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get_properties.py

Source:get_properties.py

1import os2import re3import sys4import argparse5import numpy as np6class Gaussian09:7   def __repr__(self):8        return "Extract information from Gaussian09 outputs"9   def __init__(self,output):10       self.out = open(output, 'r')11       self.lines = self.out.readlines()12       self.out.close()13   @property 14   def get_atom_labels(self):15      out_string = ''.join(self.lines)16      tmp = re.findall(r'^ [A-Z]   ', out_string, flags=re.MULTILINE)17      labels = np.asarray([i.strip() for i in tmp])18      return labels19   @property20   def get_coords(self):21      xyz_list = list()22      match = False23      count = 024      for line in self.lines:25         if 'Input orientation' in line:26            match = True27            count += 128            continue29         elif match and (count >= 5):30            if len(line.split()) != 6:31               break32            xyz = np.array(line.split()[-3:], dtype=np.float64)33            xyz = xyz.reshape(-1,3)34            xyz_list.append(xyz) 35         elif match:36            count += 137      coords = np.vstack(xyz_list)38      coords = np.expand_dims(coords, axis=0)39      return coords40   @property41   def get_forces(self):42      ua_to_kcal = 1185.821214378384643      start_reading = False44      count = 045      F_list = list()46      for line in self.lines:47         if start_reading:48            count += 149         if 'Forces (Hartrees/Bohr)' in line:50            start_reading = True51            count += 152            continue53         elif start_reading and (count >= 4):54            if len(line.split()) != 5:55               break56            xyz = np.array(line.split()[-3:], dtype=np.float64)57            xyz = xyz.reshape(-1,3)58            F_list.append(xyz)59      forces = np.vstack(F_list)60      forces *= ua_to_kcal61      forces = np.expand_dims(forces, axis=0)62      return forces63   @property64   def get_total_energy(self):65      for line in self.lines:66         if 'SCF Done' in line:67            total_energy = np.array(line.split()[4], dtype=np.float64, ndmin=2)68            total_energy *= 627.509608030592769      return total_energy70   @property71   def get_homo_lumo(self):72      for line in self.lines:73         if ' occ. ' in line:74            e_homo = float(line.split()[-1])75         if ' virt. ' in line:76            e_lumo = float(line.split()[4])77            break78      e_homo_lumo = np.array([e_homo, e_lumo])79      e_homo_lumo = e_homo_lumo.reshape(-1,2)80      e_homo_lumo *= 27.211399 # convert from Hartree to eV81      return e_homo_lumo82   @property83   def get_dipole(self):84   #    match_number = re.compile('-?\ *[0-9]+\.?[0-9]*(?:[D]\ *-?\ *[0-9]+)?')85      scinot = re.compile('[-+]?[\d]+\.?[\d]*[Dd](?:[-+]?[\d]+)?')86      for line in self.lines:87         if 'Dipole    ' in line:88            dipole = [x.replace('D','E') for x in re.findall(scinot, line)]89            dipole = np.array(dipole, dtype=np.float64)90            dipole = dipole.reshape(1,3)91            return dipole92   @property93   def get_mulliken(self):94      count = -195      start_reading = False96      charges = list()97      pattern1 = 'Mulliken charges:'98      pattern2 = 'Mulliken atomic charges:'99      for line in self.lines:100         if pattern1 in line or pattern2 in line:101            start_reading = True102            continue103         if start_reading:104            count += 1105            if count >= 1:106               if len(line.split()) != 3:107                  break108               charges.append(line.split()[-1])109      charges = np.array(charges, dtype=np.float64)110      n_atoms = len(charges)111      charges = charges.reshape(1, n_atoms, 1)112      return charges113   @property114   def get_zpve(self):115      start_reading = False116      for line in self.lines:117         if 'vibrational energy' in line:118            start_reading = True119            continue120         if start_reading:121            zpve = np.array(line.split()[0], dtype=np.float64, ndmin=2)122            return zpve123   @property124   def _get_exact_polar(self):125      for line in self.lines:126         if 'Exact polarizability' in line:127            polar = np.array(line.split()[-6:], dtype=np.float64)128            polar = polar.reshape(-1,6)129            return polar130   @property131   def get_polarizability(self):132      start_reading = False133      scinot = re.compile('[-+]?[\d]+\.?[\d]*[Dd](?:[-+]?[\d]+)?')134      for line in self.lines:135         if 'Polarizability' in line:136            start_reading = True137            p1 = [x.replace('D','E') for x in re.findall(scinot, line)]138         if start_reading:139            p2 = [x.replace('D','E') for x in re.findall(scinot, line)]140            polar = np.array((p1 + p2), dtype=np.float64)141            polar = polar.reshape(-1,6)142            return polar143   @property144   def get_rot_constants(self):145      for line in self.lines:146         if 'Rotational constants' in line:147            rot_const = np.array(line.split()[-3:], dtype=np.float64)148            rot_const = rot_const.reshape(1,3)149            return rot_const150   @property151   def get_elec_spatial_ext(self):152      for line in self.lines:153         if 'Electronic spatial extent' in line:154            r2 = np.array(line.split()[-1], dtype=np.float64, ndmin=2)155            return r2156   @property157   def get_thermal_energies(self):158      count = 0 159      thermal_energies = list()160      pattern = 'Sum of electronic and thermal'161      for line in self.lines:162         if pattern in line:163            thermal_energies.append(line.split()[-1])164            count += 1165         if count == 3:166            break167      thermal_energies = np.array(thermal_energies, dtype=np.float64)168      thermal_energies *= 627.5096080305927169      thermal_energies = thermal_energies.reshape(-1,3)170      return thermal_energies171   @property172   def get_frequencies(self):173      freq_list = list()174      pattern = "Frequencies "175      for line in self.lines:176         if pattern in line:177            f = line.split()[-3:]178            freq_list.append(f)179      freqs = np.array(freq_list, dtype=np.float64)180      freqs = freqs.flatten()181      freqs = np.expand_dims(freqs, axis=0)182      return freqs183if __name__ == "__main__":184    parser = argparse.ArgumentParser()185    parser.add_argument("-log", default=None, type=str, help = "full path to the output file")186    parser.add_argument("-prop", default=None, type=str, help = "property to be read from the output")187    if len(sys.argv) == 1:188        args = parser.parse_args(["--help"])189    else:190        args = parser.parse_args()191    log_file = args.log192    property = args.prop193    try:194       g09_output = Gaussian09(log_file)195       print(g09_output)196       print(" ")197    except:198       print("Oops! File not found. Try again.")199       sys.exit()200    all_properties = {'labels': g09_output.get_atom_labels,201                      'coords': g09_output.get_coords,202                      'Etot': g09_output.get_total_energy,203                      'e_hl': g09_output.get_homo_lumo,204                      'alpha': g09_output.get_polarizability,205                      'dipole': g09_output.get_dipole,206                      'e_vib': g09_output.get_zpve,207                      'rot': g09_output.get_rot_constants,208                      'r2': g09_output.get_elec_spatial_ext,209                      'forces': g09_output.get_forces,210                      'e_thermal': g09_output.get_thermal_energies,211                      'freqs': g09_output.get_frequencies,212                      'mulliken': g09_output.get_mulliken}213    if property is None or property == 'all':214        print('Reading all properties from file: {}'.format(log_file))215        print('-------------------------------------')216        for k, val in all_properties.items():217           print(k, val)218    else:219       if ',' in property:220          props = [p.strip() for p in property.split(',')]221          print('Reading {} properties from file: {}'.format(len(props),log_file))222          print('-------------------------------------')223          for p in props:224             try:225                print(p, all_properties[p])226             except:227                print(" ")228                print("Oops! Key not found in dictionary.\n")229                print("The available options are", list(all_properties.keys()))230       else:231           p = property.strip()232           print('Reading {} from file: {}'.format(p,log_file))233           print('-------------------------------')234           try:235               print(p, all_properties[p])236           except:237               print(" ")238               print("Oops! Key not found in dictionary.\n")...

read_xsf_example.py

Source:read_xsf_example.py

1from numpy import *2def read_example_xsf_density(filename):3    lattice=[]4    density=[]5    grid=[]6    shift=[]7    i=08    start_reading = False9    with open(filename, 'r') as f:10        for line in f:11            if "END_DATAGRID_3D" in line:12                start_reading = False13            if start_reading and i==1:14                grid=array(line.split(),dtype=int)15            if start_reading and i==2:16                shift.append(array(line.split(),dtype=float))17            if start_reading and i==3:18                lattice.append(array(line.split(),dtype=float))19            if start_reading and i==4:20                lattice.append(array(line.split(),dtype=float))21            if start_reading and i==5:22                lattice.append(array(line.split(),dtype=float))23            if start_reading and i>5:            24                density.extend(array(line.split(),dtype=float))25            if start_reading and i>0:26                i=i+127            if "DATAGRID_3D_UNKNOWN" in line:28                start_reading = True29                i=130    31    rho=zeros((grid[0],grid[1],grid[2]))32    ii=033    for k in range(grid[2]):34        for j in range(grid[1]):        35            for i in range(grid[0]):36                rho[i,j,k]=density[ii]37                ii+=138    # convert density to 1/Angstrom**3 from 1/Bohr**339    a0=0.5291772106740    a03=a0*a0*a041    rho/=a0342    # since in xsf format the lattice is given as A^T,43    # let's return A by taking the transpose, i.e., 44    # A = transpose(lattice)45    return rho, transpose(array(lattice)), grid, shift46def main():47    filename = 'dft_chargedensity1.xsf'48    rho, lattice, grid, shift = read_example_xsf_density(filename)49    50if __name__=="__main__":...

fragments.py

Source:fragments.py

1from typing import List, Set2from Bio.Seq import Seq3from Bio.SeqRecord import SeqRecord4from code.codon_group import Group, codon_group5def start_stop_fragments(6    seq_record: SeqRecord,7    minimum_fragment_length: int = 100,8    start_codons: Set[str] = {"ATG"},9    stop_codons: Set[str] = {"TAA", "TAG", "TGA"}10) -> List[Seq]:11    nucleotides: Seq = seq_record.seq12    start_stop_fragments: List[Seq] = []13    nucleotide_strand: Seq14    for nucleotide_strand in [nucleotides, nucleotides.reverse_complement()]:15        for frame in range(3):16            frame_codons: List[str] = codon_group(17                nucleotide_strand, Group.CODON, frame)18            fragment = Seq("")19            start_reading = False20            for codon in frame_codons:21                if codon in start_codons:22                    start_reading = True23                    fragment += codon24                elif start_reading:25                    fragment += codon26                    if codon in stop_codons:27                        start_reading = False28                        start_stop_fragments.append(fragment)29                        fragment = Seq("")30    return [31        fragment for fragment in start_stop_fragments32        if len(fragment) > minimum_fragment_length...

shrinkVol.py

Source:shrinkVol.py

1from numpy import *2scale = 1000.3fin = open('PPM_ABAQUS.inp', 'r')4contents = fin.readlines()5fin.close()6fout = open('PPM_ABAQUS_shrunk.inp','w')7start_reading = False8for line in contents:9    if line[0:1] == '*' and line[0:5] != '*Node':10        start_reading = False11    if start_reading == True:12        n_id = int(line.split(',')[0])13        x = double(line.split(',')[1])/1000.14        y = double(line.split(',')[2])/1000.15        z = double(line.split(',')[3])/1000.16        fout.write('%d,%f,%f,%f\n'%(n_id,x,y,z))17    else:18        fout.write(line)19    if line[0:5] == '*Node' and len(line) <= 6:20        start_reading = True...

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