molget

#!/usr/bin/env bash
# Original work by Jan Jensen (https://github.com/jensengroup/molget).
# Rewritten by Felipe Schneider.
#
#? molget 0.3
#?
#? Molget: bash script to get coordinates from chemical name using Cactus.
#?
#? Usage: molget chemical_name [chemical_name...]
#?
#?   -h         show this message
#?   -v         show version
#?   -s         assume chemical_name is a SMILES string
#?   -o [TYPE]  selects an output file type supported by OpenBabel (defaults to
#?              xyz)
#?
#? Examples:
#?
#?   ./molget methane
#?   ./molget hexacyanoiron
#?   ./molget water thf dmso dmf
#?   ./molget "propylene carbonate"
#?   ./molget -s "C(=O)N"
#?   ./molget -s "C/C=C\C" "C/C=C/C"
#?   ./molget -o gamin p-nitrobenzene
#?   ./molget -o pdb nadh nad+
#?   ./molget -o gamin -s "C#C"
#?   (remember to "chmod 755 molget")

use_smiles=false
ob_out_type="xyz"


while getopts ":hvso:" opt "$@"
do
    case $opt in
        h)  # Help message.
            grep "^#?" "$0" | cut -c 4-
            exit 0
            ;;
        v)  # Version message.
            grep "^#? molget" "$0" | cut -c 4-
            exit 0
            ;;
        s)  # Use SMILES.
            use_smiles=true
            ;;
        o)  # Set output type.
            ob_out_type=$OPTARG
            ;;
        \?)
            echo "Invalid option: -$OPTARG" >&2
            exit 1
            ;;
        :)
        echo "Option -$OPTARG requires an argument." >&2
        exit 1
        ;;
    esac
done

# Recover $@ for posterior use.
shift $((OPTIND-1))

for molecule in "$@"
do
    echo -n "$molecule"

    # Some preferences are preset, such as file types and options.
    cactus_repr="sdf"
    ob_inp_type="sdf"
    ob_ext_opts="-c"

    if [ "$use_smiles" = true ]; then
        # We need to change the input type.
        ob_inp_type="smi"
        # We also need to tell OpenBabel to generate 3D coordinates from SMILES.
        ob_ext_opts="${ob_ext_opts} --gen3d"
    fi

    # It is also wise to translate spaces in filenames to underscores.
    molecule_wo_spaces=${molecule// /_}

    # Slashes should be escaped in Linux, backslashes in Windows/Wine.
    molecule_wo_spaces=${molecule_wo_spaces//\//slash}
    molecule_wo_spaces=${molecule_wo_spaces//\\/backslash}

    # After, file names are generated.
    ob_inp_file="${molecule_wo_spaces}.${ob_inp_type}"
    ob_out_file="${molecule_wo_spaces}.${ob_out_type}"

    # Now we need to generate the input file for OpenBabel.
    if [ "$use_smiles" = true ]; then
        echo "$molecule" > "$ob_inp_file"
    else
        # A URL is then generated.
        url="https://cactus.nci.nih.gov/chemical/structure/${molecule}/${cactus_repr}"
        # Spaces in the URL should be escaped.
        url=${url// /%20}

        # The data is downloaded and transformed.
        # stderr is stored in case the exit status is not 0
        error=$( curl -# "$url" -o "$ob_inp_file" >/dev/null 2>&1  )
        check=$?
        # Check for errors. These are critical so exit program
        if [ ! $check = "0" ]
        then
            echo " FAILED"
            echo "Exit status $check of command 'curl -# $url -o $ob_inp_file':" >&2
            echo $error >&2
            rm "${ob_inp_file}"
            exit 1
        fi

        # Check for 404 error
        if grep -q "Page not found" "${ob_inp_file}"
        then
            echo " FAILED"
            rm "${ob_inp_file}"
            continue
        fi
    fi

    # Avoid cases in which the output file type is the same as the input one.
    if [ "$ob_inp_type" != "$ob_out_type" ]
    then
        error=$( obabel -i "$ob_inp_type" "$ob_inp_file" -o "$ob_out_type" -O "$ob_out_file" $ob_ext_opts >/dev/null 2>&1 )
        # Check for errors. These are critical so exit program
        check=$?
        if [ ! $check = "0" ]
        then
            echo " FAILED"
            echo ${ob_inp_file}
            echo "Exit status $check of command 'obabel -i "$ob_inp_type" "$ob_inp_file" -o "$ob_out_type" -O "$ob_out_file" $ob_ext_opts':" >&2
            echo $error >&2
            rm "${ob_inp_file}"
            exit 1
        fi
        # clean sdf input file
        rm "${ob_inp_file}"
    fi
    echo " SUCCESS"


done