x_data_coll.py

#!/usr/bin/env python3

import sys
import pandas as pd


##########################################################################
def BuildDataSet():
  return { 
          'pdb_id':None,  'pdb':None,
          'h_phi':None,   'h_psi':None,   'h_axvc':None,
          'h_norm':None,  'h_cgvc':None,  'h_scvc':None,
          'h_ca':None,    'h_cg':None,    'h_curv':None,
          'n_ca':None,    'c_ca':None,
          'n_phi':None,   'n_psi':None,
          'c_phi':None,   'c_psi':None,
          'dist_NH':None, 'dist_NC':None, 'dist_CH':None,
          'ang_NHs':None, 'ang_CHs':None,
          'r_medi':None,  'r_std':None,
          'g_resi':None,  'g_coord':None,
          'p1p1x':None,   'p2p2x':None,   'dfg_st':None,
          'v1v1x':None,   'v2v2x':None,   'dfg_vs':None,
          # d0_x/d1_x = p1/p2 without cross Ca-to-Ca vec
          'r3r3x':None,   'd0_x':None,    'd1_x':None,	
          # h_sc_x = cg_vec.sc_vec	h_cg_x = cg_vec.cb_vec
          'h_sc_x':None,  'h_cg_x':None,
          'r_curv':None,  'r_curv_m2':None,
          'c_curv':None,  'c_curv_m2':None,
          'lig_name':None,'lig_id':None,  
          'lig_ha':None,  'lig_multi':None,
          'pock_out':None,'pock_hinge':None,
          'pock_sugar':None, 'pock_up':None,
          'pock_I5':None, 'pock_I5in':None,
          'pock_I5dp':None,'pock_dfg':None,
          'pock_bp':None, 'lig_type':None,
        }


################################################
def Data2Pandas( Data, output ):

  df = pd.DataFrame.from_dict(Data, orient='index')
  df.index.name = 'pdb_id'

  # Columns of data to be reordered and to print out 
  columns = [ 'pdb_id',
              'p1p1x','p2p2x','h_cgvc','h_scvc',
              'ang_NHs','ang_CHs','dist_NH','dist_CH','dfg_st','r3r3x',
              'v1v1x','v2v2x','g_resi',
              'lig_name','lig_id','lig_ha','lig_multi','lig_type',
              'pock_out','pock_hinge','pock_sugar','pock_up','pock_I5',
              'pock_I5in','pock_I5dp','pock_dfg','pock_bp' ]
  parm_df = df[columns]

  # Output to CSV
  parm_df.to_csv(output+'.csv', sep=',', na_rep='NA', encoding='utf-8',
                  float_format='%.5f', header=True )

  # Output to Excel
  parm_df.to_excel(output+'.xlsx', header=True , na_rep='NA')

  return parm_df


##########################################################################
# 
#   Peter Man-Un Un @ MSSM
#
#   v1.0    17.03.11
#   v2.0    17.03.17    add more parameters
#   v2.1    17.04.28    add ax-cg normal vector, h-ax dot product, cg vector
#   v3.0    17.05.09	add more parameters
#   v4.0    17.08.18	add ligand-types, chean up R/C-spines
#   v5.0    17.10.07	add non-crossed DFG vectors
#   v6.0    17.12.21    only output most essential parameters
#
##########################################################################