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Chapter 10. Menu File (Alt-F)
This menu gives access to the basic operations involving file manipulation, as to open previous VolSurf projects, import series of compounds, import fields etc... The option to quit the program is in this menu.
10.1. File->Open data file... (Alt-O)
Every time VolSurf imports one or more fields it creates an output file, usually with the extension .vol. This file can be opened afterwards to reload the results of the analysis, to have access to the variables and models obtained, etc...
This command opens a file selection dialog, where the User can select the file to open.
- Files
this list shows all the files matching the filter pattern. Click on any of these files to select it. In addition, the list displays other accessible directories and allows the User to navigate through the directory tree. To see the contents of any descendent directory simply click on any item of the list. To see the contents of the parent subdirectory, click on the ".. [Parent Directory]" item.
- Select VolSurf file (.vol):
under this label the User can find three elements which can be used to select the file to open.
On the left hand side there is a drop pocket area where the User can drag and drop the icon representing the VolSurf file.
In the center there is a text input file, the User can type directly the path and the name of the file to open. By default, this input file contains the path to the current directory, the one shown in the Files list, and is updated when the User navigates by the directory three. Notice that there are buttons over the names of every individual directory in this path. By pressing those buttons the user can change directly to the corresponding directory in a fast way.
On the right hand side there is a double arrow symbol. When pressed, it shows a list with the more recent file selections.
The Filter button brings up a dialog where the User can see and edit the filter pattern. This filter pattern string uses standard wildcards characters to define the files presented in the Files list. For example, in this case the filter pattern string is *.vol and therefore the list shows only files with the extension .vol (usually the VolSurf files have this extension). To show files with different extensions press the button and enter in this dialog the appropriate wildcards.
Once the selection is done press the OK button, and this file will be read. If the file has a improper format a error message will appear and the file will be refused. Press the Cancel button to abort the operation.
After loading an .vol file, the program is at the same point it was when the User quit the program. If the User excluded objects or variables in the last run, these will be automatically excluded now. The same applies to non-standard data scaling.
10.2. File->Import
This menu gives access to the "Import" operations which could involve series of molecules or fields as well as .vol files from previous VolSurf editions.
10.2.1. File->Import->Series...
VolSurf includes part of the program GRID to generate molecular interaction field (MIF) data. VolSurf is able to reads and generates one or many 3D molecular structures written in a standard file format (GRID kout, SYBYL mol2, MDL SDFile or Multi mol2 files), and process them automatically as indicated in the scheme below
The VolSurf conversion engine starts processing the molecules or molecules defined and assigns atom types. If VolSurf is unable to assign atom types an error message will be shown and the User will be asked to continue using only the structures successfully converted. Atom type assignment is made analyzing the atomic elements and the bond orders. SYBYL atom types are not considered at all and don't need to be correctly set for a successful conversion. On the contrary, correct bond order and the presence of all the hydrogen atoms is essential. In aromatic compounds, a sensible Kekule form is preferred to aromatic bonds, even if in most cases both representations give identically good results.
Charged compound will be recognized from the structure. During the conversion, the charge assigned to the compound will be presented in the main text window. A correct charge is a good indicator that the atom assignment is working fine.
Once the GRID atom types are assigned, the program works molecule after molecule: for each one it runs GRIN producing a kout file and then it runs GRID producing a kont. VolSurf encoding engine works on the output kont files storing the results in an VolSurf output file (.vol).
Multiple structures can be imported at the same time. When it is so, the variables generated by VolSurf are stored in a X matrix representing the whole series of compounds. Multiple structures can be imported in three ways:
| wildcards | The User can type a line containing some wildcard characters. Files with names matching the wildcard string will be imported sequentially. For example: file###.mol2 will produce the import of files file000.mol2, file001.mol2 and file003.mol2 |
| list file | The User can enter the name of a file that contains a list of the files to import. A file is recognized by VolSurf as a "list file" when it has the extension .lst or .list. List files must contain inside only valid filenames, one in each line, without any other information. |
| SDFiles | A single MDL SDFile may contain inside many structures. These will be processed sequentially. |
VolSurf can import the following type of formats:
| single file | multiple files using wildcards | multiple files using list file | |
| SYBYL mol2 | yes | yes | yes |
| GRID kout | yes | yes | yes |
| MDL SDFiles | yes | no | no |
| Multi mol2 | yes | no | no |
The command opens a dialog like this:
- Series type
The User selects here the format of the files that contain the molecular structure/s. The choices are SYBYL mol2, GRID kout or MDL sdf and Multi-mol2.
- Task
For SYBYL mol2 and MDL SDFiles, the User has the choice of running the whole process, as specified in the scheme above, or run only the VolSurf convert engine and GRIN, in order to obtain the kout files.
- Input series file/s
In this text field the User can enter the name of a single file or specify multiple files either introducing the name of a list file of a string with wildcards characters. If the desired input corresponds with an actual file name of the type specified in the above Series type control, the User can press Find to open a standard file selection dialog. The file selected will be then presented in the input line immediately to the left to the button pressed. See the File->Open data file command for details about the file selection dialog.
- VolSurf new file (.vol)
in this text field the User must enter the name of the output file where the new generated variables and related information will be stored. This file can be opened afterward in order to inspect the variables, build models, export the variables in ASCII or GOLPE format, etc... We strongly recommend to assign the extension .vol to VolSurf output files. It is possible to type the file name or press the Find button to open a standard file selection dialog. The file selected will be then presented in the input line immediately to the left to the button pressed. See the File->Open data file command for details about the file selection dialog.
- probes (up to 5 selections)
in this control, the User select the probes used in the GRID analysis. For VolSurf calculations we suggest to use at least probes OH2 (water) and DRY (see the background section for more details) but other probes can be selected in special situations. For selecting a probe, simply click on the corresponding line and it will be highlighted. Up to five selections are allowed.
- grid spacing (in Å)
This control defines the spacing of the nodes used to compute the MIF in GRID. Therefore, if we want to use a grid spacing of 0.5Å in GRID, here simply we must move the sliding control up to 0.5. For most VolSurf analysis, a grid spacing of 0.5 is recommended.
- keep KONT
The results of the GRID analysis are stored in kont files, usually quite large. VolSurf can keep in the disk these files or can remove them in order to save disk space.
- Adv Options
This button opens the following dialog to protonate and/or deprotonate some chemical groups:
At the moment is possible to protonate and/or deprotonate only the carboxylic and amine groups:
COOH ionization
selecting As provided the carboxilic groups are not modified
selecting COO- the carboxilic groups are deprotonated if they have the hydrogen, they are not modified if they are already deprotonated
selecting COOH the carboxilic groups are protonated if they have not the hydrogen, they are not modified if they are already protonated
NH3 ionization
selecting As provided the amine groups are not modified
selecting NH3 the amine groups are deprotonated if they are protonated, they are not modified if they are already deprotonated
selecting NH4+ the amine groups are protonated if they are deprotonated, they are not modified if they are already protonated
Warning At the moment this process modifies unselectively all groups present in the imported structures.
Once the controls were set press OK, and VolSurf will start processing the files or press Cancel button to abort the operation.
When importing SDFiles, the program will ask the User for the name of the field label that VolSurf should use to assign the name of the molecules (often <MOLNAME>). In no input is given, VolSurf will use the contents of the first line for each molecule block. If again this is not suitable as an object name, a generic name based in the sequential order of the object into the file will be used.
If any of the files is not found, their format is incorrect or the conversion is not successful, an error message will be shown.
10.2.2. File->Import->Fields...
VolSurf includes a method to generate molecular interaction field (MIF) data on its own. However MIFs can be computed externally with GRID using the interface described above (see File->Import->Series... ) or can be imported from other programs using this command.
VolSurf supports some external MIF formats:
GRID kont, containing one or several fields for one or many molecules
GOLPE dat, containing one or several fields for one or many molecules
Gaussian ASCII mep files
GRID ASCII fields
VolSurf can import just one or a set of these files. There are two methods to define the import of multiple MIFs:
| wildcards | The User can type a line containing some wildcard characters. Files with names matching the wildcard string will be imported sequentially. For example: file###.dat will produce the import of files file000.dat, file001.dat and file003.dat |
| list file | The User can enter the name of a file that contains a list of the files to import. A file is recognized by VolSurf as a "list file" because it ends with the extension .lst or .list. List files must contain inside only valid filenames, one in each line, without any other information. |
Therefore, VolSurf can import data for multiple molecules in several ways.
Importing a single GRID or GOLPE file containing information for multiple molecules
Importing many files containing information for only one molecule
Importing many GRID or GOLPE files containing information for many molecules
When it is so, the variables generated by VolSurf are stored in a X matrix representing the whole series of compounds.
The command opens a dialog like this:
- Field type
the User defines here the format of the MIF files. Possible choices are GRID kont, GOLPE dat and GRID ASCII.
- Input field file/s
in this text field the User can enter the name of a single file or specify multiple files either introducing the name of a list file of a filename with wildcards characters. If the desired input corresponds with an actual file name of the type specified in the above Field type control, the User can press the Find button to open a standard file selection dialog. The file selected will be then presented in the input line immediately to the left to the button pressed. See the File->Open data file command for details about the file selection dialog.
- VolSurf new file (.vol)
in this text field the User must enter the name of the output file where the new generated variables and related information will be stored. This file can be opened later in order to inspect the variables, build models, export the variables in ASCII or GOLPE format, etc... We strongly recommend to assign the extension .vol to VolSurf output files. It is possible to type the file name or press the Find button to open a standard file selection dialog. The file selected will be then presented in the input line immediately to the left to the button pressed. See the File->Open data file command for details about the file selection dialog.
Once the controls were set press the OK button, and VolSurf will start processing the files or press the Cancel button to abort the operation.
If any of the files is not found, their format is incorrect or the conversion is not successful, an error message will be shown. Otherwise, the Calculation Parameters dialog is shown:
Note: this dialog will NOT appear if Default calculation definition field is set to Yes in the Miscellaneus preferences dialog (see Preferences->Miscellaneus ).
In this dialog, the User can change the different parameters that control the VolSurf encoding engine (see Calculation->Recompute... command for a detailed description of the Calculation Parameters dialog.
10.2.3. File->Import->Activity...
This command allows the User to import up to 4 dependent variables. These values are often a measure of the biological activity of the compounds and the crude values require to be transformed to logarithmic scale. This command allows to import such data and performs the required transformations in a simple and straightforward way.
The command opens a dialog like this:
- Find...
Press this button to open a standard file selection dialog. The file selected will be then presented in the input line immediately to the left to the button pressed. See the File->Open data file command for details about the file selection dialog.
- Activity File (ASCII)
Enter here the name of an ASCII file containing one line for each compound and up to five columns separated by spaces or tabs:
a reminder of the name of the compounds (optional)
up to four separated values of dependent variables
The following examples are valid ASCII activity file:
With a first column of labels
mol1 0.34 mol2 0.56 mol3 0.01 mol4 0.97
Without a first column of labels, three values of activity
0.25 0.45 0.34 0.76 1.25 0.98 0.84 0.96 1.56 3.00 2.98 3.00 0.75 1.10 0.85 1.23 1.00 1.25
Please notice that the first column is optional. However, when present, VolSurf will compare these names with the actual names of the objects in order to assign correctly the activity values. This prodedure will work also in the case of mismatch between the list of compounds imported and the list of compounds in the activity text file. Without the first column of label names the first value in this file will be assigned to the first object (in the order listed in the first read of the file), the second to the second object and so on. Here the order of compounds do matter.
- pK (-log)
If this control is selected, the numerical data x will be converted to -log(x). An error will be shown if any of the values is zero or negative. The biological data is usually provided in millimolar, micromolar or nanomolar concentrations. In this dialog is possible to select the appropriate units for the data.
- Structure names in the first field
As mentioned above, the first column can be used to write a label which reminds the User the name of the objects. If the file contains such a column, select this control to prevent VolSurf to read it as if it was numerical data.
Please notice that, when importing activity data, the new data will replace any previously loaded activity data. Activity data might contain missing values, represented as -99.000, provided that more than one column is imported. It is not allowed to import activity data that assigns only missing values to a certain object.
10.2.4. File->Import->2.x .vol file...
With this option the User can convert the old 2.x VolSurf version .vol files in VolSurf 4 compatible .vol files. This command opens a select a file dialog: see the File->Open data file command for details about the Select a File dialog.
10.2.5. File->Import->3.0.x .vol file...
With this option the User can convert the old 3.0.x VolSurf version .vol files in VolSurf 4 version compatible .vol files. This command opens the select a file dialog: see the File->Open data file command for details about the Select a File dialog.
Important: The converted .vol file has the same number and type of variables of the old version file. The new VolSurf 4 descriptors are not computed and the -99 code (missing data) will be assigned to them.
10.3. File->Expand series...
From VolSurf 4 is possible to expand a .vol file adding new molecules to the .vol binary file. The command opens the follow dialog:
This dialog is the same as the one opened with File->Import->Series... command. It is not possible to select or unselect probes because they are already saved the .vol file to expand
Important: When the User expands a .vol file containing Y values a dialog appears to inform the Y values will be lost in the expansion procedure. In order to create a PLS model with the expanded .vol file it is therefore necessary to reimport the Y values for all molecules (see File->Import->Activity... command).
10.4. File->Export data file
The results of the VolSurf encoding engine can be exported as GOLPE .dat files or as plain text files in tabular format.
In any case, the data is always exported "as it is" in the program at a certain time. If the User applies scaling or removes objects or variables, these transformations will be also applied to the data exported.
10.4.1. File->Export data file->GOLPE format
The variables produced by the VolSurf encoding engine can be exported to GOLPE using this command. It opens a standard file selection dialog where the User can introduce the name of the output file.
The command will produce the output of the .dat file plus some auxiliary files that define the blocks of variables and their names.
The commands Model->External PCA pred... and Model->External PLS pred... require as input GOLPE dat files like the ones created with this command. However, when exporting data with this purpose please make sure that the data is not scaled. Only data with RAW scaling is suitable for external predictions.
10.4.2. File->Export data file->ASCII format (tabs)
The variables produced by the VolSurf encoding engine can be exported to many applications using this command. It opens a standard file selection dialog where the User can introduce the name of the output file.
The output files have tabular, tab separated format, so the lines can be extremely long. This is not a format intended for being human-readable but to be imported into generic spreadsheets, statistical analysis or plotting programs.
10.4.3. File->Export data file->ASCII format (spaces)
The same dialog opened with the File->Export data file->ASCII format (spaces) command but the output files are spaces separated format, to obtain a human-readable text file.
10.5. File->Object type
10.5.1. File->Object type->List
Shows in the main window a summary of the type of objects and the colors associated to them.
10.5.2. File->Object type->Modify (manual)...
Often, the objects of a data set can be considered to belong to different types. For instance, they can be molecules of two chemical families, obtained from modifications of two different prototypes, or samples obtained from different sources, etc... In such cases it is interesting to highlight these peculiarities in the 2D and 3D objects plots, in order to identify any clustering of the objects related with those properties.
VolSurf allows the User to define different types of objects and to assign a different color to each type. Please notice that the types will be used only to give different colors to the objects in the plots and they have absolutely no influence in the results of the analysis.
In data files containing few objects the User can assign the colors directly. On the contrary, in data files with hundred or thousand of objects it would be more convenient to use the File->Object type->Modify (rule based)... option.
- Object Type
The User can choose here the type (color) to assign. There are 20 colours: cyan, green, red, blue, white, yellow, magenta, orange, ivory, purple, dark cyan, dark green, dark red, dark blue, dark white, dark yellow, dark magenta, dark orange and dark ivory.
- Objects:
This is a list of all the objects present in the dataset. Each time the User click on an object name, the type of the object will change to the type currently active in Object Type. By default, before making any type change, all the objects are assigned to type 1 (white).
When the OK button is pressed, the object types are stored in the disk and from this moment they can be seen in the plots. Changes can be applied at any time.
10.5.3. File->Object type->Modify (rule based)...
Often, the objects of a data set can be considered to belong to different types. For instance, they can be molecules of two chemical families, obtained from modifications of two different prototypes, or samples obtained from different sources, etc... In such cases it is interesting to highlight these peculiarities in the 2D and 3D objects plots, in order to identify any clustering of the objects related with those properties.
VolSurf allows the User to define different types of objects and to assign a different color to each type. Please notice that the types will be used only to give different colors to the objects in the plots and they have absolutely no influence in the results of the analysis.
In data files containing hundred or thousand of objects it is not practical to define the type picking one object at a time. When the type is associated with the name of the objects it is possible to define a rule, that can be then used to assign the type of the objects automatically.
- Rule definition
This input field contains initially a line of asterisks. The User should replace in this line the asterisks by the character # in those positions that distinguish the type of the objects. For example, if the data file contains a set of objects called X01, X02, X03... and other series called Y01, Y02, Y03.... the rule #************** will automatically assign different types to both series, since the first character is the key to identify the series to which belongs each object. The names of the objects can be more complicated, for instance they can be a first series of EA2748_A_01, EA2749_A_02, CAB347_A_03 ... and a second one of EA2748_B_01, EA2749_B_02, CAB347_B_03 ... In this case we can use the eighth character (A and B) to classify the objects in the two series, with the rule string *******#**********.
Formally, the rule works comparing the names of the objects only in those positions marked by the # character. If from the result of this comparison it is not similar to any previous object, it will be assigned to a new type. Since there is a maximum of 20 types (colors), type 21 will be assigned color 1 and so on.
Once the User has entered the string he should push the Apply button in order to carry out the type assignment. The results of the assignment can be inspected in the Objects names and types list. If the User is satisfied with the assignment he can press the OK button. Otherwise he can press the Cancel button and repeat the rule definition.
When the OK button is pressed, the object types are stored in the disk and from this moment they can be seen in the plots. Changes can be applied at any time.
10.5.4. File->Object type->Hide...
In some data files there are dense clusters of objects that make difficult to see some particular object in the 2D and 3D plots. In such situations it is possible to toggle the hidden or visible status of some objects in the plots. It is important to notice that this status affects only the way the objects are shown in the plots. Hidden objects participate in any analysis in the same way that visible objects.
In this dialog the visible status of the objects can be changed both picking individually the objects or using a rule definition.
- Rule definition
This input field contains initially a line of asterisks. The User should replace in this line the asterisks by any character that identify the objects to hide. For example, if the data file contains the objects called X01, X02, X03, X04, Y01, Y02 and we want to hide the two last objects the rule Y************** will automatically assign these two objects a hide visibility status.
Formally, the rule works comparing the names of the objects only in those positions not containing an asterisk. If from the result of this comparison an object is found similar to the rule, it is assigned an hidden status, if not it is assigned a visible status.
Once the User has entered the string he should push Apply in order to carry out the visibility status assignment. The results of the assignment can be inspected in the Objects names list. If the User is satisfied with the assignment he can press the OK button. Otherwise he can press the Cancel button and repeat the rule definition.
In addition the user can click on the names of individual objects in the Objects names, click to swith status list. Each click will switch the visible-hidden status of this object.
When the OK is pressed, the object visibility status are stored in the disk and from this moment they can be seen in the plots. Changes can be applied at any time.
10.5.5. File->Object type->Define spectrum...
In VolSurf it is possible to color the objects according to a chromatic scale that represents the values of a certain variable, for example the activity.
First, the User must select the variable from a list containing all the VolSurf variables, in a dialog like this:
By default the spectrum is set to the last Y variable, when present. Once a variable is selected pressing OK the following dialog is shown:
- Minimum value and Maximum value
The User can move these slides to define the maximum and the minimum between of which the spectrum will show color variation. Objects with values higher than the maximum and lower than the minimum will be assigned the to and from colors. Objects with values into the range defined by these two values can be draw in the plots with colors that take intermediate values between the color defined as from and the color defined as to.
- from and to
In these menus, the User can choose the colors associated with low values of the spectrum variable (from) and with high values of the spectrum variable (to). Both color should be different. The choices are red, blue and green.
When the OK button is pressed, the spectrum is saved to disk. From this moment, correlograms and object plots will show the option to color the points according to the defined spectrum.
10.6. File->Model library...
This command allow the User to import up to nine precomputed ADME models or own saved models, depending by the selection near the Default model library path field in Section 16.1. The ADME models included in the VolSurf package, are available either with the standard atom charge calculation method than with the AM1 atom charge calculation method.
Note: The User has to choose the model with the same atom charge calculation method of the model that he wants to project.
VulSurf predicts ADME properties of compounds such as blood-brain barrier permeation (BBB in Model Library), termodinamic solubility (SOLY in Model Library), Caco2 permeability (CACO2 in Model Library), biopharmaceutical classification (SolyPerm in Model Library), protein binding (Protein_Binding in Model Library), volume of distribution (Volume_Distribution in Model Library), hERG (HERG in Model Library), water-DMSO mixture solubility (solDMSO in Model Library) and CYP3A4 metabolic stability making it possible to check a drug's behaviour profiles in parallel.
More informations about the ADME models supplied with VolSurf are available in Chapter 8.
The command opens a dialog like this:
- Models list
The different ADME models can be selected by clicking on the appropriate row of the above window.
- Open
Press this button to retrieve the appropriate ADME model.
- Add
This button allows the User to store in the Model Library the model just built, modified or optimized with VolSurf. Only a model resident in the memory can be stored in the Model Library. When a model is stored, VolSurf asks for descriptive label for the model (i.e. Metabolic Stability). A new line will then be added to the list of the Model Library.
- Delete
This button allows the User to delete a model.
Note: Both Add and Delete buttons need write permissions in the Model Library directory to work properly, so please check your permissions on the library directory if you're experiencing problems with these two commands (see more details about it in Section 16.1).
- Expand
This button expand the selected model with the actually opened .vol file in VolSurf. After the following dailog will appears:
in the text field, insert a name for the new expanded model to add at the Model Library list and press OK to continue or Cancel to exit without expanding the model.
- Info
Retrieves the calulations parameters used in the building phase of the selected library model.
- Exit
Use this command to exit the model library dialog window.
10.7. File->Direct prediction...
This option can be used to obtain fully automatic predictions (projections on models) starting directly from the 3D structure of chemicals. No intermediate steps are required.
The command opens the following dialog:
- Series type
the User selects here the format of the files that contain the molecular structure/s. The choices are: single mol2 file, GRID kout file, MDL sdf file ot Multi-mol2 Sybyl file.
- Input series file/s
in this text field the User can enter the name of a single file or specify multiple files either introducing the name of a list file of a string with wildcards characters. If the desired input corresponds with an actual file name of the type specified in the above Series type control, the User can press the Find button to open a standard file selection dialog. The file selected will be then presented in the input line immediately to the left to the button pressed. See the File->Open data file command for details about the Select a File dialog.
- VolSurf new file (.vol)
in this text field the User must enter the name of the output file where the new generated variables and related information will be stored. This file can be opened afterward in order to inspect the variables, build models, export the variables in ASCII or GOLPE format, etc... We strongly recommend to assign the extension .vol to VolSurf output files. It is possible to type the file name or press the Find button to open a standard file selection dialog. The file selected will be then presented in the input line immediately to the left to the button pressed. See the File->Open data file command for details about the Select a File dialog.
- Activity filename
in this optional text filed the User can enter the filename of the file containing the activity values for the external molecule to predict. If the real values are unknown, the field can be left unfilled.
- Models
the list of the saved model libraries is shown here. The User can choose the model upon which to project the external compounds. If you want more informations about the library models please look in File->Model library
- Grid spacing
this control defines the spacing of the nodes used to compute the MIF in GRID. Therefore, if we want to use a grid spacing of 0.5Å in GRID here simply we must move the sliding control up to 0.5. In this case the grid spacing selection is not a critical parameter for external prediction, so even if in a model a grid spacing of 0.5 was used, prediction can be tolerated with a grid spacing up to 1.0.
- Info
method info contains the calculation parameters selected in the building phase of the current model. X refers to the number of descriptors produced by VolSurf, Y refers to the number of responses, LEV to the number of energetic levels selected for the computation of the descriptors and Objs is the number of molecules present in the dataset.
- keep KONT
the results of the GRID analysis are stored in kont files, usually quite large. the User can choose here if VolSurf has to keep in the disk these files or remove them in order to save disk space.
- Enable projection spectra
select it in order to visualize in the plots the projected compounds coloured by a X or Y variable values of the projected model.
- Adv Options
This button opens a window dialog to protonate and/or deprotonate some chemical protonable groups in the imported compounds. This dialog is the same opened with the Adv Options button in the File->Import->Series... dialog.
- Help
gives on line help
When this parameters have been set and the OK button is pressed, the calculation is made and the prediction palette will appear:
the User must first decide if to use PCA or PLS prediction. In both cases the graphic (2D, 3D or scatter plot) is activated only after PCA or PLS prediction selection. When the PLS prediction is selected, the projection values on the library are reported in the VolSurf screen in this format:
where the data fields have the following significate:
| 1 | object sequential number |
| amikacin | object name |
| < 1.14> | external y value (conventionally 0.0 is unknown) |
| PC1 to PC5 | coordinates of the object in the PC model |
| Y-LV1 to Y-LV5 | y predictions for a PLS model with 1 up to 5 components |
- 2D scores and 3D scores
the User must specify the axes for the PCA or PLS plot. X=1 and Y=2 refers to PC1 vs PC2 space. In order to show in the plot the predicted values, the show external predictions check button must be enabled.
Pressing OK the 2D or 3D score plot appears. The projected points will be reported in yellow. Whenever the spectrum color is activated it is extremely simple to predict graphically the activity behaviour of the external compounds (see how to activate the spectrum plot in the 2D plot or 3D plot sections of this manual).
- Scatter
it reports experimental vs calculated activity for the compounds in the library. The external compounds will be reported in yellow. By clicking on the compounds the calculated activity will be reported at the present dimensionality.
- Residuals
it reports the experimental activity vs the recalculated residues at the selected dimensionality. The external compounds will be reported in yellow. By clicking on the compounds the calculated residual value will be reported at the present dimensionality.
- PLS plot
the User must select the component dimensionality (the first component is always the best choice). The show external predictions button must be checked to show the predictions in the plot. The external compounds will be reported in yellow. The position of the compounds in the model (yellow line) can be used to nake a compound ranking.
Note: If the Enable projection spectra check button in the External predictions dialog is enable after pressing the buttons above and defining the dimensionalty or the X and Y axes, the following dialog appears:
Under Variables select a X or Y variable and press OK. In the dialog that will appear define the spectrum and press OK. After the plot will appear with the right mouse button in the plot, open the pop-up menu and select symbol color->spectrum projection to visualize the compounds coloured by the choosen variable.
- Similarity
This button is used to create a list of the compounds of the library model by similarity for every projected compounds. The button opens the following dialog:
Output:
the User can choose the output for the similarity list: selecting File the list is saved in the SimilarityScores.txt, selecting Main window the list is visualized in the main VolSurf window.
Sorting:
the User can choose the order of the similarity list: Score to sort from the more to the less similar compounds of the library model, Name to sort by name of compounds of the library model and No to sort by the order of the compounds in the library model.
- Exclude objects
sometimes external predicted compounds are really far from the current chemical space. These compounds often produce a graphic "compression" of the plot thus disturbing the chemical interpretation. Using this button a new window will be presented for the selection of the objects to be removed from the external prediction. To remove one or more objects, click on the compond line in order to change the status from active to excluded.
After pressing OK another prediction will be made with the exclusion of the disturbing compounds.
- Proj. 3DM
this button opens a Select a File dialog to import a new list of coumpounds to compute and project in the previous selected library model. See the File->Open data file command for details about the Select a File dialog.
| Warning |
after the command File->Direct prediction... VolSurf will mantain in memory the newly produced .vol file. To load a new model, press File->Open data file or File->Model library . |
10.8. File->Data file utils...
From VolSurf 4 it is possible to create a new .vol file merging two preexisting ones or to create a new .vol file by extracting some objects from a list file.
10.8.1. File->Data file utils...->Merge data files...
This command opens a Select a File dialog where you select the first .vol file to merge. Then another Select a File dialog appears to define the second .vol file to merge. The last Select a File dialog defines name for the merged file.
10.8.2. File->Data file utils...->Extract from data files...
This command is active only when a .vol file is opened (see File->Open data file). Selecting this command the following dialog appears:
- List file path:
Insert in this text field the name of the list file with the objects to extract. Use the Find... button to open a Select a File dialog and search the list file (see File->Open data file command).
The following is an example of the list file to use for the extraction:
The first line contains the total number of objects to extract; then each line lists the ID number and the name of the object to extract from the .vol file. The ID number can be found in the first column of the output from the command List->Activity.4 8 obj08 6 obj06 1 obj01 3 obj03
- New .vol filename:
Insert in this text field the filename for the new .vol data file or press Find... to open a Select a File dialog to search an existing file (see File->Open data file command.
10.9. File->Quit (Alt-Q)
Select this option to exit from VolSurf. A dialog window will appear to confirm the exit:
Press OK to exit from VolSurf or Cancel to close the dialog window and continue working.
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