#CONFIGURATION FILE FOR THE GNOMO SOFTWARE
#This file sets the values for some variables of the software display mode
#initial conditions

1       #1=apoptosis,2=cell sorting,3=invagination,4=epithelial directed growth,
        #5=mesenchymal directed growth,6=ECM secretion,7=migration

#visualization variables for the OpenGL environment

0.0 0.0 12.0       camera initial position

0.0     camera initial rotation around z axis
135.0     camera initial rotation around x axis

29        color code selection (see below for an explanation)
1         color palette (1-3)
0         custom colorcode (should match the color code above if you want a custom colorcode, if not leave it at 0)
1         custom colorcode maximum
0         custom colorcode minimum

0         arrow code selection (see below for an explanation)
1.0       arrow scale
0         custom arrow selection (should match the color code above if you want a custom colorcode, if not leave it at 0)
0         custom arrow maximum value
0         custom arrow minimum value

0         semitransparent shpere code selection (see below for an explanation)
1.0       sphere scale
0         custom sphere selection (should match the color code above if you want a custom colorcode, if not leave it at 0)
0         custom sphere maximum value
0         custom sphere minimum value



#draw function flags (will determine what is bein displayed)

0   cylinder spring 
0   3D box grid for neighboring
0   nothing
0   nothing
1   nodes as spheres: radius is p^EQD
0   nodes as spheres: radius is p^ADD
0   nothing
0   no spheres
1   epithelial apical nodes
1   epithelial basal nodes
0   nodes as spheres: small radius
0   connexions between cells
0   connexions within the cell
0   nothing
0   nothing
0   nothing
0   nothing
0   display box
0   display cell polarization vectors 
0   nothing 
0   display cell centroids 
1   epithelial nodes as cylinders
0   nothing
0   nothing
0   nothing
0   nothing
0   nothing
0   nothing
0   nothing
1   display epithelium
1   display mesenchyme
1   display extracellular matrix
0   nothing
0   nothing
0   nothing
1   fixed nodes (node()%hold=1)
0   plot cell contour
0   plot intercellular contour
0   plot displacement of nodes respect initial conditions
0   nothing
0   EPIGRID

#Preselection of nodes and cells

0   Selecting nodes (=1) or cells (=2), or nothing (=0)

0   Number of nodes/cells/selected





###### color code options (also applies to arrows and spheres

1 node position in x
2 node position in y
3 node postition in z
4 node energy
5 node p^EQD
6 node p^AAD
7 node p^YOU
8 node p^ADH
9 node p^REP
10 node p^REPCEL
11 node p^ER
12 node p^EST
13 node p^EQS
14 node p^HOO
15 node p^MOV
16 node p^DMO
17 node initial position in x
18 node initial position in y
19 node initial position in z
20 node accumulated extracellular matrix
21 node p^COD
22 node p^GRD
23 node p^PLD
24 node p^VOD
25 node p^DIF
26 node p^KFI
27 node p^PLA
28 node p^VOC
29 node type
30 cell index
31 epithelial node counterpart (the other one composing the cylinder
32 cell nucleus
33 node()%talone
34 nodes that are fixed in space
35 nodes that are borders of the system
36 cell cycle progression
37 node displacement in x
38 node displacement in y
39 node displacement in z
40 node total displacement
41 node's grid box index
42 node index
43 concentration of gene form 1
44 concentration of gene form 2
.
.
.
.
until the total number of genes
