gaussian_parser 0.0.1

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data/.gitignore

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+/.bundle/
+/.yardoc
+/_yardoc/
+/coverage/
+/doc/
+/pkg/
+/spec/reports/
+/tmp/
+
+# rspec failure tracking
+.rspec_status

data/.rspec

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+--format documentation
+--color
+--require spec_helper

data/.travis.yml

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+sudo: false
+language: ruby
+rvm:
+  - 2.5.1
+before_install: gem install bundler -v 1.16.2

data/CODE_OF_CONDUCT.md

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+# Contributor Covenant Code of Conduct
+
+## Our Pledge
+
+In the interest of fostering an open and welcoming environment, we as
+contributors and maintainers pledge to making participation in our project and
+our community a harassment-free experience for everyone, regardless of age, body
+size, disability, ethnicity, gender identity and expression, level of experience,
+nationality, personal appearance, race, religion, or sexual identity and
+orientation.
+
+## Our Standards
+
+Examples of behavior that contributes to creating a positive environment
+include:
+
+* Using welcoming and inclusive language
+* Being respectful of differing viewpoints and experiences
+* Gracefully accepting constructive criticism
+* Focusing on what is best for the community
+* Showing empathy towards other community members
+
+Examples of unacceptable behavior by participants include:
+
+* The use of sexualized language or imagery and unwelcome sexual attention or
+advances
+* Trolling, insulting/derogatory comments, and personal or political attacks
+* Public or private harassment
+* Publishing others' private information, such as a physical or electronic
+  address, without explicit permission
+* Other conduct which could reasonably be considered inappropriate in a
+  professional setting
+
+## Our Responsibilities
+
+Project maintainers are responsible for clarifying the standards of acceptable
+behavior and are expected to take appropriate and fair corrective action in
+response to any instances of unacceptable behavior.
+
+Project maintainers have the right and responsibility to remove, edit, or
+reject comments, commits, code, wiki edits, issues, and other contributions
+that are not aligned to this Code of Conduct, or to ban temporarily or
+permanently any contributor for other behaviors that they deem inappropriate,
+threatening, offensive, or harmful.
+
+## Scope
+
+This Code of Conduct applies both within project spaces and in public spaces
+when an individual is representing the project or its community. Examples of
+representing a project or community include using an official project e-mail
+address, posting via an official social media account, or acting as an appointed
+representative at an online or offline event. Representation of a project may be
+further defined and clarified by project maintainers.
+
+## Enforcement
+
+Instances of abusive, harassing, or otherwise unacceptable behavior may be
+reported by contacting the project team at ihnatolia3@gmail.com. All
+complaints will be reviewed and investigated and will result in a response that
+is deemed necessary and appropriate to the circumstances. The project team is
+obligated to maintain confidentiality with regard to the reporter of an incident.
+Further details of specific enforcement policies may be posted separately.
+
+Project maintainers who do not follow or enforce the Code of Conduct in good
+faith may face temporary or permanent repercussions as determined by other
+members of the project's leadership.
+
+## Attribution
+
+This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4,
+available at [http://contributor-covenant.org/version/1/4][version]
+
+[homepage]: http://contributor-covenant.org
+[version]: http://contributor-covenant.org/version/1/4/

data/Gemfile

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+source "https://rubygems.org"
+
+git_source(:github) {|repo_name| "https://github.com/#{repo_name}" }
+
+# Specify your gem's dependencies in gaussian_parser.gemspec
+gemspec

data/Gemfile.lock

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+PATH
+  remote: .
+  specs:
+    gaussian_parser (0.0.1)
+      colorize (~> 0.8.1)
+
+GEM
+  remote: https://rubygems.org/
+  specs:
+    colorize (0.8.1)
+    diff-lcs (1.3)
+    rake (10.5.0)
+    rspec (3.8.0)
+      rspec-core (~> 3.8.0)
+      rspec-expectations (~> 3.8.0)
+      rspec-mocks (~> 3.8.0)
+    rspec-core (3.8.0)
+      rspec-support (~> 3.8.0)
+    rspec-expectations (3.8.1)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.8.0)
+    rspec-mocks (3.8.0)
+      diff-lcs (>= 1.2.0, < 2.0)
+      rspec-support (~> 3.8.0)
+    rspec-support (3.8.0)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.16)
+  gaussian_parser!
+  rake (~> 10.0)
+  rspec (~> 3.0)
+
+BUNDLED WITH
+   1.16.2

data/README.md

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+# GaussianParser
+
+Welcome to your new gem! In this directory, you'll find the files you need to be able to package up your Ruby library into a gem. Put your Ruby code in the file `lib/gaussian_parser`. To experiment with that code, run `bin/console` for an interactive prompt.
+
+TODO: Delete this and the text above, and describe your gem
+
+## Installation
+
+Add this line to your application's Gemfile:
+
+```ruby
+gem 'gaussian_parser'
+```
+
+And then execute:
+
+    $ bundle
+
+Or install it yourself as:
+
+    $ gem install gaussian_parser
+
+## Usage
+
+TODO: Write usage instructions here
+
+## Development
+
+After checking out the repo, run `bin/setup` to install dependencies. Then, run `rake spec` to run the tests. You can also run `bin/console` for an interactive prompt that will allow you to experiment.
+
+To install this gem onto your local machine, run `bundle exec rake install`. To release a new version, update the version number in `version.rb`, and then run `bundle exec rake release`, which will create a git tag for the version, push git commits and tags, and push the `.gem` file to [rubygems.org](https://rubygems.org).
+
+## Contributing
+
+Bug reports and pull requests are welcome on GitHub at https://github.com/[USERNAME]/gaussian_parser. This project is intended to be a safe, welcoming space for collaboration, and contributors are expected to adhere to the [Contributor Covenant](http://contributor-covenant.org) code of conduct.
+
+## Code of Conduct
+
+Everyone interacting in the GaussianParser project’s codebases, issue trackers, chat rooms and mailing lists is expected to follow the [code of conduct](https://github.com/[USERNAME]/gaussian_parser/blob/master/CODE_OF_CONDUCT.md).

data/Rakefile

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+require "bundler/gem_tasks"
+require "rspec/core/rake_task"
+
+RSpec::Core::RakeTask.new(:spec)
+
+task :default => :spec

data/bin/console

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+#!/usr/bin/env ruby
+
+require "bundler/setup"
+require "gaussian_parser"
+
+# You can add fixtures and/or initialization code here to make experimenting
+# with your gem easier. You can also use a different console, if you like.
+
+# (If you use this, don't forget to add pry to your Gemfile!)
+# require "pry"
+# Pry.start
+
+require "irb"
+IRB.start(__FILE__)

data/bin/setup

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+#!/usr/bin/env bash
+set -euo pipefail
+IFS=$'\n\t'
+set -vx
+
+bundle install
+
+# Do any other automated setup that you need to do here

data/exe/gaussian_parser

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+#!/usr/bin/env ruby
+
+require 'gaussian_parser'
+params  = ARGV.reject {|a| a =~ /^-/}
+options = ARGV.select {|a| a =~ /^-/}
+
+GaussianParser.process({params: params, options: options})

data/gaussian_parser.gemspec

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+
+lib = File.expand_path("../lib", __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require "gaussian_parser/version"
+
+Gem::Specification.new do |spec|
+  spec.name          = "gaussian_parser"
+  spec.version       = GaussianParser::VERSION
+  spec.authors       = ["Paul I"]
+  spec.email         = ["ihnatolia3@gmail.com"]
+
+  spec.summary       = %q{Parse Gaussian output log file and structure data}
+  spec.description   = <<-DESCRIPTION
+    Gaussian (http://gaussian.com/) is one of the most popular general purpose computational chemistry
+    software packages. The output genearated by it contains a lot of data which should
+    be structured properly before evaluation.
+
+    The purpose of the Gaussian Parser is to perform routine operations for better and faster
+    log data processing. Currently it's able to parse the output file and process the data for
+
+    - Distance matrix
+    - Molecular Orbital Coefficients
+    - Harmonic frequencies
+  DESCRIPTION
+  spec.homepage      = "https://github.com/paul-ihnatolia/gaussian_parser"
+
+  # Prevent pushing this gem to RubyGems.org. To allow pushes either set the 'allowed_push_host'
+  # to allow pushing to a single host or delete this section to allow pushing to any host.
+  # if spec.respond_to?(:metadata)
+  #   spec.metadata["allowed_push_host"] = "TODO: Set to 'http://mygemserver.com'"
+  # else
+  #   raise "RubyGems 2.0 or newer is required to protect against " \
+  #     "public gem pushes."
+  # end
+
+  # Specify which files should be added to the gem when it is released.
+  # The `git ls-files -z` loads the files in the RubyGem that have been added into git.
+  spec.files         = Dir.chdir(File.expand_path('..', __FILE__)) do
+    `git ls-files -z`.split("\x0").reject { |f| f.match(%r{^(test|spec|features)/}) }
+  end
+  spec.bindir        = "exe"
+  spec.executables   = spec.files.grep(%r{^exe/}) { |f| File.basename(f) }
+  spec.require_paths = ["lib"]
+
+  spec.add_runtime_dependency "colorize", "~> 0.8.1"
+
+  spec.add_development_dependency "bundler", "~> 1.16"
+  spec.add_development_dependency "rake", "~> 10.0"
+  spec.add_development_dependency "rspec", "~> 3.0"
+end

data/lib/gaussian_parser.rb

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+require "gaussian_parser/version"
+require "gaussian_parser/parser"
+
+module GaussianParser
+  def self.process(argv)
+    GaussianParser::Parser.new(argv).process
+  end
+end

data/lib/gaussian_parser/cli.rb

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+require 'colorize'
+
+module GaussianParser
+  module Cli
+    ERROR_COLOR   = :red
+    SUCCESS_COLOR = :green
+
+    def print_as_error(message)
+      puts "Error: #{message}".colorize(ERROR_COLOR)
+    end
+
+    def print_as_success(message)
+      puts "Success: #{message}".colorize(SUCCESS_COLOR)
+    end
+
+    def print_as_usual(message)
+      puts "#{message}"
+    end
+  end
+end

data/lib/gaussian_parser/data_processor.rb

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+require "gaussian_parser/cli"
+require "gaussian_parser/processors/results_processor"
+require "gaussian_parser/processors/atom_processor"
+
+module GaussianParser
+  class DataProcessor
+    include Cli
+
+    def initialize(file)
+      @file_lines = file.readlines
+    end
+
+    def has_normal_termination?
+      # programm terminates correctly when
+      # "normal termination" line is found
+      @file_lines.each do |line|
+        if line =~ /Normal termination/
+          return true
+        end
+      end
+      return false
+    end
+
+    def parse
+      processors = {}
+
+      atom_count = {}
+      molecular_orbitals = []
+      harmonic_frequencies = []
+      index = 0
+
+      was_stationary_point = false
+      was_standard_orientation = false
+      was_mo_coefficients = false
+
+      while index < @file_lines.length
+        line = @file_lines[index]
+        if line =~ /Stationary point found/ && !was_stationary_point
+          print_as_success("Stationary point found")
+          was_stationary_point = true
+          index += 7
+          results = []
+          while @file_lines[index] =~ /^\s*!/
+            results.push(@file_lines[index])
+            index += 1
+          end
+          processors[:results_processor] = Processors::ResultsProcessor.new(results)
+        end
+
+        if line =~ /Standard orientation:/ && was_stationary_point
+          unless was_standard_orientation
+            print_as_usual("Standard orientation processing")
+            was_standard_orientation = true
+            index += 5
+            atom_data = []
+            while @file_lines[index] =~ /^(\s+\d+){3}/
+              atom_data.push(@file_lines[index])
+              index += 1
+            end
+            processors[:atom_processor] = Processors::AtomProcessor.new(atom_data)
+          end
+        end
+        
+        if line =~ /Molecular Orbital Coefficients/ && was_standard_orientation
+          unless was_mo_coefficients
+            print_as_usual("Molecular orbital processing")
+            was_mo_coefficients = true
+            mo_position = index + 1
+            current_line = @file_lines[mo_position].split(/\s+/) 
+            current_line.delete ""
+            last_number = current_line.first.to_i - 1
+            mo_regexp = generate_mo_regexp(last_number)
+            while mo_position < @file_lines.length
+              prev_zayniatist = nil
+              if @file_lines[mo_position] =~ mo_regexp &&
+                @file_lines[mo_position + 2] =~ /Eigenvalues --/                
+
+                current_line = @file_lines[mo_position].split(/\s+/)
+                last_number = current_line.last.to_i
+                mo_regexp = generate_mo_regexp(last_number)
+                current_line.delete ""
+                energy_types = @file_lines[mo_position+=1].split(/\s+/)
+                energy_types.delete ""
+                energy_values = @file_lines[mo_position+=1].scan(/-*\d+\.*\d+/)
+                energy_values.delete ""
+
+                current_line.each_with_index do |elem,i|
+                  symetry = energy_types[i].split('--').first.scan(/\w/).join
+                  zayniatist = energy_types[i].split('--').last
+                  prev_zayniatist ||= zayniatist
+                  hartri = energy_values[i]
+                  s = []
+                  s << elem
+                  s << symetry
+                  s << hartri
+                  s << hartri_to_ev(hartri) 
+                  s << zayniatist
+                  s << if prev_zayniatist != zayniatist
+                    previous = molecular_orbitals.last
+                    previous.pop()
+                    previous.push "HOMO"
+                    molecular_orbitals.pop()
+                    molecular_orbitals.push(previous) 
+                    "LUMO"
+                  else
+                    ""
+                  end
+                  prev_zayniatist = zayniatist
+                  molecular_orbitals << s
+                end
+              end
+              mo_position += 1
+            end
+          end
+        end
+        
+        if line =~ /Harmonic frequencies/
+          print_as_usual("Harmonic frequencies processing")
+          index += 4
+          current_line = @file_lines[index].split(/\s+/)
+          current_line.delete ""
+          last_number = current_line.first.to_i
+          hf_regexp = /^\s+#{last_number}/
+          while !(@file_lines[index] =~ /Thermochemistry/)
+            if @file_lines[index] =~ hf_regexp
+              harmonic_frequencies_data = []
+              # save index position for return back 
+              # if it is wrong line
+              saved_position = index + 1
+              # save current line for futher analyze
+              saved_line = @file_lines[index]
+              
+              # Begin proccessing
+              mode_numbers = @file_lines[index].split(/\s+/)
+              mode_numbers.delete ""
+              harmonic_frequencies_data << mode_numbers
+              
+              symmetries = @file_lines[index+=1].split(/\s+/)
+              symmetries.delete ""
+              harmonic_frequencies_data << symmetries
+
+              poss_frequencies = @file_lines[index+=1].split(/ --\s+/)
+              unless poss_frequencies.first =~ /Frequencies/
+                index = saved_position
+                next
+              end
+              frequencies = poss_frequencies.last.split(/\s+/)
+              harmonic_frequencies_data << frequencies
+
+              poss_red_masses = @file_lines[index+=1].split(/ --\s+/)
+              unless poss_red_masses.first =~ /Red. masses/
+                index = saved_position
+                next
+              end
+              red_masses = poss_red_masses.last.split(/\s+/)
+              harmonic_frequencies_data << red_masses
+
+              poss_frc_consts = @file_lines[index+=1].split(/ --\s+/)
+              unless poss_frc_consts.first =~ /Frc consts/
+                index = saved_position
+                next
+              end
+              frc_consts = poss_frc_consts.last.split(/\s+/)
+              harmonic_frequencies_data << frc_consts
+
+              poss_ir_inten = @file_lines[index+=1].split(/ --\s+/)
+              unless poss_ir_inten.first =~ /IR Inten/
+                index = saved_position
+                next
+              end
+              ir_inten = poss_ir_inten.last.split(/\s+/)
+              harmonic_frequencies_data << ir_inten
+
+              poss_raman_activ = @file_lines[index+=1].split(/ --\s+/)
+              unless poss_raman_activ.first =~ /Raman Activ/
+                index = saved_position
+                next
+              end
+              raman_activ = poss_raman_activ.last.split(/\s+/)
+              harmonic_frequencies_data << raman_activ
+
+              poss_depolar_p = @file_lines[index+=1].split(/ --\s+/)
+              unless poss_depolar_p.first =~ /Depolar \(P\)/
+                index = saved_position
+                next
+              end
+              depolar_p = poss_depolar_p.last.split(/\s+/)
+              harmonic_frequencies_data << depolar_p
+
+              poss_depolar_u = @file_lines[index+=1].split(/ --\s+/)
+              unless poss_depolar_u.first =~ /Depolar \(U\)/
+                index = saved_position
+                next
+              end
+              depolar_u = poss_depolar_u.last.split(/\s+/)
+              harmonic_frequencies_data << depolar_u
+
+              current_harmonic_position = harmonic_frequencies.size
+              harmonic_frequencies_data[0].size.times do |i|
+                harmonic_frequencies[current_harmonic_position + i] = []
+                harmonic_frequencies_data.each do |el|
+                  harmonic_frequencies[current_harmonic_position + i] << el[i]
+                end
+              end              
+              
+              # ex.  1                      2                      3
+              # Split line with mode numbers
+              current_line = saved_line.split(/\s+/)
+              current_line.delete ""
+              # Get last mode number for futher search
+              last_number = current_line.last.to_i
+              # next search for line that consists two neccessary numbers
+              # separated with whitespace
+              # TODO!
+              hf_regexp = /^\s+#{last_number+=1}/
+            end
+            index += 1
+          end
+          break
+        end
+
+        index += 1
+      end 
+      return [
+        processors[:results_processor].process,
+        processors[:atom_processor].process,
+        molecular_orbitals,
+        harmonic_frequencies
+      ]
+    end
+
+    def hartri_to_ev(hartri)
+      to_ev = 27.2107
+      (hartri.to_f * to_ev).round 6
+    end
+
+    def generate_mo_regexp(last_number)
+      str = (1..2).to_a.inject('^') {|memo, e| memo += "\\s+#{last_number + e}"; memo }
+      Regexp.new(str)
+    end
+  end
+end