Projects are text files in which all options required to execute a calculation are included. They contain information regarding the indices, their weighting parameters, groups and aggregation operators. Also it includes values for all the configuration parameters needed for calculations (default settings are automatically saved).
A project is very simple to configure from the GUI, it is only needed to settle the configuration for the desired calculation and to export it by using the "Save Project" (
A ProtDCal project uses unique tags to identify the different steps of the calculation process (indices, weightings, groups, aggregation operators, etc.). The general structure of a project is:
directory:
/path/to/datasets
indices:
Indices names separated by comma. The weighted indices must include two lines more specifying the index's name and the weights separated by comma.
weighted index:
Weights for the indices separated by commas. For instance:
wPhiH:It's important being careful with manual setting of tags, missing data shall cause a failure in the excecution.
user-defined:
Properties indices defined using the ProtDCal GUI.
cdk indices:
TAE indices provided by CDK library.
functions:
Functions names separated by comma.
groups:
Group names separated by comma.
invariants:
Aggregation operators separated by comma.
parameters: Parameters for calculations, in the next order: t_cont, s_cont, area, dHSG, n, Int, K, Subgraph where:
options:
Options like output format, dataset type, windex algorithm, etc. in the next order:
(decimals,armonicMeanType,geometricMeanType,windexID,datasetType,outputOrder)where:
In addition a project don't must contains any empty line, incorrect tag or bad IDs. For more information about the IDs for each tags see the next section.
Thermodynamic Indices of Folded Protein States
Gc(F) Gw(F) Gs(F) W(F) DGs HBd DGel DGw DGLJ DGtorThermodynamic Indices of the Extended Protein State
Gw(U) Gs(U) W(U)Topographic Indices
A DA DAnp wSp lnfd wR2 wDHBd wNc wFLC wNLC wCO wLCO wRWCO wCTP wCLQ wPsiH wPsiS wPsiI wPhiH wPhiS wPhiI Phi PsiProperty Based Indices
Mw HP IP ECI Vm Anp Z1 Z2 Z3 ISA At Ap Pa Pb PtResidue Basic Group
ALA ARG ASN ASP CYS GLU GLN GLY HIS ILE LEU LYS MET PHE PRO SER THR TRP TYR VALProperties Based Group
RTR BSR AHR ALR NPR ARM PLR PCR NCR UCR UFRTopographic Group
SHT HEX TRN RCL INT SUP PRTDistances
N1 N2 N3Means
Ar P2 P3 M G VStatistics
CV Q3 S RA MN K Q1 MX DE Q2 I50Classics
SI MI TI
To For up loading a project there is the "Load Project" ( ) button on the toolbar or from the File menu, and also the key combination Ctrl. + L. Any of these options will launch a window to select the desired project.