cheminformatics.yml

id: cheminformatics
items:
- id: get_data
  items:
  - id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sam_dump
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/dbbuilder/dbbuilder
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_epost/ncbi_eutils_epost
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ebi_search_rest_results/ebi_search_rest_results
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_efetch/ncbi_eutils_efetch
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esearch/ncbi_eutils_esearch
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/iedb_api/iedb_api
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_analysis_report/enasearch_retrieve_analysis_report
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_elink/ncbi_eutils_elink
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_egquery/ncbi_eutils_egquery
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/uniprot_rest_interface/uniprot
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/ecology/spocc_occ/spocc_occ
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_einfo/ncbi_eutils_einfo
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_datasets/datasets_download_gene
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fasterq_dump
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/fastq_dump
    type: tool
  - id: lftp
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_feature_info/get_feature_info
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/unipept/unipept
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ega_download_client/pyega3
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_ecitmatch/ncbi_eutils_ecitmatch
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/sra_tools/sra_pileup
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/enasearch_search_data/enasearch_search_data
    type: tool
  - id: upload1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/uniprotxml_downloader/uniprotxml_downloader
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_taxons/enasearch_retrieve_taxons
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_acc_download/ncbi_acc_download
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_eutils_esummary/ncbi_eutils_esummary
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/pysradb_search/pysradb_search
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ncbi_datasets/datasets_download_genome
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_run_report/enasearch_retrieve_run_report
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_sequences/get_sequences
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/earlhaminst/ensembl_get_genetree/get_genetree
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/enasearch_retrieve_data/enasearch_retrieve_data
    type: tool
  - id: microbial_import1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ebi_metagenomics_run_downloader/ebi_metagenomics_run_downloader
    type: tool
  name: Get Data
  type: section
- id: send_data
  items:
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ena_upload/ena_upload
    type: tool
  - id: export_remote
    type: tool
  - id: send_to_cloud
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/imgteam/curl_post/curl_post
    type: tool
  name: Send Data
  type: section
- id: collection_operations
  items:
  - id: toolshed.g2.bx.psu.edu/repos/imgteam/unzip/unzip
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/nml/collapse_collections/collapse_dataset
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column
    type: tool
  name: Collection Operations
  type: section
- id: general_text_label
  text: General Text Tools
  type: label
- id: text_manipulation
  items:
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/unique/bg_uniq
    type: tool
  - id: addValue
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/add_value/addValue
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_rows
    type: tool
  - id: Show beginning1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/basecoverage/gops_basecoverage_1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_text_file_with_recurring_lines
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/jq/jq
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/replace_column_by_key_value_file/replace_column_with_key_value_file
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/filter_tabular/filter_tabular
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/diff/diff
    type: tool
  - id: Cut1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/add_line_to_file/add_line_to_file
    type: tool
  - id: Convert characters1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regex1
    type: tool
  - id: trimmer
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool
    type: tool
  - id: secure_hash_message_digest
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_uniq_tool
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/artbio/concatenate_multiple_datasets/cat_multi_datasets
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_unfold_column_tool
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/column_maker/Add_a_column1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/get_flanks/get_flanks1
    type: tool
  - id: Remove beginning1
    type: tool
  - id: createInterval
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/imgteam/imagecoordinates_flipaxis/imagecoordinates_flipaxis
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/dna_filtering/histogram_rpy
    type: tool
  - id: wc_gnu
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_melt/melt
    type: tool
  - id: ChangeCase
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/merge/gops_merge_1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_head_tool
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_multijoin_tool
    type: tool
  - id: Paste1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_find_and_replace
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/intersect/gops_intersect_1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/mvdbeek/add_input_name_as_column/addName
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tac
    type: tool
  - id: random_lines1
    type: tool
  - id: Show tail1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/tables_arithmetic_operations/tables_arithmetic_operations
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/prinseq/prinseq
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/flanking_features/flanking_features_1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/column_order_header_sort/column_order_header_sort
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/join_files_on_column_fuzzy/join_files_on_column_fuzzy
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/merge_cols/mergeCols1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/complement/gops_complement_1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/coverage/gops_coverage_1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/sqlite_to_tabular/sqlite_to_tabular
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_easyjoin_tool
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/earlhaminst/replace_chromosome_names/replace_chromosome_names
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/table_compute/table_compute
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/subtract_query/subtract_query1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/gff3_rebase/gff3.rebase
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1
    type: tool
  - id: cat1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/cluster/gops_cluster_1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/reshape2_cast/cast
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/split_file_on_column/tp_split_on_column
    type: tool
  name: Text Manipulation
  type: section
- id: filter_and_sort
  items:
  - id: gtf_filter_by_attribute_values_list
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/jjohnson/find_in_reference/find_in_reference
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id
    type: tool
  - id: Grep1
    type: tool
  - id: Filter1
    type: tool
  - id: sort1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/column_arrange_by_header/bg_column_arrange_by_header
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids
    type: tool
  - id: gff_filter_by_feature_count
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/xpath/xpath
    type: tool
  - id: gff_filter_by_attribute
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/gffcompare/gffcompare
    type: tool
  - id: Extract_features1
    type: tool
  name: Filter and Sort
  type: section
- id: join__subtract_and_group
  items:
  - id: Grouping1
    type: tool
  - id: comp1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/collection_column_join/collection_column_join
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops/datamash_ops
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_reverse/datamash_reverse
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/subtract/gops_subtract_1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_transpose/datamash_transpose
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/datamash_ops/datamash_ops
    type: tool
  - id: join1
    type: tool
  name: Join, Subtract and Group
  type: section
- id: convert_formats
  items:
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/mz_to_sqlite/mz_to_sqlite
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/resize_coordinate_window/resize_coordinate_window
    type: tool
  - id: axt_to_concat_fasta
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert_subset
    type: tool
  - id: wig_to_bigWig
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/bed_to_protein_map/bed_to_protein_map
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/genebed_maf_to_fasta/GeneBed_Maf_Fasta2
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_montage/graphicsmagick_image_montage
    type: tool
  - id: MAF_To_Interval1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/cpt/cpt_fix_aragorn/edu.tamu.cpt.external.aragorn-gff3
    type: tool
  - id: Sff_extractor
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/crossmap_vcf/crossmap_vcf
    type: tool
  - id: axt_to_fasta
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/gffcompare_to_bed/gffcompare_to_bed
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/biom_convert/biom_convert
    type: tool
  - id: wiggle2simple1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/crossmap_wig/crossmap_wig
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/ecology/xmlstarlet/xmlstarlet
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/fasta_to_tabular/fasta2tab
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/gfa_to_fa/gfa_to_fa
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/intermine_galaxy_exchange/galaxy_intermine_exchange
    type: tool
  - id: bed_to_bigBed
    type: tool
  - id: gtf2bedgraph
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/interval2maf/Interval2Maf1
    type: tool
  - id: axt_to_lav_1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/crossmap_gff/crossmap_gff
    type: tool
  - id: MAF_To_Fasta1
    type: tool
  - id: MAF_To_BED1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/thermo_raw_file_converter/thermo_raw_file_converter
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fastq/tabular_to_fastq
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/crossmap_bam/crossmap_bam
    type: tool
  - id: bed2gff1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/graphicsmagick_image_convert/graphicsmagick_image_convert
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/samtools_bam_to_cram/samtools_bam_to_cram
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/idconvert
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/bioext_bam2msa/bioext_bam2msa
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/ecology/ab1_fastq_converter/ab1_fastq_converter
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/map_peptides_to_bed/map_peptides_to_bed
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/cpt/cpt_convert_mga/edu.tamu.cpt2.util.mga_to_gff3
    type: tool
  - id: gff2bed1
    type: tool
  - id: liftOver1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/ucsc_twobittofa/ucsc-twobittofa
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/compress_file/compress_file
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/msms_extractor/msms_extractor
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/crossmap_bed/crossmap_bed
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/crossmap_region/crossmap_region
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/idpquery/idpquery
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/bam_to_scidx/bam_to_scidx
    type: tool
  - id: lav_to_bed1
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/iuc/bax2bam/bax2bam
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/bigwig_to_bedgraph/bigwig_to_bedgraph
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/idconvert/idconvert
    type: tool
  name: Convert Formats
  type: section
- id: chemicaltoolbox
  items:
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/natural_product_likeness/ctb_np-likeness-calculator
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_remsmall/openbabel_remSmall
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsf/bio3d_rmsf
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbdock/rdock_rbdock
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_multi_obgrep/openbabel_multi_obgrep
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_cosine_analysis/mdanalysis_cosine_analysis
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_endtoend/mdanalysis_endtoend
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_editconf/gmx_editconf
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxyp/openms_openpepxl/OpenPepXL
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/fpocket/fpocket
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_genprop/openbabel_genProp
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_butina_clustering
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_standardize/ctb_im_standardize
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_setup/gmx_setup
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/chembl_structure_pipeline/chembl_structure_pipeline
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_box/prepare_box
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_rxn_maker/ctb_im_rxn_maker
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/earlhaminst/apoc/apoc
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/fpocket/dpocket
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/sucos_max_score/sucos_max_score
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openduck_run_smd/openduck_run_smd
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_sim/gmx_sim
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_hbonds/mdanalysis_hbonds
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/vmd_hbonds/vmd_hbonds
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_spectrophore_search
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_dihedral/mdanalysis_dihedral
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_rdf/mdanalysis_rdf
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbdock/rxdock_rbdock
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_sort_filter/rxdock_sort_filter
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_online_data_fetch
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_nxn_clustering
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_addh/openbabel_addh
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_angle/mdanalysis_angle
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/get_online_data/ctb_online_data_fetch
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_md/gmx_md
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/biomd_neqgamma/biomd_neqgamma
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/get_pdb/get_pdb
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/featurestein/featurestein
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_machine_learning/ctb_mds_plot
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/traj_selections_and_merge/traj_selections_and_merge
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_svg_depiction/openbabel_svg_depiction
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina/docking
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gromacs_modify_topology/gromacs_modify_topology
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_filter/openbabel_filter
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_conformers/ctb_im_conformers
    type: tool
  - id: fragmenter
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/rxdock_rbcavity/rxdock_rbcavity
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_solvate/gmx_solvate
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_subsearch/openbabel_subsearch
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_energy/gmx_energy
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_frankenstein_ligand/ctb_frankenstein_ligand
    type: tool
  - id: bgchem_fragment_merger
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_o3dalign/ctb_im_o3dalign
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/mmpbsa_mmgbsa/mmpbsa_mmgbsa
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_xcos/ctb_im_xcos
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_remIons
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_remove_protonation_state/openbabel_remove_protonation_state
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openduck_chunk/openduck_chunk
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/alchemical_analysis/alchemical_analysis
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_receptor/prepare_receptor
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_acpype/ambertools_acpype
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gromacs_extract_topology/gromacs_extract_topology
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/parmconv/parmconv
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/get_pubchem/ctb_pubchem_download_assays
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca/bio3d_pca
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/rdock_sort_filter/rdock_sort_filter
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/align_it/ctb_alignit_create_db
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_converter
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/earlhaminst/smina/smina
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/md_converter/md_slicer
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/packmol/packmol
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/padel/padel
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/sucos_clustering/sucos_clustering
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_cluster_butina/ctb_im_cluster_butina
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/mordred/ctb_mordred_descriptors
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_restraints/gmx_restraints
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_get_builtin_file/gmx_get_builtin_file
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_em/gmx_em
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_obgrep/openbabel_obgrep
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_change_title/openbabel_change_title
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_rxn_smarts_filter/ctb_im_rxn_smarts_filter
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/rdock_rbcavity/rdock_rbcavity
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_remions/openbabel_remIons
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_spectrophore_search/openbabel_spectrophore_search
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/sucos_docking_scoring/sucos_docking_scoring
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/sdf_to_tab/sdf_to_tab
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/chemical_data_sources/ctb_pubchem_download_assays
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_parmchk2/ambertools_parmchk2
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_check/gmx_check
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_rdkit_descriptors/ctb_rdkit_descriptors
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/fastpca/fastpca
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_dccm/bio3d_dccm
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_chemfp_mol2fps
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_ramachandran_plot/mdanalysis_ramachandran_plot
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/chembl/chembl_structure_pipeline
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openmg/ctb_openmg
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_structure_distance_finder/openbabel_structure_distance_finder
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_trj/gmx_trj
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/chemfp/ctb_sdf2fps
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/get_pubchem/ctb_pubchem_download_as_smiles
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_pbf_ev/ctb_im_pbf_ev
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_remduplicates/openbabel_remDuplicates
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/biomd_rmsd_clustering/biomd_rmsd_clustering
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_rg/gmx_rg
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/acpype_amber2gromacs/acpype_Amber2Gromacs
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_rmsd/gmx_rmsd
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/tleap/tleap
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/enumerate_charges/enumerate_charges
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/simsearch/ctb_simsearch
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_makendx/gmx_makendx
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_max_min_picker/ctb_im_max_min_picker
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_rmsf/gmx_rmsf
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_subsearch
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_extract_rmsd/mdanalysis_extract_rmsd
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_constrained_conf_gen/ctb_im_constrained_conf_gen
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/osra/ctb_osra
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/qed/ctb_silicos_qed
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_rmsd/bio3d_rmsd
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_screen/ctb_im_screen
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/ambertools_antechamber/ambertools_antechamber
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/bio3d_pca_visualize/bio3d_pca_visualize
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_distance/mdanalysis_distance
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/prepare_ligands_for_docking/prepare_ligands_for_docking
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/pdbfixer/pdbfixer
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/biomd_extract_clusters/biomd_extract_clusters
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/gmx_merge_topology_files/gmx_merge_topology_files
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/chemteam/mdanalysis_ramachandran_protein/mdanalysis_ramachandran_protein
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel/ctb_multi_obgrep
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/ctb_im_cluster_butina_matrix/ctb_im_cluster_butina_matrix
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/galaxy-australia/alphafold2/alphafold
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/openbabel_compound_convert/openbabel_compound_convert
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/xchem_transfs_scoring/xchem_transfs_scoring
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/autodock_vina_prepare_ligand/prepare_ligand
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/confab/ctb_confab
    type: tool
  - id: toolshed.g2.bx.psu.edu/repos/bgruening/rdconf/rdconf
    type: tool
  name: ChemicalToolBox
  type: section
name: Cheminformatics
type: activity