How to use start_reading method in keyboard

Best Python code snippet using keyboard

get_properties.py

Source:get_properties.py Github

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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")...

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read_xsf_example.py

Source:read_xsf_example.py Github

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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__":...

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fragments.py

Source:fragments.py Github

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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...

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shrinkVol.py

Source:shrinkVol.py Github

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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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