If 10 iterations are unsuccessful stop calculation Stage 10 This stage will be reached only in situations when all mentioned the geometry tests above are satisfied At this stage the MDL MOL file in the 3D MOL MOPAC Subfolder is formed based on formal connectivity information from the MDL MOL file in the MOL Subfolder and atomic coordinates from the MOPAC output file in the MOPAC Optimization step2 Subfolder Stage 11 CODESSA PRO takes all MDL MOL files in the 3D MOL MOPAC Subfolder the MOPAC output file in the SCF Subfolder and the MOPAC output file in the THERMO Subfolder to do descriptor value calculations The resulting text file with descriptor values is stored in the Descriptor s Subfolder All intermediate files are deleted from storage at this stage Only MDL MOL files in the MOL Subfolder and the 3D MOL MOPAC Subfolder and MOPAC input and output files in the SCF Subfolder and THERMO Subfolder remains If the calculation cycle is not finished at Stage 1 changes can be made to the files at the last successful stage manually usually it is editing of MOPAC keyw
15. d can be cut and pasted directly into a word processing program x Comments al 4 R2 0 7709 R2cv 0 7105 F 57 22 s 0 0436 N 2 n 37 Ranges Observed 7 35 9 17 Predicted 7 5001 9 40447 B 3 t IC Name of descriptor 0 12 8032 0 495482 25 8399 Intercept 1 0 311865 0 037522 8 31153 0 0914958 HOMO LUMO energy gap 2 0 0196488 0 0050315 3 90515 0 0914958 Vib heat capacity 300K Outliers are selected Number of outliers is 2 Correlation N 37 n 2 R2 0 770255 R2cv 0 719299 F 56 995 s2 0 0706459 Comments R2 0 7703 R2cv 0 7193 F 57 00 s 0 0437 N 2 n 37 Ranges Observed 7 35 9 17 Predicted 7 38056 9 37866 B 3 t Ic Name of descriptor 0 12 4111 0 515973 24 0538 Intercept 1 0 297124 0 0389097 7 63623 0 152585 HOMO LUMO energy gap 2 0 00796042 0 00204845 3 88607 0 152585 Complementary Information content order 2 Dutliers are selected Number of outliers is 2 a all The edit pull down menu has options to select all log copy from log paste to log and clear all log Transferring the information for several correlations to a word processing program can be accomplished by clearing all log double clicking on each of the correlations then clicking select all log finally copy from log 2 CODESSA PRO User s Manual Chapter 3 Using CODESSA PRO to start a new project 3 1 Creating a new folder for the new project You can select the drive on which it is desired to s
16. e x Property Value Log Window Property Window Show or hide Log window Workspace An on screen presentation of the current cache file Work Area The screen space for various view windows Property Window The property window depicts information about properties of the selected object and is available for almost all objects Log Window The windows purpose is protocol all operation on the storage Tool Bar Shortcuts to commonly performed tasks The task will be displayed when the pointer is positioned over the icon 16 2 2 1 Workspace EN Root All 3 Descriptors 3 Properties Models 2 Objects CODESSA PRO User s Manual al x The workspace area contains an on screen presentation of the current cache file which is essentially a directory tree Clicking on the minus will collapse a folder branch of the tree and clicking on a plus will expand a folder When a folder is expanded note the structures folder it will show the lists note All list contained in the folder The same icon is used to represent lists as folders because they are also used to contain files If a list is empty then there will be no plus or minus beside it The Structures folder is expanded to show alzi the list All The list All is also expanded to show the structure artifacts Notice the icon beside the structure artifact Each type of artifact will have a diff
17. e This file is located in the memory whenever work is being performed on the CVI module The cache file reloads each time the CVI detects a change in the storage contents The snapshot can be reloaded manually at anytime by opening the pull down menu Calculate on the menu bar then selecting Load storage or by using F5 keyboard shortcut Workspace The workspace is a window within the CVI that represents the snapshot it is located in the workspace area on the top left side of the CVI frame Folder A folder is used to store lists and is similar to a directory CODESSA PRO uses four types of folders structure descriptor property and model correlation Each of the first three folders has a system generated list named All This list will contain ALL of the structures descriptors or properties for the corresponding folder The Descriptors folder also includes system defined descriptor lists according to group and type A particular descriptor item may be contained in several lists The Correlations folder contains lists for each property item in the property folder The list is generated automatically by the system when a property item is created When correlations are 218 CODESSA PRO User s Manual calculated 50 correlation items by default will be stored in the list that corresponds to the property Structure A structure is a representation of an individual chemical object with a precise chemical constitution Example
18. e Candidate RC2 License Agreement for End Users The University of Florida Research Foundation Inc hereafter referred to as UFRE a nonstock nonprofit Florida corporation having a place of business at 223 Grinter Hall Gainesville Florida 32611 5500 grants to the licensee Licensee a non exclusive license License to utilize the CODESSA PRO Release Candidate RC2 Software and related materials described in the Software section XII subject to the following terms The CODESSA PRO Release Candidate RC2 Order Form will become part of this Agreement and must be completed for this product ordered by the Licensee and signed by an authorized representative of the Licensee I Site Definition The Site is defined as university or firm company owned machines including networks labs and stand alone machines A company is defined as multinational if it has offices in more than one country II Usage A Licensee may i provide unlimited use of the Software by staff for licensee institute business and research il make copies of the Software reasonably required for Licensee s working and archival purposes these copies of the Software will then become subject to the Terms 111 make composite programs which include portions of the Software in inseparably bound executable form only for use on the computer s at the Site s specified B Licensee may not 1 alter the Software if the Licensee elects to alter the Softw
19. eparing property files If the above is accomplished satisfactorily the final requirement prior to correlation is to prepare the property files On the CODESSA PRO window click the edit pull down menu and choose add property Then you input the name comment and property value according to the format which is indicated in the notepad and finally use the F5 keyboard shortcut for CODESSA PRO to load the data 3 4 Calculating the correlation Ensure that structures descriptors and properties of interest are selected they should all appear in boldface font If not right click the name of structures descriptors or property to show a context pop up menu then select make current to highlight them Click on the calculate pull down menu and choose HMPRO or just press the F9 keyboard shortcut instead The correlation will be finished automatically by CODESSA PRO If you just want to calculate descriptors then click on the calculate pull down menu and choose descriptors or press the F7 keyboard shortcut instead You can also choose form matrix which in addition to descriptor calculation will also form a matrix You can limit the maximum number of descriptors for your model by clicking on the option pull down menu choosing HMPRO clicking expanding then inputting the maximum number of descriptors you permit in your model 3 5 Viewing correlations When the correlations are finished you just double click model and all the models respond to eac
20. erent icon The name that is listed will be the same as the name given on the first line of the molfile The last structure artifact gives the filename of the molfile because the name was not entered on the first line of the molfile Double clicking on an artifact launches a Structures E all 4 Nitropyridine N oxide O Acenaphthene anthracene O Benzil Carbazole Diphenyl sulfone Diuron Ferrocene O Fluoranthene Monouron structure view window in the work area Es Structures Y Descriptors E all Q External E Constitutional Average atom weight Molecular weight Number of aromatic bonds al Number of benzene rings al Number of Br atoms al Number of C atoms G Number of CI atoms Number of double bonds al Number of F atoms Gi Number of H atoms ma Objects Naphthalene Phenanthrene O Pyrene 50000005 mol si ma Objects The descriptors folder is expanded to show the All External and Constitutional lists as well as several other descriptor artifacts The All list is in boldface font because it is the currently selected analysis dimension for descriptors Notice the descriptor icon is different from the structure icons pictured above If an artifact is selected its color will change from black to blue 172 CODESSA PRO User s Manual The Properties folder is expanded to show the All list and several property artifacts No
21. g again stochastically This process is continued up to 10 iterations until the gradient value test for the precise optimization is satisfied If 10 iterations are unsuccessful the calculations are stopped Stage 6 At this stage the CODESSA PRO program converts the MOPAC output files in the MOPAC Optimization step2 Subfolder into MOPAC input files for calculation of molecular properties It is possible to do this without calculation of the Hessian matrix The resulting MOPAC input file is stored in SCF Subfolder Stage 7 Next at stage 7 the CODESSA PRO program produces a set of molecular properties calculated using CMOPAC MOPAC input files The resulting output files are stored in the SCF Subfolder Stage 8 Next CODESSA PRO program takes the molecular geometries in the MOPAC Optimization step2 Subfolder prepares MOPAC input files for force calculations and stores them in the THERMO Subfolder At this stage keyword ROT 1 is added which is valid for Cl CI and CS groups of symmetry This applies to almost all organic molecules However If molecular symmetry is different from point groups C1 CI and CS mentioned above the keywords need to be edited manually To achieve manual 25 CODESSA PRO User s Manual editing open the mni files in MOPAC Optimization step1 Subfolder or MOPAC Optimization step2 Subfolder with Notepad or Wordpad and then add the desired keywords Stage 9 At this stage CODESSA PRO program cal
22. h are not shown in the picture now The picture shows the information provided xj when a descriptor artifact is selected in the 4 workspace Property Yalue Name 1X BETA polarizability DIP Comment Short name DO_MNO_POL_B1 Group Semi empirical Type Molecular typed SubType 1 NJA SubType 2 N A Defined for structures 231 F Property Value Name cyclo test 1 Comment stability File name PO000001 prp Defined for structures 74 The property window for correlation artifacts lists the details of the correlation Details displayed include the properties used in the correlation SA s When a property artifact selected information from the prp file is displayed comments and the number of structures This includes is name laix Property alue Name N 52 n 5 R2 0 916359 Comment For property logL For trans stilbene Number of descriptors Matched sublist of structures fo Number of structures Squared correlation coefficient Squared correlation coefficient Fisher criteria Standart error 5 logL For trans stilbene 52 0 916359 0 870163 100 793776 0 024032 CODESSA PRO User s Manual 2 2 4 Log Window The log window describes each operation that has been performed on the storage Double clicking on a correlation in the workspace will give a full description of the correlation as pictured below The text is in RTF format an
23. h property file will show up Then you double click the model that you want to take a look to open the correlation view window see page 17 3 6 Printing your results O CODESSA PRO User s Manual Use print from the file menu bar to print the correlation plot from the work area To print information from the log area follow the instructions given on page 19 and then print from the corresponding word processing program 3 7 Manipulating lists CODESSA PRO automatically produce one or more lists in each folder but when analyzing a property or correlation it is sometimes helpful to create a user defined list e g a list of structures containing phenyl rings The simplest method for creating a list in CODESSA PRO is to select several artifacts from one or more existing lists i e all right click to open the context pop up menu and left click on create list A list can also be formed from a group of artifacts that are linked to a common artifact If a descriptor is chosen to be the common artifact then all the structures that are defined for that descriptor could be selected for a list To create the list from a common artifact select the common artifact open the context pop up menu click on Select Linked and then select the type of artifacts that you want to add to the list To create a list from multiple common artifacts select the list that is created corresponding to each common artifact then perform the AND operation see below
24. he experimental data and molecular descriptors 1v interpret the developed models and v predict properties for compounds previously unknown or unavailable This manual presents the guidelines for the successful development of a QSAR QSPR models using the CODESSA PRO program The execution of each step of the program normally requires knowledge of the proceeding steps and the steps are therefore discussed in the sequence in which they would be accomplished This manual also provides further information concerning the features and methods available in the CODESSA PRO program their purpose and the interpretation of the results For a more detailed description of the program and the techniques employed please refer to the CODESSA PRO Reference Manual The CODESSA PRO program is designed to operate in the following Microsoft Windows environments Windows 2000 Windows XP Windows NT and Windows 9x To start CODESSA PRO double click on its icon shown above When the program starts the CODESSA PRO Visual Interface CVI window will open Click Calculate on the menu bar to open a pull down menu next click on the Load storage option to refresh the current snapshot which is then displayed on the screen Alternatively the single keystroke F5 will refresh the snapshot Before attempting to use CODESSA PRO it is necessary to understand some of the concepts and terminology used within the program CODESSA PRO User s Manual CODESSA PRO Releas
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26. ke payment within that period UFRF without prejudice to its other rights and remedies considers the license cancelled and Licensee forfeits all rights to use the Software covered under the terms of this agreement CODESSA PRO User s Manual Name of Authorized CODESSA PRO Release Candidate RC2 Software User PRINT OR TYPE SIGNATURE of Authorized CODESSA PRO Release Candidate RC2 Software User Full Name of Organization PRINT OR TYPE Professor or Lab Group Name and or Department PRINT OR TYPE Non Profit Profit State or federal government Benchmarking demonstration Other explain E mail of Authorized CODESSA PRO Release Candidate RC2 Software User Telephone and fax number Payment Method All licensing fees must be PREPAID by check money order or credit card NO purchase orders are accepted If an invoice is required for check payment please send a request to sales codessa pro com l Check Enclosed Please make the check payable to University of Florida Research Foundation Inc Mailing Address 223 Grinter Hall Gainesville Florida 32611 5500 2 2 Credit Card MasterCard Visa Number Expiration Date PRINT or TYPE the name as it appears on the card AIl orders take two weeks to process and are mailed by Postal Services The shipping is paid for by supplier Delivery is within 15 business days PRINT or TYPE the shipping addre
27. l group List of structures All group The selected dimensions are used in the formation of the descriptor property matrix Correlation A correlation represents the results of a multi linear regression between a property of interest y and one or more selected descriptors x y a a x Correlations are composed of regression coefficients a a correlation coefficient R a squared standard deviation s and a Fisher criterion F value for the set of structures used in the derivation of the correlation By default each correlation is named by its number of structures N correlation coefficient R crossvalidated correlation R cv and Fisher criterion value F and squared standard deviation s List A list is collection of the chemical structures descriptors physical and chemical or other property of interest or models correlations Lists can be either system type or user type System lists cannot be deleted by the user To select the items that it is desired to include in a new list right click to show a context pop up menu and then choose create list to make a new list To delete a list click the list that you want to delete right click to show a context pop up menu and then choose delete list 215 CODESSA PRO User s Manual 2 2 CODESSA PRO Visual Interface CODESSA PRO File Edit View Calculate Option Window Help Menu Bar asadas ess aaa O Sala Workspac
28. nety 90 days written notice of termination from Licensee to UFRF c Licensee breaches any of the Terms or any terms of any other agreement between Licensee and UFRF or if the breach can be corrected if Licensee fails to correct that breach within thirty 30 days after notification from UFRF d Licensee performs any act of insolvency or bankruptcy CODESSA PRO User s Manual Following termination Licensee may not use either the Software or the composite programs made in accordance with IJ A ii1 and must promptly return the Software and all related materials to UFRF or certify in writing that the Software and materials have been destroyed V Disclaimer of warranty and limitation of liability THE SOFTWARE IS PROVIDED AS IS EXCEPT AS EXPRESSLY SET FORTH IN THIS AGREEMENT UFRF MAKES NO REPRESENTATIONS AND EXTENDS NO WARRANTIES OF ANY KIND EITHER EXPRESS OR IMPLIED INCLUDING BUT NOT LIMITED TO WARRANTIES OF MERCHANTABILITY FITNESS FOR A PARTICULAR PURPOSE OR ANY OBLIGATION OF RESULTS WITH RESPECT TO SOFTWARE OR ANY OF THE DOCUMENTATION SUPPLIED TO LICENSEE UNDER THIS AGREEMENT WHETHER TRANSMITTED IN WRITING OR ORALLY UFRF ASSUMES NO RESPONSIBILITIES WHATSOEVER WITH RESPECT TO USE LICENSEE AGREES THAT UFRF WILL NOT BE LIABLE FOR ANY SPECIAL INDIRECT OR CONSEQUENTIAL DAMAGES HEREUNDER INCLUDING BUT NOT LIMITED TO LOSS OF USE OR THE LOSS OF DATA OR INFORMATION OF ANY KIND HOWEVER CAUSED VI Proprietary information L
29. ords and the calculations restatred If four files MDL MOL files in the MOL Subfolder and the 3D MOL MOPAC Subfolder and the MOPAC output files in the SCF Subfolder and the THERMO Subfolder are present and up to date no further calculation will be done The up to date state is defined using the modification time of the files In case it is not the calculations will be processed starting from the most recently corrected file To invoke the recalculation select from the menu Calculate Load Storage F5 or Calculate Descriptors F6 In the last case only problematic structures which show in MOPAC Optimization step1 Subfolder and MOPAC Optimization step2 Subfolder will be recalculated If the problems arise as a result of a structure s improper format you must redraw the structure in the MOL Subfolder Note Before a correlation is run you should check if everything in the storage is ready All subfolders in the storage should be empty except the following 1 MOL Subfolder this subfolder should contain all mol files of all structures 26 CODESSA PRO User s Manual 2 SCF Subfolder this subfolder should contain only mni and mno files of all structures 3 THERMO Subfolder this subfolder should contain only mni and mno files of all structures 4 3D MOL MOPAC Subfolder this subfolder should contain only mol files of all structures which are different mol files from the mol files present in the MOL Subfolder Pr
30. s of structures include a single molecule a monomeric unit of a polymer or a molecular complex with a definite composition The minimum information that a structure must include is the types of atoms involved and their connectivity Each structure must be linked with three files containing 3 D structure SCF and Force information Before a 3 dimensional structure can be input into CODESSA PRO it must be converted to MDL molfile format and be optimized The molfile structures are stored in the 3D MOL MOPAC Subfolder SCF output files are stored in the SCF Subfolder and Force output files are stored in the THERMO Subfolder SCF and Force structures will be created and properly stored automatically by the CMol3D module See Starting a New Project for instructions to create each file type It is vital that the name for a particular structure be exactly the same in each directory Structure names must be in the form Sddddddd xxx and should be added in sequential order e g S0000001 xxx S0000002 xxx which will be produced automatically by CODESSA PRO Descriptors Descriptors are defined as numerical characteristics associated with chemical structures They are derived from the structures chemical constitution topology geometry inherent wavefunction potential energy surface or some combination of these items The values of a particular descriptor can be provided by the user or calculated by the CODESSA PRO program Each descriptor value m
31. ss attention to Please include room floor or any special receiving instructions Send license and appropriate fee payment to 10 CODESSA PRO User s Manual Chapter 1 Installing CODESSA PRO 1 1 System requirements Hardware Processor Pentium class systems minimum All processors developed hereafter by Intel Corp are supported on the assembly level optimization All AMD current processors work as old Pentium with higher clock freqency no special optimization Memory 128MB minimum 256MB default tuning CD ROM A CD ROM or a compatible DVD device is required to install CODESSA PRO software Other A 3D graphics accelerator is highly recommended because of extensive use of OpenGL for presentation of molecules 2 button mouse is required Software Operation system Windows XP Professional Windows XP Home Windows 2000 Windows NT with limitation on using network drives Workstation and Server On Windows ME Windows 98 and Windows 95 the program works with many limitations and is tested not very well Operation system extensions Internet Explorer 4 0 SP2 or newer version 11 CODESSA PRO User s Manual 1 2 Installation instructions 4 5 Place the CODESSA PRO CD in your CD ROM drive If the windows Autorun feature is turned on the installation options will be displayed automatically If the installation options do not appear open the Windows Start
32. tice that the fifth property is in boldface font which indicates that it is the property dimension currently selected Notice the icon used to represent property artifacts The name of the property artifact is the same name given on the first line of the property P0000005 prp file As you can see in the picture the first four property files are named lt insert name of property here gt This is because all these four property files are presently empty therefore the first line of these property files is now lt insert name of property here gt You can alter the property files name by double click the current name and then changing it al E Root 3 Structures 3 Descriptors Q Properties All 3 lt Insert name of p Gf lt Insert name of p Zi lt Insert name of p E 0 4 lt Insert name of p gj free energies of Models lt m gt a Objects al xi The models folder has been expanded to display several lists and artifacts A list is created automatically for each property artifact If the pointer is held over a correlation artifact the E Root details of the artifact are displayed e N 74 n 1 R2 HE N 74 n 1 R2 HE N 74 n 1 R2 LE N 74 n 1 Ras Double clicking on an artifact launches correlation view 18 A Structures E Descriptors J Properties ls 0 377704 R2cv 0 343269 F 43 7006 s2 14 9882 CODESSA PRO User s
33. to the formal valence rules The model building is done deterministically for the first iteration and stochastically for subsequent iterations 24 CODESSA PRO User s Manual Stage 2 This stage is concerned with the conversion of the file from MDL MOL format in the 3D MOL Molecular Mechanic subfolder into the MOPAC input file format for preliminary geometry optimization in the MOPAC Optimization step1 subfolder Stage 3 This stage performs the preliminary geometry optimization using CMOPAC MOPAC Version 7 clone If the gradient is less than 5 0 the program automatically proceeds to Stage 4 If the gradient is more than 5 0 then the program automatically go back to Stage 1 and starts model building again stochastically This process is continued up to 10 times until the optimization stage is passes on the criteria of the gradient value being less than 5 0 If success is not achieved after 10 iterations then program stops Stage 4 During this stage the program converts the MOPAC output files in the MOPAC Optimization step1 subfolder into a MOPAC input file for precise geometry optimization and stores them in the MOPAC Optimization step2 subfolder Stage 5 CODESSA PRO is performing precise geometry optimization at this stage If the gradient value can be reduced to less than 0 5 then the program proceeds automatically to Stage 6 If the gradient is more than 0 5 then CODESSA PRO goes back to Stage 1 and does model buildin
34. ust be associated with a previously defined structure Descriptors calculated by the CODESSA PRO program are named automatically renaming descriptors is not recommended Property Property is a physical or chemical characteristic biological activity or other characteristic of interest Each property value must be associated with a structure located in the Structure folder Descriptor Property Matrix The descriptor property matrix consists of descriptor all columns except the last and property the last column values The horizontal dimension of the matrix is the descriptor property ID sequence and the vertical dimension is the structure ID sequence The matrix has two presentations binary and text The binary presentation is used for internal use while the text presentation is optimized for import into the STATISTICA and other software package at present in the CSV format 14 CODESSA PRO User s Manual Current Analysis Dimensions The dimensions used for an analysis by CODESSA PRO are the property the list of descriptors and the list of the structures All the dimensions are selected by right clicking the dimension desired this will open a context pop up menu from which should be chosen make current the one chosen will be in boldface font to indicate that it is the currently selected dimension The default dimensions for a new snapshot file are Dimension Default value Property First selected List of descriptors Al
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