Merge branch 'analyzer_tool'

GMXMMPBSA/amber_outputs.py

@@ -371,6 +371,38 @@ def fill_composite_terms(self):
 
 #-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
 
+class IEout(object):
+    """
+    Interaction Entropy output
+    """
+    def __init__(self, edata, value, frames, ie_frames, key):
+        self.data = edata
+        self.value = value
+        self.frames = frames
+        self.ieframes = ie_frames
+        self.key = key
+
+    def print_summary_csv(self, csvwriter):
+        """ Output summary of quasi-harmonic results in CSV format """
+        csvwriter.writerow([f'Iteration Entropy calculation for {self.key.upper()} from last {self.ieframes} frames...'])
+        csvwriter.writerow(['Iteration Entropy:', '{:.2f}'.format(self.value)])
+
+    def print_vectors(self, csvwriter):
+        """ Prints the energy vectors to a CSV file for easy viewing
+            in spreadsheets
+        """
+        csvwriter.writerow(['Frame #', 'Interaction Entropy'])
+        for f, d in zip(self.frames, self.edata):
+            csvwriter.writerow([f] + [d])
+
+    def print_summary(self):
+        """ Formatted summary of quasi-harmonic results """
+        ret_str =  (f'Iteration Entropy calculation for {self.key.upper()} from last {self.ieframes} frames...\n')
+        ret_str += 'Iteration Entropy: {:.2f}\n'.format(self.value)
+        return ret_str
+
+#-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-
+
 class QHout(object):
     """ Quasi-harmonic output file class. QH output files are strange so we won't
         derive from AmberOutput

GMXMMPBSA/calculation.py

@@ -37,6 +37,8 @@
 from GMXMMPBSA.exceptions import GMXMMPBSA_ERROR
 import os
 import sys
+import numpy as np
+import math
 
 #+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
 
@@ -549,3 +551,58 @@ def run(self, rank, stdout=sys.stdout, stderr=sys.stderr):
         if rank == 0: stdout.write(self.message + '\n')
 
 #+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+
+
+class InteractionEntropyCalc:
+    """
+    Class for Interaction Entropy calculation
+    :return {IE_key: data}
+    """
+    def __init__(self, ggas, key, INPUT, output):
+        self.ggas = ggas
+        self.key = key
+        self.INPUT = INPUT
+        self.output = output
+        self.data = {}
+
+        self._calculate()
+        self.save_output()
+
+    def _calculate(self):
+        # gases constant in kcal/mol
+        k = 0.001987
+        energy_int = np.array([], dtype=np.float)
+        a_energy_int = np.array([], dtype=np.float)
+        d_energy_int = np.array([], dtype=np.float)
+        exp_energy_int = np.array([], dtype=np.float)
+        ts = np.array([], dtype=np.float)
+
+        for eint in self.ggas:
+            energy_int = np.append(energy_int, eint)
+            aeint = energy_int.mean()
+            a_energy_int = np.append(a_energy_int, aeint)
+            deint = eint - aeint
+            d_energy_int = np.append(d_energy_int, deint)
+            eceint = math.exp(deint / (k * self.INPUT['entropy_temp']))
+            exp_energy_int = np.append(exp_energy_int, eceint)
+            aeceint = exp_energy_int.mean()
+            cts = k * self.INPUT['entropy_temp'] * math.log(aeceint)
+            ts = np.append(ts, cts)
+        self.IntEnt = ts
+        self.data['IE_' + self.key] = self.IntEnt
+        nframes = len(self.IntEnt)
+        self.ie_frames = math.ceil(nframes * (self.INPUT['entropy_seg'] / 100))
+        self.value = self.IntEnt[self.ie_frames:].mean()
+        self.frames = [x for x in range(self.INPUT['startframe'], self.INPUT['endframe'] + self.INPUT['interval'],
+                                       self.INPUT['interval'])]
+
+    def save_output(self):
+        with open(self.output, 'w') as out:
+            out.write(f'Calculation for last {self.ie_frames} frames:\n')
+            out.write(f'Interaction Entropy: {self.value}\n\n')
+            out.write(f'Interaction Entropy per-frame:\n')
+
+            out.write('Frame # | IE value\n')
+            for f, d in zip(self.frames, self.IntEnt):
+                out.write('{:d}  {:.2f}\n'.format(f,d))
+
+#+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+-+

GMXMMPBSA/main.py

@@ -32,14 +32,11 @@
 import logging
 # Import gmx_MMPBSA modules
 from GMXMMPBSA import utils
-from GMXMMPBSA.amber_outputs import (QHout, NMODEout, QMMMout, GBout, PBout,
-                                     PolarRISM_std_Out, RISM_std_Out,
-                                     PolarRISM_gf_Out, RISM_gf_Out,
-                                     SingleTrajBinding, MultiTrajBinding)
-from GMXMMPBSA.calculation import (CalculationList, EnergyCalculation,
-                                   PBEnergyCalculation, RISMCalculation,
-                                   NmodeCalc, QuasiHarmCalc, CopyCalc,
-                                   PrintCalc, LcpoCalc, MolsurfCalc)
+from GMXMMPBSA.amber_outputs import (QHout, NMODEout, QMMMout, GBout, PBout, PolarRISM_std_Out, RISM_std_Out,
+                                     PolarRISM_gf_Out, RISM_gf_Out, SingleTrajBinding, MultiTrajBinding, IEout)
+from GMXMMPBSA.calculation import (CalculationList, EnergyCalculation, PBEnergyCalculation, RISMCalculation,
+                                   NmodeCalc, QuasiHarmCalc, CopyCalc, PrintCalc, LcpoCalc, MolsurfCalc,
+                                   InteractionEntropyCalc)
 from GMXMMPBSA.commandlineparser import parser
 from GMXMMPBSA.createinput import create_inputs
 from GMXMMPBSA.exceptions import (MMPBSA_Error, InternalError, InputError, GMXMMPBSA_ERROR)
@@ -48,9 +45,7 @@
 from GMXMMPBSA.infofile import InfoFile
 from GMXMMPBSA.input_parser import input_file as _input_file
 from GMXMMPBSA.make_trajs import make_trajectories, make_mutant_trajectories
-from GMXMMPBSA.output_file import (write_stability_output,
-                                   write_binding_output,
-                                   write_decomp_stability_output,
+from GMXMMPBSA.output_file import (write_stability_output, write_binding_output, write_decomp_stability_output,
                                    write_decomp_binding_output)
 from GMXMMPBSA.parm_setup import MMPBSA_System
 from GMXMMPBSA.make_top import CheckMakeTop
@@ -915,39 +910,6 @@ def sync_mpi(self):
         """ Throws up a barrier """
         self.MPI.COMM_WORLD.Barrier()
 
-    def calculate_interaction_entropy(self, key, mutant=False):
-        """
-        Calculate the interaction entropy described FIXME: article
-        :param key:
-        :return:
-        """
-        # gases constant in kcal/mol
-        k = 0.001987
-        if mutant:
-            calc_types = self.calc_types['mutant']
-        else:
-            calc_types = self.calc_types
-        energy_int = np.array([], dtype=np.float)
-        a_energy_int = np.array([], dtype=np.float)
-        d_energy_int = np.array([], dtype=np.float)
-        exp_energy_int = np.array([], dtype=np.float)
-        ts = np.array([], dtype=np.float)
-
-        ggas = calc_types[key]['delta'].data['DELTA G gas']
-
-        for eint in ggas:
-            energy_int = np.append(energy_int, eint)
-            aeint = energy_int.mean()
-            a_energy_int = np.append(a_energy_int, aeint)
-            deint = eint - aeint
-            d_energy_int = np.append(d_energy_int, deint)
-            eceint = exp(deint / (k * self.INPUT['entropy_temp']))
-            exp_energy_int = np.append(exp_energy_int, eceint)
-            aeceint = exp_energy_int.mean()
-            cts = k * self.INPUT['entropy_temp'] * log(aeceint)
-            ts = np.append(ts, cts)
-            calc_types[key]['delta'].data['-TDS'] = ts
-
     def parse_output_files(self):
         """
         This parses the output files and loads them into dicts for easy access
@@ -963,11 +925,9 @@ def parse_output_files(self):
         # Quasi-harmonic analysis is a special-case, so handle that separately
         if INPUT['entropy'] == 1:
             if not INPUT['mutant_only']:
-                self.calc_types['qh'] = QHout(self.pre + 'cpptraj_entropy.out',
-                                              INPUT['temp'])
+                self.calc_types['qh'] = QHout(self.pre + 'cpptraj_entropy.out', INPUT['temp'])
             if INPUT['alarun']:
-                self.calc_types['mutant']['qh'] = QHout(self.pre +
-                                                        'mutant_cpptraj_entropy.out', INPUT['temp'])
+                self.calc_types['mutant']['qh'] = QHout(self.pre + 'mutant_cpptraj_entropy.out', INPUT['temp'])
         # Set BindingClass based on whether it's a single or multiple trajectory
         # analysis
         if self.traj_protocol == 'STP':
@@ -1017,8 +977,11 @@ def parse_output_files(self):
                         self.calc_types[key]['ligand'],
                         self.INPUT['verbose'], self.using_chamber)
 
-                    if self.INPUT['entropy'] == 2:
-                        self.calculate_interaction_entropy(key)
+                    if self.INPUT['entropy'] == 2 and key != 'nmode':
+                        edata = self.calc_types[key]['delta'].data['DELTA G gas']
+                        ie = InteractionEntropyCalc(edata, key, self.INPUT, self.pre + 'iteraction_entropy.dat')
+                        self.calc_types['ie'] = IEout(ie.data, ie.value, ie.frames, ie.ie_frames, key)
+                        # self.calc_types[self.key]['delta'].data['DELTA G gas']
                 else:
                     self.calc_types[key]['complex'].fill_composite_terms()
             # Time for mutant
@@ -1038,8 +1001,10 @@ def parse_output_files(self):
                         self.calc_types['mutant'][key]['receptor'],
                         self.calc_types['mutant'][key]['ligand'],
                         self.INPUT['verbose'], self.using_chamber)
-                    if self.INPUT['entropy'] == 2:
-                        self.calculate_interaction_entropy(key, mutant=True)
+                    if self.INPUT['entropy'] == 2 and key != 'nmode':
+                        edata = self.calc_types['mutant'][key]['delta'].data['DELTA G gas']
+                        mie = InteractionEntropyCalc(edata, key, self.INPUT, self.pre + 'mutant_iteraction_entropy.dat')
+                        self.calc_types['mutant']['ie'] = IEout(mie.data, mie.value, mie.frames, mie.ie_frames, key)
                 else:
                     self.calc_types['mutant'][key]['complex'].fill_composite_terms()
 

GMXMMPBSA/make_top.py

@@ -98,13 +98,6 @@ def __init__(self, FILES, INPUT, external_programs):
         self.receptor_str_file = self.FILES.prefix + 'REC.pdb'
         self.ligand_str_file = self.FILES.prefix + 'LIG.pdb'
 
-        self.rec_ions_pdb = self.FILES.prefix + 'REC_IONS.pdb'
-        self.lig_ions_pdb = self.FILES.prefix + 'LIG_IONS.pdb'
-
-        self.mutant_complex_pdb = self.FILES.prefix + 'MUT_COM.pdb'
-        self.mutant_receptor_pdb = self.FILES.prefix + 'MUT_REC.pdb'
-        self.mutant_ligand_pdb = self.FILES.prefix + 'MUT_LIG.pdb'
-
         if self.FILES.reference_structure:
             self.ref_str = parmed.read_PDB(self.FILES.reference_structure)
 
@@ -598,30 +591,31 @@ def res2map(self):
         res_list = {'REC': [], 'LIG': []}
         com_ndx = ndx['GMXMMPBSA_REC_GMXMMPBSA_LIG']
         com_len = len(ndx['GMXMMPBSA_REC_GMXMMPBSA_LIG'])
-        dif = 0
+        resnum = 1
+        current_res = None
         for i in range(com_len):
-            if  i == 0:
-                dif = com_str.atoms[i].residue.number - 1  # AMBER mask must be start at 1
             # We check who owns the residue corresponding to this atom
             if com_ndx[i] in ndx['GMXMMPBSA_REC']:
                 current = 'R'
                 # save residue number in the rec list
-                resnum = com_str.atoms[i].residue.number - dif
-                if not resnum in res_list['REC']:
+                if com_str.atoms[i].residue.number != current_res and not resnum in res_list['REC']:
                     res_list['REC'].append(resnum)
+                    resnum += 1
+                    current_res = com_str.atoms[i].residue.number
             else:
                 current = 'L'
                 # save residue number in the lig list
-                resnum = com_str.atoms[i].residue.number - dif
-                if not resnum in res_list['LIG']:
+                if com_str.atoms[i].residue.number != current_res and not resnum in res_list['LIG']:
                     res_list['LIG'].append(resnum)
+                    resnum += 1
+                    current_res = com_str.atoms[i].residue.number
             # check for end
             if previous and current != previous:
-                end = com_str.atoms[i-1].residue.number - dif
+                end = resnum - 2
 
             # when i is the last index
             if i == com_len - 1:
-                end = com_str.atoms[i].residue.number - dif
+                end = resnum - 1
             if end:
                 if previous == 'R':
                     masks['REC'].append([start, end])