gdock 2.0.0

Information-driven protein-protein docking using a genetic algorithm
Documentation 
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// Values taken from
// !README for CHARMM topology/parameter files for OPLS-AA (opls.rtf, opls.prm)
// !** reference for OPLS-AA for proteins:
// !** Jorgensen, W.L. et al., J. Am. Chem. Soc. 118:11225-11236 (1996)
// !** reference for OPLS-AA/M:
// !** Robertson, M.J. et al., J. Chem. Theory Comput., (2015)
// !and see additional reference below
// !
// https://traken.chem.yale.edu/doc/par_opls_aam.inp
// https://traken.chem.yale.edu/doc/top_opls_aam.inp

pub fn get_epsilon(atom: &str) -> Option<f64> {
    match atom {
        "C135" | "C136" | "C137" | "C149" | "C157" | "C158" | "C206" | "C209" | "C210" | "C214"
        | "C223" | "C224" | "C242" | "C245" | "C246" | "C267" | "C271" | "C274" | "C283"
        | "C284" | "C285" | "C292" | "C293" | "C295" | "C296" | "C307" | "C308" | "C505" => {
            Some(-0.066000)
        }
        "C145" | "C166" | "C500" | "C501" | "C502" | "C506" | "C507" | "C508" | "C509" | "C510"
        | "C514" => Some(-0.070000),
        "C235" => Some(-0.105000),
        "H140" => Some(-0.030000),
        "H146" => Some(-0.030000),
        "C302" => Some(-0.050000),
        "H155" | "H168" | "H204" | "H240" | "H241" | "H270" | "H290" | "H301" | "H304" | "H310"
        | "H504" | "H513" => Some(0.000000),
        "N237" | "N238" | "N239" | "N287" | "N300" | "N303" | "N309" | "N503" | "N511" | "N512"
        | "O154" | "O167" | "O268" => Some(-0.170000),
        "O236" | "O269" | "O272" => Some(-0.210000),
        "S200" => Some(-0.425000),
        "S202" | "S203" => Some(-0.355000),
        "OT" => Some(-0.152100),
        "HT" => Some(-0.046000),
        "SOD" => Some(-0.000500),
        "CLA" => Some(-0.710000),
        _ => None, // for atoms not listed
    }
}

pub fn get_rmin2(atom: &str) -> Option<f64> {
    match atom {
        "C135" | "C136" | "C137" | "C149" | "C157" | "C158" | "C206" | "C209" | "C210" | "C214"
        | "C223" | "C224" | "C242" | "C245" | "C246" | "C267" | "C271" | "C274" | "C283"
        | "C284" | "C285" | "C292" | "C293" | "C295" | "C296" | "C307" | "C308" | "C505" => {
            Some(1.9643086)
        }
        "C145" | "C166" | "C500" | "C501" | "C502" | "C506" | "C507" | "C508" | "C509" | "C510"
        | "C514" => Some(1.9923701),
        "C235" => Some(2.1046163),
        "H140" => Some(1.4030776),
        "H146" => Some(1.3581791),
        "C302" => Some(1.2627698),
        "H155" | "H168" | "H204" | "H240" | "H241" | "H270" | "H290" | "H301" | "H304" | "H310"
        | "H504" | "H513" => Some(0.0000000),
        "N237" | "N238" | "N239" | "N287" | "N300" | "N303" | "N309" | "N503" | "N511" | "N512" => {
            Some(1.8240008)
        }
        "O154" => Some(1.7510408),
        "O167" => Some(1.7229792),
        "O268" => Some(1.6836931),
        "O236" | "O269" | "O272" => Some(1.6612438),
        "S200" => Some(2.0204317),
        "S202" | "S203" => Some(2.0204317),
        "OT" => Some(1.768200),
        "HT" => Some(0.224500),
        "SOD" => Some(2.9969737),
        "CLA" => Some(2.2561487),
        _ => None, // for atoms not listed
    }
}
pub fn get_eps_1_4(atom: &str) -> Option<f64> {
    match atom {
        "C135" | "C136" | "C137" | "C149" | "C157" | "C158" | "C206" | "C209" | "C210" | "C214"
        | "C223" | "C224" | "C242" | "C245" | "C246" | "C267" | "C271" | "C274" | "C283"
        | "C284" | "C285" | "C292" | "C293" | "C295" | "C296" | "C307" | "C308" | "C505" => {
            Some(-0.033000)
        }
        "C145" | "C166" | "C500" | "C501" | "C502" | "C506" | "C507" | "C508" | "C509" | "C510"
        | "C514" => Some(-0.035000),
        "C235" => Some(-0.052500),
        "H140" => Some(-0.015000),
        "H146" => Some(-0.015000),
        "C302" => Some(-0.025000),
        "H155" | "H168" | "H204" | "H240" | "H241" | "H270" | "H290" | "H301" | "H304" | "H310"
        | "H504" | "H513" => Some(0.000000),
        "N237" | "N238" | "N239" | "N287" | "N300" | "N303" | "N309" | "N503" | "N511" | "N512"
        | "O154" | "O167" | "O268" => Some(-0.085000),
        "O236" | "O269" | "O272" => Some(-0.105000),
        "S200" => Some(-0.212500),
        "S202" | "S203" => Some(-0.177500),
        "OT" => Some(-0.152100),
        "HT" => Some(-0.046000),
        "SOD" => Some(-0.000500),
        "CLA" => Some(-0.710000),
        _ => None, // for atoms not listed
    }
}

pub fn get_rmin2_1_4(atom: &str) -> Option<f64> {
    match atom {
        "C135" | "C136" | "C137" | "C149" | "C157" | "C158" | "C206" | "C209" | "C210" | "C214"
        | "C223" | "C224" | "C242" | "C245" | "C246" | "C267" | "C271" | "C274" | "C283"
        | "C284" | "C285" | "C292" | "C293" | "C295" | "C296" | "C307" | "C308" | "C505" => {
            Some(1.9643086)
        }
        "C145" | "C166" | "C500" | "C501" | "C502" | "C506" | "C507" | "C508" | "C509" | "C510"
        | "C514" => Some(1.9923701),
        "C235" => Some(2.1046163),
        "H140" => Some(1.4030776),
        "H146" => Some(1.3581791),
        "C302" => Some(1.2627698),
        "H155" | "H168" | "H204" | "H240" | "H241" | "H270" | "H290" | "H301" | "H304" | "H310"
        | "H504" | "H513" => Some(0.0000000),
        "N237" | "N238" | "N239" | "N287" | "N300" | "N303" | "N309" | "N503" | "N511" | "N512" => {
            Some(1.8240008)
        }
        "O154" => Some(1.7510408),
        "O167" => Some(1.7229792),
        "O268" => Some(1.6836931),
        "O236" | "O269" | "O272" => Some(1.6612438),
        "S200" => Some(2.0204317),
        "S202" | "S203" => Some(2.0204317),
        "OT" => Some(1.768200),
        "HT" => Some(0.224500),
        "SOD" => Some(2.9969737),
        "CLA" => Some(2.2561487),
        _ => None, // for atoms not listed
    }
}

// fn get_mass(atom: &str) -> Option<f64> {
//     match atom {
//         "C135" | "C136" | "C137" | "C145" | "C149" | "C157" | "C158" | "C166" | "C206" | "C209"
//         | "C210" | "C214" | "C223" | "C224" | "C235" | "C242" | "C245" | "C246" | "C267"
//         | "C271" | "C274" | "C283" | "C284" | "C285" | "C292" | "C293" | "C295" | "C296"
//         | "C302" | "C307" | "C308" | "C500" | "C501" | "C502" | "C505" | "C506" | "C507"
//         | "C508" | "C509" | "C510" | "C514" => Some(12.01100),
//         "H140" | "H146" | "H155" | "H168" | "H204" | "H240" | "H241" | "H270" | "H290" | "H301"
//         | "H304" | "H310" | "H504" | "H513" => Some(1.00800),
//         "N237" | "N238" | "N239" | "N287" | "N300" | "N303" | "N309" | "N503" | "N511" | "N512" => {
//             Some(14.00700)
//         }
//         "O154" | "O167" | "O236" | "O268" | "O269" | "O272" | "OT" => Some(15.99940),
//         "S200" | "S202" | "S203" => Some(32.06000),
//         "HT" => Some(1.00800),
//         "SOD" => Some(22.98977),
//         "CLA" => Some(35.45000),
//         _ => None, // for atoms not listed
//     }
// }

pub fn get_atom(residue_name: &str, atom_name: &str) -> Option<&'static str> {
    match residue_name {
        "ALA" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C135"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "HB3" => Some("H140"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "ARG" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C136"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C308"),
            "HG1" => Some("H140"),
            "HG2" => Some("H140"),
            "CD" => Some("C307"),
            "HD1" => Some("H140"),
            "HD2" => Some("H140"),
            "NE" => Some("N303"),
            "HE" => Some("H304"),
            "CZ" => Some("C302"),
            "NH1" => Some("N300"),
            "HH11" => Some("H301"),
            "HH12" => Some("H301"),
            "NH2" => Some("N300"),
            "HH21" => Some("H301"),
            "HH22" => Some("H301"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "ASN" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C136"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C235"),
            "OD1" => Some("O236"),
            "ND2" => Some("N237"),
            "HD21" => Some("H240"),
            "HD22" => Some("H240"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "ASP" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C274"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C271"),
            "OD1" => Some("O272"),
            "OD2" => Some("O272"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "CYS" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C206"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "SG" => Some("S200"),
            "HG1" => Some("H204"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "GLN" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C136"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C136"),
            "HG1" => Some("H140"),
            "HG2" => Some("H140"),
            "CD" => Some("C235"),
            "OE1" => Some("O236"),
            "NE2" => Some("N237"),
            "HE21" => Some("H240"),
            "HE22" => Some("H240"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "GLU" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C136"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C274"),
            "HG1" => Some("H140"),
            "HG2" => Some("H140"),
            "CD" => Some("C271"),
            "OE1" => Some("O272"),
            "OE2" => Some("O272"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "GLY" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C223"),
            "HA1" => Some("H140"),
            "HA2" => Some("H140"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "HIS" | "HSD" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C505"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "ND1" => Some("N503"),
            "HD1" => Some("H504"),
            "CG" => Some("C508"),
            "CE1" => Some("C506"),
            "HE1" => Some("H146"),
            "NE2" => Some("N511"),
            "CD2" => Some("C507"),
            "HD2" => Some("H146"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "HSE" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C505"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "ND1" => Some("N511"),
            "CG" => Some("C507"),
            "CE1" => Some("C506"),
            "HE1" => Some("H146"),
            "NE2" => Some("N503"),
            "HE2" => Some("H504"),
            "CD2" => Some("C508"),
            "HD2" => Some("H146"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "HSP" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C505"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CD2" => Some("C510"),
            "HD2" => Some("H146"),
            "CG" => Some("C510"),
            "NE2" => Some("N512"),
            "HE2" => Some("H513"),
            "ND1" => Some("N512"),
            "HD1" => Some("H513"),
            "CE1" => Some("C509"),
            "HE1" => Some("H146"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "ILE" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C137"),
            "HB" => Some("H140"),
            "CG2" => Some("C135"),
            "HG21" => Some("H140"),
            "HG22" => Some("H140"),
            "HG23" => Some("H140"),
            "CG1" => Some("C136"),
            "HG11" => Some("H140"),
            "HG12" => Some("H140"),
            "CD" => Some("C135"),
            "HD1" => Some("H140"),
            "HD2" => Some("H140"),
            "HD3" => Some("H140"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "LEU" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C136"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C137"),
            "HG" => Some("H140"),
            "CD1" => Some("C135"),
            "HD11" => Some("H140"),
            "HD12" => Some("H140"),
            "HD13" => Some("H140"),
            "CD2" => Some("C135"),
            "HD21" => Some("H140"),
            "HD22" => Some("H140"),
            "HD23" => Some("H140"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "LYS" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C136"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C136"),
            "HG1" => Some("H140"),
            "HG2" => Some("H140"),
            "CD" => Some("C136"),
            "HD1" => Some("H140"),
            "HD2" => Some("H140"),
            "CE" => Some("C292"),
            "HE1" => Some("H140"),
            "HE2" => Some("H140"),
            "NZ" => Some("N287"),
            "HZ1" => Some("H290"),
            "HZ2" => Some("H290"),
            "HZ3" => Some("H290"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "MET" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C136"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C210"),
            "HG1" => Some("H140"),
            "HG2" => Some("H140"),
            "SD" => Some("S202"),
            "CE" => Some("C209"),
            "HE1" => Some("H140"),
            "HE2" => Some("H140"),
            "HE3" => Some("H140"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "PHE" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C149"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C145"),
            "CD1" => Some("C145"),
            "HD1" => Some("H146"),
            "CE1" => Some("C145"),
            "HE1" => Some("H146"),
            "CZ" => Some("C145"),
            "HZ" => Some("H146"),
            "CD2" => Some("C145"),
            "HD2" => Some("H146"),
            "CE2" => Some("C145"),
            "HE2" => Some("H146"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "PRO" => match atom_name {
            "N" => Some("N239"),
            "CD" => Some("C245"),
            "HD1" => Some("H140"),
            "HD2" => Some("H140"),
            "CA" => Some("C246"),
            "HA" => Some("H140"),
            "CB" => Some("C136"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C136"),
            "HG1" => Some("H140"),
            "HG2" => Some("H140"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "SER" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C157"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "OG" => Some("O154"),
            "HG1" => Some("H155"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "THR" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C158"),
            "HB" => Some("H140"),
            "OG1" => Some("O154"),
            "HG1" => Some("H155"),
            "CG2" => Some("C135"),
            "HG21" => Some("H140"),
            "HG22" => Some("H140"),
            "HG23" => Some("H140"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "TRP" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C136"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C500"),
            "CD1" => Some("C514"),
            "HD1" => Some("H146"),
            "NE1" => Some("N503"),
            "HE1" => Some("H504"),
            "CE2" => Some("C502"),
            "CD2" => Some("C501"),
            "CE3" => Some("C145"),
            "HE3" => Some("H146"),
            "CZ3" => Some("C145"),
            "HZ3" => Some("H146"),
            "CZ2" => Some("C145"),
            "HZ2" => Some("H146"),
            "CH2" => Some("C145"),
            "HH2" => Some("H146"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "TYR" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C149"),
            "HB1" => Some("H140"),
            "HB2" => Some("H140"),
            "CG" => Some("C145"),
            "CD1" => Some("C145"),
            "HD1" => Some("H146"),
            "CE1" => Some("C145"),
            "HE1" => Some("H146"),
            "CZ" => Some("C166"),
            "OH" => Some("O167"),
            "HH" => Some("H168"),
            "CD2" => Some("C145"),
            "HD2" => Some("H146"),
            "CE2" => Some("C145"),
            "HE2" => Some("H146"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        "VAL" => match atom_name {
            "N" => Some("N238"),
            "HN" => Some("H241"),
            "CA" => Some("C224"),
            "HA" => Some("H140"),
            "CB" => Some("C137"),
            "HB" => Some("H140"),
            "CG1" => Some("C135"),
            "HG11" => Some("H140"),
            "HG12" => Some("H140"),
            "HG13" => Some("H140"),
            "CG2" => Some("C135"),
            "HG21" => Some("H140"),
            "HG22" => Some("H140"),
            "HG23" => Some("H140"),
            "C" => Some("C235"),
            "O" => Some("O236"),
            _ => None,
        },
        _ => None,
    }
}

pub fn get_charge(atom: &str) -> Option<f64> {
    match atom {
        "N238" => Some(-0.500),
        "H241" => Some(0.300),
        "C224" => Some(0.140),
        "H140" => Some(0.060),
        "C136" => Some(-0.120),
        "C210" => Some(0.0475),
        "S202" => Some(-0.335),
        "C209" => Some(-0.0125),
        "C235" => Some(0.500),
        "O236" => Some(-0.500),
        "C135" => Some(-0.180),
        "C308" => Some(-0.050),
        "C307" => Some(0.190),
        "N303" => Some(-0.700),
        "H304" => Some(0.440),
        "C302" => Some(0.640),
        "N300" => Some(-0.800),
        "H301" => Some(0.460),
        "N237" => Some(-0.760),
        "H240" => Some(0.380),
        "C274" => Some(-0.220),
        "C271" => Some(0.700),
        "O272" => Some(-0.800),
        "C206" => Some(0.060),
        "S200" => Some(-0.335),
        "H204" => Some(0.155),
        "C505" => Some(-0.005),
        "N503" => Some(-0.570),
        "H504" => Some(0.420),
        "C508" => Some(0.015),
        "C506" => Some(0.295),
        "H146" => Some(0.115),
        "N511" => Some(-0.490),
        "C507" => Some(-0.015),
        "C510" => Some(0.215),
        "N512" => Some(-0.540),
        "H513" => Some(0.460),
        "C509" => Some(0.385),
        "C137" => Some(-0.060),
        "C500" => Some(0.075),
        "C514" => Some(-0.115),
        "C502" => Some(0.130),
        "C501" => Some(-0.055),
        "C145" => Some(-0.115),
        "C166" => Some(0.150),
        "O167" => Some(-0.585),
        "H168" => Some(0.435),
        "N239" => Some(-0.140),
        "C245" => Some(-0.050),
        "C246" => Some(0.010),
        "C157" => Some(0.145),
        "O154" => Some(-0.683),
        "H155" => Some(0.418),
        "C158" => Some(0.205),
        "C149" => Some(-0.005),
        "N287" => Some(-0.300),
        "H290" => Some(0.330),
        "C293" => Some(0.250),
        "C292" => Some(0.190),
        "N309" => Some(-0.200),
        "H310" => Some(0.310),
        "C296" => Some(0.170),
        "C295" => Some(0.230),
        "C283" => Some(0.040),
        "C267" => Some(0.52),
        "O269" => Some(-0.44),
        "O268" => Some(-0.53),
        "H270" => Some(0.45),
        "C223" => Some(0.08),
        "C242" => Some(0.020),
        "C284" => Some(-0.020),
        "C285" => Some(-0.090),
        "C214" => Some(0.0975),
        "S203" => Some(-0.2175),
        "OT" => Some(-0.834),
        "HT" => Some(0.417),
        _ => None, // for atoms not listed
    }
}

#[cfg(test)]
mod tests {
    use super::*;

    #[test]
    fn test_get_epsilon_carbon() {
        let epsilon = get_epsilon("C135");
        assert!(epsilon.is_some());
        assert!((epsilon.unwrap() - (-0.066000)).abs() < 1e-6);
    }

    #[test]
    fn test_get_epsilon_nitrogen() {
        let epsilon = get_epsilon("N238");
        assert!(epsilon.is_some());
        assert!((epsilon.unwrap() - (-0.170000)).abs() < 1e-6);
    }

    #[test]
    fn test_get_epsilon_unknown() {
        let epsilon = get_epsilon("UNKNOWN");
        assert!(epsilon.is_none());
    }

    #[test]
    fn test_get_rmin2_carbon() {
        let rmin2 = get_rmin2("C135");
        assert!(rmin2.is_some());
        assert!((rmin2.unwrap() - 1.9643086).abs() < 1e-6);
    }

    #[test]
    fn test_get_rmin2_hydrogen() {
        let rmin2 = get_rmin2("H140");
        assert!(rmin2.is_some());
        assert!((rmin2.unwrap() - 1.4030776).abs() < 1e-6);
    }

    #[test]
    fn test_get_rmin2_unknown() {
        let rmin2 = get_rmin2("INVALID");
        assert!(rmin2.is_none());
    }

    #[test]
    fn test_get_eps_1_4_carbon() {
        let eps = get_eps_1_4("C135");
        assert!(eps.is_some());
        assert!((eps.unwrap() - (-0.033000)).abs() < 1e-6);
    }

    #[test]
    fn test_get_eps_1_4_sulfur() {
        let eps = get_eps_1_4("S200");
        assert!(eps.is_some());
        assert!((eps.unwrap() - (-0.212500)).abs() < 1e-6);
    }

    #[test]
    fn test_get_eps_1_4_unknown() {
        let eps = get_eps_1_4("NOTFOUND");
        assert!(eps.is_none());
    }

    #[test]
    fn test_get_rmin2_1_4_oxygen() {
        let rmin2 = get_rmin2_1_4("O154");
        assert!(rmin2.is_some());
        assert!((rmin2.unwrap() - 1.7510408).abs() < 1e-6);
    }

    #[test]
    fn test_get_rmin2_1_4_chloride() {
        let rmin2 = get_rmin2_1_4("CLA");
        assert!(rmin2.is_some());
        assert!((rmin2.unwrap() - 2.2561487).abs() < 1e-6);
    }

    #[test]
    fn test_get_rmin2_1_4_unknown() {
        let rmin2 = get_rmin2_1_4("XYZ");
        assert!(rmin2.is_none());
    }

    #[test]
    fn test_get_atom_alanine() {
        assert_eq!(get_atom("ALA", "N"), Some("N238"));
        assert_eq!(get_atom("ALA", "CA"), Some("C224"));
        assert_eq!(get_atom("ALA", "CB"), Some("C135"));
        assert_eq!(get_atom("ALA", "C"), Some("C235"));
        assert_eq!(get_atom("ALA", "O"), Some("O236"));
    }

    #[test]
    fn test_get_atom_glycine() {
        assert_eq!(get_atom("GLY", "N"), Some("N238"));
        assert_eq!(get_atom("GLY", "CA"), Some("C223"));
        assert_eq!(get_atom("GLY", "C"), Some("C235"));
        assert_eq!(get_atom("GLY", "O"), Some("O236"));
    }

    #[test]
    fn test_get_atom_proline() {
        assert_eq!(get_atom("PRO", "N"), Some("N239"));
        assert_eq!(get_atom("PRO", "CD"), Some("C245"));
        assert_eq!(get_atom("PRO", "CA"), Some("C246"));
    }

    #[test]
    fn test_get_atom_arginine() {
        assert_eq!(get_atom("ARG", "NE"), Some("N303"));
        assert_eq!(get_atom("ARG", "CZ"), Some("C302"));
        assert_eq!(get_atom("ARG", "NH1"), Some("N300"));
        assert_eq!(get_atom("ARG", "NH2"), Some("N300"));
    }

    #[test]
    fn test_get_atom_tryptophan() {
        assert_eq!(get_atom("TRP", "NE1"), Some("N503"));
        assert_eq!(get_atom("TRP", "CG"), Some("C500"));
        assert_eq!(get_atom("TRP", "CD2"), Some("C501"));
    }

    #[test]
    fn test_get_atom_unknown_residue() {
        let atom = get_atom("XXX", "CA");
        assert!(atom.is_none());
    }

    #[test]
    fn test_get_atom_unknown_atom() {
        let atom = get_atom("ALA", "NOTEXIST");
        assert!(atom.is_none());
    }

    #[test]
    fn test_get_charge_backbone() {
        assert_eq!(get_charge("N238"), Some(-0.500));
        assert_eq!(get_charge("H241"), Some(0.300));
        assert_eq!(get_charge("C235"), Some(0.500));
        assert_eq!(get_charge("O236"), Some(-0.500));
    }

    #[test]
    fn test_get_charge_lysine_sidechain() {
        assert_eq!(get_charge("N287"), Some(-0.300));
        assert_eq!(get_charge("H290"), Some(0.330));
    }

    #[test]
    fn test_get_charge_arginine_sidechain() {
        assert_eq!(get_charge("N303"), Some(-0.700));
        assert_eq!(get_charge("H304"), Some(0.440));
        assert_eq!(get_charge("C302"), Some(0.640));
        assert_eq!(get_charge("N300"), Some(-0.800));
    }

    #[test]
    fn test_get_charge_aspartate() {
        assert_eq!(get_charge("C271"), Some(0.700));
        assert_eq!(get_charge("O272"), Some(-0.800));
    }

    #[test]
    fn test_get_charge_unknown() {
        let charge = get_charge("NOTFOUND");
        assert!(charge.is_none());
    }

    #[test]
    fn test_get_charge_sulfur() {
        assert_eq!(get_charge("S200"), Some(-0.335));
        assert_eq!(get_charge("S202"), Some(-0.335));
    }

    #[test]
    fn test_get_atom_histidine_variants() {
        // HSD (neutral histidine, proton on ND1)
        assert_eq!(get_atom("HSD", "ND1"), Some("N503"));
        assert_eq!(get_atom("HSD", "NE2"), Some("N511"));

        // HSE (neutral histidine, proton on NE2)
        assert_eq!(get_atom("HSE", "ND1"), Some("N511"));
        assert_eq!(get_atom("HSE", "NE2"), Some("N503"));

        // HSP (protonated histidine)
        assert_eq!(get_atom("HSP", "ND1"), Some("N512"));
        assert_eq!(get_atom("HSP", "NE2"), Some("N512"));

        // HIS (alias for HSD)
        assert_eq!(get_atom("HIS", "ND1"), Some("N503"));
    }

    #[test]
    fn test_parameters_consistency() {
        // Test that C135 has all four parameters
        let test_atom = "C135";
        assert!(get_epsilon(test_atom).is_some());
        assert!(get_rmin2(test_atom).is_some());
        assert!(get_eps_1_4(test_atom).is_some());
        assert!(get_rmin2_1_4(test_atom).is_some());
    }

    #[test]
    fn test_complete_alanine_mapping() {
        // Verify all alanine atoms can be mapped
        let ala_atoms = vec!["N", "HN", "CA", "HA", "CB", "HB1", "HB2", "HB3", "C", "O"];
        for atom_name in ala_atoms {
            assert!(
                get_atom("ALA", atom_name).is_some(),
                "Failed to map ALA {}",
                atom_name
            );
        }
    }
}