Config file colormap fix

lintools/lintools.py

@@ -1,4 +1,3 @@
-
 from argparse import ArgumentParser
 import os
 import shutil
@@ -38,13 +37,12 @@ class Lintools(object):
         * end_frame * - end frame(s) for trajectory analysis (can be different for each trajectory)
         * skip * - number of frames to skip (can be different for each trajectory)
         * analysis_cutoff * - a fraction of time a residue has to fullfil the analysis parameters for (default - 0.3)
-        * sasa * - set this to 1 to turn on solvent accessible surface area calculation (currently only works across whole trajectory)
         * diagram_type * - string of the selected diagram type (e.g. "amino" or "clocks")
         * output_name * - name of the folder with results and the final SVG file
 
     """
-    __version__ = "06.2018"
-    def __init__(self,topology,trajectory,mol_file,ligand,offset,cutoff,start_frame,end_frame,skip,analysis_cutoff,sasa,diagram_type,output_name,cfg):
+    __version__ = "09.2016"
+    def __init__(self,topology,trajectory,mol_file,ligand,offset,cutoff,start_frame,end_frame,skip,analysis_cutoff,diagram_type,output_name,cfg):
         """Defines the input variables."""
         self.topology = os.path.abspath(topology)
         try:
@@ -69,7 +67,6 @@ def __init__(self,topology,trajectory,mol_file,ligand,offset,cutoff,start_frame,
             self.end = end_frame
             self.skip = skip
         self.analysis_cutoff = analysis_cutoff
-        self.sasa = sasa
         self.diagram_type = diagram_type
         self.output_name = output_name
     def data_input_and_res_time_analysis(self):
@@ -93,17 +90,16 @@ def analysis_of_prot_lig_interactions(self):
         """
         self.hbonds = HBonds(self.topol_data,self.trajectory,self.start,self.end,self.skip,self.analysis_cutoff,distance=3)
         self.pistacking = PiStacking(self.topol_data,self.trajectory,self.start,self.end,self.skip, self.analysis_cutoff)
-        if self.sasa==1:
-            self.sasa = SASA(self.topol_data,self.trajectory)
+        self.sasa = SASA(self.topol_data,self.trajectory)
         self.lig_descr = LigDescr(self.topol_data)
         if self.trajectory!=[]:
             self.rmsf = RMSF_measurements(self.topol_data,self.topology,self.trajectory,self.ligand,self.start,self.end,self.skip)
         self.salt_bridges = SaltBridges(self.topol_data,self.trajectory,self.lig_descr,self.start,self.end,self.skip,self.analysis_cutoff)
-    def plot_residues(self):
+    def plot_residues(self, colormap):
         """
         Calls Plot() that plots the residues with the required diagram_type.
         """
-        self.plots = Plots(self.topol_data,self.diagram_type)
+        self.plots = Plots(self.topol_data, self.diagram_type, colormap)
     def draw_figure(self,data_for_color=None, data_for_size=None, data_for_clouds=None, rot_bonds=None, color_for_clouds="Blues", color_type_color="viridis"):
         """
         Draws molecule through Molecule() and then puts the final figure together with
@@ -149,7 +145,6 @@ def write_config_file(self, cfg):
                             'offset': self.offset,
                             'distance cutoff': self.cutoff,
                             'analysis cutoff': self.analysis_cutoff,
-                            'sasa': self.sasa,
                             'diagram type': self.diagram_type,
                             'output name': self.output_name},
                     'representation':{
@@ -173,7 +168,6 @@ def remove_files(self):
             if os.path.isfile(f)==True:
                 os.remove(f)
 
-
 if __name__ == '__main__':
 
     #################################################################################################################
@@ -188,16 +182,13 @@ def remove_files(self):
     parser.add_argument('-o', '--outname', dest = "output_name", help='Name for output folder and file')
     parser.add_argument('-c', '--cutoff', dest = "cutoff", default = 3.5, help='Cutoff distance in angstroms.')
     parser.add_argument('-ac', '--analysis_cutoff', dest = "analysis_cutoff", default=0.3, help='Analysis cutoff - a feature has to appear for at least a fraction of the simulation to be plotted.')
-    parser.add_argument('-sasa', '--sasa', dest = "sasa", default = 0, help='Perform solvent accessible surface area (sasa) calculation')
 
     args = parser.parse_args()
 
     ####################################################################################################################
 
-
-
     if args.config!=None:
-        #If config file exists, args.will be ingnored
+        #If config file exists, args.will be ignored
         print "#####################################################################"
         print "WARNING"
         print "The arguments from command line will be ignored,"
@@ -209,7 +200,7 @@ def remove_files(self):
             cfg = yaml.load(ymlfile)
         ## Check config file input - mainly topology and output file, also handling bad input
 
-        lintools = Lintools(cfg['input']['topology'],cfg['input']['trajectory'],cfg['input']['mol file'],cfg['input']['ligand'],cfg['input']['offset'],float(cfg['input']['distance cutoff']),cfg['input']['traj start'],cfg['input']['traj end'],cfg['input']['traj skip'],cfg['input']['analysis cutoff'],cfg['input']['sasa'],cfg['input']['diagram type'],cfg['input']['output name'],cfg=True)
+        lintools = Lintools(cfg['input']['topology'],cfg['input']['trajectory'],cfg['input']['mol file'],cfg['input']['ligand'],cfg['input']['offset'],float(cfg['input']['distance cutoff']),cfg['input']['traj start'],cfg['input']['traj end'],cfg['input']['traj skip'],cfg['input']['analysis cutoff'],cfg['input']['diagram type'],cfg['input']['output name'],cfg=True)
         lintools.save_files()
         lintools.data_input_and_res_time_analysis()
         lintools.analysis_of_prot_lig_interactions()
@@ -281,7 +272,7 @@ def find_diagram_type():
         ligand_name = find_ligand_name()
         diagram_type = find_diagram_type()
 
-        lintools = Lintools(args.topology,args.trajectory,None,ligand_name,0,args.cutoff,args.start_frame,args.end_frame,args.skip,float(args.analysis_cutoff),args.sasa,diagram_type,args.output_name,cfg=False)
+        lintools = Lintools(args.topology,args.trajectory,None,ligand_name,0,args.cutoff,args.start_frame,args.end_frame,args.skip,float(args.analysis_cutoff),diagram_type,args.output_name,cfg=False)
         lintools.save_files()
         lintools.data_input_and_res_time_analysis()
         lintools.analysis_of_prot_lig_interactions()

lintools/plots.py

@@ -4,7 +4,6 @@
 from matplotlib import pylab
 import numpy
 
-
 class Plots(object):
     """
     This module plots the residue data.
@@ -23,21 +22,28 @@ class Plots(object):
     """
     __version__ = "09.2016"
     matplotlib.rcParams['svg.fonttype'] = 'none'
-    matplotlib.rcParams['font.weight']=900
+    matplotlib.rcParams['font.weight'] = 900
     matplotlib.rcParams['text.usetex'] = False
     matplotlib.rcParams['patch.linewidth'] = 0
-    def __init__(self, topology_data_object,diagram_type,colormap='summer'):
+    def __init__(self, topology_data_object, diagram_type, colormap='summer'):
         self.topology_data = topology_data_object
-        self.colors_amino_acids = {"acidic":"#D9774B", "basic":"#889DCC",
-                                   "aromatic":"#9FC74A", "polar":"#D06AC1",
-                                   "hydrophobic":"#6AC297","lipids":"#ffff99",
-                                   "water":"turquoise","ions":"gold"}
-        self.amino_acids = {"ASP":"acidic","GLU":"acidic","LYS":"basic","ARG":"basic",
-                       "PHE":"aromatic","TYR":"aromatic","TRP":"aromatic","SER":"polar",
-                       "THR":"polar","ASN":"polar","GLN":"polar","CYS":"polar",
-                       "HIS":"polar","ALA":"hydrophobic","VAL":"hydrophobic",
-                       "ILE":"hydrophobic","LEU":"hydrophobic","MET":"hydrophobic","GLY":"hydrophobic","PRO":"hydrophobic",
-                       "PC":"lipids","HOH":"water","SOL":"water"}
+        self.colors_amino_acids = {"acidic": "#D9774B", "basic": "#889DCC",
+                                   "aromatic": "#9FC74A", "polar": "#D06AC1",
+                                   "hydrophobic": "#6AC297", 
+                                   "lipids": "#ffff99", "water": "turquoise",
+                                   "ions": "gold"}
+        self.amino_acids = {"ASP": "acidic","GLU": "acidic","LYS": "basic",
+                            "ARG": "basic", "PHE": "aromatic", 
+                            "TYR": "aromatic", "TRP": "aromatic", 
+                            "SER": "polar", "THR": "polar", "ASN": "polar",
+                            "GLN": "polar", "CYS": "polar", "HIS": "polar",
+                            "ALA": "hydrophobic", "VAL": "hydrophobic",
+                            "ILE": "hydrophobic", "LEU": "hydrophobic",
+                            "MET": "hydrophobic", "GLY": "hydrophobic", 
+                            "PRO": "hydrophobic", "PC": "lipids",
+                            "HOH": "water", "SOL": "water"}
+        # Let's try to fix this so that default config works
+        self.colormap = colormap
         if diagram_type == "amino":
             self.plot_amino_diagrams()
         if diagram_type == "domains":