/
parms.dat
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parms.dat
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parms_list = {
## some graphics
'colorblind':0,
'chain_colors':[[0.25,0.25,0.90],[0.90,0.90,0.25],[0.90,0.25,0.25],
[0.25,0.90,0.25],[0.25,0.90,0.90],[0.90,0.25,0.90],
[0.05,0.05,0.50],[0.50,0.50,0.05],[0.50,0.05,0.05],
[0.05,0.50,0.05],[0.05,0.50,0.50],[0.50,0.05,0.50]],
'colorblind_chain_colors':[[0.15,0.15,0.80],[0.80,0.80,0.15],[0.15,0.80,0.15],
[0.00,0.00,0.50],[0.50,0.50,0.00],[0.00,0.50,0.00],
[0.55,0.55,0.99],[0.99,0.99,0.55],[0.55,0.99,0.55],
[0.35,0.35,0.90],[0.90,0.90,0.35],[0.35,0.90,0.35]],
'atom_color_list':['chain1','chain2','chain3','chain4','chain5','chain6',
'chain7','chain8','chain9','chain10','chain11','chain12',
'white', 'blue', 'red','orange','yellow','cyan','magenta', 'grey'],
# the first twelve have to be guaranteed, for the chain colors to cycle through
'colormap':{ 'chain1':[0.25,0.25,0.90], 'chain2':[0.90,0.90,0.25], 'chain3':[0.90,0.25,0.25],
'chain4':[0.25,0.90,0.25], 'chain5':[0.25,0.90,0.90], 'chain6':[0.90,0.25,0.90],
'chain7':[0.05,0.05,0.50], 'chain8':[0.50,0.50,0.05], 'chain9':[0.50,0.05,0.05],
'chain10':[0.05,0.50,0.05],'chain11':[0.05,0.50,0.50],'chain12':[0.50,0.05,0.50],
'white':[1.00,1.00,1.00], 'blue':[0.00,0.00,1.00], 'red':[1.00,0.00,0.00],
'orange':[1,0.5,0], 'yellow':[1,1,0], 'cyan':[0,1,1],
'magenta':[1.0,0.0,0.5], 'grey':[0.8,0.8,0.8]},
'colorblind_colormap':{'chain1':[0.15,0.15,0.80],'chain2':[0.80,0.80,0.15],'chain3':[0.15,0.80,0.15],
'chain4':[0.00,0.00,0.50],'chain5':[0.50,0.50,0.00],'chain6':[0.00,0.50,0.00],
'chain7':[0.55,0.55,0.99],'chain8':[0.99,0.99,0.55],'chain7':[0.55,0.99,0.55],
'chain10':[0.35,0.35,0.90],'chain11':[0.90,0.90,0.35],'chain12':[0.35,0.90,0.35],
'white':[1,1,1], 'blue':[0,0,1], 'red':[0,1,1],
'orange':[1,1,0],'yellow':[1,1,0],'cyan':[0,1,1],
'magenta':[0,0,0.3], 'grey':[0.8,0.8,0.8]},
# graphics options
'graphics_transparency': 1.0,
'graphics_quality':30,
'graphics_contours':0.20,
## 3-letter types recognized by Bliss
'AATypes':["ALA",
"CYS", "CYD", "CYZ", "CYX", # all cystine
"ASP", "GLU", "PHE", "GLY",
"HIS", "HID", "HIE",
"ILE", "LEU", "LYS", "MET", "ASN", "PRO", "GLN",
"ARG", "SER", "THR", "VAL", "TRP", "TYR"],
'NUCTypes':[" A", " C", " G", " T", " U"],
'WATTypes':["HOH", "WAT", "H2O", "IP3", "SOL"],
## graphics
'deselected_opacity':0.05,
## the following parameters are used in ModificationViewer
'global_x_scale':1,
# defaults for MS axes
'x_axis_mark_every':50,
'y_axis_mark_every':10,
'label_font_size':7,
# for window smoothing
'smoothing_gap':0,
# defaults for standards selection
'standard_options_parm_scaler':10,
'minimum_width_of_low_region':250,
'max_height_for_boxing':2.0,
'box_distance_from_peak':100,
# defaults for analysis selection
'analysis_options_parm_scaler':10,
'min_weight':800, # the starting point for identifying peaks... nothing smaller is recognized
'min_peak_height':1.0,
'height_thresh':1.0,
'svsl_peak_thresh':0.5,
# if true the mini-viewer plots are scaled
'scale_mini_plots':1,
#ScopDomainViewer
'gifs_dir': "C:\\CourseWork\\CS499\\MyTest\\",
'pdb_dir': "C:\\CourseWork\\CS499\\MyTest\\SCOP_Pdbs\\",
'profilesPath': "C:\\CourseWork\\CS499\\MyTest\\SCOPSearchProfiles\\",
'scopClassification': "C:\\CourseWork\\CS499\\MyTest\\dir.cla.scop.txt_1.65.txt",
'scopDescription': "C:\\CourseWork\\CS499\\MyTest\\dir.des.scop.txt_1.65.txt",
'scopHierarchy': "C:\\CourseWork\\CS499\\MyTest\\dir.hie.scop.txt_1.65.txt",
'dirNamesDonotIncludelist': ['(', ')', ':', '-', '.', ',', ';', '\\', '/', '"', '\'', '`', '&', '@', '!'],
'scopComments': "C:\\CourseWork\\CS499\\MyTest\\dir.com.scop.txt_1.65.txt",
# 'scopClassification': "C:\\CourseWork\\CS499\\MyTest\\clatest.txt",
# 'scopDescription': "C:\\CourseWork\\CS499\\MyTest\\destest.txt",
# 'scopHierarchy': "C:\\CourseWork\\CS499\\MyTest\\hietest.txt",
# Donot Change the order
'nameHierarchy': {'cl':1, 'cf':2, 'sf':3, 'fa':4, 'dm':5, 'sp':6, 'px':7, '':0},
#'nameHierarchy': {'cl':0, 'cf':1, 'sf':2, 'fa':3, 'dm':4, 'sp':5, 'px':6, '':0},
'scopPDBsLocation': "D:\\pdbstyle-1.65-1\\pdbstyle-1.65\\",
#ScopSearch
'keywordsFile':"C:\\CourseWork\\CS499\\MyTest\\SCOPSearchProfiles\\keywords.ini",
'saveResultsin':"C:\\CourseWork\\CS499\\MyTest\\SCOPSearchProfiles\\CurrentSearchResults\\",
'classifications': ['cl', 'cf', 'sf', 'fa', 'dm', 'sp', 'px'],
'classifications_fullname': {'cl': 'Class', 'cf': 'Fold', 'sf': 'Superfamily', 'fa': 'Family', 'dm': 'Protein', 'sp': 'Species', 'px': 'Domain'},
}